BL_genes.md
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@@ -11,121 +11,121 @@ link-citations: true
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## Tier 1, high-confidence BL genes
13 13
14
-### *28 total*
14
+### *32 total*
15 15
16 16
|Gene|Summary| First BL study | Other entities | QC result |
17 17
|:-:|:--:|:-:|:-|:-|
18
-|[ARID1A](ARID1A)|Tier 1 GE[@loveGeneticLandscapeMutations2012], FE[@barisicARID1AOrchestratesSWI2024], aSHM|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@krysiakRecurrentSomaticMutations2017b; @rossiCodingGenomeSplenic2012c; @wienandGenomicAnalysesFlowsorted2019b; @zhangGeneticHeterogeneityDiffuse2013]||
18
+|[ARID1A](ARID1A)|Tier 1 GE[@loveGeneticLandscapeMutations2012], FE[@barisicARID1AOrchestratesSWI2024]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@krysiakRecurrentSomaticMutations2017; @rossiCodingGenomeSplenic2012; @wienandGenomicAnalysesFlowsorted2019; @zhangGeneticHeterogeneityDiffuse2013]||
19 19
|[BACH2](BACH2)|Tier 1 GE[@grandeGenomewideDiscoverySomatic2019]|[Grande et al](papers/grandeGenomewideDiscoverySomatic2019)|||
20
-|[BCL7A](BCL7A)|Tier 1 GE[@grandeGenomewideDiscoverySomatic2019], FE[@balinas-gaviraFrequentMutationsAminoterminal2020b], aSHM|[Grande et al](papers/grandeGenomewideDiscoverySomatic2019)|[@krysiakRecurrentSomaticMutations2017b; @morinFrequentMutationHistonemodifying2011; @reichelFlowSortingExome2015a]||
20
+|[BCL6](BCL6)|Tier 1 GE[@loveGeneticLandscapeMutations2012], FE[@masclePointMutationsBCL62003], aSHM|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@drevalGeneticSubdivisionsFollicular2023; @morinFrequentMutationHistonemodifying2011]|PASS|
21
+|[BCL7A](BCL7A)|Tier 1 GE[@grandeGenomewideDiscoverySomatic2019], FE[@balinas-gaviraFrequentMutationsAminoterminal2020], aSHM|[Grande et al](papers/grandeGenomewideDiscoverySomatic2019)|[@krysiakRecurrentSomaticMutations2017; @morinFrequentMutationHistonemodifying2011; @reichelFlowSortingExome2015]||
21 22
|[BMP7](BMP7)|Tier 1 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)|||
22
-|[CCND3](CCND3)|Tier 1 GE[@richterRecurrentMutationID32012a], FE[@schmitzBurkittLymphomaPathogenesis2012], aSHM|[Richter et al](papers/richterRecurrentMutationID32012a)|[@deschGenotypingCirculatingTumor2020; @jalladesExomeSequencingIdentifies2017; @morinFrequentMutationHistonemodifying2011]||
23
+|[CCND3](CCND3)|Tier 1 GE[@richterRecurrentMutationID32012], FE[@schmitzBurkittLymphomaPathogenesis2012]|[Richter et al](papers/richterRecurrentMutationID32012)|[@deschGenotypingCirculatingTumor2020; @jalladesExomeSequencingIdentifies2017; @morinFrequentMutationHistonemodifying2011]||
23 24
|[CHD8](CHD8)|Tier 1 GE[@grandeGenomewideDiscoverySomatic2019]|[Grande et al](papers/grandeGenomewideDiscoverySomatic2019)|||
24
-|[DDX3X](DDX3X)|Tier 1 GE[@schmitzBurkittLymphomaPathogenesis2012], FE[@gongSequentialInverseDysregulation2021], CE[@kizhakeyilDDX3XLossAdverse2021], aSHM|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|[@mottokIntegrativeGenomicAnalysis2019b; @reddyGeneticFunctionalDrivers2017]||
25
-|[FBXO11](FBXO11)|Tier 1 GE[@richterRecurrentMutationID32012a], FE[@schneiderFBXO11InactivationLeads2016b], aSHM|[Richter et al](papers/richterRecurrentMutationID32012a)|[@hubschmannMutationalMechanismsShaping2021b; @parryWholeExomeSequencing2013]||
26
-|[FOXO1](FOXO1)|Tier 1 GE[@schmitzBurkittLymphomaPathogenesis2012], FE[@trinhAnalysisFOXO1Mutations], CE[@trinhAnalysisFOXO1Mutations], aSHM|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|[@dunsCharacterizationDLBCLPMBL2021b; @morinFrequentMutationHistonemodifying2011]||
27
-|[GNA13](GNA13)|Tier 1 GE[@loveGeneticLandscapeMutations2012], FE[@muppidiLossSignalingGa132014b], aSHM|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@morinFrequentMutationHistonemodifying2011; @reichelFlowSortingExome2015a]||
28
-|[GNAI2](GNAI2)|Tier 1 GE[@grandeGenomewideDiscoverySomatic2019], aSHM|[Grande et al](papers/grandeGenomewideDiscoverySomatic2019)|[@morinMutationalStructuralAnalysis2013]||
29
-|[HNRNPU](HNRNPU)|Tier 1 GE[@paneaWholeGenomeLandscape2019], aSHM|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@reddyGeneticFunctionalDrivers2017]||
30
-|[ID3](ID3)|Tier 1 GE[@richterRecurrentMutationID32012a], FE[@richterRecurrentMutationID32012a], aSHM|[Richter et al](papers/richterRecurrentMutationID32012a)|[@schmitzBurkittLymphomaPathogenesis2012; @spinaGeneticsNodalMarginal2016b]||
31
-|[KMT2D](KMT2D)|Tier 1 GE[@grandeGenomewideDiscoverySomatic2019], FE[@liLossCREBBPKMT2D2024], CE[@rushtonGeneticEvolutionaryPatterns2020], aSHM|[Grande et al](papers/grandeGenomewideDiscoverySomatic2019)|[@beaLandscapeSomaticMutations2013; @deschGenotypingCirculatingTumor2020; @morinFrequentMutationHistonemodifying2011; @rossiCodingGenomeSplenic2012c]||
32
-|[MYC](MYC)|Tier 1 GE[@johnstonCmycHypermutationBurkitt1992], FE[@giallongoIdentificationCmycOncogene1983], CE[@christieCMYCTranslocation142008], aSHM|[Johnston et al](papers/johnstonCmycHypermutationBurkitt1992)|[@dunsCharacterizationDLBCLPMBL2021b; @jalladesExomeSequencingIdentifies2017; @pasqualucciHypermutationMultipleProtooncogenes2001a]||
33
-|[P2RY8](P2RY8)|Tier 1 GE[@muppidiLossSignalingGa132014b], FE[@muppidiLossSignalingGa132014b], aSHM|[Muppidi et al](papers/muppidiLossSignalingGa132014b)|[@drevalGeneticSubdivisionsFollicular2023; @lohrDiscoveryPrioritizationSomatic2012a]||
34
-|[PHF6](PHF6)|Tier 1 GE[@thomasGeneticSubgroupsInform2023], aSHM|[Thomas et al](papers/thomasGeneticSubgroupsInform2023)|[@reddyGeneticFunctionalDrivers2017]||
35
-|[PTEN](PTEN)|Tier 1 GE[@loveGeneticLandscapeMutations2012], aSHM|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@reddyGeneticFunctionalDrivers2017]||
36
-|[RFX7](RFX7)|Tier 1 GE[@grandeGenomewideDiscoverySomatic2019], aSHM|[Grande et al](papers/grandeGenomewideDiscoverySomatic2019)|[@arthurGenomewideDiscoverySomatic2018]||
37
-|[RHOA](RHOA)|Tier 1 GE[@richterRecurrentMutationID32012a], FE[@ohayreInactivatingMutationsGNA132016], aSHM|[Richter et al](papers/richterRecurrentMutationID32012a)|[@zhangGeneticHeterogeneityDiffuse2013]||
38
-|[SIN3A](SIN3A)|Tier 1 GE[@grandeGenomewideDiscoverySomatic2019], aSHM|[Grande et al](papers/grandeGenomewideDiscoverySomatic2019)|[@chapuyMolecularSubtypesDiffuse2018b; @rossiCodingGenomeSplenic2012c]||
39
-|[SMARCA4](SMARCA4)|Tier 1 GE[@richterRecurrentMutationID32012a], FE[@dengSMARCA4HaploinsufficientCell2024], aSHM|[Richter et al](papers/richterRecurrentMutationID32012a)|[@krysiakRecurrentSomaticMutations2017b; @nadeuGenomicEpigenomicInsights2020b; @reddyGeneticFunctionalDrivers2017]||
40
-|[TCF3](TCF3)|Tier 1 GE[@schmitzBurkittLymphomaPathogenesis2012], FE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|||
25
+|[CREBBP](CREBBP)|Tier 1 GE[@loveGeneticLandscapeMutations2012], FE[@pasqualucciInactivatingMutationsAcetyltransferase2011]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@dunsCharacterizationDLBCLPMBL2021; @parryWholeExomeSequencing2013; @pasqualucciInactivatingMutationsAcetyltransferase2011]|PASS|
26
+|[DDX3X](DDX3X)|Tier 1 GE[@schmitzBurkittLymphomaPathogenesis2012], FE[@gongSequentialInverseDysregulation2021]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|[@mottokIntegrativeGenomicAnalysis2019; @reddyGeneticFunctionalDrivers2017]||
27
+|[FBXO11](FBXO11)|Tier 1 GE[@richterRecurrentMutationID32012], FE[@duanFBXO11TargetsBCL62011]|[Richter et al](papers/richterRecurrentMutationID32012)|[@arthurGenomewideDiscoverySomatic2018; @parryWholeExomeSequencing2013]||
28
+|[FOXO1](FOXO1)|Tier 1 GE[@schmitzBurkittLymphomaPathogenesis2012], FE[@trinhAnalysisFOXO1Mutations]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|[@dunsCharacterizationDLBCLPMBL2021; @morinFrequentMutationHistonemodifying2011]||
29
+|[GNA13](GNA13)|Tier 1 GE[@loveGeneticLandscapeMutations2012], FE[@muppidiLossSignalingGa132014]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@morinFrequentMutationHistonemodifying2011; @reichelFlowSortingExome2015]||
30
+|[GNAI2](GNAI2)|Tier 1 GE[@grandeGenomewideDiscoverySomatic2019], FE[@muppidiLossSignalingGa132014]|[Grande et al](papers/grandeGenomewideDiscoverySomatic2019)|[@drevalGeneticSubdivisionsFollicular2023; @morinMutationalStructuralAnalysis2013]||
31
+|[HIST1H1E](HIST1H1E)|Tier 1 GE[@grandeGenomewideDiscoverySomatic2019], aSHM|[Grande et al](papers/grandeGenomewideDiscoverySomatic2019)|[@krysiakRecurrentSomaticMutations2017; @lohrDiscoveryPrioritizationSomatic2012; @reichelFlowSortingExome2015]||
32
+|[HNRNPU](HNRNPU)|Tier 1 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@reddyGeneticFunctionalDrivers2017]||
33
+|[ID3](ID3)|Tier 1 GE[@richterRecurrentMutationID32012]|[Richter et al](papers/richterRecurrentMutationID32012)|[@schmitzGeneticsPathogenesisDiffuse2018; @spinaGeneticsNodalMarginal2016]||
34
+|[KMT2D](KMT2D)|Tier 1 GE[@grandeGenomewideDiscoverySomatic2019], FE[@zhangDisruptionKMT2DPerturbs2015]|[Grande et al](papers/grandeGenomewideDiscoverySomatic2019)|[@beaLandscapeSomaticMutations2013; @deschGenotypingCirculatingTumor2020; @morinFrequentMutationHistonemodifying2011; @rossiCodingGenomeSplenic2012]||
35
+|[MYC](MYC)|Tier 1 GE[@johnstonCmycHypermutationBurkitt1992], FE[@freieGermlinePointMutation2024], aSHM|[Johnston et al](papers/johnstonCmycHypermutationBurkitt1992)|[@dunsCharacterizationDLBCLPMBL2021; @jalladesExomeSequencingIdentifies2017; @pasqualucciHypermutationMultipleProtooncogenes2001]||
36
+|[P2RY8](P2RY8)|Tier 1 GE[@muppidiLossSignalingGa132014], FE[@muppidiLossSignalingGa132014]|[Muppidi et al](papers/muppidiLossSignalingGa132014)|[@drevalGeneticSubdivisionsFollicular2023; @lohrDiscoveryPrioritizationSomatic2012]||
37
+|[PCBP1](PCBP1)|Tier 1 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|||
38
+|[PHF6](PHF6)|Tier 1 GE[@thomasGeneticSubgroupsInform2023]|[Thomas et al](papers/thomasGeneticSubgroupsInform2023)|[@reddyGeneticFunctionalDrivers2017]||
39
+|[PTEN](PTEN)|Tier 1 GE[@loveGeneticLandscapeMutations2012], FE[@pfeiferPTENLossDefines2013]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@reddyGeneticFunctionalDrivers2017]||
40
+|[RFX7](RFX7)|Tier 1 GE[@grandeGenomewideDiscoverySomatic2019], FE[@weberPiggyBacTransposonTools2019]|[Grande et al](papers/grandeGenomewideDiscoverySomatic2019)|[@arthurGenomewideDiscoverySomatic2018]||
41
+|[RHOA](RHOA)|Tier 1 GE[@richterRecurrentMutationID32012], FE[@ohayreInactivatingMutationsGNA132016]|[Richter et al](papers/richterRecurrentMutationID32012)|[@zhangGeneticHeterogeneityDiffuse2013]||
42
+|[SIN3A](SIN3A)|Tier 1 GE[@grandeGenomewideDiscoverySomatic2019]|[Grande et al](papers/grandeGenomewideDiscoverySomatic2019)|[@chapuyMolecularSubtypesDiffuse2018; @rossiCodingGenomeSplenic2012]||
43
+|[SMARCA4](SMARCA4)|Tier 1 GE[@richterRecurrentMutationID32012], FE[@fernandoFunctionalCharacterizationSMARCA42020]|[Richter et al](papers/richterRecurrentMutationID32012)|[@krysiakRecurrentSomaticMutations2017; @nadeuGenomicEpigenomicInsights2020b; @reddyGeneticFunctionalDrivers2017]||
44
+|[TCF3](TCF3)|Tier 1 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|||
41 45
|[TCL1A](TCL1A)|Tier 1 GE[@grandeGenomewideDiscoverySomatic2019], aSHM|[Grande et al](papers/grandeGenomewideDiscoverySomatic2019)|[@reddyGeneticFunctionalDrivers2017]||
42
-|[TFAP4](TFAP4)|Tier 1 GE[@grandeGenomewideDiscoverySomatic2019], FE[@toncUnexpectedSuppressionTumorigenesis2021]|[Grande et al](papers/grandeGenomewideDiscoverySomatic2019)|||
43
-|[TP53](TP53)|Tier 1 GE[@wildaInactivationARFMDM2p53Pathway2004], FE[@rowhTp53DeletionLineage2011], aSHM|[Wilda et al](papers/wildaInactivationARFMDM2p53Pathway2004)|[@beaLandscapeSomaticMutations2013; @lohrDiscoveryPrioritizationSomatic2012a; @morinFrequentMutationHistonemodifying2011; @rossiCodingGenomeSplenic2012c; @tiacciPervasiveMutationsJAKSTAT2018b]||
44
-|[USP7](USP7)|Tier 1 GE[@grandeGenomewideDiscoverySomatic2019], aSHM|[Grande et al](papers/grandeGenomewideDiscoverySomatic2019)|[@arthurGenomewideDiscoverySomatic2018]||
45
-|[WNK1](WNK1)|Tier 1 GE[@thomasGeneticSubgroupsInform2023], aSHM|[Thomas et al](papers/thomasGeneticSubgroupsInform2023)|[@hubschmannMutationalMechanismsShaping2021b; @jalladesExomeSequencingIdentifies2017]||
46
+|[TFAP4](TFAP4)|Tier 1 GE[@grandeGenomewideDiscoverySomatic2019]|[Grande et al](papers/grandeGenomewideDiscoverySomatic2019)|||
47
+|[TP53](TP53)|Tier 1 GE[@wildaInactivationARFMDM2p53Pathway2004], FE[@katoUnderstandingFunctionstructureFunctionmutation2003]|[Wilda et al](papers/wildaInactivationARFMDM2p53Pathway2004)|[@beaLandscapeSomaticMutations2013; @morinFrequentMutationHistonemodifying2011; @rossiCodingGenomeSplenic2012; @tiacciPervasiveMutationsJAKSTAT2018]||
48
+|[USP7](USP7)|Tier 1 GE[@grandeGenomewideDiscoverySomatic2019]|[Grande et al](papers/grandeGenomewideDiscoverySomatic2019)|[@arthurGenomewideDiscoverySomatic2018]||
49
+|[WNK1](WNK1)|Tier 1 GE[@thomasGeneticSubgroupsInform2023]|[Thomas et al](papers/thomasGeneticSubgroupsInform2023)|[@hubschmannMutationalMechanismsShaping2021; @jalladesExomeSequencingIdentifies2017]||
46 50
47 51
## Tier 2, low-confidence BL genes
48 52
49
-### *76 total*
53
+### *72 total*
50 54
51 55
|Gene|Summary| First BL study | Other entities | QC result |
52 56
|:-:|:--:|:-:|:-|:-|
53
-|[ADAMTS5](ADAMTS5)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022b]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022b)|||
54
-|[ADNP](ADNP)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022b]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022b)|||
55
-|[AGO4](AGO4)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022b]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022b)|||
56
-|[ARHGEF1](ARHGEF1)|Tier 2 GE[@muppidiLossSignalingGa132014b]|[Muppidi et al](papers/muppidiLossSignalingGa132014b)|||
57
-|[BCL2](BCL2)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022b], FE[@balSuperenhancerHypermutationAlters2022], aSHM|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022b)|[@morinFrequentMutationHistonemodifying2011; @sarkozyMutationalLandscapeGray2021a; @tanakaFrequentIncidenceSomatic1992]||
58
-|[BCL6](BCL6)|Tier 2 GE[@loveGeneticLandscapeMutations2012], FE[@balSuperenhancerHypermutationAlters2022], aSHM|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@drevalGeneticSubdivisionsFollicular2023; @morinFrequentMutationHistonemodifying2011]|PASS|
59
-|[BTG1](BTG1)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022b], FE[@mlynarczykBTG1MutationYields2023b], aSHM|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022b)|[@drevalGeneticSubdivisionsFollicular2023; @morinFrequentMutationHistonemodifying2011; @sarkozyMutationalLandscapeGray2021a]||
57
+|[ADAMTS5](ADAMTS5)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|||
58
+|[ADNP](ADNP)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|||
59
+|[AGO4](AGO4)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|||
60
+|[ARHGEF1](ARHGEF1)|Tier 2 GE[@muppidiLossSignalingGa132014]|[Muppidi et al](papers/muppidiLossSignalingGa132014)|||
61
+|[BCL2](BCL2)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022], aSHM|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|[@morinFrequentMutationHistonemodifying2011; @sarkozyMutationalLandscapeGray2021; @tanakaFrequentIncidenceSomatic1992]||
62
+|[BTG1](BTG1)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022], FE[@almasmoumFrequentLossBTG12021], aSHM|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|[@drevalGeneticSubdivisionsFollicular2023; @morinFrequentMutationHistonemodifying2011; @sarkozyMutationalLandscapeGray2021]||
60 63
|[C16orf48](C16orf48)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|||
61 64
|[CARD4](CARD4)|Tier 2 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||PASS|
62
-|[CCNF](CCNF)|Tier 2 GE[@abateDistinctViralMutational2015a], aSHM|[Abate et al](papers/abateDistinctViralMutational2015a)|[@zhangGeneticHeterogeneityDiffuse2013]||
63
-|[CD79A](CD79A)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022b]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022b)|[@rossiCodingGenomeSplenic2012c]||
64
-|[CD83](CD83)|Tier 2 GE[@paneaWholeGenomeLandscape2019], aSHM|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@dunsCharacterizationDLBCLPMBL2021b; @morinMutationalStructuralAnalysis2013; @russler-germainMutationsAssociatedProgression2023b]|PASS|
65
-|[CDC73](CDC73)|Tier 2 GE[@loveGeneticLandscapeMutations2012], aSHM|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@reddyGeneticFunctionalDrivers2017]|PASS|
66
-|[CDKN2A](CDKN2A)|Tier 2 GE[@grandeGenomewideDiscoverySomatic2019], CE[@jardinDiffuseLargeBcell2010a], aSHM|[Grande et al](papers/grandeGenomewideDiscoverySomatic2019)|[@morinMutationalStructuralAnalysis2013; @spinaGeneticsNodalMarginal2016b]||
65
+|[CCNF](CCNF)|Tier 2 GE[@abateDistinctViralMutational2015]|[Abate et al](papers/abateDistinctViralMutational2015)|[@zhangGeneticHeterogeneityDiffuse2013]||
66
+|[CD79A](CD79A)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|[@rossiCodingGenomeSplenic2012]||
67
+|[CD83](CD83)|Tier 2 GE[@paneaWholeGenomeLandscape2019], aSHM|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@dunsCharacterizationDLBCLPMBL2021; @morinMutationalStructuralAnalysis2013; @russler-germainMutationsAssociatedProgression2023]|PASS|
68
+|[CDC73](CDC73)|Tier 2 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@reddyGeneticFunctionalDrivers2017]|PASS|
69
+|[CDKN2A](CDKN2A)|Tier 2 GE[@grandeGenomewideDiscoverySomatic2019], FE[@kannengiesserFunctionalStructuralGenetic2009]|[Grande et al](papers/grandeGenomewideDiscoverySomatic2019)|[@morinMutationalStructuralAnalysis2013; @spinaGeneticsNodalMarginal2016]||
67 70
|[CDKN2C](CDKN2C)|Tier 2 GE[@thomasGeneticSubgroupsInform2023]|[Thomas et al](papers/thomasGeneticSubgroupsInform2023)|||
68
-|[CHD4](CHD4)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022b]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022b)|||
69
-|[CPXM2](CPXM2)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022b]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022b)|||
70
-|[CREBBP](CREBBP)|Tier 2 GE[@loveGeneticLandscapeMutations2012], FE[@pasqualucciInactivatingMutationsAcetyltransferase2011a], aSHM|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@dunsCharacterizationDLBCLPMBL2021b; @parryWholeExomeSequencing2013; @pasqualucciInactivatingMutationsAcetyltransferase2011a]|PASS|
71
-|[CXCR4](CXCR4)|Tier 2 GE[@paneaWholeGenomeLandscape2019], aSHM|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@khodabakhshiRecurrentTargetsAberrant2012; @krysiakRecurrentSomaticMutations2017b]|PASS|
71
+|[CHD4](CHD4)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|||
72
+|[CPXM2](CPXM2)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|||
73
+|[CXCR4](CXCR4)|Tier 2 GE[@paneaWholeGenomeLandscape2019], FE[@zmajkovicovaGenotypephenotypeCorrelationsWHIM2022], aSHM|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@khodabakhshiRecurrentTargetsAberrant2012; @krysiakRecurrentSomaticMutations2017]|PASS|
72 74
|[DHCR7](DHCR7)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|||
73
-|[E2F2](E2F2)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022b]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022b)|||
74
-|[EBF1](EBF1)|Tier 2 GE[@thomasGeneticSubgroupsInform2023], aSHM|[Thomas et al](papers/thomasGeneticSubgroupsInform2023)|[@bohleRoleEarlyBcell2013; @reichelFlowSortingExome2015a]||
75
-|[EDNRB](EDNRB)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022b]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022b)|||
75
+|[E2F2](E2F2)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|||
76
+|[EBF1](EBF1)|Tier 2 GE[@thomasGeneticSubgroupsInform2023], FE[@ramirez-komoSpontaneousLossLineage2017], aSHM|[Thomas et al](papers/thomasGeneticSubgroupsInform2023)|[@bohleRoleEarlyBcell2013; @drevalGeneticSubdivisionsFollicular2023; @reichelFlowSortingExome2015]||
77
+|[EDNRB](EDNRB)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|||
76 78
|[EHD1](EHD1)|Tier 2 GE[@thomasGeneticSubgroupsInform2023]|[Thomas et al](papers/thomasGeneticSubgroupsInform2023)|||
77 79
|[EIF4A1](EIF4A1)|Tier 2 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)|||
78 80
|[ELP2](ELP2)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|||
79 81
|[EPPK1](EPPK1)|Tier 2 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)|||
80
-|[ERAP1](ERAP1)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022b]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022b)|||
82
+|[ERAP1](ERAP1)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|||
81 83
|[EXOSC6](EXOSC6)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|||
82
-|[EZH2](EZH2)|Tier 2 GE[@loveGeneticLandscapeMutations2012], FE[@yapSomaticMutationsEZH22011b], aSHM|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@morinSomaticMutationsAltering2010a; @mottokIntegrativeGenomicAnalysis2019b]|PASS|
84
+|[EZH2](EZH2)|Tier 2 GE[@loveGeneticLandscapeMutations2012], FE[@sneeringerCoordinatedActivitiesWildtype2010]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@morinSomaticMutationsAltering2010; @mottokIntegrativeGenomicAnalysis2019]|PASS|
83 85
|[FLYWCH1](FLYWCH1)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|||
84 86
|[GGTLA4](GGTLA4)|Tier 2 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||PASS|
85 87
|[GTSE1](GTSE1)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|||
86
-|[HIST1H1E](HIST1H1E)|Tier 2 GE[@grandeGenomewideDiscoverySomatic2019], aSHM|[Grande et al](papers/grandeGenomewideDiscoverySomatic2019)|[@krysiakRecurrentSomaticMutations2017b; @lohrDiscoveryPrioritizationSomatic2012a; @reichelFlowSortingExome2015a]||
87 88
|[HIST1H3D](HIST1H3D)|Tier 2 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||PASS|
88
-|[HIST1H3I](HIST1H3I)|Tier 2 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@krysiakRecurrentSomaticMutations2017b]|PASS|
89
-|[HIST1H4J](HIST1H4J)|Tier 2 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@mottokIntegrativeGenomicAnalysis2019b]|PASS|
90
-|[HLA-DQB1](HLA-DQB1)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022b]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022b)|||
91
-|[IGLL5](IGLL5)|Tier 2 GE[@paneaWholeGenomeLandscape2019], aSHM|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@chapuyMolecularSubtypesDiffuse2018b; @deschGenotypingCirculatingTumor2020; @russler-germainMutationsAssociatedProgression2023b]|PASS|
92
-|[IKZF3](IKZF3)|Tier 2 GE[@paneaWholeGenomeLandscape2019], aSHM|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@morinFrequentMutationHistonemodifying2011]|PASS|
93
-|[IRF8](IRF8)|Tier 2 GE[@paneaWholeGenomeLandscape2019], FE[@qiuIRF8mutantCellLymphoma2024], aSHM|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@morinFrequentMutationHistonemodifying2011; @mottokIntegrativeGenomicAnalysis2019b]|PASS|
89
+|[HIST1H3I](HIST1H3I)|Tier 2 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@krysiakRecurrentSomaticMutations2017]|PASS|
90
+|[HIST1H4J](HIST1H4J)|Tier 2 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@mottokIntegrativeGenomicAnalysis2019]|PASS|
91
+|[HLA-DQB1](HLA-DQB1)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|||
92
+|[IGLL5](IGLL5)|Tier 2 GE[@paneaWholeGenomeLandscape2019], aSHM|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@chapuyMolecularSubtypesDiffuse2018; @deschGenotypingCirculatingTumor2020; @russler-germainMutationsAssociatedProgression2023]|PASS|
93
+|[IKZF3](IKZF3)|Tier 2 GE[@paneaWholeGenomeLandscape2019], FE[@lazarianHotspotMutationTranscription2021]|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@morinFrequentMutationHistonemodifying2011]|PASS|
94
+|[IRF8](IRF8)|Tier 2 GE[@paneaWholeGenomeLandscape2019], FE[@qiuIRF8mutantCellLymphoma2024], aSHM|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@morinFrequentMutationHistonemodifying2011; @mottokIntegrativeGenomicAnalysis2019]|PASS|
94 95
|[KANK2](KANK2)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|||
95
-|[KLHL26](KLHL26)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022b]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022b)|||
96
-|[KMT2C](KMT2C)|Tier 2 GE[@zhouSporadicEndemicBurkitt2019], aSHM|[Zhou et al](papers/zhouSporadicEndemicBurkitt2019)|[@sarkozyMutationalLandscapeGray2021a; @zhangGeneticHeterogeneityDiffuse2013; @zhangGenomicLandscapeMantle2014]||
97
-|[MCL1](MCL1)|Tier 2 GE[@paneaWholeGenomeLandscape2019], aSHM|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@dunsCharacterizationDLBCLPMBL2021b; @reddyGeneticFunctionalDrivers2017]|PASS|
98
-|[MIR142](MIR142)|Tier 2 GE[@grandeGenomewideDiscoverySomatic2019], aSHM|[Grande et al](papers/grandeGenomewideDiscoverySomatic2019)|[@kwanhianMicroRNA142Mutated202012b]||
99
-|[MKI67](MKI67)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|[@russler-germainMutationsAssociatedProgression2023b]||
96
+|[KLHL26](KLHL26)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|||
97
+|[KMT2C](KMT2C)|Tier 2 GE[@zhouSporadicEndemicBurkitt2019]|[Zhou et al](papers/zhouSporadicEndemicBurkitt2019)|[@sarkozyMutationalLandscapeGray2021; @zhangGeneticHeterogeneityDiffuse2013; @zhangGenomicLandscapeMantle2014]||
98
+|[MCL1](MCL1)|Tier 2 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@dunsCharacterizationDLBCLPMBL2021; @reddyGeneticFunctionalDrivers2017]|PASS|
99
+|[MIR142](MIR142)|Tier 2 GE[@grandeGenomewideDiscoverySomatic2019], FE[@trissalMIR142LossofFunctionMutations2018], aSHM|[Grande et al](papers/grandeGenomewideDiscoverySomatic2019)|[@kwanhianMicroRNA142Mutated202012]||
100
+|[MKI67](MKI67)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|[@russler-germainMutationsAssociatedProgression2023]||
100 101
|[MYO18A](MYO18A)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|||
101 102
|[NBEAL1](NBEAL1)|Tier 2 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||PASS|
102
-|[NCOR2](NCOR2)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012], aSHM|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|[@sarkozyMutationalLandscapeGray2021a; @spinaGeneticsNodalMarginal2016b]||
103
-|[NOA1](NOA1)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022b]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022b)|||
103
+|[NCOR2](NCOR2)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|[@sarkozyMutationalLandscapeGray2021; @spinaGeneticsNodalMarginal2016]||
104
+|[NOA1](NOA1)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|||
104 105
|[P2RY2](P2RY2)|Tier 2 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||PASS|
105
-|[PCBP1](PCBP1)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012], aSHM|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|||
106 106
|[PDCD11](PDCD11)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|||
107
-|[PIM1](PIM1)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022b], CE[@guoSGK1MutationStatus2022b], aSHM|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022b)|[@drevalGeneticSubdivisionsFollicular2023; @dunsCharacterizationDLBCLPMBL2021b; @pasqualucciHypermutationMultipleProtooncogenes2001a]||
108
-|[PLCG2](PLCG2)|Tier 2 GE[@paneaWholeGenomeLandscape2019], aSHM|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@fanComprehensiveCharacterizationDriver2020b]|PASS|
109
-|[PPP6R2](PPP6R2)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022b]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022b)|||
110
-|[PREX1](PREX1)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022b]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022b)|||
107
+|[PIM1](PIM1)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022], FE[@kuoRolePIM1Ibrutinibresistant2016], aSHM|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|[@drevalGeneticSubdivisionsFollicular2023; @dunsCharacterizationDLBCLPMBL2021; @pasqualucciHypermutationMultipleProtooncogenes2001]||
108
+|[PLCG2](PLCG2)|Tier 2 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@fanComprehensiveCharacterizationDriver2020]|PASS|
109
+|[PPP6R2](PPP6R2)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|||
110
+|[PREX1](PREX1)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|||
111 111
|[RANBP6](RANBP6)|Tier 2 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||PASS|
112
-|[REV3L](REV3L)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022b]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022b)|||
112
+|[REV3L](REV3L)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|||
113 113
|[RNF144B](RNF144B)|Tier 2 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||PASS|
114
-|[RPL10](RPL10)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022b]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022b)|||
115
-|[S1PR2](S1PR2)|Tier 2 GE[@muppidiLossSignalingGa132014b], FE[@floriHematopoieticOncoproteinFOXP12016], aSHM|[Muppidi et al](papers/muppidiLossSignalingGa132014b)|[@drevalGeneticSubdivisionsFollicular2023; @morinFrequentMutationHistonemodifying2011]||
116
-|[SAL3](SAL3)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022b]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022b)|||
117
-|[TET2](TET2)|Tier 2 GE[@thomasGeneticSubgroupsInform2023], aSHM|[Thomas et al](papers/thomasGeneticSubgroupsInform2023)|[@albuquerqueEnhancingKnowledgeDiscovery2017a]||
114
+|[RPL10](RPL10)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|||
115
+|[S1PR2](S1PR2)|Tier 2 GE[@muppidiLossSignalingGa132014], FE[@muppidiLossSignalingGa132014], aSHM|[Muppidi et al](papers/muppidiLossSignalingGa132014)|[@drevalGeneticSubdivisionsFollicular2023; @morinFrequentMutationHistonemodifying2011]||
116
+|[SAL3](SAL3)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|||
117
+|[TET2](TET2)|Tier 2 GE[@thomasGeneticSubgroupsInform2023], FE[@asmarGenomewideProfilingIdentifies2013]|[Thomas et al](papers/thomasGeneticSubgroupsInform2023)|[@albuquerqueEnhancingKnowledgeDiscovery2017]||
118 118
|[TOP2A](TOP2A)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|||
119
-|[TTN](TTN)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022b]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022b)|||
120
-|[VWA7](VWA7)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022b]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022b)|||
119
+|[TTN](TTN)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|||
120
+|[VWA7](VWA7)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|||
121 121
|[WDR90](WDR90)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|||
122 122
|[WHAMM](WHAMM)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|||
123 123
|[WNK2](WNK2)|Tier 2 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||PASS|
124 124
|[YY1AP1](YY1AP1)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|||
125
-|[ZAN](ZAN)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022b]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022b)|||
126
-|[ZBTB7A](ZBTB7A)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022b], aSHM|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022b)|[@reddyGeneticFunctionalDrivers2017]||
127
-|[ZFP36L1](ZFP36L1)|Tier 2 GE[@paneaWholeGenomeLandscape2019], aSHM|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@morinFrequentMutationHistonemodifying2011; @reichelFlowSortingExome2015a]|PASS|
128
-|[ZNF85](ZNF85)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022b]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022b)|||
125
+|[ZAN](ZAN)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|||
126
+|[ZBTB7A](ZBTB7A)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|[@reddyGeneticFunctionalDrivers2017]||
127
+|[ZFP36L1](ZFP36L1)|Tier 2 GE[@paneaWholeGenomeLandscape2019], aSHM|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@morinFrequentMutationHistonemodifying2011; @reichelFlowSortingExome2015]|PASS|
128
+|[ZNF85](ZNF85)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)|||
129 129
130 130
## Tier 3, retired BL genes
131 131
... ...
@@ -134,24 +134,24 @@ link-citations: true
134 134
|Gene|Summary| First BL study | Other entities | QC result |
135 135
|:-:|:--:|:-:|:-|:-|
136 136
|[ACAD9](ACAD9)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
137
-|[ACE](ACE)|Tier 3 GE[@loveGeneticLandscapeMutations2012], aSHM|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@zhangGeneticHeterogeneityDiffuse2013]|FAIL|
137
+|[ACE](ACE)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@zhangGeneticHeterogeneityDiffuse2013]|FAIL|
138 138
|[ALPK2](ALPK2)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||FAIL|
139 139
|[ATP2C2](ATP2C2)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
140
-|[BRAF](BRAF)|Tier 3 GE[@loveGeneticLandscapeMutations2012], aSHM|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@tiacciBRAFMutationsHairycell2011a]|FAIL|
141
-|[BRD4](BRD4)|Tier 3 GE[@loveGeneticLandscapeMutations2012], aSHM|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@zhangGeneticHeterogeneityDiffuse2013]|FAIL|
142
-|[BTG2](BTG2)|Tier 3 GE[@loveGeneticLandscapeMutations2012], CE[@guoMutationBTG2Gene2022b], aSHM|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@drevalGeneticSubdivisionsFollicular2023; @morinFrequentMutationHistonemodifying2011]|FAIL|
140
+|[BRAF](BRAF)|Tier 3 GE[@loveGeneticLandscapeMutations2012], FE[@wanMechanismActivationRAFERK2004]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@tiacciBRAFMutationsHairycell2011]|FAIL|
141
+|[BRD4](BRD4)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@zhangGeneticHeterogeneityDiffuse2013]|FAIL|
142
+|[BTG2](BTG2)|Tier 3 GE[@loveGeneticLandscapeMutations2012], aSHM|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@drevalGeneticSubdivisionsFollicular2023; @morinFrequentMutationHistonemodifying2011]|FAIL|
143 143
|[C6orf27](C6orf27)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
144
-|[CAD](CAD)|Tier 3 GE[@loveGeneticLandscapeMutations2012], aSHM|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@zhangGeneticHeterogeneityDiffuse2013]|FAIL|
144
+|[CAD](CAD)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@zhangGeneticHeterogeneityDiffuse2013]|FAIL|
145 145
|[CCT6B](CCT6B)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
146
-|[CD79B](CD79B)|Tier 3 GE[@paneaWholeGenomeLandscape2019], FE[@davisChronicActiveBcellreceptor2010], aSHM|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@drevalGeneticSubdivisionsFollicular2023; @morinFrequentMutationHistonemodifying2011]|FAIL|
146
+|[CD79B](CD79B)|Tier 3 GE[@paneaWholeGenomeLandscape2019], FE[@davisChronicActiveBcellreceptor2010]|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@davisChronicActiveBcellreceptor2010; @drevalGeneticSubdivisionsFollicular2023]|FAIL|
147 147
|[CDH17](CDH17)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
148 148
|[COL4A2](COL4A2)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
149 149
|[CTCF](CTCF)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||FAIL|
150 150
|[CYB5D1](CYB5D1)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
151 151
|[CYP4F22](CYP4F22)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
152
-|[DLGAP1](DLGAP1)|Tier 3 GE[@loveGeneticLandscapeMutations2012], aSHM|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@zhangGeneticHeterogeneityDiffuse2013]|FAIL|
152
+|[DLGAP1](DLGAP1)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@zhangGeneticHeterogeneityDiffuse2013]|FAIL|
153 153
|[DNMT1](DNMT1)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||FAIL|
154
-|[DTX1](DTX1)|Tier 3 GE[@loveGeneticLandscapeMutations2012], FE[@demirandaExomeSequencingReveals2014], CE[@merirantaDeltex1MutationsPredict2017b], aSHM|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@gomezUltraDeepSequencingReveals2023; @rossiCodingGenomeSplenic2012c; @zhangGeneticHeterogeneityDiffuse2013]|FAIL|
154
+|[DTX1](DTX1)|Tier 3 GE[@loveGeneticLandscapeMutations2012], aSHM|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@gomezUltraDeepSequencingReveals2023; @rossiCodingGenomeSplenic2012; @zhangGeneticHeterogeneityDiffuse2013]|FAIL|
155 155
|[EIF2C4](EIF2C4)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
156 156
|[EML2](EML2)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
157 157
|[ENTPD3](ENTPD3)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
... ...
@@ -163,37 +163,37 @@ link-citations: true
163 163
|[FZD3](FZD3)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||FAIL|
164 164
|[GRIK5](GRIK5)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
165 165
|[HIST1H1C](HIST1H1C)|Tier 3 GE[@paneaWholeGenomeLandscape2019], aSHM|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@morinFrequentMutationHistonemodifying2011]|FAIL|
166
-|[HIST1H2AG](HIST1H2AG)|Tier 3 GE[@paneaWholeGenomeLandscape2019], aSHM|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@krysiakRecurrentSomaticMutations2017b; @morinMutationalStructuralAnalysis2013; @rossiCodingGenomeSplenic2012c]|FAIL|
167
-|[HIST1H2AM](HIST1H2AM)|Tier 3 GE[@paneaWholeGenomeLandscape2019], aSHM|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@chapuyMolecularSubtypesDiffuse2018b; @krysiakRecurrentSomaticMutations2017b]|FAIL|
168
-|[HIST1H2BK](HIST1H2BK)|Tier 3 GE[@paneaWholeGenomeLandscape2019], aSHM|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@rossiCodingGenomeSplenic2012c; @zhangGeneticHeterogeneityDiffuse2013]|FAIL|
166
+|[HIST1H2AG](HIST1H2AG)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@krysiakRecurrentSomaticMutations2017; @morinMutationalStructuralAnalysis2013; @rossiCodingGenomeSplenic2012]|FAIL|
167
+|[HIST1H2AM](HIST1H2AM)|Tier 3 GE[@paneaWholeGenomeLandscape2019], aSHM|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@chapuyMolecularSubtypesDiffuse2018; @krysiakRecurrentSomaticMutations2017]|FAIL|
168
+|[HIST1H2BK](HIST1H2BK)|Tier 3 GE[@paneaWholeGenomeLandscape2019], aSHM|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@rossiCodingGenomeSplenic2012; @zhangGeneticHeterogeneityDiffuse2013]|FAIL|
169 169
|[HIST1H3H](HIST1H3H)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||FAIL|
170 170
|[HIST1H3J](HIST1H3J)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||FAIL|
171 171
|[ICK](ICK)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
172
-|[ITPR3](ITPR3)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@tiacciPervasiveMutationsJAKSTAT2018b]|FAIL|
172
+|[ITPR3](ITPR3)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@tiacciPervasiveMutationsJAKSTAT2018]|FAIL|
173 173
|[KCNK10](KCNK10)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||FAIL|
174 174
|[KIFC3](KIFC3)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
175 175
|[MAP3K6](MAP3K6)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
176 176
|[MME](MME)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||FAIL|
177
-|[MTOR](MTOR)|Tier 3 GE[@paneaWholeGenomeLandscape2019], aSHM|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@zhangGeneticHeterogeneityDiffuse2013]|FAIL|
177
+|[MTOR](MTOR)|Tier 3 GE[@paneaWholeGenomeLandscape2019], FE[@grabinerDiverseArrayCancerassociated2014]|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@zhangGeneticHeterogeneityDiffuse2013]|FAIL|
178 178
|[MYH10](MYH10)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
179
-|[NOTCH1](NOTCH1)|Tier 3 GE[@loveGeneticLandscapeMutations2012], CE[@kridelWholeTranscriptomeSequencing2012], aSHM|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@beaLandscapeSomaticMutations2013; @pasqualucciAnalysisCodingGenome2011; @rossiCodingGenomeSplenic2012c]|FAIL|
180
-|[NRXN2](NRXN2)|Tier 3 GE[@loveGeneticLandscapeMutations2012], aSHM|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@zhangGeneticHeterogeneityDiffuse2013]|FAIL|
179
+|[NOTCH1](NOTCH1)|Tier 3 GE[@loveGeneticLandscapeMutations2012], FE[@ryanCellRegulomeLinks2017]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@beaLandscapeSomaticMutations2013; @pasqualucciAnalysisCodingGenome2011; @rossiCodingGenomeSplenic2012]|FAIL|
180
+|[NRXN2](NRXN2)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@zhangGeneticHeterogeneityDiffuse2013]|FAIL|
181 181
|[PABPC4L](PABPC4L)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||FAIL|
182 182
|[PC](PC)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
183 183
|[PCDHA11](PCDHA11)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||FAIL|
184
-|[PDZRN3](PDZRN3)|Tier 3 GE[@paneaWholeGenomeLandscape2019], aSHM|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@zhangGeneticHeterogeneityDiffuse2013]|FAIL|
185
-|[PIK3R1](PIK3R1)|Tier 3 GE[@paneaWholeGenomeLandscape2019], aSHM|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@zhangGeneticHeterogeneityDiffuse2013]|FAIL|
184
+|[PDZRN3](PDZRN3)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@zhangGeneticHeterogeneityDiffuse2013]|FAIL|
185
+|[PIK3R1](PIK3R1)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@zhangGeneticHeterogeneityDiffuse2013]|FAIL|
186 186
|[POLRMT](POLRMT)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
187 187
|[POR](POR)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
188 188
|[PRSS22](PRSS22)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
189 189
|[PTPRN](PTPRN)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
190 190
|[PXDNL](PXDNL)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||FAIL|
191
-|[RBP3](RBP3)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
192
-|[RET](RET)|Tier 3 GE[@loveGeneticLandscapeMutations2012], aSHM|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@fanComprehensiveCharacterizationDriver2020b]|FAIL|
191
+|[RBP3](RBP3)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@lohrDiscoveryPrioritizationSomatic2012]|FAIL|
192
+|[RET](RET)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@fanComprehensiveCharacterizationDriver2020]|FAIL|
193 193
|[SALL3](SALL3)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@zhangGenomicLandscapeMantle2014]|FAIL|
194 194
|[SAPS2](SAPS2)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
195 195
|[SBF1](SBF1)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
196
-|[SF3B1](SF3B1)|Tier 3 GE[@loveGeneticLandscapeMutations2012], aSHM|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@reddyGeneticFunctionalDrivers2017]|FAIL|
196
+|[SF3B1](SF3B1)|Tier 3 GE[@loveGeneticLandscapeMutations2012], FE[@cazzolaBiologicClinicalSignificance2013]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@reddyGeneticFunctionalDrivers2017]|FAIL|
197 197
|[SHANK1](SHANK1)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
198 198
|[SLC29A2](SLC29A2)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL|
199 199
|[SNTB2](SNTB2)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||FAIL|
BTK.md
... ...
@@ -20,8 +20,8 @@ timeline
20 20
21 21
|Entity|Tier|Description |
22 22
|:------:|:----:|--------------------------|
23
-|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene[@albuquerqueEnhancingKnowledgeDiscovery2017a; @reddyGeneticFunctionalDrivers2017]|
24
-|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene [@krysiakRecurrentSomaticMutations2017b]|
23
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene[@albuquerqueEnhancingKnowledgeDiscovery2017; @reddyGeneticFunctionalDrivers2017]|
24
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene [@krysiakRecurrentSomaticMutations2017]|
25 25
26 26
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
27 27
DLBCL_genes.md
... ...
@@ -11,715 +11,746 @@ link-citations: true
11 11
12 12
## Tier 1, high-confidence DLBCL genes
13 13
14
-### *126 total*
14
+### *125 total*
15 15
16 16
|Gene|Summary| First DLBCL study | Other entities | QC result |
17 17
|:-:|:--:|:-:|:-|:-|
18
-|[ACTB](ACTB)|Tier 1 GE[@lohrDiscoveryPrioritizationSomatic2012a], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012a)|[@drevalGeneticSubdivisionsFollicular2023; @wienandGenomicAnalysesFlowsorted2019b]||
19
-|[ACTG1](ACTG1)|Tier 1 GE[@hubschmannMutationalMechanismsShaping2021b], aSHM|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)|[@deschGenotypingCirculatingTumor2020; @spinaGeneticsNodalMarginal2016b]||
20
-|[ARID1A](ARID1A)|Tier 1 GE[@zhangGeneticHeterogeneityDiffuse2013], FE[@barisicARID1AOrchestratesSWI2024], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@krysiakRecurrentSomaticMutations2017b; @loveGeneticLandscapeMutations2012; @rossiCodingGenomeSplenic2012c; @wienandGenomicAnalysesFlowsorted2019b]||
21
-|[ATM](ATM)|Tier 1 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@beaLandscapeSomaticMutations2013; @braggioGenomicAnalysisMarginal2012]||
22
-|[B2M](B2M)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@challa-malladiCombinedGeneticInactivationa], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@pararajalingamCodingNoncodingDrivers2020; @reichelFlowSortingExome2015a]||
23
-|[BCL10](BCL10)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@xiaBCL10MutationsDefine2022], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@russler-germainMutationsAssociatedProgression2023b; @spinaGeneticsNodalMarginal2016b]||
24
-|[BCL2](BCL2)|Tier 1 GE[@tanakaFrequentIncidenceSomatic1992], FE[@balSuperenhancerHypermutationAlters2022], aSHM|[Tanaka et al](papers/tanakaFrequentIncidenceSomatic1992)|[@burkhardtClinicalRelevanceMolecular2022b; @morinFrequentMutationHistonemodifying2011; @sarkozyMutationalLandscapeGray2021a]||
25
-|[BCL6](BCL6)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@balSuperenhancerHypermutationAlters2022], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@drevalGeneticSubdivisionsFollicular2023; @loveGeneticLandscapeMutations2012]||
26
-|[BCL7A](BCL7A)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@balinas-gaviraFrequentMutationsAminoterminal2020b], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@grandeGenomewideDiscoverySomatic2019; @krysiakRecurrentSomaticMutations2017b; @reichelFlowSortingExome2015a]||
27
-|[BIRC6](BIRC6)|Tier 1 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@sarkozyMutationalLandscapeGray2021a]||
28
-|[BRAF](BRAF)|Tier 1 GE[@tiacciBRAFMutationsHairycell2011a], aSHM|[Tiacci et al](papers/tiacciBRAFMutationsHairycell2011a)|[@loveGeneticLandscapeMutations2012]||
29
-|[BTG1](BTG1)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@mlynarczykBTG1MutationYields2023b], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@burkhardtClinicalRelevanceMolecular2022b; @drevalGeneticSubdivisionsFollicular2023; @sarkozyMutationalLandscapeGray2021a]||
30
-|[BTG2](BTG2)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], CE[@guoMutationBTG2Gene2022b], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@drevalGeneticSubdivisionsFollicular2023; @loveGeneticLandscapeMutations2012]||
31
-|[BTK](BTK)|Tier 1 GE[@albuquerqueEnhancingKnowledgeDiscovery2017a], aSHM|[Albuquerque et al](papers/albuquerqueEnhancingKnowledgeDiscovery2017a)|[@krysiakRecurrentSomaticMutations2017b]||
32
-|[CARD11](CARD11)|Tier 1 GE[@lenzOncogenicCARD11Mutations2008], FE[@lenzOncogenicCARD11Mutations2008], CE[@zhaoExpressionPrognosticValue2016], aSHM|[Lenz et al](papers/lenzOncogenicCARD11Mutations2008)|[@morinFrequentMutationHistonemodifying2011; @wuGeneticHeterogeneityPrimary2016; @yanBCRTLRSignaling2012a]||
33
-|[CCND3](CCND3)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@schmitzBurkittLymphomaPathogenesis2012], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@deschGenotypingCirculatingTumor2020; @jalladesExomeSequencingIdentifies2017; @richterRecurrentMutationID32012a]||
34
-|[CD58](CD58)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@challa-malladiCombinedGeneticInactivationa], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@schneiderAlterationsCD58Gene2015a]||
35
-|[CD70](CD70)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@russler-germainMutationsAssociatedProgression2023b]||
36
-|[CD79B](CD79B)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@davisChronicActiveBcellreceptor2010], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@drevalGeneticSubdivisionsFollicular2023; @paneaWholeGenomeLandscape2019]||
37
-|[CD83](CD83)|Tier 1 GE[@morinMutationalStructuralAnalysis2013], aSHM|[Morin et al](papers/morinMutationalStructuralAnalysis2013)|[@dunsCharacterizationDLBCLPMBL2021b; @paneaWholeGenomeLandscape2019; @russler-germainMutationsAssociatedProgression2023b]||
38
-|[CDKN2A](CDKN2A)|Tier 1 GE[@morinMutationalStructuralAnalysis2013], CE[@jardinDiffuseLargeBcell2010a], aSHM|[Morin et al](papers/morinMutationalStructuralAnalysis2013)|[@grandeGenomewideDiscoverySomatic2019; @spinaGeneticsNodalMarginal2016b]||
39
-|[CIITA](CIITA)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], CE[@guoSGK1MutationStatus2022b], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@mottokGenomicAlterationsCIITA2015b]||
40
-|[CREBBP](CREBBP)|Tier 1 GE[@pasqualucciInactivatingMutationsAcetyltransferase2011a], FE[@pasqualucciInactivatingMutationsAcetyltransferase2011a], aSHM|[Pasqualucci et al](papers/pasqualucciInactivatingMutationsAcetyltransferase2011a)|[@dunsCharacterizationDLBCLPMBL2021b; @loveGeneticLandscapeMutations2012; @parryWholeExomeSequencing2013]||
41
-|[CXCR4](CXCR4)|Tier 1 GE[@khodabakhshiRecurrentTargetsAberrant2012], aSHM|[Khodabakhshi et al](papers/khodabakhshiRecurrentTargetsAberrant2012)|[@krysiakRecurrentSomaticMutations2017b; @paneaWholeGenomeLandscape2019]||
42
-|[CXCR5](CXCR5)|Tier 1 GE[@schmitzGeneticsPathogenesisDiffuse2018a], aSHM|[Schmitz et al](papers/schmitzGeneticsPathogenesisDiffuse2018a)|[@mottokIntegrativeGenomicAnalysis2019b]||
43
-|[DDX3X](DDX3X)|Tier 1 GE[@reddyGeneticFunctionalDrivers2017], FE[@gongSequentialInverseDysregulation2021], CE[@kizhakeyilDDX3XLossAdverse2021], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@mottokIntegrativeGenomicAnalysis2019b; @schmitzBurkittLymphomaPathogenesis2012]||
44
-|[DTX1](DTX1)|Tier 1 GE[@zhangGeneticHeterogeneityDiffuse2013], FE[@demirandaExomeSequencingReveals2014], CE[@merirantaDeltex1MutationsPredict2017b], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@gomezUltraDeepSequencingReveals2023; @loveGeneticLandscapeMutations2012; @rossiCodingGenomeSplenic2012c]||
45
-|[DUSP2](DUSP2)|Tier 1 GE[@lohrDiscoveryPrioritizationSomatic2012a], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012a)|[@drevalGeneticSubdivisionsFollicular2023; @dunsCharacterizationDLBCLPMBL2021b]||
46
-|[EBF1](EBF1)|Tier 1 GE[@bohleRoleEarlyBcell2013], aSHM|[Bohle et al](papers/bohleRoleEarlyBcell2013)|[@reichelFlowSortingExome2015a; @thomasGeneticSubgroupsInform2023]||
47
-|[EEF1A1](EEF1A1)|Tier 1 GE[@hubschmannMutationalMechanismsShaping2021b], CE[@gongExpressionClinicalValue2021], aSHM|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)|[@reichelFlowSortingExome2015a]||
48
-|[EP300](EP300)|Tier 1 GE[@pasqualucciInactivatingMutationsAcetyltransferase2011a], FE[@pasqualucciInactivatingMutationsAcetyltransferase2011a], aSHM|[Pasqualucci et al](papers/pasqualucciInactivatingMutationsAcetyltransferase2011a)|[@rossiCodingGenomeSplenic2012c]||
18
+|[ACTB](ACTB)|Tier 1 GE[@lohrDiscoveryPrioritizationSomatic2012], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012)|[@drevalGeneticSubdivisionsFollicular2023; @wienandGenomicAnalysesFlowsorted2019]||
19
+|[ACTG1](ACTG1)|Tier 1 GE[@fanComprehensiveCharacterizationDriver2020], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|[@deschGenotypingCirculatingTumor2020; @hubschmannMutationalMechanismsShaping2021; @spinaGeneticsNodalMarginal2016]||
20
+|[ARID1A](ARID1A)|Tier 1 GE[@zhangGeneticHeterogeneityDiffuse2013], FE[@barisicARID1AOrchestratesSWI2024]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@krysiakRecurrentSomaticMutations2017; @loveGeneticLandscapeMutations2012; @rossiCodingGenomeSplenic2012; @wienandGenomicAnalysesFlowsorted2019]||
21
+|[ATM](ATM)|Tier 1 GE[@reddyGeneticFunctionalDrivers2017], FE[@camachoATMGeneInactivation2002]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@beaLandscapeSomaticMutations2013; @braggioGenomicAnalysisMarginal2012]||
22
+|[B2M](B2M)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@challa-malladiCombinedGeneticInactivation2011]|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@pararajalingamCodingNoncodingDrivers2020; @reichelFlowSortingExome2015]||
23
+|[BCL10](BCL10)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@xiaBCL10MutationsDefine2022]|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@russler-germainMutationsAssociatedProgression2023; @spinaGeneticsNodalMarginal2016]||
24
+|[BCL2](BCL2)|Tier 1 GE[@tanakaFrequentIncidenceSomatic1992], aSHM|[Tanaka et al](papers/tanakaFrequentIncidenceSomatic1992)|[@burkhardtClinicalRelevanceMolecular2022; @morinFrequentMutationHistonemodifying2011; @sarkozyMutationalLandscapeGray2021]||
25
+|[BCL6](BCL6)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@masclePointMutationsBCL62003], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@drevalGeneticSubdivisionsFollicular2023; @loveGeneticLandscapeMutations2012]||
26
+|[BCL7A](BCL7A)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@balinas-gaviraFrequentMutationsAminoterminal2020], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@grandeGenomewideDiscoverySomatic2019; @krysiakRecurrentSomaticMutations2017; @reichelFlowSortingExome2015]||
27
+|[BIRC6](BIRC6)|Tier 1 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@sarkozyMutationalLandscapeGray2021]||
28
+|[BRAF](BRAF)|Tier 1 GE[@tiacciBRAFMutationsHairycell2011], FE[@wanMechanismActivationRAFERK2004]|[Tiacci et al](papers/tiacciBRAFMutationsHairycell2011)|[@loveGeneticLandscapeMutations2012]||
29
+|[BTG1](BTG1)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@almasmoumFrequentLossBTG12021], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@burkhardtClinicalRelevanceMolecular2022; @drevalGeneticSubdivisionsFollicular2023; @sarkozyMutationalLandscapeGray2021]||
30
+|[BTG2](BTG2)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@drevalGeneticSubdivisionsFollicular2023; @loveGeneticLandscapeMutations2012]||
31
+|[BTK](BTK)|Tier 1 GE[@albuquerqueEnhancingKnowledgeDiscovery2017], FE[@huFollicularLymphomaassociatedBTK2021]|[Albuquerque et al](papers/albuquerqueEnhancingKnowledgeDiscovery2017)|[@krysiakRecurrentSomaticMutations2017]||
32
+|[CARD11](CARD11)|Tier 1 GE[@lenzOncogenicCARD11Mutations2008], FE[@lenzOncogenicCARD11Mutations2008]|[Lenz et al](papers/lenzOncogenicCARD11Mutations2008)|[@morinFrequentMutationHistonemodifying2011; @wuGeneticHeterogeneityPrimary2016; @yanBCRTLRSignaling2012]||
33
+|[CCND3](CCND3)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@schmitzBurkittLymphomaPathogenesis2012]|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@deschGenotypingCirculatingTumor2020; @jalladesExomeSequencingIdentifies2017; @richterRecurrentMutationID32012]||
34
+|[CD58](CD58)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@challa-malladiCombinedGeneticInactivation2011]|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@schneiderAlterationsCD58Gene2015]||
35
+|[CD70](CD70)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@nieDualRoleCD702022]|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@russler-germainMutationsAssociatedProgression2023]||
36
+|[CD79B](CD79B)|Tier 1 GE[@davisChronicActiveBcellreceptor2010], FE[@davisChronicActiveBcellreceptor2010]|[Davis et al](papers/davisChronicActiveBcellreceptor2010)|[@drevalGeneticSubdivisionsFollicular2023; @paneaWholeGenomeLandscape2019]||
37
+|[CD83](CD83)|Tier 1 GE[@morinMutationalStructuralAnalysis2013], aSHM|[Morin et al](papers/morinMutationalStructuralAnalysis2013)|[@dunsCharacterizationDLBCLPMBL2021; @paneaWholeGenomeLandscape2019; @russler-germainMutationsAssociatedProgression2023]||
38
+|[CDKN2A](CDKN2A)|Tier 1 GE[@morinMutationalStructuralAnalysis2013], FE[@kannengiesserFunctionalStructuralGenetic2009]|[Morin et al](papers/morinMutationalStructuralAnalysis2013)|[@grandeGenomewideDiscoverySomatic2019; @spinaGeneticsNodalMarginal2016]||
39
+|[CIITA](CIITA)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@mottokGenomicAlterationsCIITA2015], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@mottokGenomicAlterationsCIITA2015]||
40
+|[CREBBP](CREBBP)|Tier 1 GE[@pasqualucciInactivatingMutationsAcetyltransferase2011], FE[@pasqualucciInactivatingMutationsAcetyltransferase2011]|[Pasqualucci et al](papers/pasqualucciInactivatingMutationsAcetyltransferase2011)|[@dunsCharacterizationDLBCLPMBL2021; @loveGeneticLandscapeMutations2012; @parryWholeExomeSequencing2013]||
41
+|[CXCR4](CXCR4)|Tier 1 GE[@khodabakhshiRecurrentTargetsAberrant2012], FE[@zmajkovicovaGenotypephenotypeCorrelationsWHIM2022], aSHM|[Khodabakhshi et al](papers/khodabakhshiRecurrentTargetsAberrant2012)|[@krysiakRecurrentSomaticMutations2017; @paneaWholeGenomeLandscape2019]||
42
+|[DDX3X](DDX3X)|Tier 1 GE[@reddyGeneticFunctionalDrivers2017], FE[@gongSequentialInverseDysregulation2021]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@mottokIntegrativeGenomicAnalysis2019; @schmitzBurkittLymphomaPathogenesis2012]||
43
+|[DTX1](DTX1)|Tier 1 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@gomezUltraDeepSequencingReveals2023; @loveGeneticLandscapeMutations2012; @rossiCodingGenomeSplenic2012]||
44
+|[DUSP2](DUSP2)|Tier 1 GE[@lohrDiscoveryPrioritizationSomatic2012], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012)|[@drevalGeneticSubdivisionsFollicular2023; @dunsCharacterizationDLBCLPMBL2021]||
45
+|[EBF1](EBF1)|Tier 1 GE[@bohleRoleEarlyBcell2013], FE[@ramirez-komoSpontaneousLossLineage2017], aSHM|[Bohle et al](papers/bohleRoleEarlyBcell2013)|[@drevalGeneticSubdivisionsFollicular2023; @reichelFlowSortingExome2015; @thomasGeneticSubgroupsInform2023]||
46
+|[EEF1A1](EEF1A1)|Tier 1 GE[@chapuyMolecularSubtypesDiffuse2018]|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018)|[@hubschmannMutationalMechanismsShaping2021; @reichelFlowSortingExome2015]||
47
+|[EP300](EP300)|Tier 1 GE[@pasqualucciInactivatingMutationsAcetyltransferase2011], FE[@pasqualucciInactivatingMutationsAcetyltransferase2011]|[Pasqualucci et al](papers/pasqualucciInactivatingMutationsAcetyltransferase2011)|[@rossiCodingGenomeSplenic2012]||
49 48
|[ETS1](ETS1)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@paneaWholeGenomeLandscape2019]||
50
-|[ETV6](ETV6)|Tier 1 GE[@lohrDiscoveryPrioritizationSomatic2012a], CE[@guoSGK1MutationStatus2022b], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012a)|||
51
-|[EZH2](EZH2)|Tier 1 GE[@morinSomaticMutationsAltering2010a], FE[@yapSomaticMutationsEZH22011b], aSHM|[Morin et al](papers/morinSomaticMutationsAltering2010a)|[@loveGeneticLandscapeMutations2012; @mottokIntegrativeGenomicAnalysis2019b]||
52
-|[FAS](FAS)|Tier 1 GE[@schollMutationsRegionFAS2007], FE[@seebergerLossFasCD952001], aSHM|[Scholl et al](papers/schollMutationsRegionFAS2007)|[@spinaGeneticsNodalMarginal2016b]||
53
-|[FBXO11](FBXO11)|Tier 1 GE[@hubschmannMutationalMechanismsShaping2021b], FE[@schneiderFBXO11InactivationLeads2016b], aSHM|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)|[@parryWholeExomeSequencing2013; @richterRecurrentMutationID32012a]||
54
-|[FBXW7](FBXW7)|Tier 1 GE[@zhangGeneticHeterogeneityDiffuse2013], FE[@saffieFBXW7TriggersDegradation2020b], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
55
-|[FOXO1](FOXO1)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@trinhAnalysisFOXO1Mutations], CE[@trinhAnalysisFOXO1Mutations], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@dunsCharacterizationDLBCLPMBL2021b; @schmitzBurkittLymphomaPathogenesis2012]||
56
-|[GNA13](GNA13)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@muppidiLossSignalingGa132014b], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@loveGeneticLandscapeMutations2012; @reichelFlowSortingExome2015a]||
57
-|[GNAI2](GNAI2)|Tier 1 GE[@morinMutationalStructuralAnalysis2013], aSHM|[Morin et al](papers/morinMutationalStructuralAnalysis2013)|[@grandeGenomewideDiscoverySomatic2019]||
58
-|[GRB2](GRB2)|Tier 1 GE[@pasqualucciAnalysisCodingGenome2011], aSHM|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|||
59
-|[GRHPR](GRHPR)|Tier 1 GE[@arthurGenomewideDiscoverySomatic2018], aSHM|[Arthur et al](papers/arthurGenomewideDiscoverySomatic2018)|||
60
-|[HIST1H1B](HIST1H1B)|Tier 1 GE[@chapuyMolecularSubtypesDiffuse2018b], aSHM|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018b)|[@krysiakRecurrentSomaticMutations2017b; @sarkozyMutationalLandscapeGray2021a]||
49
+|[ETV6](ETV6)|Tier 1 GE[@lohrDiscoveryPrioritizationSomatic2012], FE[@wangETV6MutationCohort2014], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012)|||
50
+|[EZH2](EZH2)|Tier 1 GE[@morinSomaticMutationsAltering2010], FE[@sneeringerCoordinatedActivitiesWildtype2010]|[Morin et al](papers/morinSomaticMutationsAltering2010)|[@loveGeneticLandscapeMutations2012; @mottokIntegrativeGenomicAnalysis2019]||
51
+|[FAS](FAS)|Tier 1 GE[@schollMutationsRegionFAS2007], FE[@wangFasFADDDeathDomain2010]|[Scholl et al](papers/schollMutationsRegionFAS2007)|[@morinFrequentMutationHistonemodifying2011; @spinaGeneticsNodalMarginal2016]||
52
+|[FBXO11](FBXO11)|Tier 1 GE[@arthurGenomewideDiscoverySomatic2018], FE[@duanFBXO11TargetsBCL62011]|[Arthur et al](papers/arthurGenomewideDiscoverySomatic2018)|[@parryWholeExomeSequencing2013; @richterRecurrentMutationID32012]||
53
+|[FBXW7](FBXW7)|Tier 1 GE[@zhangGeneticHeterogeneityDiffuse2013], FE[@saffieFBXW7TriggersDegradation2020]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
54
+|[FOXO1](FOXO1)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@trinhAnalysisFOXO1Mutations]|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@dunsCharacterizationDLBCLPMBL2021; @schmitzBurkittLymphomaPathogenesis2012]||
55
+|[GNA13](GNA13)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@muppidiLossSignalingGa132014]|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@loveGeneticLandscapeMutations2012; @reichelFlowSortingExome2015]||
56
+|[GNAI2](GNAI2)|Tier 1 GE[@morinMutationalStructuralAnalysis2013], FE[@muppidiLossSignalingGa132014]|[Morin et al](papers/morinMutationalStructuralAnalysis2013)|[@drevalGeneticSubdivisionsFollicular2023; @grandeGenomewideDiscoverySomatic2019]||
57
+|[GRB2](GRB2)|Tier 1 GE[@pasqualucciAnalysisCodingGenome2011]|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|||
58
+|[GRHPR](GRHPR)|Tier 1 GE[@schmitzGeneticsPathogenesisDiffuse2018], aSHM|[Schmitz et al](papers/schmitzGeneticsPathogenesisDiffuse2018)|||
59
+|[HIST1H1B](HIST1H1B)|Tier 1 GE[@chapuyMolecularSubtypesDiffuse2018], aSHM|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018)|[@krysiakRecurrentSomaticMutations2017; @sarkozyMutationalLandscapeGray2021]||
61 60
|[HIST1H1C](HIST1H1C)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@paneaWholeGenomeLandscape2019]||
62
-|[HIST1H1D](HIST1H1D)|Tier 1 GE[@morinMutationalStructuralAnalysis2013], aSHM|[Morin et al](papers/morinMutationalStructuralAnalysis2013)|[@jalladesExomeSequencingIdentifies2017; @krysiakRecurrentSomaticMutations2017b]||
63
-|[HIST1H1E](HIST1H1E)|Tier 1 GE[@lohrDiscoveryPrioritizationSomatic2012a], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012a)|[@grandeGenomewideDiscoverySomatic2019; @krysiakRecurrentSomaticMutations2017b; @reichelFlowSortingExome2015a]||
64
-|[HIST1H2AC](HIST1H2AC)|Tier 1 GE[@morinMutationalStructuralAnalysis2013], aSHM|[Morin et al](papers/morinMutationalStructuralAnalysis2013)|[@krysiakRecurrentSomaticMutations2017b]||
65
-|[HIST1H2AM](HIST1H2AM)|Tier 1 GE[@chapuyMolecularSubtypesDiffuse2018b], aSHM|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018b)|[@krysiakRecurrentSomaticMutations2017b; @paneaWholeGenomeLandscape2019]||
66
-|[HIST1H2BC](HIST1H2BC)|Tier 1 GE[@lohrDiscoveryPrioritizationSomatic2012a], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012a)|[@krysiakRecurrentSomaticMutations2017b; @mottokIntegrativeGenomicAnalysis2019b]||
67
-|[HIST1H2BK](HIST1H2BK)|Tier 1 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@paneaWholeGenomeLandscape2019; @rossiCodingGenomeSplenic2012c]||
68
-|[HIST1H3B](HIST1H3B)|Tier 1 GE[@lohrDiscoveryPrioritizationSomatic2012a], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012a)|[@reichelFlowSortingExome2015a]||
69
-|[HIST2H2BE](HIST2H2BE)|Tier 1 GE[@schmitzGeneticsPathogenesisDiffuse2018a], aSHM|[Schmitz et al](papers/schmitzGeneticsPathogenesisDiffuse2018a)|||
70
-|[HLA-A](HLA-A)|Tier 1 GE[@lohrDiscoveryPrioritizationSomatic2012a], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012a)|[@deschGenotypingCirculatingTumor2020]||
71
-|[HLA-B](HLA-B)|Tier 1 GE[@lohrDiscoveryPrioritizationSomatic2012a], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012a)|[@wienandGenomicAnalysesFlowsorted2019b]||
72
-|[HLA-C](HLA-C)|Tier 1 GE[@chapuyMolecularSubtypesDiffuse2018b], aSHM|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018b)|[@gomezUltraDeepSequencingReveals2023]||
73
-|[HLA-DMB](HLA-DMB)|Tier 1 GE[@hubschmannMutationalMechanismsShaping2021b], aSHM|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)|||
74
-|[HNRNPU](HNRNPU)|Tier 1 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@paneaWholeGenomeLandscape2019]||
75
-|[HVCN1](HVCN1)|Tier 1 GE[@chapuyMolecularSubtypesDiffuse2018b], aSHM|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018b)|[@krysiakRecurrentSomaticMutations2017b]||
76
-|[IKZF3](IKZF3)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@paneaWholeGenomeLandscape2019]||
77
-|[IL4R](IL4R)|Tier 1 GE[@dunsCharacterizationDLBCLPMBL2021b], FE[@viganoSomaticIL4RMutations2018b], aSHM|[Duns et al](papers/dunsCharacterizationDLBCLPMBL2021b)|[@viganoSomaticIL4RMutations2018b]||
78
-|[IRF4](IRF4)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@drevalGeneticSubdivisionsFollicular2023; @mottokIntegrativeGenomicAnalysis2019b]||
79
-|[IRF8](IRF8)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@qiuIRF8mutantCellLymphoma2024], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@mottokIntegrativeGenomicAnalysis2019b; @paneaWholeGenomeLandscape2019]||
80
-|[ITPKB](ITPKB)|Tier 1 GE[@schmitzGeneticsPathogenesisDiffuse2018a], aSHM|[Schmitz et al](papers/schmitzGeneticsPathogenesisDiffuse2018a)|[@drevalGeneticSubdivisionsFollicular2023; @reichelFlowSortingExome2015a]||
81
-|[JUNB](JUNB)|Tier 1 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@mottokIntegrativeGenomicAnalysis2019b]|PASS|
61
+|[HIST1H1D](HIST1H1D)|Tier 1 GE[@morinMutationalStructuralAnalysis2013], aSHM|[Morin et al](papers/morinMutationalStructuralAnalysis2013)|[@jalladesExomeSequencingIdentifies2017; @krysiakRecurrentSomaticMutations2017]||
62
+|[HIST1H1E](HIST1H1E)|Tier 1 GE[@lohrDiscoveryPrioritizationSomatic2012], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012)|[@grandeGenomewideDiscoverySomatic2019; @krysiakRecurrentSomaticMutations2017; @reichelFlowSortingExome2015]||
63
+|[HIST1H2AC](HIST1H2AC)|Tier 1 GE[@morinMutationalStructuralAnalysis2013], aSHM|[Morin et al](papers/morinMutationalStructuralAnalysis2013)|[@krysiakRecurrentSomaticMutations2017]||
64
+|[HIST1H2AM](HIST1H2AM)|Tier 1 GE[@chapuyMolecularSubtypesDiffuse2018], aSHM|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018)|[@krysiakRecurrentSomaticMutations2017; @paneaWholeGenomeLandscape2019]||
65
+|[HIST1H2BC](HIST1H2BC)|Tier 1 GE[@lohrDiscoveryPrioritizationSomatic2012], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012)|[@krysiakRecurrentSomaticMutations2017; @mottokIntegrativeGenomicAnalysis2019]||
66
+|[HIST1H2BK](HIST1H2BK)|Tier 1 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@paneaWholeGenomeLandscape2019; @rossiCodingGenomeSplenic2012]||
67
+|[HIST1H3B](HIST1H3B)|Tier 1 GE[@lohrDiscoveryPrioritizationSomatic2012], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012)|[@reichelFlowSortingExome2015]||
68
+|[HIST2H2BE](HIST2H2BE)|Tier 1 GE[@chapuyMolecularSubtypesDiffuse2018], aSHM|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018)|||
69
+|[HLA-A](HLA-A)|Tier 1 GE[@lohrDiscoveryPrioritizationSomatic2012], FE[@fangazioGeneticMechanismsHLAI2021]|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012)|[@deschGenotypingCirculatingTumor2020]||
70
+|[HLA-B](HLA-B)|Tier 1 GE[@lohrDiscoveryPrioritizationSomatic2012], FE[@fangazioGeneticMechanismsHLAI2021]|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012)|[@wienandGenomicAnalysesFlowsorted2019]||
71
+|[HLA-C](HLA-C)|Tier 1 GE[@chapuyMolecularSubtypesDiffuse2018], FE[@fangazioGeneticMechanismsHLAI2021]|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018)|[@gomezUltraDeepSequencingReveals2023]||
72
+|[HLA-DMB](HLA-DMB)|Tier 1 GE[@hubschmannMutationalMechanismsShaping2021]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021)|||
73
+|[HNRNPU](HNRNPU)|Tier 1 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@paneaWholeGenomeLandscape2019]||
74
+|[HVCN1](HVCN1)|Tier 1 GE[@chapuyMolecularSubtypesDiffuse2018]|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018)|[@krysiakRecurrentSomaticMutations2017]||
75
+|[IKZF3](IKZF3)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@lazarianHotspotMutationTranscription2021]|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@paneaWholeGenomeLandscape2019]||
76
+|[IL4R](IL4R)|Tier 1 GE[@dunsCharacterizationDLBCLPMBL2021], FE[@viganoSomaticIL4RMutations2018], aSHM|[Duns et al](papers/dunsCharacterizationDLBCLPMBL2021)|[@viganoSomaticIL4RMutations2018]||
77
+|[IRF4](IRF4)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@drevalGeneticSubdivisionsFollicular2023; @mottokIntegrativeGenomicAnalysis2019]||
78
+|[IRF8](IRF8)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@qiuIRF8mutantCellLymphoma2024], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@mottokIntegrativeGenomicAnalysis2019; @paneaWholeGenomeLandscape2019]||
79
+|[ITPKB](ITPKB)|Tier 1 GE[@schmitzGeneticsPathogenesisDiffuse2018], FE[@tiacciPervasiveMutationsJAKSTAT2018], aSHM|[Schmitz et al](papers/schmitzGeneticsPathogenesisDiffuse2018)|[@drevalGeneticSubdivisionsFollicular2023; @reichelFlowSortingExome2015]||
80
+|[JUNB](JUNB)|Tier 1 GE[@lohrDiscoveryPrioritizationSomatic2012]|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012)|[@mottokIntegrativeGenomicAnalysis2019]|PASS|
82 81
|[KLF2](KLF2)|Tier 1 GE[@pasqualucciAnalysisCodingGenome2011], aSHM|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|[@deschGenotypingCirculatingTumor2020; @drevalGeneticSubdivisionsFollicular2023; @jalladesExomeSequencingIdentifies2017]||
83
-|[KLHL14](KLHL14)|Tier 1 GE[@zhangGeneticHeterogeneityDiffuse2013], FE[@choiRegulationCellReceptordependent2020], CE[@hodkinsonBiomarkersResponseIbrutinib2021], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
84
-|[KLHL6](KLHL6)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@merirantaDisruptionKLHL6Fuels2024], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@ganapathiGeneticLandscapeDural2016]||
85
-|[KMT2C](KMT2C)|Tier 1 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@sarkozyMutationalLandscapeGray2021a; @zhangGenomicLandscapeMantle2014; @zhouSporadicEndemicBurkitt2019]||
86
-|[KMT2D](KMT2D)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@liLossCREBBPKMT2D2024], CE[@rushtonGeneticEvolutionaryPatterns2020], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@beaLandscapeSomaticMutations2013; @deschGenotypingCirculatingTumor2020; @grandeGenomewideDiscoverySomatic2019; @rossiCodingGenomeSplenic2012c]||
87
-|[KRAS](KRAS)|Tier 1 GE[@lohrDiscoveryPrioritizationSomatic2012a], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012a)|||
88
-|[LCOR](LCOR)|Tier 1 GE[@arthurGenomewideDiscoverySomatic2018], aSHM|[Arthur et al](papers/arthurGenomewideDiscoverySomatic2018)|||
89
-|[LRRN3](LRRN3)|Tier 1 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@sarkozyMutationalLandscapeGray2021a]||
90
-|[LTB](LTB)|Tier 1 GE[@chapuyMolecularSubtypesDiffuse2018b], aSHM|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018b)|[@deschGenotypingCirculatingTumor2020; @drevalGeneticSubdivisionsFollicular2023]||
91
-|[MEF2B](MEF2B)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@yingMEF2BMutationsLead], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@beaLandscapeSomaticMutations2013]||
92
-|[MEF2C](MEF2C)|Tier 1 GE[@arthurGenomewideDiscoverySomatic2018], FE[@jingjingNovelMEF2CMutation2020], aSHM|[Arthur et al](papers/arthurGenomewideDiscoverySomatic2018)|||
93
-|[MGA](MGA)|Tier 1 GE[@reddyGeneticFunctionalDrivers2017], CE[@guoSGK1MutationStatus2022b], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@jalladesExomeSequencingIdentifies2017]||
94
-|[MIR142](MIR142)|Tier 1 GE[@kwanhianMicroRNA142Mutated202012b], aSHM|[Kwanhian et al](papers/kwanhianMicroRNA142Mutated202012b)|[@grandeGenomewideDiscoverySomatic2019]||
95
-|[MPEG1](MPEG1)|Tier 1 GE[@morinMutationalStructuralAnalysis2013], CE[@guoSGK1MutationStatus2022b], aSHM|[Morin et al](papers/morinMutationalStructuralAnalysis2013)|||
96
-|[MS4A1](MS4A1)|Tier 1 GE[@rushtonGeneticEvolutionaryPatterns2020], FE[@rushtonGeneticEvolutionaryPatterns2020], CE[@rushtonGeneticEvolutionaryPatterns2020], aSHM|[Rushton et al](papers/rushtonGeneticEvolutionaryPatterns2020)|[@mottokIntegrativeGenomicAnalysis2019b]||
97
-|[MTOR](MTOR)|Tier 1 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@paneaWholeGenomeLandscape2019]||
98
-|[MYC](MYC)|Tier 1 GE[@pasqualucciHypermutationMultipleProtooncogenes2001a], FE[@giallongoIdentificationCmycOncogene1983], CE[@christieCMYCTranslocation142008], aSHM|[Pasqualucci et al](papers/pasqualucciHypermutationMultipleProtooncogenes2001a)|[@dunsCharacterizationDLBCLPMBL2021b; @jalladesExomeSequencingIdentifies2017; @johnstonCmycHypermutationBurkitt1992]||
99
-|[MYD88](MYD88)|Tier 1 GE[@ngoOncogenicallyActiveMYD882011a], FE[@ngoOncogenicallyActiveMYD882011a], CE[@guoSGK1MutationStatus2022b], aSHM|[Ngo et al](papers/ngoOncogenicallyActiveMYD882011a)|[@drevalGeneticSubdivisionsFollicular2023; @yanBCRTLRSignaling2012a]||
100
-|[NFKBIA](NFKBIA)|Tier 1 GE[@thomasMutationalAnalysisIkappaBalpha2004], aSHM|[Thomas et al](papers/thomasMutationalAnalysisIkappaBalpha2004)|[@russler-germainMutationsAssociatedProgression2023b; @wienandGenomicAnalysesFlowsorted2019b]||
101
-|[NFKBIE](NFKBIE)|Tier 1 GE[@morinGeneticLandscapesRelapsed2016], FE[@mansouriFrequentNFKBIEDeletions2016], aSHM|[Morin et al](papers/morinGeneticLandscapesRelapsed2016)|[@mansouriFrequentNFKBIEDeletions2016; @pararajalingamCodingNoncodingDrivers2020]||
82
+|[KLHL14](KLHL14)|Tier 1 GE[@zhangGeneticHeterogeneityDiffuse2013], FE[@choiRegulationCellReceptordependent2020]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
83
+|[KLHL6](KLHL6)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@choiLossKLHL6Promotes2018], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@ganapathiGeneticLandscapeDural2016]||
84
+|[KMT2C](KMT2C)|Tier 1 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@sarkozyMutationalLandscapeGray2021; @zhangGenomicLandscapeMantle2014; @zhouSporadicEndemicBurkitt2019]||
85
+|[KMT2D](KMT2D)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@zhangDisruptionKMT2DPerturbs2015]|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@beaLandscapeSomaticMutations2013; @deschGenotypingCirculatingTumor2020; @grandeGenomewideDiscoverySomatic2019; @rossiCodingGenomeSplenic2012]||
86
+|[KRAS](KRAS)|Tier 1 GE[@lohrDiscoveryPrioritizationSomatic2012], FE[@scheffzekRasRasGAPComplexStructural1997]|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012)|||
87
+|[LRRN3](LRRN3)|Tier 1 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@sarkozyMutationalLandscapeGray2021]||
88
+|[LTB](LTB)|Tier 1 GE[@chapuyMolecularSubtypesDiffuse2018], aSHM|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018)|[@deschGenotypingCirculatingTumor2020; @drevalGeneticSubdivisionsFollicular2023]||
89
+|[MEF2B](MEF2B)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@ponMEF2BMutationsNonHodgkin2015], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@beaLandscapeSomaticMutations2013]||
90
+|[MEF2C](MEF2C)|Tier 1 GE[@hubschmannMutationalMechanismsShaping2021], aSHM|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021)|||
91
+|[MGA](MGA)|Tier 1 GE[@reddyGeneticFunctionalDrivers2017], FE[@depaoliMGASuppressorMYC2013]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@jalladesExomeSequencingIdentifies2017]||
92
+|[MIR142](MIR142)|Tier 1 GE[@kwanhianMicroRNA142Mutated202012], FE[@trissalMIR142LossofFunctionMutations2018], aSHM|[Kwanhian et al](papers/kwanhianMicroRNA142Mutated202012)|[@grandeGenomewideDiscoverySomatic2019]||
93
+|[MPEG1](MPEG1)|Tier 1 GE[@morinMutationalStructuralAnalysis2013]|[Morin et al](papers/morinMutationalStructuralAnalysis2013)|||
94
+|[MS4A1](MS4A1)|Tier 1 GE[@rushtonGeneticEvolutionaryPatterns2020], FE[@rushtonGeneticEvolutionaryPatterns2020], aSHM|[Rushton et al](papers/rushtonGeneticEvolutionaryPatterns2020)|[@mottokIntegrativeGenomicAnalysis2019]||
95
+|[MTOR](MTOR)|Tier 1 GE[@zhangGeneticHeterogeneityDiffuse2013], FE[@grabinerDiverseArrayCancerassociated2014]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@paneaWholeGenomeLandscape2019]||
96
+|[MYC](MYC)|Tier 1 GE[@pasqualucciHypermutationMultipleProtooncogenes2001], FE[@freieGermlinePointMutation2024], aSHM|[Pasqualucci et al](papers/pasqualucciHypermutationMultipleProtooncogenes2001)|[@dunsCharacterizationDLBCLPMBL2021; @jalladesExomeSequencingIdentifies2017; @johnstonCmycHypermutationBurkitt1992]||
97
+|[MYD88](MYD88)|Tier 1 GE[@ngoOncogenicallyActiveMYD882011], FE[@ngoOncogenicallyActiveMYD882011]|[Ngo et al](papers/ngoOncogenicallyActiveMYD882011)|[@drevalGeneticSubdivisionsFollicular2023; @yanBCRTLRSignaling2012]||
98
+|[NFKBIA](NFKBIA)|Tier 1 GE[@thomasMutationalAnalysisIkappaBalpha2004], FE[@jungnickelClonalDeleteriousMutations2000]|[Thomas et al](papers/thomasMutationalAnalysisIkappaBalpha2004)|[@russler-germainMutationsAssociatedProgression2023; @wienandGenomicAnalysesFlowsorted2019]||
99
+|[NFKBIE](NFKBIE)|Tier 1 GE[@morinGeneticLandscapesRelapsed2016], FE[@mansouriFunctionalLossIkBe2015]|[Morin et al](papers/morinGeneticLandscapesRelapsed2016)|[@mansouriFrequentNFKBIEDeletions2016; @pararajalingamCodingNoncodingDrivers2020]||
102 100
|[NFKBIZ](NFKBIZ)|Tier 1 GE[@morinGeneticLandscapesRelapsed2016], FE[@arthurGenomewideDiscoverySomatic2018], aSHM|[Morin et al](papers/morinGeneticLandscapesRelapsed2016)|||
103
-|[NOL9](NOL9)|Tier 1 GE[@schmitzGeneticsPathogenesisDiffuse2018a], aSHM|[Schmitz et al](papers/schmitzGeneticsPathogenesisDiffuse2018a)|[@spinaGeneticsNodalMarginal2016b]||
104
-|[NOTCH1](NOTCH1)|Tier 1 GE[@pasqualucciAnalysisCodingGenome2011], CE[@kridelWholeTranscriptomeSequencing2012], aSHM|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|[@beaLandscapeSomaticMutations2013; @loveGeneticLandscapeMutations2012; @rossiCodingGenomeSplenic2012c]||
105
-|[NOTCH2](NOTCH2)|Tier 1 GE[@zhangGeneticHeterogeneityDiffuse2013], CE[@campos-martinClinicalDiagnosticRelevance2017], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@beaLandscapeSomaticMutations2013; @rossiCodingGenomeSplenic2012c]||
106
-|[OSBPL10](OSBPL10)|Tier 1 GE[@zhangGeneticHeterogeneityDiffuse2013], CE[@dobashiTP53OSBPL10Alterations2018b], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
107
-|[P2RY8](P2RY8)|Tier 1 GE[@lohrDiscoveryPrioritizationSomatic2012a], FE[@muppidiLossSignalingGa132014b], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012a)|[@drevalGeneticSubdivisionsFollicular2023; @muppidiLossSignalingGa132014b]||
108
-|[PIM1](PIM1)|Tier 1 GE[@pasqualucciHypermutationMultipleProtooncogenes2001a], CE[@guoSGK1MutationStatus2022b], aSHM|[Pasqualucci et al](papers/pasqualucciHypermutationMultipleProtooncogenes2001a)|[@burkhardtClinicalRelevanceMolecular2022b; @drevalGeneticSubdivisionsFollicular2023; @dunsCharacterizationDLBCLPMBL2021b]||
109
-|[PIM2](PIM2)|Tier 1 GE[@arthurGenomewideDiscoverySomatic2018], aSHM|[Arthur et al](papers/arthurGenomewideDiscoverySomatic2018)|[@reichelFlowSortingExome2015a]||
110
-|[POU2AF1](POU2AF1)|Tier 1 GE[@chapuyMolecularSubtypesDiffuse2018b], aSHM|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018b)|[@krysiakRecurrentSomaticMutations2017b]||
111
-|[POU2F2](POU2F2)|Tier 1 GE[@lohrDiscoveryPrioritizationSomatic2012a], FE[@hodsonRegulationNormalBcell2016a], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012a)|[@krysiakRecurrentSomaticMutations2017b]||
112
-|[PRDM1](PRDM1)|Tier 1 GE[@pasqualucciInactivationPRDM1BLIMP12006a], FE[@pasqualucciInactivationPRDM1BLIMP12006a], aSHM|[Pasqualucci et al](papers/pasqualucciInactivationPRDM1BLIMP12006a)|||
113
-|[PTEN](PTEN)|Tier 1 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@loveGeneticLandscapeMutations2012]||
114
-|[RB1](RB1)|Tier 1 GE[@morinMutationalStructuralAnalysis2013], aSHM|[Morin et al](papers/morinMutationalStructuralAnalysis2013)|[@zhangGenomicLandscapeMantle2014]||
115
-|[RFX7](RFX7)|Tier 1 GE[@arthurGenomewideDiscoverySomatic2018], aSHM|[Arthur et al](papers/arthurGenomewideDiscoverySomatic2018)|[@grandeGenomewideDiscoverySomatic2019]||
116
-|[RHOA](RHOA)|Tier 1 GE[@zhangGeneticHeterogeneityDiffuse2013], FE[@ohayreInactivatingMutationsGNA132016], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@richterRecurrentMutationID32012a]||
117
-|[RRAGC](RRAGC)|Tier 1 GE[@okosunRecurrentMTORC1activatingRRAGC2016a], FE[@ortega-molinaOncogenicRagGTPase2019b], aSHM|[Okosun et al](papers/okosunRecurrentMTORC1activatingRRAGC2016a)|||
118
-|[S1PR2](S1PR2)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@floriHematopoieticOncoproteinFOXP12016], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@drevalGeneticSubdivisionsFollicular2023; @muppidiLossSignalingGa132014b]||
119
-|[SETD1B](SETD1B)|Tier 1 GE[@albuquerqueEnhancingKnowledgeDiscovery2017a], aSHM|[Albuquerque et al](papers/albuquerqueEnhancingKnowledgeDiscovery2017a)|||
120
-|[SF3B1](SF3B1)|Tier 1 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@loveGeneticLandscapeMutations2012]||
121
-|[SGK1](SGK1)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@hartmannHighlyRecurrentMutations2016b], CE[@guoSGK1MutationStatus2022b], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@dunsCharacterizationDLBCLPMBL2021b]||
122
-|[SIN3A](SIN3A)|Tier 1 GE[@chapuyMolecularSubtypesDiffuse2018b], aSHM|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018b)|[@grandeGenomewideDiscoverySomatic2019; @rossiCodingGenomeSplenic2012c]||
123
-|[SMARCA4](SMARCA4)|Tier 1 GE[@reddyGeneticFunctionalDrivers2017], FE[@dengSMARCA4HaploinsufficientCell2024], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@krysiakRecurrentSomaticMutations2017b; @nadeuGenomicEpigenomicInsights2020b; @richterRecurrentMutationID32012a]||
124
-|[SOCS1](SOCS1)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@melznerBiallelicMutationSOCS12005a], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@drevalGeneticSubdivisionsFollicular2023; @wenigerMutationsTumorSuppressor2006a]||
125
-|[SPEN](SPEN)|Tier 1 GE[@albuquerqueEnhancingKnowledgeDiscovery2017a], CE[@guoSGK1MutationStatus2022b], aSHM|[Albuquerque et al](papers/albuquerqueEnhancingKnowledgeDiscovery2017a)|[@rossiCodingGenomeSplenic2012c; @sarkozyMutationalLandscapeGray2021a]||
126
-|[STAT3](STAT3)|Tier 1 GE[@lohrDiscoveryPrioritizationSomatic2012a], FE[@huNovelMissenseM206K2013b], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012a)|||
127
-|[STAT6](STAT6)|Tier 1 GE[@yildizActivatingSTAT6Mutations2015c], FE[@yildizActivatingSTAT6Mutations2015c], aSHM|[Yildiz et al](papers/yildizActivatingSTAT6Mutations2015c)|[@ritzRecurrentMutationsSTAT62009a]||
128
-|[TAF1](TAF1)|Tier 1 GE[@morinMutationalStructuralAnalysis2013], aSHM|[Morin et al](papers/morinMutationalStructuralAnalysis2013)|[@spinaGeneticsNodalMarginal2016b]||
129
-|[TBL1XR1](TBL1XR1)|Tier 1 GE[@lohrDiscoveryPrioritizationSomatic2012a], FE[@venturuttiTBL1XR1MutationsDrive2020b], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012a)|[@rossiCodingGenomeSplenic2012c]||
130
-|[TET2](TET2)|Tier 1 GE[@albuquerqueEnhancingKnowledgeDiscovery2017a], aSHM|[Albuquerque et al](papers/albuquerqueEnhancingKnowledgeDiscovery2017a)|[@thomasGeneticSubgroupsInform2023]||
131
-|[TMEM30A](TMEM30A)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@ennishiTMEM30ALossoffunctionMutations2020b], CE[@ennishiTMEM30ALossoffunctionMutations2020b], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|||
132
-|[TMSB4X](TMSB4X)|Tier 1 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
133
-|[TNFAIP3](TNFAIP3)|Tier 1 GE[@compagnoMutationsMultipleGenes2009a], FE[@compagnoMutationsMultipleGenes2009a], aSHM|[Compagno et al](papers/compagnoMutationsMultipleGenes2009a)|[@rossiAlterationBIRC3Multiple2011a; @schmitzTNFAIP3A20Tumor2009a]||
134
-|[TNFRSF14](TNFRSF14)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], CE[@guoSGK1MutationStatus2022b], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@cheungAcquiredTNFRSF14Mutations2010a; @spinaGeneticsNodalMarginal2016b]||
135
-|[TOX](TOX)|Tier 1 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|||
136
-|[TP53](TP53)|Tier 1 GE[@lohrDiscoveryPrioritizationSomatic2012a], FE[@rowhTp53DeletionLineage2011], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012a)|[@beaLandscapeSomaticMutations2013; @morinFrequentMutationHistonemodifying2011; @rossiCodingGenomeSplenic2012c; @tiacciPervasiveMutationsJAKSTAT2018b; @wildaInactivationARFMDM2p53Pathway2004]||
137
-|[UBE2A](UBE2A)|Tier 1 GE[@lohrDiscoveryPrioritizationSomatic2012a], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012a)|[@reichelFlowSortingExome2015a]||
138
-|[WEE1](WEE1)|Tier 1 GE[@schmitzGeneticsPathogenesisDiffuse2018a], aSHM|[Schmitz et al](papers/schmitzGeneticsPathogenesisDiffuse2018a)|[@reichelFlowSortingExome2015a]||
139
-|[XPO1](XPO1)|Tier 1 GE[@mareschalWholeExomeSequencing2016], aSHM|[Mareschal et al](papers/mareschalWholeExomeSequencing2016)|[@jardinRecurrentMutationsExportin2016a]||
140
-|[ZC3H12A](ZC3H12A)|Tier 1 GE[@chapuyMolecularSubtypesDiffuse2018b], aSHM|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018b)|||
141
-|[ZFP36L1](ZFP36L1)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@paneaWholeGenomeLandscape2019; @reichelFlowSortingExome2015a]||
142
-|[ZNF292](ZNF292)|Tier 1 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|||
143
-|[ZNF608](ZNF608)|Tier 1 GE[@morinMutationalStructuralAnalysis2013], aSHM|[Morin et al](papers/morinMutationalStructuralAnalysis2013)|[@krysiakRecurrentSomaticMutations2017b]||
101
+|[NOL9](NOL9)|Tier 1 GE[@schmitzGeneticsPathogenesisDiffuse2018]|[Schmitz et al](papers/schmitzGeneticsPathogenesisDiffuse2018)|[@spinaGeneticsNodalMarginal2016]||
102
+|[NOTCH1](NOTCH1)|Tier 1 GE[@pasqualucciAnalysisCodingGenome2011], FE[@ryanCellRegulomeLinks2017]|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|[@beaLandscapeSomaticMutations2013; @loveGeneticLandscapeMutations2012; @rossiCodingGenomeSplenic2012]||
103
+|[NOTCH2](NOTCH2)|Tier 1 GE[@zhangGeneticHeterogeneityDiffuse2013], FE[@leeGainoffunctionMutationsCopy2009]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@beaLandscapeSomaticMutations2013; @rossiCodingGenomeSplenic2012]||
104
+|[OSBPL10](OSBPL10)|Tier 1 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
105
+|[P2RY8](P2RY8)|Tier 1 GE[@lohrDiscoveryPrioritizationSomatic2012], FE[@muppidiLossSignalingGa132014]|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012)|[@drevalGeneticSubdivisionsFollicular2023; @muppidiLossSignalingGa132014]||
106
+|[PIM1](PIM1)|Tier 1 GE[@pasqualucciHypermutationMultipleProtooncogenes2001], FE[@kuoRolePIM1Ibrutinibresistant2016], aSHM|[Pasqualucci et al](papers/pasqualucciHypermutationMultipleProtooncogenes2001)|[@burkhardtClinicalRelevanceMolecular2022; @drevalGeneticSubdivisionsFollicular2023; @dunsCharacterizationDLBCLPMBL2021]||
107
+|[PIM2](PIM2)|Tier 1 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@reichelFlowSortingExome2015]||
108
+|[POU2AF1](POU2AF1)|Tier 1 GE[@chapuyMolecularSubtypesDiffuse2018], FE[@gonzalez-rinconUnravelingTransformationFollicular2019], aSHM|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018)|[@krysiakRecurrentSomaticMutations2017]||
109
+|[POU2F2](POU2F2)|Tier 1 GE[@lohrDiscoveryPrioritizationSomatic2012], FE[@hodsonRegulationNormalBcell2016]|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012)|[@krysiakRecurrentSomaticMutations2017]||
110
+|[PRDM1](PRDM1)|Tier 1 GE[@pasqualucciInactivationPRDM1BLIMP12006], FE[@pasqualucciInactivationPRDM1BLIMP12006]|[Pasqualucci et al](papers/pasqualucciInactivationPRDM1BLIMP12006)|||
111
+|[PTEN](PTEN)|Tier 1 GE[@reddyGeneticFunctionalDrivers2017], FE[@pfeiferPTENLossDefines2013]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@loveGeneticLandscapeMutations2012]||
112
+|[PTPN6](PTPN6)|Tier 1 GE[@reddyGeneticFunctionalDrivers2017], FE[@demosthenousLossFunctionMutations2015]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||PASS|
113
+|[RB1](RB1)|Tier 1 GE[@morinMutationalStructuralAnalysis2013], FE[@pinyolInactivationRB1Mantlecell2007]|[Morin et al](papers/morinMutationalStructuralAnalysis2013)|[@zhangGenomicLandscapeMantle2014]||
114
+|[RFX7](RFX7)|Tier 1 GE[@arthurGenomewideDiscoverySomatic2018], FE[@weberPiggyBacTransposonTools2019]|[Arthur et al](papers/arthurGenomewideDiscoverySomatic2018)|[@grandeGenomewideDiscoverySomatic2019]||
115
+|[RHOA](RHOA)|Tier 1 GE[@zhangGeneticHeterogeneityDiffuse2013], FE[@ohayreInactivatingMutationsGNA132016]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@richterRecurrentMutationID32012]||
116
+|[RRAGC](RRAGC)|Tier 1 GE[@okosunRecurrentMTORC1activatingRRAGC2016], FE[@okosunRecurrentMTORC1activatingRRAGC2016]|[Okosun et al](papers/okosunRecurrentMTORC1activatingRRAGC2016)|||
117
+|[S1PR2](S1PR2)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@muppidiLossSignalingGa132014], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@drevalGeneticSubdivisionsFollicular2023; @muppidiLossSignalingGa132014]||
118
+|[SETD1B](SETD1B)|Tier 1 GE[@albuquerqueEnhancingKnowledgeDiscovery2017], FE[@]|[Albuquerque et al](papers/albuquerqueEnhancingKnowledgeDiscovery2017)|||
119
+|[SF3B1](SF3B1)|Tier 1 GE[@reddyGeneticFunctionalDrivers2017], FE[@cazzolaBiologicClinicalSignificance2013]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@loveGeneticLandscapeMutations2012]||
120
+|[SGK1](SGK1)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@gaoSGK1MutationsDLBCL2021], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@dunsCharacterizationDLBCLPMBL2021]||
121
+|[SIN3A](SIN3A)|Tier 1 GE[@chapuyMolecularSubtypesDiffuse2018]|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018)|[@grandeGenomewideDiscoverySomatic2019; @rossiCodingGenomeSplenic2012]||
122
+|[SMARCA4](SMARCA4)|Tier 1 GE[@reddyGeneticFunctionalDrivers2017], FE[@fernandoFunctionalCharacterizationSMARCA42020]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@krysiakRecurrentSomaticMutations2017; @nadeuGenomicEpigenomicInsights2020b; @richterRecurrentMutationID32012]||
123
+|[SOCS1](SOCS1)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@melznerBiallelicMutationSOCS12005], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@drevalGeneticSubdivisionsFollicular2023; @wenigerMutationsTumorSuppressor2006]||
124
+|[SPEN](SPEN)|Tier 1 GE[@albuquerqueEnhancingKnowledgeDiscovery2017]|[Albuquerque et al](papers/albuquerqueEnhancingKnowledgeDiscovery2017)|[@rossiCodingGenomeSplenic2012; @sarkozyMutationalLandscapeGray2021]||
125
+|[STAT3](STAT3)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@huNovelMissenseM206K2013]|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|||
126
+|[STAT6](STAT6)|Tier 1 GE[@yildizActivatingSTAT6Mutations2015], FE[@mentzPARP14NovelTarget2022]|[Yildiz et al](papers/yildizActivatingSTAT6Mutations2015)|[@ritzRecurrentMutationsSTAT62009]||
127
+|[TAF1](TAF1)|Tier 1 GE[@morinMutationalStructuralAnalysis2013]|[Morin et al](papers/morinMutationalStructuralAnalysis2013)|[@spinaGeneticsNodalMarginal2016]||
128
+|[TBL1XR1](TBL1XR1)|Tier 1 GE[@lohrDiscoveryPrioritizationSomatic2012], FE[@venturuttiTBL1XR1MutationsDrive2020]|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012)|[@drevalGeneticSubdivisionsFollicular2023; @rossiCodingGenomeSplenic2012]||
129
+|[TET2](TET2)|Tier 1 GE[@albuquerqueEnhancingKnowledgeDiscovery2017], FE[@asmarGenomewideProfilingIdentifies2013]|[Albuquerque et al](papers/albuquerqueEnhancingKnowledgeDiscovery2017)|[@thomasGeneticSubgroupsInform2023]||
130
+|[TMEM30A](TMEM30A)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@ennishiTMEM30ALossoffunctionMutations2020]|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|||
131
+|[TMSB4X](TMSB4X)|Tier 1 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@drevalGeneticSubdivisionsFollicular2023]||
132
+|[TNFAIP3](TNFAIP3)|Tier 1 GE[@compagnoMutationsMultipleGenes2009], FE[@compagnoMutationsMultipleGenes2009]|[Compagno et al](papers/compagnoMutationsMultipleGenes2009)|[@drevalGeneticSubdivisionsFollicular2023; @rossiAlterationBIRC3Multiple2011; @schmitzTNFAIP3A20Tumor2009]||
133
+|[TNFRSF14](TNFRSF14)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@]|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@cheungAcquiredTNFRSF14Mutations2010; @spinaGeneticsNodalMarginal2016]||
134
+|[TOX](TOX)|Tier 1 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|||
135
+|[TP53](TP53)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@katoUnderstandingFunctionstructureFunctionmutation2003]|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@beaLandscapeSomaticMutations2013; @rossiCodingGenomeSplenic2012; @tiacciPervasiveMutationsJAKSTAT2018; @wildaInactivationARFMDM2p53Pathway2004]||
136
+|[UBE2A](UBE2A)|Tier 1 GE[@lohrDiscoveryPrioritizationSomatic2012]|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012)|[@reichelFlowSortingExome2015]||
137
+|[WEE1](WEE1)|Tier 1 GE[@schmitzGeneticsPathogenesisDiffuse2018]|[Schmitz et al](papers/schmitzGeneticsPathogenesisDiffuse2018)|[@reichelFlowSortingExome2015]||
138
+|[XPO1](XPO1)|Tier 1 GE[@mareschalWholeExomeSequencing2016], FE[@miloudiXPO1E571KMutationModifies2020]|[Mareschal et al](papers/mareschalWholeExomeSequencing2016)|[@jardinRecurrentMutationsExportin2016]||
139
+|[ZC3H12A](ZC3H12A)|Tier 1 GE[@chapuyMolecularSubtypesDiffuse2018], FE[@skalniakRegulatoryFeedbackLoop2009]|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018)|||
140
+|[ZFP36L1](ZFP36L1)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@paneaWholeGenomeLandscape2019; @reichelFlowSortingExome2015]||
141
+|[ZNF292](ZNF292)|Tier 1 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|||
142
+|[ZNF608](ZNF608)|Tier 1 GE[@morinMutationalStructuralAnalysis2013]|[Morin et al](papers/morinMutationalStructuralAnalysis2013)|[@krysiakRecurrentSomaticMutations2017]||
144 143
145 144
## Tier 2, low-confidence DLBCL genes
146 145
147
-### *179 total*
146
+### *210 total*
148 147
149 148
|Gene|Summary| First DLBCL study | Other entities | QC result |
150 149
|:-:|:--:|:-:|:-|:-|
151
-|[ABI3BP](ABI3BP)|Tier 2 GE[@morinMutationalStructuralAnalysis2013], aSHM|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||PASS|
152
-|[ADAMTS1](ADAMTS1)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021b], aSHM|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)||PASS|
150
+|[ABI3BP](ABI3BP)|Tier 2 GE[@morinMutationalStructuralAnalysis2013]|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||PASS|
151
+|[ADAMTS1](ADAMTS1)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021)||PASS|
152
+|[ADAMTSL3](ADAMTSL3)|Tier 2 GE[@pasqualucciAnalysisCodingGenome2011]|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|||
153 153
|[AICDA](AICDA)|Tier 2 GE[@arthurGenomewideDiscoverySomatic2018], aSHM|[Arthur et al](papers/arthurGenomewideDiscoverySomatic2018)|||
154
-|[ANKRD12](ANKRD12)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021b], aSHM|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)||PASS|
155
-|[ANKRD17](ANKRD17)|Tier 2 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
156
-|[ARID5B](ARID5B)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@gomezUltraDeepSequencingReveals2023]|PASS|
157
-|[ASXL3](ASXL3)|Tier 2 GE[@albuquerqueEnhancingKnowledgeDiscovery2017a], aSHM|[Albuquerque et al](papers/albuquerqueEnhancingKnowledgeDiscovery2017a)|||
158
-|[ATR](ATR)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||PASS|
159
-|[BCL11A](BCL11A)|Tier 2 GE[@chapuyMolecularSubtypesDiffuse2018b], aSHM|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018b)|||
160
-|[BCOR](BCOR)|Tier 2 GE, aSHM||[@jalladesExomeSequencingIdentifies2017; @nadeuGenomicEpigenomicInsights2020b]||
161
-|[BCR](BCR)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012a], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012a)|||
162
-|[BIRC3](BIRC3)|Tier 2 GE[@arthurGenomewideDiscoverySomatic2018], aSHM|[Arthur et al](papers/arthurGenomewideDiscoverySomatic2018)|[@beaLandscapeSomaticMutations2013; @dunsCharacterizationDLBCLPMBL2021b; @rossiAlterationBIRC3Multiple2011a]||
154
+|[AKAP8](AKAP8)|Tier 2 GE[@pasqualucciAnalysisCodingGenome2011]|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|||
155
+|[ANKLE2](ANKLE2)|Tier 2 GE[@pasqualucciAnalysisCodingGenome2011]|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|||
156
+|[ANKRD12](ANKRD12)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021)||PASS|
157
+|[ANKRD17](ANKRD17)|Tier 2 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
158
+|[ARAP2](ARAP2)|Tier 2 GE[@morinMutationalStructuralAnalysis2013]|[Morin et al](papers/morinMutationalStructuralAnalysis2013)|||
159
+|[ARID5B](ARID5B)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@gomezUltraDeepSequencingReveals2023]|PASS|
160
+|[ASXL3](ASXL3)|Tier 2 GE[@albuquerqueEnhancingKnowledgeDiscovery2017]|[Albuquerque et al](papers/albuquerqueEnhancingKnowledgeDiscovery2017)|||
161
+|[ATR](ATR)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||PASS|
162
+|[BCL11A](BCL11A)|Tier 2 GE[@chapuyMolecularSubtypesDiffuse2018], aSHM|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018)|||
163
+|[BCL2L10](BCL2L10)|Tier 2 GE[@pasqualucciAnalysisCodingGenome2011]|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|||
164
+|[BCR](BCR)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012]|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012)|||
165
+|[BIRC3](BIRC3)|Tier 2 GE[@arthurGenomewideDiscoverySomatic2018], aSHM|[Arthur et al](papers/arthurGenomewideDiscoverySomatic2018)|[@beaLandscapeSomaticMutations2013; @dunsCharacterizationDLBCLPMBL2021; @rossiAlterationBIRC3Multiple2011]||
163 166
|[BLK](BLK)|Tier 2 GE, aSHM||||
164
-|[BRINP3](BRINP3)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||PASS|
165
-|[BTBD3](BTBD3)|Tier 2 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
166
-|[CADPS2](CADPS2)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021b], aSHM|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)||PASS|
167
-|[CASP8](CASP8)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017], FE[@hakemCaspase8EssentialMaintaining2012], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|||
168
-|[CD22](CD22)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||PASS|
169
-|[CD274](CD274)|Tier 2 GE[@morinFrequentMutationHistonemodifying2011], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|||
170
-|[CD36](CD36)|Tier 2 GE[@pasqualucciAnalysisCodingGenome2011], aSHM|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|||
167
+|[BRINP3](BRINP3)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||PASS|
168
+|[BRSK1](BRSK1)|Tier 2 GE[@pasqualucciAnalysisCodingGenome2011]|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|||
169
+|[BTBD3](BTBD3)|Tier 2 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
170
+|[C12orf35](C12orf35)|Tier 2 GE[@pasqualucciAnalysisCodingGenome2011]|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|||
171
+|[CADPS2](CADPS2)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021)||PASS|
172
+|[CAMTA1](CAMTA1)|Tier 2 GE[@pasqualucciAnalysisCodingGenome2011]|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|||
173
+|[CASP8](CASP8)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|||
174
+|[CD22](CD22)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||PASS|
175
+|[CD274](CD274)|Tier 2 GE[@morinFrequentMutationHistonemodifying2011]|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|||
176
+|[CD36](CD36)|Tier 2 GE[@pasqualucciAnalysisCodingGenome2011]|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|||
171 177
|[CD44](CD44)|Tier 2 GE[@arthurGenomewideDiscoverySomatic2018], aSHM|[Arthur et al](papers/arthurGenomewideDiscoverySomatic2018)|||
172 178
|[CD74](CD74)|Tier 2 GE[@arthurGenomewideDiscoverySomatic2018], aSHM|[Arthur et al](papers/arthurGenomewideDiscoverySomatic2018)|||
173
-|[CDH9](CDH9)|Tier 2 GE[@morinMutationalStructuralAnalysis2013], aSHM|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||PASS|
174
-|[CEP164](CEP164)|Tier 2 GE[@albuquerqueEnhancingKnowledgeDiscovery2017a], aSHM|[Albuquerque et al](papers/albuquerqueEnhancingKnowledgeDiscovery2017a)|||
175
-|[CNOT2](CNOT2)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021b], aSHM|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)||PASS|
176
-|[CNTNAP5](CNTNAP5)|Tier 2 GE[@morinMutationalStructuralAnalysis2013], aSHM|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||PASS|
177
-|[COQ7](COQ7)|Tier 2 GE[@chapuyMolecularSubtypesDiffuse2018b], aSHM|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018b)||PASS|
178
-|[CPS1](CPS1)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012a], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012a)|||
179
-|[CRIP1](CRIP1)|Tier 2 GE[@chapuyMolecularSubtypesDiffuse2018b], aSHM|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018b)||PASS|
180
-|[DAZAP1](DAZAP1)|Tier 2 GE[@pararajalingamCodingNoncodingDrivers2020], aSHM|[Pararajalingam et al](papers/pararajalingamCodingNoncodingDrivers2020)|||
181
-|[DDX10](DDX10)|Tier 2 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
182
-|[DHX16](DHX16)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021b], aSHM|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)||PASS|
183
-|[DNAH5](DNAH5)|Tier 2 GE[@morinMutationalStructuralAnalysis2013], aSHM|[Morin et al](papers/morinMutationalStructuralAnalysis2013)|[@jalladesExomeSequencingIdentifies2017]|PASS|
184
-|[DNM2](DNM2)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021b], aSHM|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)||PASS|
185
-|[DNMT3B](DNMT3B)|Tier 2 GE[@albuquerqueEnhancingKnowledgeDiscovery2017a], aSHM|[Albuquerque et al](papers/albuquerqueEnhancingKnowledgeDiscovery2017a)|||
186
-|[DOCK1](DOCK1)|Tier 2 GE[@chapuyMolecularSubtypesDiffuse2018b], aSHM|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018b)||PASS|
187
-|[DSG4](DSG4)|Tier 2 GE[@morinMutationalStructuralAnalysis2013], aSHM|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||PASS|
188
-|[EIF2AK3](EIF2AK3)|Tier 2 GE, aSHM||||
189
-|[ERAP2](ERAP2)|Tier 2 GE[@albuquerqueEnhancingKnowledgeDiscovery2017a], aSHM|[Albuquerque et al](papers/albuquerqueEnhancingKnowledgeDiscovery2017a)|||
179
+|[CDH9](CDH9)|Tier 2 GE[@morinMutationalStructuralAnalysis2013]|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||PASS|
180
+|[CEP164](CEP164)|Tier 2 GE[@albuquerqueEnhancingKnowledgeDiscovery2017]|[Albuquerque et al](papers/albuquerqueEnhancingKnowledgeDiscovery2017)|||
181
+|[CNOT2](CNOT2)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021)||PASS|
182
+|[CNTNAP5](CNTNAP5)|Tier 2 GE[@morinMutationalStructuralAnalysis2013]|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||PASS|
183
+|[COQ7](COQ7)|Tier 2 GE[@chapuyMolecularSubtypesDiffuse2018]|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018)||PASS|
184
+|[CPS1](CPS1)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012]|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012)|||
185
+|[CRIP1](CRIP1)|Tier 2 GE[@chapuyMolecularSubtypesDiffuse2018]|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018)||PASS|
186
+|[CXCR5](CXCR5)|Tier 2 GE[@schmitzGeneticsPathogenesisDiffuse2018]|[Schmitz et al](papers/schmitzGeneticsPathogenesisDiffuse2018)|[@mottokIntegrativeGenomicAnalysis2019]||
187
+|[CYTSB](CYTSB)|Tier 2 GE[@pasqualucciAnalysisCodingGenome2011]|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|||
188
+|[DAZAP1](DAZAP1)|Tier 2 GE[@pararajalingamCodingNoncodingDrivers2020]|[Pararajalingam et al](papers/pararajalingamCodingNoncodingDrivers2020)|||
189
+|[DCHS1](DCHS1)|Tier 2 GE[@pasqualucciAnalysisCodingGenome2011]|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|||
190
+|[DDX10](DDX10)|Tier 2 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
191
+|[DHX16](DHX16)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021)||PASS|
192
+|[DNAH5](DNAH5)|Tier 2 GE[@morinMutationalStructuralAnalysis2013]|[Morin et al](papers/morinMutationalStructuralAnalysis2013)|[@jalladesExomeSequencingIdentifies2017]|PASS|
193
+|[DNM2](DNM2)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021)||PASS|
194
+|[DNMT3B](DNMT3B)|Tier 2 GE[@albuquerqueEnhancingKnowledgeDiscovery2017]|[Albuquerque et al](papers/albuquerqueEnhancingKnowledgeDiscovery2017)|||
195
+|[DOCK1](DOCK1)|Tier 2 GE[@chapuyMolecularSubtypesDiffuse2018]|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018)||PASS|
196
+|[DPYD](DPYD)|Tier 2 GE[@pasqualucciAnalysisCodingGenome2011]|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|||
197
+|[DSC3](DSC3)|Tier 2 GE[@pasqualucciAnalysisCodingGenome2011]|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|||
198
+|[DSEL](DSEL)|Tier 2 GE[@morinMutationalStructuralAnalysis2013]|[Morin et al](papers/morinMutationalStructuralAnalysis2013)|||
199
+|[DSG4](DSG4)|Tier 2 GE[@morinMutationalStructuralAnalysis2013]|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||PASS|
200
+|[DUSP27](DUSP27)|Tier 2 GE[@pasqualucciAnalysisCodingGenome2011]|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|||
201
+|[DUSP9](DUSP9)|Tier 2 GE[@pasqualucciAnalysisCodingGenome2011]|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|||
202
+|[EIF2AK3](EIF2AK3)|Tier 2 GE[@schmitzGeneticsPathogenesisDiffuse2018], aSHM|[Schmitz et al](papers/schmitzGeneticsPathogenesisDiffuse2018)|||
203
+|[ERAP2](ERAP2)|Tier 2 GE[@albuquerqueEnhancingKnowledgeDiscovery2017]|[Albuquerque et al](papers/albuquerqueEnhancingKnowledgeDiscovery2017)|||
190 204
|[EZR](EZR)|Tier 2 GE, aSHM||[@deschGenotypingCirculatingTumor2020]||
191 205
|[FAM102A](FAM102A)|Tier 2 GE, aSHM||||
192 206
|[FANK1](FANK1)|Tier 2 GE, aSHM||||
193
-|[FAT2](FAT2)|Tier 2 GE[@morinFrequentMutationHistonemodifying2011], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|||
194
-|[FAT4](FAT4)|Tier 2 GE[@morinMutationalStructuralAnalysis2013], aSHM|[Morin et al](papers/morinMutationalStructuralAnalysis2013)|[@parryWholeExomeSequencing2013; @zhangGenomicLandscapeMantle2014]|PASS|
207
+|[FAT2](FAT2)|Tier 2 GE[@morinFrequentMutationHistonemodifying2011]|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|||
208
+|[FAT4](FAT4)|Tier 2 GE[@morinMutationalStructuralAnalysis2013]|[Morin et al](papers/morinMutationalStructuralAnalysis2013)|[@parryWholeExomeSequencing2013; @zhangGenomicLandscapeMantle2014]|PASS|
209
+|[FBXO31](FBXO31)|Tier 2 GE[@pasqualucciAnalysisCodingGenome2011]|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|||
195 210
|[FCRL3](FCRL3)|Tier 2 GE, aSHM||||
196 211
|[FNBP1](FNBP1)|Tier 2 GE, aSHM||||
197
-|[FOXC1](FOXC1)|Tier 2 GE[@schmitzGeneticsPathogenesisDiffuse2018a], aSHM|[Schmitz et al](papers/schmitzGeneticsPathogenesisDiffuse2018a)|||
212
+|[FOXC1](FOXC1)|Tier 2 GE[@schmitzGeneticsPathogenesisDiffuse2018]|[Schmitz et al](papers/schmitzGeneticsPathogenesisDiffuse2018)|||
198 213
|[FOXP1](FOXP1)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||PASS|
199
-|[FUBP1](FUBP1)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||PASS|
200
-|[GABRA1](GABRA1)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012a], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012a)|||
201
-|[GABRA2](GABRA2)|Tier 2 GE[@chapuyMolecularSubtypesDiffuse2018b], aSHM|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018b)|||
202
-|[GOLGA5](GOLGA5)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||PASS|
203
-|[GPC5](GPC5)|Tier 2 GE[@schmitzGeneticsPathogenesisDiffuse2018a], aSHM|[Schmitz et al](papers/schmitzGeneticsPathogenesisDiffuse2018a)|||
204
-|[GSG2](GSG2)|Tier 2 GE[@schmitzGeneticsPathogenesisDiffuse2018a], aSHM|[Schmitz et al](papers/schmitzGeneticsPathogenesisDiffuse2018a)|||
205
-|[H1FOO](H1FOO)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012a], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012a)|||
206
-|[HDAC7](HDAC7)|Tier 2 GE[@morinMutationalStructuralAnalysis2013], aSHM|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||PASS|
207
-|[HIST1H2AG](HIST1H2AG)|Tier 2 GE[@morinMutationalStructuralAnalysis2013], aSHM|[Morin et al](papers/morinMutationalStructuralAnalysis2013)|[@krysiakRecurrentSomaticMutations2017b; @paneaWholeGenomeLandscape2019; @rossiCodingGenomeSplenic2012c]|PASS|
208
-|[HIST1H2AL](HIST1H2AL)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012a], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012a)|||
209
-|[HIST1H2BO](HIST1H2BO)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012a], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012a)|||
210
-|[HLA-DMA](HLA-DMA)|Tier 2 GE[@chapuyMolecularSubtypesDiffuse2018b], aSHM|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018b)|||
211
-|[HNF1B](HNF1B)|Tier 2 GE[@pasqualucciAnalysisCodingGenome2011], aSHM|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|||
212
-|[HNRNPD](HNRNPD)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|||
213
-|[HNRNPH1](HNRNPH1)|Tier 2 GE[@pararajalingamCodingNoncodingDrivers2020], FE[@pararajalingamCodingNoncodingDrivers2020], CE[@pararajalingamCodingNoncodingDrivers2020], aSHM|[Pararajalingam et al](papers/pararajalingamCodingNoncodingDrivers2020)|||
214
-|[ID3](ID3)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012], FE[@richterRecurrentMutationID32012a], aSHM|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)|[@richterRecurrentMutationID32012a; @spinaGeneticsNodalMarginal2016b]||
215
-|[IFNGR1](IFNGR1)|Tier 2 GE[@morinMutationalStructuralAnalysis2013], aSHM|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||PASS|
216
-|[IGLL5](IGLL5)|Tier 2 GE[@chapuyMolecularSubtypesDiffuse2018b], aSHM|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018b)|[@deschGenotypingCirculatingTumor2020; @paneaWholeGenomeLandscape2019; @russler-germainMutationsAssociatedProgression2023b]||
217
-|[IKBKB](IKBKB)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@rossiAlterationBIRC3Multiple2011a; @wienandGenomicAnalysesFlowsorted2019b]|PASS|
218
-|[IKBKE](IKBKE)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021b], aSHM|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)||PASS|
219
-|[IL16](IL16)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|||
220
-|[IL6](IL6)|Tier 2 GE[@chapuyMolecularSubtypesDiffuse2018b], aSHM|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018b)||PASS|
221
-|[INO80](INO80)|Tier 2 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
222
-|[IRF1](IRF1)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021b], aSHM|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)||PASS|
223
-|[JAK1](JAK1)|Tier 2 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@mottokIntegrativeGenomicAnalysis2019b]||
224
-|[JAK3](JAK3)|Tier 2 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
225
-|[KCMF1](KCMF1)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||PASS|
226
-|[KLHL21](KLHL21)|Tier 2 GE[@schmitzGeneticsPathogenesisDiffuse2018a], aSHM|[Schmitz et al](papers/schmitzGeneticsPathogenesisDiffuse2018a)|||
227
-|[KRTAP5-5](KRTAP5-5)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012a], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012a)|||
228
-|[LAMA5](LAMA5)|Tier 2 GE[@schmitzGeneticsPathogenesisDiffuse2018a], aSHM|[Schmitz et al](papers/schmitzGeneticsPathogenesisDiffuse2018a)|||
229
-|[LAPTM5](LAPTM5)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021b], aSHM|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)||PASS|
214
+|[FUBP1](FUBP1)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||PASS|
215
+|[GABRA1](GABRA1)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012]|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012)|||
216
+|[GABRA2](GABRA2)|Tier 2 GE[@chapuyMolecularSubtypesDiffuse2018]|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018)|||
217
+|[GOLGA5](GOLGA5)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||PASS|
218
+|[GPC5](GPC5)|Tier 2 GE[@schmitzGeneticsPathogenesisDiffuse2018]|[Schmitz et al](papers/schmitzGeneticsPathogenesisDiffuse2018)|||
219
+|[GSG2](GSG2)|Tier 2 GE[@schmitzGeneticsPathogenesisDiffuse2018]|[Schmitz et al](papers/schmitzGeneticsPathogenesisDiffuse2018)|||
220
+|[H1FOO](H1FOO)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012]|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012)|||
221
+|[HDAC7](HDAC7)|Tier 2 GE[@morinMutationalStructuralAnalysis2013]|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||PASS|
222
+|[HIST1H2AG](HIST1H2AG)|Tier 2 GE[@morinMutationalStructuralAnalysis2013]|[Morin et al](papers/morinMutationalStructuralAnalysis2013)|[@krysiakRecurrentSomaticMutations2017; @paneaWholeGenomeLandscape2019; @rossiCodingGenomeSplenic2012]|PASS|
223
+|[HIST1H2AL](HIST1H2AL)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012]|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012)|||
224
+|[HIST1H2BO](HIST1H2BO)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012]|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012)|||
225
+|[HIST1H3A](HIST1H3A)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012]|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012)|||
226
+|[HLA-DMA](HLA-DMA)|Tier 2 GE[@chapuyMolecularSubtypesDiffuse2018]|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018)|||
227
+|[HMGB1](HMGB1)|Tier 2 GE[@pasqualucciAnalysisCodingGenome2011]|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|||
228
+|[HNF1B](HNF1B)|Tier 2 GE[@pasqualucciAnalysisCodingGenome2011]|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|||
229
+|[HNRNPD](HNRNPD)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|||
230
+|[HNRNPH1](HNRNPH1)|Tier 2 GE[@pararajalingamCodingNoncodingDrivers2020]|[Pararajalingam et al](papers/pararajalingamCodingNoncodingDrivers2020)|||
231
+|[ID3](ID3)|Tier 2 GE[@schmitzGeneticsPathogenesisDiffuse2018]|[Schmitz et al](papers/schmitzGeneticsPathogenesisDiffuse2018)|[@richterRecurrentMutationID32012; @spinaGeneticsNodalMarginal2016]||
232
+|[IFNGR1](IFNGR1)|Tier 2 GE[@morinMutationalStructuralAnalysis2013]|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||PASS|
233
+|[IGLL5](IGLL5)|Tier 2 GE[@chapuyMolecularSubtypesDiffuse2018], aSHM|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018)|[@deschGenotypingCirculatingTumor2020; @paneaWholeGenomeLandscape2019; @russler-germainMutationsAssociatedProgression2023]||
234
+|[IKBKB](IKBKB)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@rossiAlterationBIRC3Multiple2011; @wienandGenomicAnalysesFlowsorted2019]|PASS|
235
+|[IKBKE](IKBKE)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021)||PASS|
236
+|[IL16](IL16)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|||
237
+|[IL6](IL6)|Tier 2 GE[@chapuyMolecularSubtypesDiffuse2018]|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018)||PASS|
238
+|[INO80](INO80)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|||
239
+|[IRF1](IRF1)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021], aSHM|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021)||PASS|
240
+|[JAK1](JAK1)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@mottokIntegrativeGenomicAnalysis2019]||
241
+|[JAK3](JAK3)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|||
242
+|[KCMF1](KCMF1)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||PASS|
243
+|[KDM2B](KDM2B)|Tier 2 GE[@pasqualucciAnalysisCodingGenome2011]|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|||
244
+|[KLHL21](KLHL21)|Tier 2 GE[@schmitzGeneticsPathogenesisDiffuse2018]|[Schmitz et al](papers/schmitzGeneticsPathogenesisDiffuse2018)|||
245
+|[KRTAP5-5](KRTAP5-5)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012]|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012)|||
246
+|[LAMA5](LAMA5)|Tier 2 GE[@schmitzGeneticsPathogenesisDiffuse2018]|[Schmitz et al](papers/schmitzGeneticsPathogenesisDiffuse2018)|||
247
+|[LAPTM5](LAPTM5)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021], aSHM|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021)||PASS|
248
+|[LCOR](LCOR)|Tier 2 GE[@]||||
230 249
|[LPP](LPP)|Tier 2 GE[@arthurGenomewideDiscoverySomatic2018], aSHM|[Arthur et al](papers/arthurGenomewideDiscoverySomatic2018)|||
231
-|[LRP12](LRP12)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021b], aSHM|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)||PASS|
232
-|[LYN](LYN)|Tier 2 GE[@chapuyMolecularSubtypesDiffuse2018b], aSHM|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018b)||PASS|
233
-|[MAGT1](MAGT1)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||PASS|
250
+|[LRP12](LRP12)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021)||PASS|
251
+|[LYN](LYN)|Tier 2 GE[@chapuyMolecularSubtypesDiffuse2018]|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018)||PASS|
252
+|[MAGEC3](MAGEC3)|Tier 2 GE[@pasqualucciAnalysisCodingGenome2011]|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|||
253
+|[MAGT1](MAGT1)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||PASS|
234 254
|[MALAT1](MALAT1)|Tier 2 GE[@arthurGenomewideDiscoverySomatic2018], aSHM|[Arthur et al](papers/arthurGenomewideDiscoverySomatic2018)|||
235
-|[MAP2K1](MAP2K1)|Tier 2 GE[@shinBRAFV600EMAP2K12015], aSHM|[Shin et al](papers/shinBRAFV600EMAP2K12015)|[@louissaintPediatrictypeNodalFollicular2016a]||
236
-|[MCL1](MCL1)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@dunsCharacterizationDLBCLPMBL2021b; @paneaWholeGenomeLandscape2019]|PASS|
237
-|[MECOM](MECOM)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||PASS|
238
-|[MET](MET)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||PASS|
255
+|[MAP2K1](MAP2K1)|Tier 2 GE[@shinBRAFV600EMAP2K12015]|[Shin et al](papers/shinBRAFV600EMAP2K12015)|[@louissaintPediatrictypeNodalFollicular2016]||
256
+|[MCL1](MCL1)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@dunsCharacterizationDLBCLPMBL2021; @paneaWholeGenomeLandscape2019]|PASS|
257
+|[MECOM](MECOM)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||PASS|
258
+|[MED12L](MED12L)|Tier 2 GE[@pasqualucciAnalysisCodingGenome2011]|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|||
259
+|[MET](MET)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||PASS|
239 260
|[MIR155HG](MIR155HG)|Tier 2 GE, aSHM||||
240
-|[MPDZ](MPDZ)|Tier 2 GE[@morinMutationalStructuralAnalysis2013], aSHM|[Morin et al](papers/morinMutationalStructuralAnalysis2013)|[@reichelFlowSortingExome2015a]|PASS|
241
-|[MSH6](MSH6)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||PASS|
242
-|[MYBPC2](MYBPC2)|Tier 2 GE[@schmitzGeneticsPathogenesisDiffuse2018a], aSHM|[Schmitz et al](papers/schmitzGeneticsPathogenesisDiffuse2018a)|||
243
-|[MYO1E](MYO1E)|Tier 2 GE, aSHM||||
244
-|[MYOM2](MYOM2)|Tier 2 GE[@pasqualucciAnalysisCodingGenome2011], aSHM|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|||
245
-|[NAV1](NAV1)|Tier 2 GE[@chapuyMolecularSubtypesDiffuse2018b], aSHM|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018b)|||
261
+|[MPDZ](MPDZ)|Tier 2 GE[@morinMutationalStructuralAnalysis2013]|[Morin et al](papers/morinMutationalStructuralAnalysis2013)|[@reichelFlowSortingExome2015]|PASS|
262
+|[MSH6](MSH6)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||PASS|
263
+|[MTMR8](MTMR8)|Tier 2 GE[@pasqualucciAnalysisCodingGenome2011]|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|||
264
+|[MYBPC2](MYBPC2)|Tier 2 GE[@schmitzGeneticsPathogenesisDiffuse2018]|[Schmitz et al](papers/schmitzGeneticsPathogenesisDiffuse2018)|||
265
+|[MYO1G](MYO1G)|Tier 2 GE[@pasqualucciAnalysisCodingGenome2011]|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|||
266
+|[MYOM2](MYOM2)|Tier 2 GE[@pasqualucciAnalysisCodingGenome2011]|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|||
267
+|[NAV1](NAV1)|Tier 2 GE[@chapuyMolecularSubtypesDiffuse2018]|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018)|||
246 268
|[NCOA3](NCOA3)|Tier 2 GE, aSHM||||
247
-|[NCOR2](NCOR2)|Tier 2 GE, aSHM||[@sarkozyMutationalLandscapeGray2021a; @schmitzBurkittLymphomaPathogenesis2012; @spinaGeneticsNodalMarginal2016b]||
248 269
|[NEAT1](NEAT1)|Tier 2 GE[@arthurGenomewideDiscoverySomatic2018], aSHM|[Arthur et al](papers/arthurGenomewideDiscoverySomatic2018)|||
249
-|[NF1](NF1)|Tier 2 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
250
-|[NFKB1](NFKB1)|Tier 2 GE, aSHM||||
251
-|[NLRC5](NLRC5)|Tier 2 GE, aSHM||||
252
-|[NLRP5](NLRP5)|Tier 2 GE[@morinMutationalStructuralAnalysis2013], aSHM|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||PASS|
253
-|[ODZ3](ODZ3)|Tier 2 GE[@morinMutationalStructuralAnalysis2013], aSHM|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||PASS|
254
-|[OR6K3](OR6K3)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012a], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012a)|||
270
+|[NF1](NF1)|Tier 2 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
271
+|[NLRP5](NLRP5)|Tier 2 GE[@morinMutationalStructuralAnalysis2013]|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||PASS|
272
+|[ODZ2](ODZ2)|Tier 2 GE[@morinMutationalStructuralAnalysis2013]|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||PASS|
273
+|[OFD1](OFD1)|Tier 2 GE[@pasqualucciAnalysisCodingGenome2011]|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|||
274
+|[OR6K3](OR6K3)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012]|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012)|||
255 275
|[P2RX5](P2RX5)|Tier 2 GE[@morinMutationalStructuralAnalysis2013], aSHM|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||PASS|
256
-|[PAPOLG](PAPOLG)|Tier 2 GE[@schmitzGeneticsPathogenesisDiffuse2018a], aSHM|[Schmitz et al](papers/schmitzGeneticsPathogenesisDiffuse2018a)|||
257
-|[PASD1](PASD1)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012a], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012a)|||
258
-|[PASK](PASK)|Tier 2 GE[@morinMutationalStructuralAnalysis2013], aSHM|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||PASS|
259
-|[PAX5](PAX5)|Tier 2 GE[@pasqualucciHypermutationMultipleProtooncogenes2001a], aSHM|[Pasqualucci et al](papers/pasqualucciHypermutationMultipleProtooncogenes2001a)|||
260
-|[PCBP1](PCBP1)|Tier 2 GE, aSHM||[@schmitzBurkittLymphomaPathogenesis2012]||
261
-|[PCDHB11](PCDHB11)|Tier 2 GE[@morinMutationalStructuralAnalysis2013], aSHM|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||PASS|
262
-|[PCDHB6](PCDHB6)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012a], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012a)|||
263
-|[PCLO](PCLO)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012a], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012a)|||
264
-|[PDGFC](PDGFC)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012a], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012a)|||
265
-|[PDS5B](PDS5B)|Tier 2 GE[@morinMutationalStructuralAnalysis2013], aSHM|[Morin et al](papers/morinMutationalStructuralAnalysis2013)|[@hubschmannMutationalMechanismsShaping2021b]|PASS|
266
-|[PIK3CD](PIK3CD)|Tier 2 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
267
-|[PIK3R1](PIK3R1)|Tier 2 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@paneaWholeGenomeLandscape2019]||
268
-|[PNPO](PNPO)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021b], aSHM|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)||PASS|
269
-|[PPP1R9B](PPP1R9B)|Tier 2 GE, aSHM||||
270
-|[PRKCB](PRKCB)|Tier 2 GE[@morinMutationalStructuralAnalysis2013], aSHM|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||PASS|
271
-|[PRKDC](PRKDC)|Tier 2 GE[@schmitzGeneticsPathogenesisDiffuse2018a], aSHM|[Schmitz et al](papers/schmitzGeneticsPathogenesisDiffuse2018a)|[@hubschmannMutationalMechanismsShaping2021b]||
272
-|[PRPS1](PRPS1)|Tier 2 GE[@chapuyMolecularSubtypesDiffuse2018b], aSHM|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018b)||PASS|
273
-|[PTMA](PTMA)|Tier 2 GE, aSHM||||
274
-|[PTPN1](PTPN1)|Tier 2 GE, aSHM||[@gunawardanaRecurrentSomaticMutations2014c]||
275
-|[PTPN6](PTPN6)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||PASS|
276
-|[PTPRD](PTPRD)|Tier 2 GE, aSHM||[@drevalGeneticSubdivisionsFollicular2023; @spinaGeneticsNodalMarginal2016b]||
277
-|[RAC2](RAC2)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021b], aSHM|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)||PASS|
278
-|[RAPGEF1](RAPGEF1)|Tier 2 GE[@morinFrequentMutationHistonemodifying2011], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|||
276
+|[PAPOLG](PAPOLG)|Tier 2 GE[@schmitzGeneticsPathogenesisDiffuse2018]|[Schmitz et al](papers/schmitzGeneticsPathogenesisDiffuse2018)|||
277
+|[PASD1](PASD1)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012]|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012)|||
278
+|[PASK](PASK)|Tier 2 GE[@morinMutationalStructuralAnalysis2013]|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||PASS|
279
+|[PAX5](PAX5)|Tier 2 GE[@pasqualucciHypermutationMultipleProtooncogenes2001], aSHM|[Pasqualucci et al](papers/pasqualucciHypermutationMultipleProtooncogenes2001)|||
280
+|[PCDHB11](PCDHB11)|Tier 2 GE[@morinMutationalStructuralAnalysis2013]|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||PASS|
281
+|[PCDHB6](PCDHB6)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012]|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012)|||
282
+|[PCLO](PCLO)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012]|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012)|||
283
+|[PDGFC](PDGFC)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012]|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012)|||
284
+|[PDS5B](PDS5B)|Tier 2 GE[@morinMutationalStructuralAnalysis2013]|[Morin et al](papers/morinMutationalStructuralAnalysis2013)|[@hubschmannMutationalMechanismsShaping2021]|PASS|
285
+|[PIK3CD](PIK3CD)|Tier 2 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
286
+|[PIK3R1](PIK3R1)|Tier 2 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@paneaWholeGenomeLandscape2019]||
287
+|[PMS1](PMS1)|Tier 2 GE[@pasqualucciAnalysisCodingGenome2011]|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|||
288
+|[PNPO](PNPO)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021)||PASS|
289
+|[PPP2R5A](PPP2R5A)|Tier 2 GE[@pasqualucciAnalysisCodingGenome2011]|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|||
290
+|[PRKCB](PRKCB)|Tier 2 GE[@morinMutationalStructuralAnalysis2013]|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||PASS|
291
+|[PRKDC](PRKDC)|Tier 2 GE[@schmitzGeneticsPathogenesisDiffuse2018]|[Schmitz et al](papers/schmitzGeneticsPathogenesisDiffuse2018)|[@hubschmannMutationalMechanismsShaping2021]||
292
+|[PRPS1](PRPS1)|Tier 2 GE[@chapuyMolecularSubtypesDiffuse2018]|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018)||PASS|
293
+|[PTPN21](PTPN21)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012]|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012)|||
294
+|[PTPRD](PTPRD)|Tier 2 GE[@drevalGeneticSubdivisionsFollicular2023]|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@spinaGeneticsNodalMarginal2016]||
295
+|[RAC2](RAC2)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021)||PASS|
296
+|[RAPGEF1](RAPGEF1)|Tier 2 GE[@morinFrequentMutationHistonemodifying2011]|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|||
297
+|[RASGEF1A](RASGEF1A)|Tier 2 GE[@pasqualucciAnalysisCodingGenome2011]|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|||
298
+|[RBP3](RBP3)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012]|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012)|[@loveGeneticLandscapeMutations2012]||
279 299
|[RCC](RCC)|Tier 2 GE, aSHM||||
280
-|[RFTN1](RFTN1)|Tier 2 GE[@arthurGenomewideDiscoverySomatic2018], aSHM|[Arthur et al](papers/arthurGenomewideDiscoverySomatic2018)|[@dunsCharacterizationDLBCLPMBL2021b]||
281
-|[RFXAP](RFXAP)|Tier 2 GE, aSHM||||
282
-|[RHEX](RHEX)|Tier 2 GE, aSHM||||
283
-|[RHOH](RHOH)|Tier 2 GE[@pasqualucciHypermutationMultipleProtooncogenes2001a], aSHM|[Pasqualucci et al](papers/pasqualucciHypermutationMultipleProtooncogenes2001a)|||
300
+|[RFTN1](RFTN1)|Tier 2 GE[@arthurGenomewideDiscoverySomatic2018], aSHM|[Arthur et al](papers/arthurGenomewideDiscoverySomatic2018)|[@dunsCharacterizationDLBCLPMBL2021]||
301
+|[RFXAP](RFXAP)|Tier 2 GE||||
302
+|[RGAG1](RGAG1)|Tier 2 GE[@pasqualucciAnalysisCodingGenome2011]|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|||
303
+|[RHEX](RHEX)|Tier 2 GE[@arthurGenomewideDiscoverySomatic2018], aSHM|[Arthur et al](papers/arthurGenomewideDiscoverySomatic2018)|||
304
+|[RHOH](RHOH)|Tier 2 GE[@pasqualucciHypermutationMultipleProtooncogenes2001], aSHM|[Pasqualucci et al](papers/pasqualucciHypermutationMultipleProtooncogenes2001)|||
284 305
|[RUBCNL](RUBCNL)|Tier 2 GE, aSHM||||
285
-|[S1PR1](S1PR1)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012a], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012a)|[@pararajalingamCodingNoncodingDrivers2020]||
286
-|[SAMD9L](SAMD9L)|Tier 2 GE[@morinMutationalStructuralAnalysis2013], aSHM|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||PASS|
287
-|[SEL1L3](SEL1L3)|Tier 2 GE, aSHM||||
306
+|[S1PR1](S1PR1)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012]|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012)|[@pararajalingamCodingNoncodingDrivers2020]||
307
+|[SAMD9L](SAMD9L)|Tier 2 GE[@morinMutationalStructuralAnalysis2013]|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||PASS|
308
+|[SEL1L3](SEL1L3)|Tier 2 GE[@schmitzGeneticsPathogenesisDiffuse2018], aSHM|[Schmitz et al](papers/schmitzGeneticsPathogenesisDiffuse2018)|||
288 309
|[SEPTIN9](SEPTIN9)|Tier 2 GE, aSHM||||
310
+|[SERPINA1](SERPINA1)|Tier 2 GE[@pasqualucciAnalysisCodingGenome2011]|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|||
289 311
|[SERPINA9](SERPINA9)|Tier 2 GE[@arthurGenomewideDiscoverySomatic2018], aSHM|[Arthur et al](papers/arthurGenomewideDiscoverySomatic2018)|||
290
-|[SETD2](SETD2)|Tier 2 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
291
-|[SETD5](SETD5)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@tiacciPervasiveMutationsJAKSTAT2018b]|PASS|
292
-|[SIAH2](SIAH2)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021b], aSHM|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)|[@reichelFlowSortingExome2015a]|PASS|
293
-|[SLC34A2](SLC34A2)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021b], aSHM|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)||PASS|
294
-|[SLC38A8](SLC38A8)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012a], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012a)|||
295
-|[SLITRK6](SLITRK6)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012a], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012a)|||
296
-|[SMEK1](SMEK1)|Tier 2 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
297
-|[SRPX](SRPX)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012a], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012a)|||
298
-|[SRRM2](SRRM2)|Tier 2 GE[@morinMutationalStructuralAnalysis2013], aSHM|[Morin et al](papers/morinMutationalStructuralAnalysis2013)|[@russler-germainMutationsAssociatedProgression2023b]|PASS|
312
+|[SETD2](SETD2)|Tier 2 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
313
+|[SETD5](SETD5)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@tiacciPervasiveMutationsJAKSTAT2018]|PASS|
314
+|[SIAH2](SIAH2)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021)|[@reichelFlowSortingExome2015]|PASS|
315
+|[SLC34A2](SLC34A2)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021)||PASS|
316
+|[SLC38A8](SLC38A8)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012]|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012)|||
317
+|[SLITRK6](SLITRK6)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012]|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012)|||
318
+|[SMARCA1](SMARCA1)|Tier 2 GE[@pasqualucciAnalysisCodingGenome2011]|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|||
319
+|[SMEK1](SMEK1)|Tier 2 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
320
+|[SRPX](SRPX)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012]|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012)|||
321
+|[SRRM2](SRRM2)|Tier 2 GE[@morinMutationalStructuralAnalysis2013]|[Morin et al](papers/morinMutationalStructuralAnalysis2013)|[@russler-germainMutationsAssociatedProgression2023]|PASS|
299 322
|[ST6GAL1](ST6GAL1)|Tier 2 GE[@arthurGenomewideDiscoverySomatic2018], aSHM|[Arthur et al](papers/arthurGenomewideDiscoverySomatic2018)|||
300
-|[STAT5B](STAT5B)|Tier 2 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@tiacciPervasiveMutationsJAKSTAT2018b]||
301
-|[SYN2](SYN2)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012a], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012a)|||
302
-|[SYPL1](SYPL1)|Tier 2 GE[@morinMutationalStructuralAnalysis2013], aSHM|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||PASS|
303
-|[TAP1](TAP1)|Tier 2 GE[@schmitzGeneticsPathogenesisDiffuse2018a], aSHM|[Schmitz et al](papers/schmitzGeneticsPathogenesisDiffuse2018a)|||
323
+|[STAT5B](STAT5B)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@tiacciPervasiveMutationsJAKSTAT2018]||
324
+|[SYN2](SYN2)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012]|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012)|||
325
+|[SYPL1](SYPL1)|Tier 2 GE[@morinMutationalStructuralAnalysis2013]|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||PASS|
326
+|[TAP1](TAP1)|Tier 2 GE[@schmitzGeneticsPathogenesisDiffuse2018]|[Schmitz et al](papers/schmitzGeneticsPathogenesisDiffuse2018)|||
304 327
|[TBC1D4](TBC1D4)|Tier 2 GE[@arthurGenomewideDiscoverySomatic2018], aSHM|[Arthur et al](papers/arthurGenomewideDiscoverySomatic2018)|||
328
+|[TBP](TBP)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012]|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012)|||
305 329
|[TCL1A](TCL1A)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@grandeGenomewideDiscoverySomatic2019]||
306
-|[TGFBR2](TGFBR2)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||PASS|
307
-|[TIPARP](TIPARP)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||PASS|
308
-|[TLR2](TLR2)|Tier 2 GE[@chapuyMolecularSubtypesDiffuse2018b], aSHM|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018b)|[@beaLandscapeSomaticMutations2013]|PASS|
309
-|[TMSL3](TMSL3)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012a], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012a)|||
310
-|[TNF](TNF)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012a], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012a)|||
311
-|[TRAF3](TRAF3)|Tier 2 GE[@pasqualucciAnalysisCodingGenome2011], aSHM|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|[@ottoGeneticLesionsTRAF32012a; @rossiAlterationBIRC3Multiple2011a]||
312
-|[TRAF6](TRAF6)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021b], aSHM|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)||PASS|
313
-|[TRIP12](TRIP12)|Tier 2 GE, aSHM||||
314
-|[UBE2J1](UBE2J1)|Tier 2 GE, aSHM||||
315
-|[UBR5](UBR5)|Tier 2 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@pararajalingamCodingNoncodingDrivers2020]||
316
-|[UHRF1BP1](UHRF1BP1)|Tier 2 GE[@albuquerqueEnhancingKnowledgeDiscovery2017a], aSHM|[Albuquerque et al](papers/albuquerqueEnhancingKnowledgeDiscovery2017a)|||
317
-|[UNC5B](UNC5B)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021b], aSHM|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)||PASS|
318
-|[UNC5C](UNC5C)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012a], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012a)|||
319
-|[UNC5D](UNC5D)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012a], aSHM|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012a)|||
320
-|[USP7](USP7)|Tier 2 GE[@arthurGenomewideDiscoverySomatic2018], aSHM|[Arthur et al](papers/arthurGenomewideDiscoverySomatic2018)|[@grandeGenomewideDiscoverySomatic2019]||
321
-|[WDFY3](WDFY3)|Tier 2 GE[@morinMutationalStructuralAnalysis2013], aSHM|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||PASS|
322
-|[WNK1](WNK1)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021b], aSHM|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)|[@jalladesExomeSequencingIdentifies2017; @thomasGeneticSubgroupsInform2023]|PASS|
330
+|[TGFBR2](TGFBR2)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||PASS|
331
+|[TIPARP](TIPARP)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||PASS|
332
+|[TLL2](TLL2)|Tier 2 GE[@pasqualucciAnalysisCodingGenome2011]|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|||
333
+|[TLR2](TLR2)|Tier 2 GE[@chapuyMolecularSubtypesDiffuse2018]|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018)|[@beaLandscapeSomaticMutations2013]|PASS|
334
+|[TMSL3](TMSL3)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012]|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012)|||
335
+|[TNF](TNF)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012]|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012)|||
336
+|[TRAF3](TRAF3)|Tier 2 GE[@pasqualucciAnalysisCodingGenome2011]|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|[@ottoGeneticLesionsTRAF32012; @rossiAlterationBIRC3Multiple2011]||
337
+|[TRAF6](TRAF6)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021)||PASS|
338
+|[TRIP12](TRIP12)|Tier 2 GE||||
339
+|[TSC22D1](TSC22D1)|Tier 2 GE[@pasqualucciAnalysisCodingGenome2011]|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|||
340
+|[UBE2J1](UBE2J1)|Tier 2 GE[@schmitzGeneticsPathogenesisDiffuse2018], aSHM|[Schmitz et al](papers/schmitzGeneticsPathogenesisDiffuse2018)|||
341
+|[UBR5](UBR5)|Tier 2 GE[@albuquerqueEnhancingKnowledgeDiscovery2017]|[Albuquerque et al](papers/albuquerqueEnhancingKnowledgeDiscovery2017)|[@pararajalingamCodingNoncodingDrivers2020]||
342
+|[UHRF1BP1](UHRF1BP1)|Tier 2 GE[@albuquerqueEnhancingKnowledgeDiscovery2017]|[Albuquerque et al](papers/albuquerqueEnhancingKnowledgeDiscovery2017)|||
343
+|[UNC5B](UNC5B)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021)||PASS|
344
+|[UNC5C](UNC5C)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012]|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012)|||
345
+|[UNC5D](UNC5D)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012]|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012)|||
346
+|[USP7](USP7)|Tier 2 GE[@arthurGenomewideDiscoverySomatic2018]|[Arthur et al](papers/arthurGenomewideDiscoverySomatic2018)|[@grandeGenomewideDiscoverySomatic2019]||
347
+|[VAX1](VAX1)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012]|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012)|||
348
+|[WDFY3](WDFY3)|Tier 2 GE[@morinMutationalStructuralAnalysis2013]|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||PASS|
349
+|[WNK1](WNK1)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021)|[@jalladesExomeSequencingIdentifies2017; @thomasGeneticSubgroupsInform2023]|PASS|
323 350
|[XBP1](XBP1)|Tier 2 GE, aSHM||||
324
-|[YY1](YY1)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||PASS|
351
+|[YY1](YY1)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||PASS|
325 352
|[ZCCHC7](ZCCHC7)|Tier 2 GE[@arthurGenomewideDiscoverySomatic2018], aSHM|[Arthur et al](papers/arthurGenomewideDiscoverySomatic2018)|||
326
-|[ZEB2](ZEB2)|Tier 2 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
327
-|[ZFX](ZFX)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||PASS|
328
-|[ZNF217](ZNF217)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021b], aSHM|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)|[@reichelFlowSortingExome2015a]|PASS|
329
-|[ZNF423](ZNF423)|Tier 2 GE[@chapuyMolecularSubtypesDiffuse2018b], aSHM|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018b)||PASS|
353
+|[ZEB2](ZEB2)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|||
354
+|[ZFX](ZFX)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||PASS|
355
+|[ZNF217](ZNF217)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021)|[@reichelFlowSortingExome2015]|PASS|
356
+|[ZNF385B](ZNF385B)|Tier 2 GE[@lohrDiscoveryPrioritizationSomatic2012]|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012)|||
357
+|[ZNF423](ZNF423)|Tier 2 GE[@chapuyMolecularSubtypesDiffuse2018]|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018)||PASS|
358
+|[ZNF521](ZNF521)|Tier 2 GE[@pasqualucciAnalysisCodingGenome2011]|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|||
359
+|[ZWILCH](ZWILCH)|Tier 2 GE[@pasqualucciAnalysisCodingGenome2011]|[Pasqualucci et al](papers/pasqualucciAnalysisCodingGenome2011)|||
330 360
331 361
## Tier 3, retired DLBCL genes
332 362
333
-### *386 total*
363
+### *387 total*
334 364
335 365
|Gene|Summary| First DLBCL study | Other entities | QC result |
336 366
|:-:|:--:|:-:|:-|:-|
337
-|[ABCA3](ABCA3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@beaLandscapeSomaticMutations2013]||
338
-|[ABCA4](ABCA4)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
339
-|[ABCB1](ABCB1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
340
-|[ACE](ACE)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@loveGeneticLandscapeMutations2012]||
341
-|[ACSM3](ACSM3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
342
-|[ACSS2](ACSS2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
343
-|[ACSS3](ACSS3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
344
-|[ACTN1](ACTN1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
345
-|[ADAM2](ADAM2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
346
-|[ADAMTS15](ADAMTS15)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
347
-|[ADH7](ADH7)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
348
-|[AFAP1L2](AFAP1L2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
349
-|[AGA](AGA)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
350
-|[AHR](AHR)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
351
-|[AKAP9](AKAP9)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
352
-|[ALAS1](ALAS1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
353
-|[ALDH1L2](ALDH1L2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
354
-|[AMAC1](AMAC1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
355
-|[AMIGO3](AMIGO3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
356
-|[AMPH](AMPH)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
357
-|[ANK2](ANK2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@zhangGenomicLandscapeMantle2014]||
358
-|[ANKRD44](ANKRD44)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
359
-|[ANTXR1](ANTXR1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
360
-|[AP1G2](AP1G2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
361
-|[APBB1](APBB1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
362
-|[APC](APC)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
363
-|[APMAP](APMAP)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
364
-|[APOA5](APOA5)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
365
-|[APP](APP)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
366
-|[ARID1B](ARID1B)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||FAIL|
367
-|[ATIC](ATIC)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
368
-|[ATP10A](ATP10A)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
369
-|[ATP1A2](ATP1A2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
370
-|[ATP2A3](ATP2A3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
371
-|[ATP6V0A1](ATP6V0A1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
372
-|[B4GALNT2](B4GALNT2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
373
-|[BAZ1A](BAZ1A)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
374
-|[BCAT2](BCAT2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
375
-|[BLM](BLM)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
376
-|[BMPR1A](BMPR1A)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
377
-|[BRCA1](BRCA1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
378
-|[BRCA2](BRCA2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
379
-|[BRD4](BRD4)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@loveGeneticLandscapeMutations2012]||
380
-|[BSCL2](BSCL2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
381
-|[BTAF1](BTAF1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
382
-|[C9](C9)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
383
-|[CAD](CAD)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@loveGeneticLandscapeMutations2012]||
384
-|[CAPN5](CAPN5)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
385
-|[CAPN7](CAPN7)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
386
-|[CBLB](CBLB)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||FAIL|
387
-|[CBX3](CBX3)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
388
-|[CCDC132](CCDC132)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
389
-|[CCDC46](CCDC46)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
390
-|[CCDC97](CCDC97)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
391
-|[CCL4](CCL4)|Tier 3 GE[@chapuyMolecularSubtypesDiffuse2018b], aSHM|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018b)||FAIL|
392
-|[CCNF](CCNF)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@abateDistinctViralMutational2015a]||
393
-|[CDC123](CDC123)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
394
-|[CDC73](CDC73)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@loveGeneticLandscapeMutations2012]|FAIL|
395
-|[CDH10](CDH10)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
396
-|[CDH7](CDH7)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
397
-|[CDH8](CDH8)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@zhangGenomicLandscapeMantle2014]|FAIL|
398
-|[CDK3](CDK3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
399
-|[CDKN1A](CDKN1A)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
400
-|[CECR1](CECR1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
401
-|[CELSR2](CELSR2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
402
-|[CGN](CGN)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
403
-|[CHD1](CHD1)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||FAIL|
404
-|[CHD3](CHD3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
405
-|[CHEK2](CHEK2)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
406
-|[CHRM5](CHRM5)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
407
-|[CHST2](CHST2)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||FAIL|
408
-|[CIC](CIC)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
409
-|[CNGA4](CNGA4)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
410
-|[CNOT6](CNOT6)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
411
-|[CNP](CNP)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
412
-|[CNTN6](CNTN6)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
413
-|[COL5A2](COL5A2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
414
-|[CORO2A](CORO2A)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
415
-|[CORO7](CORO7)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
416
-|[CRELD2](CRELD2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
417
-|[CRTC3](CRTC3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
418
-|[CSNK1A1](CSNK1A1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
419
-|[CSNK2A1](CSNK2A1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
420
-|[CST7](CST7)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
421
-|[CTNNA3](CTNNA3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
422
-|[CYP24A1](CYP24A1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
423
-|[CYP2C18](CYP2C18)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
424
-|[CYYR1](CYYR1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
425
-|[DCAF6](DCAF6)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||FAIL|
426
-|[DDB1](DDB1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
427
-|[DGCR8](DGCR8)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
428
-|[DHX33](DHX33)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
429
-|[DIAPH3](DIAPH3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
430
-|[DICER1](DICER1)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||FAIL|
431
-|[DIP2B](DIP2B)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
432
-|[DLGAP1](DLGAP1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@loveGeneticLandscapeMutations2012]||
433
-|[DMXL1](DMXL1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
434
-|[DNMT3A](DNMT3A)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||FAIL|
435
-|[DOCK2](DOCK2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
436
-|[DOCK5](DOCK5)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
437
-|[DOLK](DOLK)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
438
-|[DSC2](DSC2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
439
-|[DSCAML1](DSCAML1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
440
-|[DSG2](DSG2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
441
-|[DSP](DSP)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
442
-|[DUOXA2](DUOXA2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
443
-|[DUPD1](DUPD1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
444
-|[DYNC1H1](DYNC1H1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
445
-|[DYNC1I1](DYNC1I1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
446
-|[ECGF1](ECGF1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
447
-|[ECT2L](ECT2L)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
448
-|[EGFR](EGFR)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
449
-|[EPHA3](EPHA3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
450
-|[EPHA5](EPHA5)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
451
-|[EPHA7](EPHA7)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@mottokIntegrativeGenomicAnalysis2019b]||
452
-|[ERBB3](ERBB3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
453
-|[ERN2](ERN2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
454
-|[ETNPPL](ETNPPL)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
455
-|[EXTL3](EXTL3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
456
-|[FAIM](FAIM)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
457
-|[FAM161A](FAM161A)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
458
-|[FAM38B](FAM38B)|Tier 3 GE[@morinMutationalStructuralAnalysis2013], aSHM|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||FAIL|
459
-|[FAM62C](FAM62C)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
460
-|[FANCD2](FANCD2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
461
-|[FGD3](FGD3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
462
-|[FGFR1](FGFR1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
463
-|[FIGN](FIGN)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
464
-|[FLNA](FLNA)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
465
-|[FLNC](FLNC)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
466
-|[FLT1](FLT1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
467
-|[FMO2](FMO2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
468
-|[FN1](FN1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
469
-|[FNDC1](FNDC1)|Tier 3 GE[@morinMutationalStructuralAnalysis2013], aSHM|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||FAIL|
470
-|[FRMPD1](FRMPD1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
471
-|[FUT5](FUT5)|Tier 3 GE[@chapuyMolecularSubtypesDiffuse2018b], aSHM|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018b)||FAIL|
472
-|[FZD1](FZD1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
473
-|[GABRG1](GABRG1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
474
-|[GAK](GAK)|Tier 3 GE[@hubschmannMutationalMechanismsShaping2021b], aSHM|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)||FAIL|
475
-|[GATA2](GATA2)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
476
-|[GATA3](GATA3)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
477
-|[GCN1L1](GCN1L1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
478
-|[GJA8](GJA8)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
479
-|[GJB4](GJB4)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
480
-|[GNAS](GNAS)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||FAIL|
481
-|[GOPC](GOPC)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
482
-|[GPD2](GPD2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
483
-|[GPR133](GPR133)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
484
-|[GPR15](GPR15)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
485
-|[GREM2](GREM2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
486
-|[GRIA2](GRIA2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
487
-|[GRM5](GRM5)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
488
-|[H6PD](H6PD)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
489
-|[HACE1](HACE1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
490
-|[HCK](HCK)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
491
-|[HFE](HFE)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
492
-|[HIPK3](HIPK3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
493
-|[HIST1H4I](HIST1H4I)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
494
-|[HK3](HK3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
495
-|[HLA-DQA1](HLA-DQA1)|Tier 3 GE[@hubschmannMutationalMechanismsShaping2021b], aSHM|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)||FAIL|
496
-|[HLA-DRB1](HLA-DRB1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
497
-|[HNRNPR](HNRNPR)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
498
-|[HRAS](HRAS)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@jalladesExomeSequencingIdentifies2017]|FAIL|
499
-|[HSF2](HSF2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
500
-|[IDH1](IDH1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
501
-|[IER2](IER2)|Tier 3 GE[@morinMutationalStructuralAnalysis2013], aSHM|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||FAIL|
502
-|[IL6ST](IL6ST)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
503
-|[INSC](INSC)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
504
-|[INTS6](INTS6)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
505
-|[IQGAP1](IQGAP1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
506
-|[IQUB](IQUB)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
507
-|[ITGA2](ITGA2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
508
-|[ITGA8](ITGA8)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
509
-|[ITGB3](ITGB3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
510
-|[ITGB4](ITGB4)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
511
-|[ITPR1](ITPR1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
512
-|[JAG1](JAG1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
513
-|[JAKMIP2](JAKMIP2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
514
-|[KCNA3](KCNA3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
515
-|[KCNAB3](KCNAB3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
516
-|[KCNJ6](KCNJ6)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
517
-|[KCNT2](KCNT2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
518
-|[KDR](KDR)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
519
-|[KIF21B](KIF21B)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
520
-|[KIT](KIT)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
521
-|[KITLG](KITLG)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
522
-|[KLB](KLB)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
523
-|[KLC3](KLC3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
524
-|[KLF4](KLF4)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
525
-|[KLRC4](KLRC4)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
526
-|[KRT6A](KRT6A)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
527
-|[LEPR](LEPR)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
528
-|[LEPREL1](LEPREL1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
529
-|[LIFR](LIFR)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
530
-|[LILRA2](LILRA2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
531
-|[LIN54](LIN54)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||FAIL|
532
-|[LIN7C](LIN7C)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
533
-|[LPHN2](LPHN2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
534
-|[LRAP](LRAP)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
535
-|[LRIG3](LRIG3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
536
-|[LRP1](LRP1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
537
-|[LRP10](LRP10)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
538
-|[LRP1B](LRP1B)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@spinaGeneticsNodalMarginal2016b]||
539
-|[LRP3](LRP3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
540
-|[LYST](LYST)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
541
-|[MAP2K3](MAP2K3)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
542
-|[MAP4K4](MAP4K4)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||FAIL|
543
-|[MARCHF7](MARCHF7)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
544
-|[MARK1](MARK1)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||FAIL|
545
-|[MBL2](MBL2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
546
-|[MCM8](MCM8)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
547
-|[MED13L](MED13L)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
548
-|[MIB1](MIB1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
549
-|[MLH1](MLH1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
550
-|[MMEL1](MMEL1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
551
-|[MN1](MN1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
552
-|[MORC2](MORC2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
553
-|[MPL](MPL)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
554
-|[MSH2](MSH2)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||FAIL|
555
-|[MSN](MSN)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
556
-|[MTMR3](MTMR3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
557
-|[MYB](MYB)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@deschGenotypingCirculatingTumor2020]|FAIL|
558
-|[MYL7](MYL7)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
559
-|[MYO5C](MYO5C)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
560
-|[MYRIP](MYRIP)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
561
-|[NANOG](NANOG)|Tier 3 GE[@chapuyMolecularSubtypesDiffuse2018b], aSHM|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018b)||FAIL|
562
-|[NCOR1](NCOR1)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||FAIL|
563
-|[NDUFS1](NDUFS1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
564
-|[NELL2](NELL2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
565
-|[NFIB](NFIB)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
566
-|[NFKB2](NFKB2)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@mottokIntegrativeGenomicAnalysis2019b]|FAIL|
567
-|[NFX1](NFX1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
568
-|[NGFR](NGFR)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
569
-|[NIPBL](NIPBL)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
570
-|[NLGN2](NLGN2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
571
-|[NLRP7](NLRP7)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
572
-|[NLRP8](NLRP8)|Tier 3 GE[@chapuyMolecularSubtypesDiffuse2018b], aSHM|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018b)||FAIL|
573
-|[NOTCH3](NOTCH3)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
574
-|[NPHP1](NPHP1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
575
-|[NPY2R](NPY2R)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
576
-|[NR2F2](NR2F2)|Tier 3 GE[@hubschmannMutationalMechanismsShaping2021b], aSHM|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)||FAIL|
577
-|[NRXN2](NRXN2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@loveGeneticLandscapeMutations2012]||
578
-|[NSD1](NSD1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
579
-|[NSD2](NSD2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@beaLandscapeSomaticMutations2013]||
580
-|[NUP153](NUP153)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
581
-|[ONECUT1](ONECUT1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
582
-|[PABPC1](PABPC1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
583
-|[PADI1](PADI1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
584
-|[PAPPA2](PAPPA2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
585
-|[PBX1](PBX1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
586
-|[PCCB](PCCB)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
587
-|[PCDE1C](PCDE1C)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
588
-|[PCDH7](PCDH7)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
589
-|[PCDHB1](PCDHB1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
590
-|[PCDHB15](PCDHB15)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
591
-|[PCDHB3](PCDHB3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
592
-|[PCDHB5](PCDHB5)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
593
-|[PCDHGA2](PCDHGA2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
594
-|[PDE1C](PDE1C)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
595
-|[PDE4DIP](PDE4DIP)|Tier 3 GE[@chapuyMolecularSubtypesDiffuse2018b], aSHM|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018b)||FAIL|
596
-|[PDGFRA](PDGFRA)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
597
-|[PDGFRB](PDGFRB)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
598
-|[PDIA2](PDIA2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
599
-|[PDZRN3](PDZRN3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@paneaWholeGenomeLandscape2019]||
600
-|[PDZRN4](PDZRN4)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
601
-|[PFN1](PFN1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
602
-|[PGR](PGR)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
603
-|[PHF6](PHF6)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@thomasGeneticSubgroupsInform2023]|FAIL|
604
-|[PKD1](PKD1)|Tier 3 GE[@morinMutationalStructuralAnalysis2013], aSHM|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||FAIL|
605
-|[PLA2G4B](PLA2G4B)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
606
-|[PLCB4](PLCB4)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
607
-|[PLCG2](PLCG2)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|[@paneaWholeGenomeLandscape2019]||
608
-|[PLEKHA7](PLEKHA7)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
609
-|[PNLIPRP1](PNLIPRP1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
610
-|[PNPT1](PNPT1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
611
-|[POGZ](POGZ)|Tier 3 GE[@morinMutationalStructuralAnalysis2013], aSHM|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||FAIL|
612
-|[POLD3](POLD3)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
613
-|[POLE](POLE)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
614
-|[POLQ](POLQ)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
615
-|[PPARGC1A](PPARGC1A)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
616
-|[PPP2R2B](PPP2R2B)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
617
-|[PPWD1](PPWD1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
618
-|[PRDM16](PRDM16)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
619
-|[PRKCB1](PRKCB1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
620
-|[PRKCQ](PRKCQ)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
621
-|[PROS1](PROS1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
622
-|[PRSS7](PRSS7)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
623
-|[PTCH1](PTCH1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
624
-|[PTPN14](PTPN14)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
625
-|[PTPN23](PTPN23)|Tier 3 GE[@morinMutationalStructuralAnalysis2013], aSHM|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||FAIL|
626
-|[PTPRF](PTPRF)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
627
-|[PTPRK](PTPRK)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||FAIL|
628
-|[PTPRT](PTPRT)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
629
-|[PXK](PXK)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
630
-|[RAB3GAP1](RAB3GAP1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
631
-|[RAD9A](RAD9A)|Tier 3 GE[@chapuyMolecularSubtypesDiffuse2018b], aSHM|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018b)||FAIL|
632
-|[RAF1](RAF1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|[@jalladesExomeSequencingIdentifies2017]||
633
-|[RAPGEF2](RAPGEF2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
634
-|[RAPGEF3](RAPGEF3)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
635
-|[RARA](RARA)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||FAIL|
636
-|[RBM15B](RBM15B)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
637
-|[RECQL4](RECQL4)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
638
-|[RELN](RELN)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@sarkozyMutationalLandscapeGray2021a]||
639
-|[RET](RET)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|[@loveGeneticLandscapeMutations2012]||
640
-|[RFC1](RFC1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
641
-|[RGS1](RGS1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@mottokIntegrativeGenomicAnalysis2019b]||
642
-|[RHPN2](RHPN2)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
643
-|[RIF1](RIF1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
644
-|[RIMS4](RIMS4)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
645
-|[ROR2](ROR2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
646
-|[RPTOR](RPTOR)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
647
-|[RSL1D1](RSL1D1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
648
-|[RUNDC1](RUNDC1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
649
-|[RUNX1](RUNX1)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||FAIL|
650
-|[RYR1](RYR1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
651
-|[SAPS3](SAPS3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
652
-|[SARM1](SARM1)|Tier 3 GE[@morinMutationalStructuralAnalysis2013], aSHM|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||FAIL|
653
-|[SCYL1](SCYL1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
654
-|[SEMA3A](SEMA3A)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
655
-|[SEMA3D](SEMA3D)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
656
-|[SEMA5A](SEMA5A)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
657
-|[SERINC2](SERINC2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
658
-|[SH3PXD2B](SH3PXD2B)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
659
-|[SHMT2](SHMT2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
660
-|[SIGLEC10](SIGLEC10)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
661
-|[SLC16A7](SLC16A7)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
662
-|[SLC16A8](SLC16A8)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
663
-|[SLC4A8](SLC4A8)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
664
-|[SLC5A1](SLC5A1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
665
-|[SLC9A5](SLC9A5)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
666
-|[SMO](SMO)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
667
-|[SOS2](SOS2)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
668
-|[SOX6](SOX6)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
669
-|[SPEG](SPEG)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
670
-|[SPTBN1](SPTBN1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
671
-|[ST8SIA3](ST8SIA3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
672
-|[SULF2](SULF2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
673
-|[SYK](SYK)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||FAIL|
674
-|[TAF1L](TAF1L)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
675
-|[TAF4B](TAF4B)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
676
-|[TECRL](TECRL)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
677
-|[THBS4](THBS4)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
678
-|[TIMM50](TIMM50)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
679
-|[TLN1](TLN1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
680
-|[TLN2](TLN2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
681
-|[TLR4](TLR4)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
682
-|[TMC1](TMC1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
683
-|[TMEM161A](TMEM161A)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
684
-|[TMEM16E](TMEM16E)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
685
-|[TMEM63A](TMEM63A)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
686
-|[TNPO1](TNPO1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
687
-|[TPR](TPR)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
688
-|[TPRKB](TPRKB)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
689
-|[TRIM37](TRIM37)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
690
-|[TRIP11](TRIP11)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@reichelFlowSortingExome2015a]||
691
-|[TRRAP](TRRAP)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@rossiCodingGenomeSplenic2012c]||
692
-|[TSC2](TSC2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
693
-|[TSHZ2](TSHZ2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
694
-|[TYRO3](TYRO3)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
695
-|[UBXN11](UBXN11)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
696
-|[UBXN2B](UBXN2B)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
697
-|[UHRF1BP1L](UHRF1BP1L)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
698
-|[UNC13B](UNC13B)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
699
-|[UQCRC1](UQCRC1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
700
-|[VANGL1](VANGL1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
701
-|[VPS13A](VPS13A)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
702
-|[WAC](WAC)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@rossiCodingGenomeSplenic2012c]|FAIL|
703
-|[WDR65](WDR65)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
704
-|[WDR66](WDR66)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
705
-|[WDR67](WDR67)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
706
-|[WIF1](WIF1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
707
-|[WNK4](WNK4)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
708
-|[WT1](WT1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
709
-|[XDH](XDH)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
710
-|[ZBTB7A](ZBTB7A)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@burkhardtClinicalRelevanceMolecular2022b]|FAIL|
711
-|[ZFAT](ZFAT)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017], aSHM|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||FAIL|
712
-|[ZIC4](ZIC4)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
713
-|[ZMYM4](ZMYM4)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
714
-|[ZNF354A](ZNF354A)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
715
-|[ZNF366](ZNF366)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
716
-|[ZNF439](ZNF439)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
717
-|[ZNF474](ZNF474)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
718
-|[ZNF700](ZNF700)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
719
-|[ZNF790](ZNF790)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
720
-|[ZNF814](ZNF814)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020b], aSHM|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020b)|||
721
-|[ZNF91](ZNF91)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
722
-|[ZP1](ZP1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013], aSHM|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
367
+|[ABCA3](ABCA3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@beaLandscapeSomaticMutations2013]||
368
+|[ABCA4](ABCA4)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
369
+|[ABCB1](ABCB1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
370
+|[ACE](ACE)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@loveGeneticLandscapeMutations2012]||
371
+|[ACSM3](ACSM3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
372
+|[ACSS2](ACSS2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
373
+|[ACSS3](ACSS3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
374
+|[ACTN1](ACTN1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
375
+|[ADAM2](ADAM2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
376
+|[ADAMTS15](ADAMTS15)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
377
+|[ADH7](ADH7)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
378
+|[AFAP1L2](AFAP1L2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
379
+|[AGA](AGA)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
380
+|[AHR](AHR)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
381
+|[AKAP9](AKAP9)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
382
+|[ALAS1](ALAS1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
383
+|[ALDH1L2](ALDH1L2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
384
+|[AMAC1](AMAC1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
385
+|[AMIGO3](AMIGO3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
386
+|[AMPH](AMPH)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
387
+|[ANK2](ANK2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@zhangGenomicLandscapeMantle2014]||
388
+|[ANKRD44](ANKRD44)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
389
+|[ANTXR1](ANTXR1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
390
+|[AP1G2](AP1G2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
391
+|[APBB1](APBB1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
392
+|[APC](APC)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
393
+|[APMAP](APMAP)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
394
+|[APOA5](APOA5)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
395
+|[APP](APP)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
396
+|[ARID1B](ARID1B)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||FAIL|
397
+|[ATIC](ATIC)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
398
+|[ATP10A](ATP10A)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
399
+|[ATP1A2](ATP1A2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
400
+|[ATP2A3](ATP2A3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
401
+|[ATP6V0A1](ATP6V0A1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
402
+|[B4GALNT2](B4GALNT2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
403
+|[BAZ1A](BAZ1A)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
404
+|[BCAT2](BCAT2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
405
+|[BLM](BLM)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
406
+|[BMPR1A](BMPR1A)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
407
+|[BRCA1](BRCA1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
408
+|[BRCA2](BRCA2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
409
+|[BRD4](BRD4)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@loveGeneticLandscapeMutations2012]||
410
+|[BSCL2](BSCL2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
411
+|[BTAF1](BTAF1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
412
+|[C9](C9)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
413
+|[CAD](CAD)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@loveGeneticLandscapeMutations2012]||
414
+|[CAPN5](CAPN5)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
415
+|[CAPN7](CAPN7)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
416
+|[CBLB](CBLB)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||FAIL|
417
+|[CBX3](CBX3)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
418
+|[CCDC132](CCDC132)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
419
+|[CCDC46](CCDC46)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
420
+|[CCDC97](CCDC97)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
421
+|[CCL4](CCL4)|Tier 3 GE[@chapuyMolecularSubtypesDiffuse2018]|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018)||FAIL|
422
+|[CCNF](CCNF)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@abateDistinctViralMutational2015]||
423
+|[CDC123](CDC123)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
424
+|[CDC73](CDC73)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@loveGeneticLandscapeMutations2012]|FAIL|
425
+|[CDH1](CDH1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
426
+|[CDH10](CDH10)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
427
+|[CDH7](CDH7)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
428
+|[CDH8](CDH8)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@zhangGenomicLandscapeMantle2014]|FAIL|
429
+|[CDK3](CDK3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
430
+|[CDKN1A](CDKN1A)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
431
+|[CECR1](CECR1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
432
+|[CELSR2](CELSR2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
433
+|[CGN](CGN)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
434
+|[CHD1](CHD1)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||FAIL|
435
+|[CHD3](CHD3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
436
+|[CHEK2](CHEK2)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
437
+|[CHRM5](CHRM5)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
438
+|[CHST2](CHST2)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||FAIL|
439
+|[CIC](CIC)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
440
+|[CNGA4](CNGA4)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
441
+|[CNOT6](CNOT6)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
442
+|[CNP](CNP)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
443
+|[CNTN6](CNTN6)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
444
+|[COL5A2](COL5A2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
445
+|[CORO2A](CORO2A)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
446
+|[CORO7](CORO7)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
447
+|[CRELD2](CRELD2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
448
+|[CRTC3](CRTC3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
449
+|[CSNK1A1](CSNK1A1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
450
+|[CSNK2A1](CSNK2A1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
451
+|[CST7](CST7)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
452
+|[CTNNA3](CTNNA3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
453
+|[CYP24A1](CYP24A1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
454
+|[CYP2C18](CYP2C18)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
455
+|[CYYR1](CYYR1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
456
+|[DCAF6](DCAF6)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||FAIL|
457
+|[DDB1](DDB1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
458
+|[DGCR8](DGCR8)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
459
+|[DHX33](DHX33)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
460
+|[DIAPH3](DIAPH3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
461
+|[DICER1](DICER1)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||FAIL|
462
+|[DIP2B](DIP2B)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
463
+|[DLGAP1](DLGAP1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@loveGeneticLandscapeMutations2012]||
464
+|[DMXL1](DMXL1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
465
+|[DNMT3A](DNMT3A)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||FAIL|
466
+|[DOCK2](DOCK2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
467
+|[DOCK5](DOCK5)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
468
+|[DOLK](DOLK)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
469
+|[DSC2](DSC2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
470
+|[DSCAML1](DSCAML1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
471
+|[DSG2](DSG2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
472
+|[DSP](DSP)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
473
+|[DUOXA2](DUOXA2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
474
+|[DUPD1](DUPD1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
475
+|[DYNC1H1](DYNC1H1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
476
+|[DYNC1I1](DYNC1I1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
477
+|[ECGF1](ECGF1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
478
+|[ECT2L](ECT2L)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
479
+|[EGFR](EGFR)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
480
+|[EPHA3](EPHA3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
481
+|[EPHA5](EPHA5)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
482
+|[EPHA7](EPHA7)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@mottokIntegrativeGenomicAnalysis2019]||
483
+|[ERBB3](ERBB3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
484
+|[ERN2](ERN2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
485
+|[ETNPPL](ETNPPL)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
486
+|[EXTL3](EXTL3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
487
+|[FAIM](FAIM)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
488
+|[FAM161A](FAM161A)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
489
+|[FAM38B](FAM38B)|Tier 3 GE[@morinMutationalStructuralAnalysis2013]|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||FAIL|
490
+|[FAM62C](FAM62C)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
491
+|[FANCD2](FANCD2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
492
+|[FGD3](FGD3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
493
+|[FGFR1](FGFR1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
494
+|[FIGN](FIGN)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
495
+|[FLNA](FLNA)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
496
+|[FLNC](FLNC)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
497
+|[FLT1](FLT1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
498
+|[FMO2](FMO2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
499
+|[FN1](FN1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
500
+|[FNDC1](FNDC1)|Tier 3 GE[@morinMutationalStructuralAnalysis2013]|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||FAIL|
501
+|[FRMPD1](FRMPD1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
502
+|[FUT5](FUT5)|Tier 3 GE[@chapuyMolecularSubtypesDiffuse2018]|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018)||FAIL|
503
+|[FZD1](FZD1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
504
+|[GABRG1](GABRG1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
505
+|[GAK](GAK)|Tier 3 GE[@hubschmannMutationalMechanismsShaping2021]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021)||FAIL|
506
+|[GATA2](GATA2)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
507
+|[GATA3](GATA3)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
508
+|[GCN1L1](GCN1L1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
509
+|[GJA8](GJA8)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
510
+|[GJB4](GJB4)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
511
+|[GNAS](GNAS)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||FAIL|
512
+|[GOPC](GOPC)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
513
+|[GPD2](GPD2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
514
+|[GPR133](GPR133)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
515
+|[GPR15](GPR15)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
516
+|[GREM2](GREM2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
517
+|[GRIA2](GRIA2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
518
+|[GRM5](GRM5)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
519
+|[H6PD](H6PD)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
520
+|[HACE1](HACE1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
521
+|[HCK](HCK)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
522
+|[HFE](HFE)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
523
+|[HIPK3](HIPK3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
524
+|[HIST1H4I](HIST1H4I)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
525
+|[HK3](HK3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
526
+|[HLA-DQA1](HLA-DQA1)|Tier 3 GE[@hubschmannMutationalMechanismsShaping2021]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021)||FAIL|
527
+|[HLA-DRB1](HLA-DRB1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
528
+|[HNRNPR](HNRNPR)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
529
+|[HRAS](HRAS)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@jalladesExomeSequencingIdentifies2017]|FAIL|
530
+|[HSF2](HSF2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
531
+|[IDH1](IDH1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
532
+|[IER2](IER2)|Tier 3 GE[@morinMutationalStructuralAnalysis2013]|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||FAIL|
533
+|[IL6ST](IL6ST)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
534
+|[INSC](INSC)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
535
+|[INTS6](INTS6)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
536
+|[IQGAP1](IQGAP1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
537
+|[IQUB](IQUB)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
538
+|[ITGA2](ITGA2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
539
+|[ITGA8](ITGA8)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
540
+|[ITGB3](ITGB3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
541
+|[ITGB4](ITGB4)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
542
+|[ITPR1](ITPR1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
543
+|[JAG1](JAG1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
544
+|[JAKMIP2](JAKMIP2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
545
+|[KCNA3](KCNA3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
546
+|[KCNAB3](KCNAB3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
547
+|[KCNJ6](KCNJ6)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
548
+|[KCNT2](KCNT2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
549
+|[KDR](KDR)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
550
+|[KIF21B](KIF21B)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
551
+|[KIT](KIT)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
552
+|[KITLG](KITLG)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
553
+|[KLB](KLB)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
554
+|[KLC3](KLC3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
555
+|[KLF4](KLF4)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
556
+|[KLRC4](KLRC4)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
557
+|[KRT6A](KRT6A)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
558
+|[LEPR](LEPR)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
559
+|[LEPREL1](LEPREL1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
560
+|[LIFR](LIFR)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
561
+|[LILRA2](LILRA2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
562
+|[LIN54](LIN54)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||FAIL|
563
+|[LIN7C](LIN7C)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
564
+|[LPHN2](LPHN2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
565
+|[LRAP](LRAP)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
566
+|[LRIG3](LRIG3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
567
+|[LRP1](LRP1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
568
+|[LRP10](LRP10)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
569
+|[LRP1B](LRP1B)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@spinaGeneticsNodalMarginal2016]||
570
+|[LRP3](LRP3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
571
+|[LYST](LYST)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
572
+|[MAP2K3](MAP2K3)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
573
+|[MAP4K4](MAP4K4)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||FAIL|
574
+|[MARCHF7](MARCHF7)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
575
+|[MARK1](MARK1)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||FAIL|
576
+|[MBL2](MBL2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
577
+|[MCM8](MCM8)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
578
+|[MED13L](MED13L)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
579
+|[MIB1](MIB1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
580
+|[MLH1](MLH1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
581
+|[MMEL1](MMEL1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
582
+|[MN1](MN1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
583
+|[MORC2](MORC2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
584
+|[MPL](MPL)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
585
+|[MSH2](MSH2)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||FAIL|
586
+|[MSN](MSN)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
587
+|[MTMR3](MTMR3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
588
+|[MYB](MYB)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@deschGenotypingCirculatingTumor2020]|FAIL|
589
+|[MYL7](MYL7)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
590
+|[MYO5C](MYO5C)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
591
+|[MYRIP](MYRIP)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
592
+|[NANOG](NANOG)|Tier 3 GE[@chapuyMolecularSubtypesDiffuse2018]|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018)||FAIL|
593
+|[NCOR1](NCOR1)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||FAIL|
594
+|[NDUFS1](NDUFS1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
595
+|[NELL2](NELL2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
596
+|[NFIB](NFIB)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
597
+|[NFKB2](NFKB2)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@mottokIntegrativeGenomicAnalysis2019]|FAIL|
598
+|[NFX1](NFX1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
599
+|[NGFR](NGFR)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
600
+|[NIPBL](NIPBL)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
601
+|[NLGN2](NLGN2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
602
+|[NLRP7](NLRP7)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
603
+|[NLRP8](NLRP8)|Tier 3 GE[@chapuyMolecularSubtypesDiffuse2018]|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018)||FAIL|
604
+|[NOTCH3](NOTCH3)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
605
+|[NPHP1](NPHP1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
606
+|[NPY2R](NPY2R)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
607
+|[NR2F2](NR2F2)|Tier 3 GE[@hubschmannMutationalMechanismsShaping2021]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021)||FAIL|
608
+|[NRXN2](NRXN2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@loveGeneticLandscapeMutations2012]||
609
+|[NSD1](NSD1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
610
+|[NSD2](NSD2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@beaLandscapeSomaticMutations2013]||
611
+|[NUP153](NUP153)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
612
+|[ONECUT1](ONECUT1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
613
+|[PABPC1](PABPC1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
614
+|[PADI1](PADI1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
615
+|[PAPPA2](PAPPA2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
616
+|[PBX1](PBX1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
617
+|[PCCB](PCCB)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
618
+|[PCDE1C](PCDE1C)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
619
+|[PCDH7](PCDH7)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
620
+|[PCDHB1](PCDHB1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
621
+|[PCDHB15](PCDHB15)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
622
+|[PCDHB3](PCDHB3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
623
+|[PCDHB5](PCDHB5)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
624
+|[PCDHGA2](PCDHGA2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
625
+|[PDE1C](PDE1C)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
626
+|[PDE4DIP](PDE4DIP)|Tier 3 GE[@chapuyMolecularSubtypesDiffuse2018]|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018)||FAIL|
627
+|[PDGFRA](PDGFRA)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
628
+|[PDGFRB](PDGFRB)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
629
+|[PDIA2](PDIA2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
630
+|[PDZRN3](PDZRN3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@paneaWholeGenomeLandscape2019]||
631
+|[PDZRN4](PDZRN4)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
632
+|[PFN1](PFN1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
633
+|[PGR](PGR)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
634
+|[PHF6](PHF6)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@thomasGeneticSubgroupsInform2023]|FAIL|
635
+|[PKD1](PKD1)|Tier 3 GE[@morinMutationalStructuralAnalysis2013]|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||FAIL|
636
+|[PLA2G4B](PLA2G4B)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
637
+|[PLCB4](PLCB4)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
638
+|[PLCG2](PLCG2)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|[@paneaWholeGenomeLandscape2019]||
639
+|[PLEKHA7](PLEKHA7)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
640
+|[PNLIPRP1](PNLIPRP1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
641
+|[PNPT1](PNPT1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
642
+|[POGZ](POGZ)|Tier 3 GE[@morinMutationalStructuralAnalysis2013]|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||FAIL|
643
+|[POLD3](POLD3)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
644
+|[POLE](POLE)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
645
+|[POLQ](POLQ)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
646
+|[PPARGC1A](PPARGC1A)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
647
+|[PPP2R2B](PPP2R2B)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
648
+|[PPWD1](PPWD1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
649
+|[PRDM16](PRDM16)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
650
+|[PRKCB1](PRKCB1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
651
+|[PRKCQ](PRKCQ)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
652
+|[PROS1](PROS1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
653
+|[PRSS7](PRSS7)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
654
+|[PTCH1](PTCH1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
655
+|[PTPN14](PTPN14)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
656
+|[PTPN23](PTPN23)|Tier 3 GE[@morinMutationalStructuralAnalysis2013]|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||FAIL|
657
+|[PTPRF](PTPRF)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
658
+|[PTPRK](PTPRK)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||FAIL|
659
+|[PTPRT](PTPRT)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
660
+|[PXK](PXK)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
661
+|[RAB3GAP1](RAB3GAP1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
662
+|[RAD9A](RAD9A)|Tier 3 GE[@chapuyMolecularSubtypesDiffuse2018]|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018)||FAIL|
663
+|[RAF1](RAF1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|[@jalladesExomeSequencingIdentifies2017]||
664
+|[RAPGEF2](RAPGEF2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
665
+|[RAPGEF3](RAPGEF3)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
666
+|[RARA](RARA)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||FAIL|
667
+|[RBM15B](RBM15B)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
668
+|[RECQL4](RECQL4)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
669
+|[RELN](RELN)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@sarkozyMutationalLandscapeGray2021]||
670
+|[RET](RET)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|[@loveGeneticLandscapeMutations2012]||
671
+|[RFC1](RFC1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
672
+|[RGS1](RGS1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@mottokIntegrativeGenomicAnalysis2019]||
673
+|[RHPN2](RHPN2)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
674
+|[RIF1](RIF1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
675
+|[RIMS4](RIMS4)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
676
+|[ROR2](ROR2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
677
+|[RPTOR](RPTOR)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
678
+|[RSL1D1](RSL1D1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
679
+|[RUNDC1](RUNDC1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
680
+|[RUNX1](RUNX1)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||FAIL|
681
+|[RYR1](RYR1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
682
+|[SAPS3](SAPS3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
683
+|[SARM1](SARM1)|Tier 3 GE[@morinMutationalStructuralAnalysis2013]|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||FAIL|
684
+|[SCYL1](SCYL1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
685
+|[SEMA3A](SEMA3A)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
686
+|[SEMA3D](SEMA3D)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
687
+|[SEMA5A](SEMA5A)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
688
+|[SERINC2](SERINC2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
689
+|[SH3PXD2B](SH3PXD2B)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
690
+|[SHMT2](SHMT2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
691
+|[SIGLEC10](SIGLEC10)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
692
+|[SLC16A7](SLC16A7)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
693
+|[SLC16A8](SLC16A8)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
694
+|[SLC4A8](SLC4A8)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
695
+|[SLC5A1](SLC5A1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
696
+|[SLC9A5](SLC9A5)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
697
+|[SMO](SMO)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
698
+|[SOS2](SOS2)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
699
+|[SOX6](SOX6)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
700
+|[SPEG](SPEG)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
701
+|[SPTBN1](SPTBN1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
702
+|[ST8SIA3](ST8SIA3)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
703
+|[SULF2](SULF2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
704
+|[SYK](SYK)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||FAIL|
705
+|[TAF1L](TAF1L)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
706
+|[TAF4B](TAF4B)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
707
+|[TECRL](TECRL)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
708
+|[THBS4](THBS4)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
709
+|[TIMM50](TIMM50)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
710
+|[TLN1](TLN1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
711
+|[TLN2](TLN2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
712
+|[TLR4](TLR4)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
713
+|[TMC1](TMC1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
714
+|[TMEM161A](TMEM161A)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
715
+|[TMEM16E](TMEM16E)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
716
+|[TMEM63A](TMEM63A)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
717
+|[TNPO1](TNPO1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
718
+|[TPR](TPR)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
719
+|[TPRKB](TPRKB)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
720
+|[TRIM37](TRIM37)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
721
+|[TRIP11](TRIP11)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@reichelFlowSortingExome2015]||
722
+|[TRRAP](TRRAP)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@rossiCodingGenomeSplenic2012]||
723
+|[TSC2](TSC2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
724
+|[TSHZ2](TSHZ2)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
725
+|[TYRO3](TYRO3)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
726
+|[UBXN11](UBXN11)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
727
+|[UBXN2B](UBXN2B)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
728
+|[UHRF1BP1L](UHRF1BP1L)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
729
+|[UNC13B](UNC13B)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
730
+|[UQCRC1](UQCRC1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
731
+|[VANGL1](VANGL1)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
732
+|[VPS13A](VPS13A)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
733
+|[WAC](WAC)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@rossiCodingGenomeSplenic2012]|FAIL|
734
+|[WDR65](WDR65)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
735
+|[WDR66](WDR66)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
736
+|[WDR67](WDR67)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
737
+|[WIF1](WIF1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
738
+|[WNK4](WNK4)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
739
+|[WT1](WT1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
740
+|[XDH](XDH)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
741
+|[ZBTB7A](ZBTB7A)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@burkhardtClinicalRelevanceMolecular2022]|FAIL|
742
+|[ZFAT](ZFAT)|Tier 3 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||FAIL|
743
+|[ZIC4](ZIC4)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
744
+|[ZMYM4](ZMYM4)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
745
+|[ZNF354A](ZNF354A)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
746
+|[ZNF366](ZNF366)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
747
+|[ZNF439](ZNF439)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
748
+|[ZNF474](ZNF474)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
749
+|[ZNF700](ZNF700)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
750
+|[ZNF790](ZNF790)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
751
+|[ZNF814](ZNF814)|Tier 3 GE[@fanComprehensiveCharacterizationDriver2020]|[Fan et al](papers/fanComprehensiveCharacterizationDriver2020)|||
752
+|[ZNF91](ZNF91)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
753
+|[ZP1](ZP1)|Tier 3 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|||
723 754
724 755
725 756
# References
EBF1.md
... ...
@@ -29,8 +29,8 @@ timeline
29 29
30 30
|Entity|Tier|Description |
31 31
|:------:|:----:|--------------------------------------|
32
-|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene[@reichelFlowSortingExome2015a]|
33
-|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene [@bohleRoleEarlyBcell2013; @albuquerqueEnhancingKnowledgeDiscovery2017a; @morinMutationalStructuralAnalysis2013]|
32
+|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene[@reichelFlowSortingExome2015]|
33
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene [@bohleRoleEarlyBcell2013; @albuquerqueEnhancingKnowledgeDiscovery2017; @morinMutationalStructuralAnalysis2013]|
34 34
|![FL](images/icons/FL_tier1.png) |1-a | aSHM target and high-confidence FL gene |
35 35
|![BL](images/icons/BL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous [@thomasGeneticSubgroupsInform2023]|
36 36
FL_genes.md
... ...
@@ -11,130 +11,130 @@ link-citations: true
11 11
12 12
## Tier 1, high-confidence FL genes
13 13
14
-### *57 total*
14
+### *54 total*
15 15
16 16
|Gene|Summary| First FL study | Other entities | QC result |
17 17
|:-:|:--:|:-:|:-|:-|
18
-|[ACTB](ACTB)|Tier 1 GE[@drevalGeneticSubdivisionsFollicular2023], aSHM|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@lohrDiscoveryPrioritizationSomatic2012a; @wienandGenomicAnalysesFlowsorted2019b]||
19
-|[ARID1A](ARID1A)|Tier 1 GE[@krysiakRecurrentSomaticMutations2017b], FE[@barisicARID1AOrchestratesSWI2024], aSHM|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017b)|[@loveGeneticLandscapeMutations2012; @rossiCodingGenomeSplenic2012c; @wienandGenomicAnalysesFlowsorted2019b; @zhangGeneticHeterogeneityDiffuse2013]||
20
-|[ATP6AP1](ATP6AP1)|Tier 1 GE[@okosunRecurrentMTORC1activatingRRAGC2016a]|[Okosun et al](papers/okosunRecurrentMTORC1activatingRRAGC2016a)|||
21
-|[ATP6V1B2](ATP6V1B2)|Tier 1 GE[@okosunRecurrentMTORC1activatingRRAGC2016a]|[Okosun et al](papers/okosunRecurrentMTORC1activatingRRAGC2016a)|||
22
-|[B2M](B2M)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@challa-malladiCombinedGeneticInactivationa], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@pararajalingamCodingNoncodingDrivers2020; @reichelFlowSortingExome2015a]||
23
-|[BCL10](BCL10)|Tier 1 GE[@russler-germainMutationsAssociatedProgression2023b], FE[@xiaBCL10MutationsDefine2022], aSHM|[Russler-germain et al](papers/russler-germainMutationsAssociatedProgression2023b)|[@morinFrequentMutationHistonemodifying2011; @spinaGeneticsNodalMarginal2016b]||
24
-|[BCL2](BCL2)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@balSuperenhancerHypermutationAlters2022], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@burkhardtClinicalRelevanceMolecular2022b; @sarkozyMutationalLandscapeGray2021a; @tanakaFrequentIncidenceSomatic1992]||
25
-|[BCL6](BCL6)|Tier 1 GE[@drevalGeneticSubdivisionsFollicular2023], FE[@balSuperenhancerHypermutationAlters2022], aSHM|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@loveGeneticLandscapeMutations2012; @morinFrequentMutationHistonemodifying2011]||
26
-|[BCL7A](BCL7A)|Tier 1 GE[@krysiakRecurrentSomaticMutations2017b], FE[@balinas-gaviraFrequentMutationsAminoterminal2020b], aSHM|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017b)|[@grandeGenomewideDiscoverySomatic2019; @morinFrequentMutationHistonemodifying2011; @reichelFlowSortingExome2015a]||
27
-|[BTK](BTK)|Tier 1 GE[@krysiakRecurrentSomaticMutations2017b], aSHM|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017b)|[@albuquerqueEnhancingKnowledgeDiscovery2017a]||
28
-|[CARD11](CARD11)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@lenzOncogenicCARD11Mutations2008], CE[@zhaoExpressionPrognosticValue2016], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@lenzOncogenicCARD11Mutations2008; @wuGeneticHeterogeneityPrimary2016; @yanBCRTLRSignaling2012a]||
29
-|[CCND3](CCND3)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@schmitzBurkittLymphomaPathogenesis2012], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@deschGenotypingCirculatingTumor2020; @jalladesExomeSequencingIdentifies2017; @richterRecurrentMutationID32012a]||
30
-|[CD83](CD83)|Tier 1 GE[@russler-germainMutationsAssociatedProgression2023b], aSHM|[Russler-germain et al](papers/russler-germainMutationsAssociatedProgression2023b)|[@dunsCharacterizationDLBCLPMBL2021b; @morinMutationalStructuralAnalysis2013; @paneaWholeGenomeLandscape2019]||
31
-|[CREBBP](CREBBP)|Tier 1 GE[@pasqualucciInactivatingMutationsAcetyltransferase2011a], FE[@pasqualucciInactivatingMutationsAcetyltransferase2011a], aSHM|[Pasqualucci et al](papers/pasqualucciInactivatingMutationsAcetyltransferase2011a)|[@dunsCharacterizationDLBCLPMBL2021b; @loveGeneticLandscapeMutations2012; @parryWholeExomeSequencing2013]||
32
-|[CTSS](CTSS)|Tier 1 GE[@barariaCathepsinAlterationsInduce2020c]|[Bararia et al](papers/barariaCathepsinAlterationsInduce2020c)|||
33
-|[EBF1](EBF1)|Tier 1 GE, aSHM||[@bohleRoleEarlyBcell2013; @reichelFlowSortingExome2015a; @thomasGeneticSubgroupsInform2023]||
34
-|[EEF1A1](EEF1A1)|Tier 1 GE[@hubschmannMutationalMechanismsShaping2021b], CE[@gongExpressionClinicalValue2021], aSHM|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)|[@reichelFlowSortingExome2015a]||
35
-|[EP300](EP300)|Tier 1 GE[@pasqualucciInactivatingMutationsAcetyltransferase2011a], FE[@pasqualucciInactivatingMutationsAcetyltransferase2011a], aSHM|[Pasqualucci et al](papers/pasqualucciInactivatingMutationsAcetyltransferase2011a)|[@rossiCodingGenomeSplenic2012c]||
36
-|[EZH2](EZH2)|Tier 1 GE[@morinSomaticMutationsAltering2010a], FE[@yapSomaticMutationsEZH22011b], aSHM|[Morin et al](papers/morinSomaticMutationsAltering2010a)|[@loveGeneticLandscapeMutations2012; @mottokIntegrativeGenomicAnalysis2019b]||
37
-|[FAS](FAS)|Tier 1 GE, FE[@seebergerLossFasCD952001], aSHM||[@schollMutationsRegionFAS2007; @spinaGeneticsNodalMarginal2016b]||
38
-|[FOXO1](FOXO1)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@trinhAnalysisFOXO1Mutations], CE[@trinhAnalysisFOXO1Mutations], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@dunsCharacterizationDLBCLPMBL2021b; @schmitzBurkittLymphomaPathogenesis2012]||
39
-|[GNA13](GNA13)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@muppidiLossSignalingGa132014b], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@loveGeneticLandscapeMutations2012; @reichelFlowSortingExome2015a]||
40
-|[GNAI2](GNAI2)|Tier 1 GE, aSHM||[@grandeGenomewideDiscoverySomatic2019; @morinMutationalStructuralAnalysis2013]||
41
-|[HIST1H1B](HIST1H1B)|Tier 1 GE[@krysiakRecurrentSomaticMutations2017b], aSHM|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017b)|[@chapuyMolecularSubtypesDiffuse2018b; @sarkozyMutationalLandscapeGray2021a]||
18
+|[ACTB](ACTB)|Tier 1 GE[@drevalGeneticSubdivisionsFollicular2023], aSHM|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@lohrDiscoveryPrioritizationSomatic2012; @wienandGenomicAnalysesFlowsorted2019]||
19
+|[ARID1A](ARID1A)|Tier 1 GE[@krysiakRecurrentSomaticMutations2017], FE[@barisicARID1AOrchestratesSWI2024]|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017)|[@loveGeneticLandscapeMutations2012; @rossiCodingGenomeSplenic2012; @wienandGenomicAnalysesFlowsorted2019; @zhangGeneticHeterogeneityDiffuse2013]||
20
+|[ATP6AP1](ATP6AP1)|Tier 1 GE[@okosunRecurrentMTORC1activatingRRAGC2016]|[Okosun et al](papers/okosunRecurrentMTORC1activatingRRAGC2016)|||
21
+|[ATP6V1B2](ATP6V1B2)|Tier 1 GE[@okosunRecurrentMTORC1activatingRRAGC2016]|[Okosun et al](papers/okosunRecurrentMTORC1activatingRRAGC2016)|||
22
+|[B2M](B2M)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@challa-malladiCombinedGeneticInactivation2011]|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@pararajalingamCodingNoncodingDrivers2020; @reichelFlowSortingExome2015]||
23
+|[BCL10](BCL10)|Tier 1 GE[@russler-germainMutationsAssociatedProgression2023], FE[@xiaBCL10MutationsDefine2022]|[Russler-germain et al](papers/russler-germainMutationsAssociatedProgression2023)|[@morinFrequentMutationHistonemodifying2011; @spinaGeneticsNodalMarginal2016]||
24
+|[BCL2](BCL2)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@burkhardtClinicalRelevanceMolecular2022; @sarkozyMutationalLandscapeGray2021; @tanakaFrequentIncidenceSomatic1992]||
25
+|[BCL6](BCL6)|Tier 1 GE[@drevalGeneticSubdivisionsFollicular2023], FE[@masclePointMutationsBCL62003], aSHM|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@loveGeneticLandscapeMutations2012; @morinFrequentMutationHistonemodifying2011]||
26
+|[BCL7A](BCL7A)|Tier 1 GE[@krysiakRecurrentSomaticMutations2017], FE[@balinas-gaviraFrequentMutationsAminoterminal2020], aSHM|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017)|[@grandeGenomewideDiscoverySomatic2019; @morinFrequentMutationHistonemodifying2011; @reichelFlowSortingExome2015]||
27
+|[BTK](BTK)|Tier 1 GE[@krysiakRecurrentSomaticMutations2017], FE[@huFollicularLymphomaassociatedBTK2021]|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017)|[@albuquerqueEnhancingKnowledgeDiscovery2017]||
28
+|[CARD11](CARD11)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@lenzOncogenicCARD11Mutations2008]|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@lenzOncogenicCARD11Mutations2008; @wuGeneticHeterogeneityPrimary2016; @yanBCRTLRSignaling2012]||
29
+|[CCND3](CCND3)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@schmitzBurkittLymphomaPathogenesis2012]|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@deschGenotypingCirculatingTumor2020; @jalladesExomeSequencingIdentifies2017; @richterRecurrentMutationID32012]||
30
+|[CD83](CD83)|Tier 1 GE[@russler-germainMutationsAssociatedProgression2023], aSHM|[Russler-germain et al](papers/russler-germainMutationsAssociatedProgression2023)|[@dunsCharacterizationDLBCLPMBL2021; @morinMutationalStructuralAnalysis2013; @paneaWholeGenomeLandscape2019]||
31
+|[CREBBP](CREBBP)|Tier 1 GE[@pasqualucciInactivatingMutationsAcetyltransferase2011], FE[@pasqualucciInactivatingMutationsAcetyltransferase2011]|[Pasqualucci et al](papers/pasqualucciInactivatingMutationsAcetyltransferase2011)|[@dunsCharacterizationDLBCLPMBL2021; @loveGeneticLandscapeMutations2012; @parryWholeExomeSequencing2013]||
32
+|[CTSS](CTSS)|Tier 1 GE[@barariaCathepsinAlterationsInduce2020]|[Bararia et al](papers/barariaCathepsinAlterationsInduce2020)|||
33
+|[EBF1](EBF1)|Tier 1 GE[@drevalGeneticSubdivisionsFollicular2023], FE[@ramirez-komoSpontaneousLossLineage2017], aSHM|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@bohleRoleEarlyBcell2013; @reichelFlowSortingExome2015; @thomasGeneticSubgroupsInform2023]||
34
+|[EEF1A1](EEF1A1)|Tier 1 GE[@hubschmannMutationalMechanismsShaping2021]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021)|[@chapuyMolecularSubtypesDiffuse2018; @reichelFlowSortingExome2015]||
35
+|[EP300](EP300)|Tier 1 GE[@pasqualucciInactivatingMutationsAcetyltransferase2011], FE[@pasqualucciInactivatingMutationsAcetyltransferase2011]|[Pasqualucci et al](papers/pasqualucciInactivatingMutationsAcetyltransferase2011)|[@rossiCodingGenomeSplenic2012]||
36
+|[EZH2](EZH2)|Tier 1 GE[@morinSomaticMutationsAltering2010], FE[@sneeringerCoordinatedActivitiesWildtype2010]|[Morin et al](papers/morinSomaticMutationsAltering2010)|[@loveGeneticLandscapeMutations2012; @mottokIntegrativeGenomicAnalysis2019]||
37
+|[FAS](FAS)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@wangFasFADDDeathDomain2010]|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@schollMutationsRegionFAS2007; @spinaGeneticsNodalMarginal2016]||
38
+|[FOXO1](FOXO1)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@trinhAnalysisFOXO1Mutations]|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@dunsCharacterizationDLBCLPMBL2021; @schmitzBurkittLymphomaPathogenesis2012]||
39
+|[GNA13](GNA13)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@muppidiLossSignalingGa132014]|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@loveGeneticLandscapeMutations2012; @reichelFlowSortingExome2015]||
40
+|[GNAI2](GNAI2)|Tier 1 GE[@drevalGeneticSubdivisionsFollicular2023], FE[@muppidiLossSignalingGa132014]|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@grandeGenomewideDiscoverySomatic2019; @morinMutationalStructuralAnalysis2013]||
41
+|[HIST1H1B](HIST1H1B)|Tier 1 GE[@krysiakRecurrentSomaticMutations2017], aSHM|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017)|[@chapuyMolecularSubtypesDiffuse2018; @sarkozyMutationalLandscapeGray2021]||
42 42
|[HIST1H1C](HIST1H1C)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@paneaWholeGenomeLandscape2019]||
43
-|[HIST1H1D](HIST1H1D)|Tier 1 GE[@krysiakRecurrentSomaticMutations2017b], aSHM|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017b)|[@jalladesExomeSequencingIdentifies2017; @morinMutationalStructuralAnalysis2013]||
44
-|[HIST1H1E](HIST1H1E)|Tier 1 GE[@krysiakRecurrentSomaticMutations2017b], aSHM|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017b)|[@grandeGenomewideDiscoverySomatic2019; @lohrDiscoveryPrioritizationSomatic2012a; @reichelFlowSortingExome2015a]||
45
-|[HIST1H2AC](HIST1H2AC)|Tier 1 GE[@krysiakRecurrentSomaticMutations2017b], aSHM|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017b)|[@morinMutationalStructuralAnalysis2013]||
46
-|[HIST1H2AG](HIST1H2AG)|Tier 1 GE[@krysiakRecurrentSomaticMutations2017b], aSHM|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017b)|[@morinMutationalStructuralAnalysis2013; @paneaWholeGenomeLandscape2019; @rossiCodingGenomeSplenic2012c]||
47
-|[HIST1H2AM](HIST1H2AM)|Tier 1 GE[@krysiakRecurrentSomaticMutations2017b], aSHM|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017b)|[@chapuyMolecularSubtypesDiffuse2018b; @paneaWholeGenomeLandscape2019]||
48
-|[HIST1H2BC](HIST1H2BC)|Tier 1 GE[@krysiakRecurrentSomaticMutations2017b], aSHM|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017b)|[@lohrDiscoveryPrioritizationSomatic2012a; @mottokIntegrativeGenomicAnalysis2019b]||
49
-|[HIST1H2BD](HIST1H2BD)|Tier 1 GE[@krysiakRecurrentSomaticMutations2017b]|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017b)|||
50
-|[HIST1H2BG](HIST1H2BG)|Tier 1 GE[@krysiakRecurrentSomaticMutations2017b]|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017b)|||
51
-|[HIST1H3G](HIST1H3G)|Tier 1 GE[@krysiakRecurrentSomaticMutations2017b]|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017b)|||
52
-|[HIST1H3I](HIST1H3I)|Tier 1 GE[@krysiakRecurrentSomaticMutations2017b]|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017b)|[@paneaWholeGenomeLandscape2019]||
53
-|[HVCN1](HVCN1)|Tier 1 GE[@krysiakRecurrentSomaticMutations2017b], aSHM|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017b)|[@chapuyMolecularSubtypesDiffuse2018b]||
54
-|[IRF4](IRF4)|Tier 1 GE[@drevalGeneticSubdivisionsFollicular2023], aSHM|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@morinFrequentMutationHistonemodifying2011; @mottokIntegrativeGenomicAnalysis2019b]||
55
-|[IRF8](IRF8)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@qiuIRF8mutantCellLymphoma2024], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@mottokIntegrativeGenomicAnalysis2019b; @paneaWholeGenomeLandscape2019]||
56
-|[KLHL6](KLHL6)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@merirantaDisruptionKLHL6Fuels2024], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@ganapathiGeneticLandscapeDural2016]||
57
-|[KMT2D](KMT2D)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@liLossCREBBPKMT2D2024], CE[@rushtonGeneticEvolutionaryPatterns2020], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@beaLandscapeSomaticMutations2013; @deschGenotypingCirculatingTumor2020; @grandeGenomewideDiscoverySomatic2019; @rossiCodingGenomeSplenic2012c]||
58
-|[MAP2K1](MAP2K1)|Tier 1 GE[@louissaintPediatrictypeNodalFollicular2016a], aSHM|[Louissaint et al](papers/louissaintPediatrictypeNodalFollicular2016a)|[@shinBRAFV600EMAP2K12015]||
59
-|[MEF2B](MEF2B)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@yingMEF2BMutationsLead], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@beaLandscapeSomaticMutations2013]||
60
-|[MYC](MYC)|Tier 1 GE, FE[@giallongoIdentificationCmycOncogene1983], CE[@christieCMYCTranslocation142008], aSHM||[@dunsCharacterizationDLBCLPMBL2021b; @jalladesExomeSequencingIdentifies2017; @johnstonCmycHypermutationBurkitt1992; @pasqualucciHypermutationMultipleProtooncogenes2001a]||
61
-|[PIM1](PIM1)|Tier 1 GE[@drevalGeneticSubdivisionsFollicular2023], CE[@guoSGK1MutationStatus2022b], aSHM|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@burkhardtClinicalRelevanceMolecular2022b; @dunsCharacterizationDLBCLPMBL2021b; @pasqualucciHypermutationMultipleProtooncogenes2001a]||
62
-|[POU2AF1](POU2AF1)|Tier 1 GE[@krysiakRecurrentSomaticMutations2017b], aSHM|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017b)|[@chapuyMolecularSubtypesDiffuse2018b]||
63
-|[POU2F2](POU2F2)|Tier 1 GE[@krysiakRecurrentSomaticMutations2017b], FE[@hodsonRegulationNormalBcell2016a], aSHM|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017b)|[@lohrDiscoveryPrioritizationSomatic2012a]||
64
-|[RRAGC](RRAGC)|Tier 1 GE[@okosunRecurrentMTORC1activatingRRAGC2016a], FE[@ortega-molinaOncogenicRagGTPase2019b], aSHM|[Okosun et al](papers/okosunRecurrentMTORC1activatingRRAGC2016a)|||
65
-|[SGK1](SGK1)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@hartmannHighlyRecurrentMutations2016b], CE[@guoSGK1MutationStatus2022b], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@dunsCharacterizationDLBCLPMBL2021b]||
66
-|[SMARCA4](SMARCA4)|Tier 1 GE[@krysiakRecurrentSomaticMutations2017b], FE[@dengSMARCA4HaploinsufficientCell2024], aSHM|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017b)|[@nadeuGenomicEpigenomicInsights2020b; @reddyGeneticFunctionalDrivers2017; @richterRecurrentMutationID32012a]||
67
-|[SOCS1](SOCS1)|Tier 1 GE[@drevalGeneticSubdivisionsFollicular2023], FE[@melznerBiallelicMutationSOCS12005a], aSHM|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@morinFrequentMutationHistonemodifying2011; @wenigerMutationsTumorSuppressor2006a]||
68
-|[STAT6](STAT6)|Tier 1 GE[@yildizActivatingSTAT6Mutations2015c], FE[@yildizActivatingSTAT6Mutations2015c], aSHM|[Yildiz et al](papers/yildizActivatingSTAT6Mutations2015c)|[@ritzRecurrentMutationsSTAT62009a]||
69
-|[TBL1XR1](TBL1XR1)|Tier 1 GE, FE[@venturuttiTBL1XR1MutationsDrive2020b], aSHM||[@lohrDiscoveryPrioritizationSomatic2012a; @rossiCodingGenomeSplenic2012c]||
70
-|[TMSB4X](TMSB4X)|Tier 1 GE, aSHM||[@zhangGeneticHeterogeneityDiffuse2013]||
71
-|[TNFAIP3](TNFAIP3)|Tier 1 GE, FE[@compagnoMutationsMultipleGenes2009a], aSHM||[@compagnoMutationsMultipleGenes2009a; @rossiAlterationBIRC3Multiple2011a; @schmitzTNFAIP3A20Tumor2009a]||
72
-|[TNFRSF14](TNFRSF14)|Tier 1 GE[@cheungAcquiredTNFRSF14Mutations2010a], CE[@guoSGK1MutationStatus2022b], aSHM|[Cheung et al](papers/cheungAcquiredTNFRSF14Mutations2010a)|[@morinFrequentMutationHistonemodifying2011; @spinaGeneticsNodalMarginal2016b]||
73
-|[TP53](TP53)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@rowhTp53DeletionLineage2011], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@beaLandscapeSomaticMutations2013; @lohrDiscoveryPrioritizationSomatic2012a; @rossiCodingGenomeSplenic2012c; @tiacciPervasiveMutationsJAKSTAT2018b; @wildaInactivationARFMDM2p53Pathway2004]||
74
-|[VMA21](VMA21)|Tier 1 GE[@hubschmannMutationalMechanismsShaping2021b]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)|||
43
+|[HIST1H1D](HIST1H1D)|Tier 1 GE[@krysiakRecurrentSomaticMutations2017], aSHM|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017)|[@jalladesExomeSequencingIdentifies2017; @morinMutationalStructuralAnalysis2013]||
44
+|[HIST1H1E](HIST1H1E)|Tier 1 GE[@krysiakRecurrentSomaticMutations2017], aSHM|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017)|[@grandeGenomewideDiscoverySomatic2019; @lohrDiscoveryPrioritizationSomatic2012; @reichelFlowSortingExome2015]||
45
+|[HIST1H2AC](HIST1H2AC)|Tier 1 GE[@krysiakRecurrentSomaticMutations2017], aSHM|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017)|[@morinMutationalStructuralAnalysis2013]||
46
+|[HIST1H2AG](HIST1H2AG)|Tier 1 GE[@krysiakRecurrentSomaticMutations2017]|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017)|[@morinMutationalStructuralAnalysis2013; @paneaWholeGenomeLandscape2019; @rossiCodingGenomeSplenic2012]||
47
+|[HIST1H2AM](HIST1H2AM)|Tier 1 GE[@krysiakRecurrentSomaticMutations2017], aSHM|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017)|[@chapuyMolecularSubtypesDiffuse2018; @paneaWholeGenomeLandscape2019]||
48
+|[HIST1H2BC](HIST1H2BC)|Tier 1 GE[@krysiakRecurrentSomaticMutations2017], aSHM|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017)|[@lohrDiscoveryPrioritizationSomatic2012; @mottokIntegrativeGenomicAnalysis2019]||
49
+|[HIST1H2BG](HIST1H2BG)|Tier 1 GE[@krysiakRecurrentSomaticMutations2017]|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017)|||
50
+|[HVCN1](HVCN1)|Tier 1 GE[@krysiakRecurrentSomaticMutations2017]|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017)|[@chapuyMolecularSubtypesDiffuse2018]||
51
+|[IRF4](IRF4)|Tier 1 GE[@drevalGeneticSubdivisionsFollicular2023], aSHM|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@morinFrequentMutationHistonemodifying2011; @mottokIntegrativeGenomicAnalysis2019]||
52
+|[IRF8](IRF8)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@qiuIRF8mutantCellLymphoma2024], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@mottokIntegrativeGenomicAnalysis2019; @paneaWholeGenomeLandscape2019]||
53
+|[KLHL6](KLHL6)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@choiLossKLHL6Promotes2018], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@ganapathiGeneticLandscapeDural2016]||
54
+|[KMT2D](KMT2D)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@zhangDisruptionKMT2DPerturbs2015]|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@beaLandscapeSomaticMutations2013; @deschGenotypingCirculatingTumor2020; @grandeGenomewideDiscoverySomatic2019; @rossiCodingGenomeSplenic2012]||
55
+|[MAP2K1](MAP2K1)|Tier 1 GE[@louissaintPediatrictypeNodalFollicular2016]|[Louissaint et al](papers/louissaintPediatrictypeNodalFollicular2016)|[@shinBRAFV600EMAP2K12015]||
56
+|[MEF2B](MEF2B)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@ponMEF2BMutationsNonHodgkin2015], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@beaLandscapeSomaticMutations2013]||
57
+|[MYC](MYC)|Tier 1 GE, FE[@freieGermlinePointMutation2024], aSHM||[@dunsCharacterizationDLBCLPMBL2021; @jalladesExomeSequencingIdentifies2017; @johnstonCmycHypermutationBurkitt1992; @pasqualucciHypermutationMultipleProtooncogenes2001]||
58
+|[PIM1](PIM1)|Tier 1 GE[@drevalGeneticSubdivisionsFollicular2023], FE[@kuoRolePIM1Ibrutinibresistant2016], aSHM|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@burkhardtClinicalRelevanceMolecular2022; @dunsCharacterizationDLBCLPMBL2021; @pasqualucciHypermutationMultipleProtooncogenes2001]||
59
+|[POU2AF1](POU2AF1)|Tier 1 GE[@krysiakRecurrentSomaticMutations2017], FE[@gonzalez-rinconUnravelingTransformationFollicular2019], aSHM|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017)|[@chapuyMolecularSubtypesDiffuse2018]||
60
+|[POU2F2](POU2F2)|Tier 1 GE[@krysiakRecurrentSomaticMutations2017], FE[@hodsonRegulationNormalBcell2016]|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017)|[@lohrDiscoveryPrioritizationSomatic2012]||
61
+|[RRAGC](RRAGC)|Tier 1 GE[@okosunRecurrentMTORC1activatingRRAGC2016], FE[@okosunRecurrentMTORC1activatingRRAGC2016]|[Okosun et al](papers/okosunRecurrentMTORC1activatingRRAGC2016)|||
62
+|[SGK1](SGK1)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@gaoSGK1MutationsDLBCL2021], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@dunsCharacterizationDLBCLPMBL2021]||
63
+|[SMARCA4](SMARCA4)|Tier 1 GE[@krysiakRecurrentSomaticMutations2017], FE[@fernandoFunctionalCharacterizationSMARCA42020]|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017)|[@nadeuGenomicEpigenomicInsights2020b; @reddyGeneticFunctionalDrivers2017; @richterRecurrentMutationID32012]||
64
+|[SOCS1](SOCS1)|Tier 1 GE[@drevalGeneticSubdivisionsFollicular2023], FE[@melznerBiallelicMutationSOCS12005], aSHM|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@morinFrequentMutationHistonemodifying2011; @wenigerMutationsTumorSuppressor2006]||
65
+|[STAT6](STAT6)|Tier 1 GE[@yildizActivatingSTAT6Mutations2015], FE[@mentzPARP14NovelTarget2022]|[Yildiz et al](papers/yildizActivatingSTAT6Mutations2015)|[@ritzRecurrentMutationsSTAT62009]||
66
+|[TBL1XR1](TBL1XR1)|Tier 1 GE[@drevalGeneticSubdivisionsFollicular2023], FE[@venturuttiTBL1XR1MutationsDrive2020]|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@lohrDiscoveryPrioritizationSomatic2012; @rossiCodingGenomeSplenic2012]||
67
+|[TMSB4X](TMSB4X)|Tier 1 GE[@drevalGeneticSubdivisionsFollicular2023], aSHM|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@reddyGeneticFunctionalDrivers2017]||
68
+|[TNFAIP3](TNFAIP3)|Tier 1 GE[@drevalGeneticSubdivisionsFollicular2023], FE[@compagnoMutationsMultipleGenes2009]|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@compagnoMutationsMultipleGenes2009; @rossiAlterationBIRC3Multiple2011; @schmitzTNFAIP3A20Tumor2009]||
69
+|[TNFRSF14](TNFRSF14)|Tier 1 GE[@cheungAcquiredTNFRSF14Mutations2010], FE[@]|[Cheung et al](papers/cheungAcquiredTNFRSF14Mutations2010)|[@morinFrequentMutationHistonemodifying2011; @spinaGeneticsNodalMarginal2016]||
70
+|[TP53](TP53)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@katoUnderstandingFunctionstructureFunctionmutation2003]|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@beaLandscapeSomaticMutations2013; @rossiCodingGenomeSplenic2012; @tiacciPervasiveMutationsJAKSTAT2018; @wildaInactivationARFMDM2p53Pathway2004]||
71
+|[VMA21](VMA21)|Tier 1 GE[@hubschmannMutationalMechanismsShaping2021]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021)|||
75 72
76 73
## Tier 2, low-confidence FL genes
77 74
78
-### *56 total*
75
+### *59 total*
79 76
80 77
|Gene|Summary| First FL study | Other entities | QC result |
81 78
|:-:|:--:|:-:|:-|:-|
82
-|[ABL2](ABL2)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023b]|[Russler-germain et al](papers/russler-germainMutationsAssociatedProgression2023b)|||
83
-|[ACTG1](ACTG1)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021b], aSHM|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)|[@deschGenotypingCirculatingTumor2020; @spinaGeneticsNodalMarginal2016b]||
84
-|[ATP6V1A](ATP6V1A)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021b]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)|||
85
-|[BIRC6](BIRC6)|Tier 2 GE, aSHM||[@reddyGeneticFunctionalDrivers2017; @sarkozyMutationalLandscapeGray2021a]||
86
-|[BTG1](BTG1)|Tier 2 GE[@drevalGeneticSubdivisionsFollicular2023], FE[@mlynarczykBTG1MutationYields2023b], aSHM|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@burkhardtClinicalRelevanceMolecular2022b; @morinFrequentMutationHistonemodifying2011; @sarkozyMutationalLandscapeGray2021a]||
87
-|[BTG2](BTG2)|Tier 2 GE[@drevalGeneticSubdivisionsFollicular2023], CE[@guoMutationBTG2Gene2022b], aSHM|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@loveGeneticLandscapeMutations2012; @morinFrequentMutationHistonemodifying2011]||
88
-|[CD70](CD70)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023b], aSHM|[Russler-germain et al](papers/russler-germainMutationsAssociatedProgression2023b)|[@morinFrequentMutationHistonemodifying2011]||
89
-|[CD79B](CD79B)|Tier 2 GE[@drevalGeneticSubdivisionsFollicular2023], FE[@davisChronicActiveBcellreceptor2010], aSHM|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@morinFrequentMutationHistonemodifying2011; @paneaWholeGenomeLandscape2019]||
90
-|[CDC42BPB](CDC42BPB)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021b]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)|[@spinaGeneticsNodalMarginal2016b]||
91
-|[CILP](CILP)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023b]|[Russler-germain et al](papers/russler-germainMutationsAssociatedProgression2023b)|||
92
-|[CPNE8](CPNE8)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021b]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)|||
93
-|[CXCR4](CXCR4)|Tier 2 GE[@krysiakRecurrentSomaticMutations2017b], aSHM|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017b)|[@khodabakhshiRecurrentTargetsAberrant2012; @paneaWholeGenomeLandscape2019]||
94
-|[CYP2A6](CYP2A6)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023b]|[Russler-germain et al](papers/russler-germainMutationsAssociatedProgression2023b)|||
95
-|[DDX3X](DDX3X)|Tier 2 GE, FE[@gongSequentialInverseDysregulation2021], CE[@kizhakeyilDDX3XLossAdverse2021], aSHM||[@mottokIntegrativeGenomicAnalysis2019b; @reddyGeneticFunctionalDrivers2017; @schmitzBurkittLymphomaPathogenesis2012]||
96
-|[DHX15](DHX15)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021b]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)|||
97
-|[DTX1](DTX1)|Tier 2 GE, FE[@demirandaExomeSequencingReveals2014], CE[@merirantaDeltex1MutationsPredict2017b], aSHM||[@gomezUltraDeepSequencingReveals2023; @loveGeneticLandscapeMutations2012; @rossiCodingGenomeSplenic2012c; @zhangGeneticHeterogeneityDiffuse2013]||
98
-|[DUSP2](DUSP2)|Tier 2 GE[@drevalGeneticSubdivisionsFollicular2023], aSHM|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@dunsCharacterizationDLBCLPMBL2021b; @lohrDiscoveryPrioritizationSomatic2012a]||
99
-|[EGR1](EGR1)|Tier 2 GE[@krysiakRecurrentSomaticMutations2017b]|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017b)|[@reichelFlowSortingExome2015a; @rossiCodingGenomeSplenic2012c]||
100
-|[FZR1](FZR1)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021b]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)|||
101
-|[GBP7](GBP7)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023b]|[Russler-germain et al](papers/russler-germainMutationsAssociatedProgression2023b)|||
102
-|[GRM6](GRM6)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023b]|[Russler-germain et al](papers/russler-germainMutationsAssociatedProgression2023b)|||
103
-|[HIST1H2BM](HIST1H2BM)|Tier 2 GE[@krysiakRecurrentSomaticMutations2017b]|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017b)|||
104
-|[HIST1H3B](HIST1H3B)|Tier 2 GE, aSHM||[@lohrDiscoveryPrioritizationSomatic2012a; @reichelFlowSortingExome2015a]||
105
-|[HLA-B](HLA-B)|Tier 2 GE, aSHM||[@lohrDiscoveryPrioritizationSomatic2012a; @wienandGenomicAnalysesFlowsorted2019b]||
106
-|[IGLL5](IGLL5)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023b], aSHM|[Russler-germain et al](papers/russler-germainMutationsAssociatedProgression2023b)|[@chapuyMolecularSubtypesDiffuse2018b; @deschGenotypingCirculatingTumor2020; @paneaWholeGenomeLandscape2019]||
107
-|[ITPKB](ITPKB)|Tier 2 GE[@drevalGeneticSubdivisionsFollicular2023], aSHM|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@reichelFlowSortingExome2015a; @schmitzGeneticsPathogenesisDiffuse2018a]||
108
-|[JUP](JUP)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021b]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)|||
109
-|[KIR3DL1](KIR3DL1)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023b]|[Russler-germain et al](papers/russler-germainMutationsAssociatedProgression2023b)|||
79
+|[ABL2](ABL2)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023]|[Russler-germain et al](papers/russler-germainMutationsAssociatedProgression2023)|||
80
+|[ACTG1](ACTG1)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021], aSHM|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021)|[@deschGenotypingCirculatingTumor2020; @fanComprehensiveCharacterizationDriver2020; @spinaGeneticsNodalMarginal2016]||
81
+|[ATP6V1A](ATP6V1A)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021)|||
82
+|[BIRC6](BIRC6)|Tier 2 GE||[@reddyGeneticFunctionalDrivers2017; @sarkozyMutationalLandscapeGray2021]||
83
+|[BTG1](BTG1)|Tier 2 GE[@drevalGeneticSubdivisionsFollicular2023], FE[@almasmoumFrequentLossBTG12021], aSHM|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@burkhardtClinicalRelevanceMolecular2022; @morinFrequentMutationHistonemodifying2011; @sarkozyMutationalLandscapeGray2021]||
84
+|[BTG2](BTG2)|Tier 2 GE[@drevalGeneticSubdivisionsFollicular2023], aSHM|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@loveGeneticLandscapeMutations2012; @morinFrequentMutationHistonemodifying2011]||
85
+|[CD70](CD70)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023], FE[@nieDualRoleCD702022]|[Russler-germain et al](papers/russler-germainMutationsAssociatedProgression2023)|[@morinFrequentMutationHistonemodifying2011]||
86
+|[CD79B](CD79B)|Tier 2 GE[@drevalGeneticSubdivisionsFollicular2023], FE[@davisChronicActiveBcellreceptor2010]|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@davisChronicActiveBcellreceptor2010; @paneaWholeGenomeLandscape2019]||
87
+|[CDC42BPB](CDC42BPB)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021)|[@spinaGeneticsNodalMarginal2016]||
88
+|[CILP](CILP)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023]|[Russler-germain et al](papers/russler-germainMutationsAssociatedProgression2023)|||
89
+|[CPNE8](CPNE8)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021)|||
90
+|[CXCR4](CXCR4)|Tier 2 GE[@krysiakRecurrentSomaticMutations2017], FE[@zmajkovicovaGenotypephenotypeCorrelationsWHIM2022], aSHM|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017)|[@khodabakhshiRecurrentTargetsAberrant2012; @paneaWholeGenomeLandscape2019]||
91
+|[CYP2A6](CYP2A6)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023]|[Russler-germain et al](papers/russler-germainMutationsAssociatedProgression2023)|||
92
+|[DDX3X](DDX3X)|Tier 2 GE, FE[@gongSequentialInverseDysregulation2021]||[@mottokIntegrativeGenomicAnalysis2019; @reddyGeneticFunctionalDrivers2017; @schmitzBurkittLymphomaPathogenesis2012]||
93
+|[DHX15](DHX15)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021)|||
94
+|[DTX1](DTX1)|Tier 2 GE, aSHM||[@gomezUltraDeepSequencingReveals2023; @loveGeneticLandscapeMutations2012; @rossiCodingGenomeSplenic2012; @zhangGeneticHeterogeneityDiffuse2013]||
95
+|[DUSP2](DUSP2)|Tier 2 GE[@drevalGeneticSubdivisionsFollicular2023], aSHM|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@dunsCharacterizationDLBCLPMBL2021; @lohrDiscoveryPrioritizationSomatic2012]||
96
+|[EGR1](EGR1)|Tier 2 GE[@krysiakRecurrentSomaticMutations2017]|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017)|[@reichelFlowSortingExome2015; @rossiCodingGenomeSplenic2012]||
97
+|[FZR1](FZR1)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021)|||
98
+|[GBP7](GBP7)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023]|[Russler-germain et al](papers/russler-germainMutationsAssociatedProgression2023)|||
99
+|[GRM6](GRM6)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023]|[Russler-germain et al](papers/russler-germainMutationsAssociatedProgression2023)|||
100
+|[HIST1H2BD](HIST1H2BD)|Tier 2 GE[@krysiakRecurrentSomaticMutations2017]|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017)|||
101
+|[HIST1H2BM](HIST1H2BM)|Tier 2 GE[@krysiakRecurrentSomaticMutations2017]|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017)|||
102
+|[HIST1H3B](HIST1H3B)|Tier 2 GE, aSHM||[@lohrDiscoveryPrioritizationSomatic2012; @reichelFlowSortingExome2015]||
103
+|[HIST1H3G](HIST1H3G)|Tier 2 GE[@krysiakRecurrentSomaticMutations2017]|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017)|||
104
+|[HIST1H3I](HIST1H3I)|Tier 2 GE[@krysiakRecurrentSomaticMutations2017]|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017)|[@paneaWholeGenomeLandscape2019]||
105
+|[HLA-B](HLA-B)|Tier 2 GE, FE[@fangazioGeneticMechanismsHLAI2021]||[@lohrDiscoveryPrioritizationSomatic2012; @wienandGenomicAnalysesFlowsorted2019]||
106
+|[IGLL5](IGLL5)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023], aSHM|[Russler-germain et al](papers/russler-germainMutationsAssociatedProgression2023)|[@chapuyMolecularSubtypesDiffuse2018; @deschGenotypingCirculatingTumor2020; @paneaWholeGenomeLandscape2019]||
107
+|[ITPKB](ITPKB)|Tier 2 GE[@drevalGeneticSubdivisionsFollicular2023], FE[@tiacciPervasiveMutationsJAKSTAT2018], aSHM|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@reichelFlowSortingExome2015; @schmitzGeneticsPathogenesisDiffuse2018]||
108
+|[JUP](JUP)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021)|||
109
+|[KIR3DL1](KIR3DL1)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023]|[Russler-germain et al](papers/russler-germainMutationsAssociatedProgression2023)|||
110 110
|[KLF2](KLF2)|Tier 2 GE[@drevalGeneticSubdivisionsFollicular2023], aSHM|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@deschGenotypingCirculatingTumor2020; @jalladesExomeSequencingIdentifies2017; @pasqualucciAnalysisCodingGenome2011]||
111
-|[LAPTM5](LAPTM5)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021b], aSHM|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)|||
112
-|[LTB](LTB)|Tier 2 GE[@drevalGeneticSubdivisionsFollicular2023], aSHM|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@chapuyMolecularSubtypesDiffuse2018b; @deschGenotypingCirculatingTumor2020]||
113
-|[MAGEC1](MAGEC1)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023b]|[Russler-germain et al](papers/russler-germainMutationsAssociatedProgression2023b)|||
114
-|[MAP7D1](MAP7D1)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023b]|[Russler-germain et al](papers/russler-germainMutationsAssociatedProgression2023b)|||
115
-|[MEF2C](MEF2C)|Tier 2 GE, FE[@jingjingNovelMEF2CMutation2020], aSHM||[@arthurGenomewideDiscoverySomatic2018]||
116
-|[MGEA5](MGEA5)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021b]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)|||
117
-|[MKI67](MKI67)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023b]|[Russler-germain et al](papers/russler-germainMutationsAssociatedProgression2023b)|[@schmitzBurkittLymphomaPathogenesis2012]||
118
-|[MYCBP2](MYCBP2)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021b]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)|||
119
-|[MYD88](MYD88)|Tier 2 GE[@drevalGeneticSubdivisionsFollicular2023], FE[@ngoOncogenicallyActiveMYD882011a], CE[@guoSGK1MutationStatus2022b], aSHM|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@ngoOncogenicallyActiveMYD882011a; @yanBCRTLRSignaling2012a]||
120
-|[NFKBIA](NFKBIA)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023b], aSHM|[Russler-germain et al](papers/russler-germainMutationsAssociatedProgression2023b)|[@thomasMutationalAnalysisIkappaBalpha2004; @wienandGenomicAnalysesFlowsorted2019b]||
121
-|[OR8H2](OR8H2)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023b]|[Russler-germain et al](papers/russler-germainMutationsAssociatedProgression2023b)|||
122
-|[P2RY8](P2RY8)|Tier 2 GE[@drevalGeneticSubdivisionsFollicular2023], FE[@muppidiLossSignalingGa132014b], aSHM|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@lohrDiscoveryPrioritizationSomatic2012a; @muppidiLossSignalingGa132014b]||
123
-|[PDS5B](PDS5B)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021b], aSHM|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)|[@morinMutationalStructuralAnalysis2013]||
124
-|[PPP4C](PPP4C)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021b]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)|||
125
-|[PRKDC](PRKDC)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021b], aSHM|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)|[@schmitzGeneticsPathogenesisDiffuse2018a]||
126
-|[PTPRD](PTPRD)|Tier 2 GE[@drevalGeneticSubdivisionsFollicular2023], aSHM|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@spinaGeneticsNodalMarginal2016b]||
127
-|[PZP](PZP)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023b]|[Russler-germain et al](papers/russler-germainMutationsAssociatedProgression2023b)|||
128
-|[RBM6](RBM6)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021b]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)|||
129
-|[S1PR2](S1PR2)|Tier 2 GE[@drevalGeneticSubdivisionsFollicular2023], FE[@floriHematopoieticOncoproteinFOXP12016], aSHM|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@morinFrequentMutationHistonemodifying2011; @muppidiLossSignalingGa132014b]||
130
-|[SHROOM3](SHROOM3)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023b]|[Russler-germain et al](papers/russler-germainMutationsAssociatedProgression2023b)|||
131
-|[SRRM2](SRRM2)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023b], aSHM|[Russler-germain et al](papers/russler-germainMutationsAssociatedProgression2023b)|[@morinMutationalStructuralAnalysis2013]||
132
-|[STAB2](STAB2)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023b]|[Russler-germain et al](papers/russler-germainMutationsAssociatedProgression2023b)|||
133
-|[TMEM30A](TMEM30A)|Tier 2 GE[@morinFrequentMutationHistonemodifying2011], FE[@ennishiTMEM30ALossoffunctionMutations2020b], CE[@ennishiTMEM30ALossoffunctionMutations2020b], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|||
134
-|[TPP1](TPP1)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021b]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)|||
135
-|[XIRP2](XIRP2)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023b]|[Russler-germain et al](papers/russler-germainMutationsAssociatedProgression2023b)|||
136
-|[ZC3H12A](ZC3H12A)|Tier 2 GE, aSHM||[@chapuyMolecularSubtypesDiffuse2018b]||
137
-|[ZNF608](ZNF608)|Tier 2 GE[@krysiakRecurrentSomaticMutations2017b], aSHM|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017b)|[@morinMutationalStructuralAnalysis2013]||
111
+|[LAPTM5](LAPTM5)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021], aSHM|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021)|||
112
+|[LTB](LTB)|Tier 2 GE[@drevalGeneticSubdivisionsFollicular2023], aSHM|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@chapuyMolecularSubtypesDiffuse2018; @deschGenotypingCirculatingTumor2020]||
113
+|[MAGEC1](MAGEC1)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023]|[Russler-germain et al](papers/russler-germainMutationsAssociatedProgression2023)|||
114
+|[MAP7D1](MAP7D1)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023]|[Russler-germain et al](papers/russler-germainMutationsAssociatedProgression2023)|||
115
+|[MEF2C](MEF2C)|Tier 2 GE, aSHM||[@hubschmannMutationalMechanismsShaping2021]||
116
+|[MGEA5](MGEA5)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021)|||
117
+|[MKI67](MKI67)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023]|[Russler-germain et al](papers/russler-germainMutationsAssociatedProgression2023)|[@schmitzBurkittLymphomaPathogenesis2012]||
118
+|[MYCBP2](MYCBP2)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021)|||
119
+|[MYD88](MYD88)|Tier 2 GE[@drevalGeneticSubdivisionsFollicular2023], FE[@ngoOncogenicallyActiveMYD882011]|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@ngoOncogenicallyActiveMYD882011; @yanBCRTLRSignaling2012]||
120
+|[NFKBIA](NFKBIA)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023], FE[@jungnickelClonalDeleteriousMutations2000]|[Russler-germain et al](papers/russler-germainMutationsAssociatedProgression2023)|[@thomasMutationalAnalysisIkappaBalpha2004; @wienandGenomicAnalysesFlowsorted2019]||
121
+|[OR8H2](OR8H2)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023]|[Russler-germain et al](papers/russler-germainMutationsAssociatedProgression2023)|||
122
+|[P2RY8](P2RY8)|Tier 2 GE[@drevalGeneticSubdivisionsFollicular2023], FE[@muppidiLossSignalingGa132014]|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@lohrDiscoveryPrioritizationSomatic2012; @muppidiLossSignalingGa132014]||
123
+|[PDS5B](PDS5B)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021)|[@morinMutationalStructuralAnalysis2013]||
124
+|[PPP4C](PPP4C)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021)|||
125
+|[PRKDC](PRKDC)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021)|[@schmitzGeneticsPathogenesisDiffuse2018]||
126
+|[PTPRD](PTPRD)|Tier 2 GE[@drevalGeneticSubdivisionsFollicular2023]|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@spinaGeneticsNodalMarginal2016]||
127
+|[PZP](PZP)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023]|[Russler-germain et al](papers/russler-germainMutationsAssociatedProgression2023)|||
128
+|[RBM6](RBM6)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021)|||
129
+|[S1PR2](S1PR2)|Tier 2 GE[@drevalGeneticSubdivisionsFollicular2023], FE[@muppidiLossSignalingGa132014], aSHM|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@morinFrequentMutationHistonemodifying2011; @muppidiLossSignalingGa132014]||
130
+|[SHROOM3](SHROOM3)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023]|[Russler-germain et al](papers/russler-germainMutationsAssociatedProgression2023)|||
131
+|[SRRM2](SRRM2)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023]|[Russler-germain et al](papers/russler-germainMutationsAssociatedProgression2023)|[@morinMutationalStructuralAnalysis2013]||
132
+|[STAB2](STAB2)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023]|[Russler-germain et al](papers/russler-germainMutationsAssociatedProgression2023)|||
133
+|[TMEM30A](TMEM30A)|Tier 2 GE[@morinFrequentMutationHistonemodifying2011], FE[@ennishiTMEM30ALossoffunctionMutations2020]|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|||
134
+|[TPP1](TPP1)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021)|||
135
+|[XIRP2](XIRP2)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023]|[Russler-germain et al](papers/russler-germainMutationsAssociatedProgression2023)|||
136
+|[ZC3H12A](ZC3H12A)|Tier 2 GE, FE[@skalniakRegulatoryFeedbackLoop2009]||[@chapuyMolecularSubtypesDiffuse2018]||
137
+|[ZNF608](ZNF608)|Tier 2 GE[@krysiakRecurrentSomaticMutations2017]|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017)|[@morinMutationalStructuralAnalysis2013]||
138 138
139 139
## Tier 3, retired FL genes
140 140
FL_test_sankey.md
... ...
@@ -0,0 +1,16 @@
1
+```mermaid
2
+---
3
+config:
4
+ sankey:
5
+ showValues: true
6
+ linkColor: target
7
+ width: 600
8
+ nodeAlignment: right
9
+---
10
+sankey-beta
11
+FL, GC-like, 56
12
+FL, MEM-like, 50
13
+GC-like, dFL, 37
14
+GC-like, cFL, 19
15
+MEM-like, dFL, 17
16
+MEM-like, cFL, 33
Home.md
... ...
@@ -18,9 +18,10 @@ To get started, select one of the gene lists from the table below then select th
18 18
19 19
|Entity|Tier 1 (high-confidence)|Tier 2 (low-confidence)|Tier 3 (retired) |
20 20
|:-:|:-:|:-:|:-:|
21
-|BL [(tsv)](https://raw.githubusercontent.com/morinlab/LLMPP/main/resources/curated/bl_genes.tsv)|[28 genes](BL_genes#tier-1-bl-genes)|[76 genes](BL_genes#tier-2-bl-genes)|[70 genes](BL_genes#tier-3-bl-genes)|
22
-|DLBCL [(tsv)](https://raw.githubusercontent.com/morinlab/LLMPP/main/resources/curated/dlbcl_genes.tsv)|[126 genes](DLBCL_genes#tier-1-dlbcl-genes)|[179 genes](DLBCL_genes#tier-2-dlbcl-genes)|[386 genes](DLBCL_genes#tier-3-dlbcl-genes)|
23
-|FL [(tsv)](https://raw.githubusercontent.com/morinlab/LLMPP/main/resources/curated/fl_genes.tsv)|[57 genes](FL_genes#tier-1-fl-genes)|[56 genes](FL_genes#tier-2-fl-genes)|[0 genes](FL_genes#tier-3-fl-genes)|
21
+|BL [(tsv)](https://raw.githubusercontent.com/morinlab/LLMPP/main/resources/curated/bl_genes.tsv)|[32 genes](BL_genes#tier-1-bl-genes)|[72 genes](BL_genes#tier-2-bl-genes)|[70 genes](BL_genes#tier-3-bl-genes)|
22
+|DLBCL [(tsv)](https://raw.githubusercontent.com/morinlab/LLMPP/main/resources/curated/dlbcl_genes.tsv)|[125 genes](DLBCL_genes#tier-1-dlbcl-genes)|[210 genes](DLBCL_genes#tier-2-dlbcl-genes)|[387 genes](DLBCL_genes#tier-3-dlbcl-genes)|
23
+|FL [(tsv)](https://raw.githubusercontent.com/morinlab/LLMPP/main/resources/curated/fl_genes.tsv)|[54 genes](FL_genes#tier-1-fl-genes)|[59 genes](FL_genes#tier-2-fl-genes)|[0 genes](FL_genes#tier-3-fl-genes)|
24
+
24 25
25 26
26 27
### History of lymphoma genes in common entities
... ...
@@ -281,8 +282,8 @@ PMBL panel, Desch 2020, 10
281 282
|[@morinMutationalStructuralAnalysis2013](papers/morinMutationalStructuralAnalysis2013)|WGS|DLBCL|9|7 (24%)|
282 283
|[@reddyGeneticFunctionalDrivers2017](papers/reddyGeneticFunctionalDrivers2017)|Exome|DLBCL|6|29 (55%)|
283 284
|[@paneaWholeGenomeLandscape2019](papers/paneaWholeGenomeLandscape2019)|Exome/RNA-seq|BL|4|22 (55%)|
284
-|[@chapuyMolecularSubtypesDiffuse2018b](papers/chapuyMolecularSubtypesDiffuse2018b)|Exome|DLBCL|2| 7 (41%) |
285
-|[@hubschmannMutationalMechanismsShaping2021b](papers/hubschmannMutationalMechanismsShaping2021b)|WGS|DLBCL,FL|4|3 (9%)|
285
+|[@chapuyMolecularSubtypesDiffuse2018](papers/chapuyMolecularSubtypesDiffuse2018)|Exome|DLBCL|2| 7 (41%) |
286
+|[@hubschmannMutationalMechanismsShaping2021](papers/hubschmannMutationalMechanismsShaping2021)|WGS|DLBCL,FL|4|3 (9%)|
286 287
287 288
## Categorization of genes
288 289
MCL_genes.md
... ...
@@ -7,97 +7,97 @@ link-citations: true
7 7
8 8
## Origins of MCL genes
9 9
10
-![](MCL_sankey-1.svg)
10
+![](MCL_sankey1-1.svg)
11 11
12
-## Tier 1 MCL genes
12
+## Tier 1, high-confidence MCL genes
13 13
14 14
### *23 total*
15 15
16
-|Gene|Tier| First MCL evidence | Other entities |
17
-|:-:|:-:|:--|:-|
18
-|[ATM](ATM)|1|[Bea et al](papers/beaLandscapeSomaticMutations2013)[@beaLandscapeSomaticMutations2013]|[@braggioGenomicAnalysisMarginal2012; @reddyGeneticFunctionalDrivers2017]|
19
-|[BIRC3](BIRC3)|1|[Bea et al](papers/beaLandscapeSomaticMutations2013)[@beaLandscapeSomaticMutations2013]|[@dunsCharacterizationDLBCLPMBL2021b; @rossiAlterationBIRC3Multiple2011a; @arthurGenomewideDiscoverySomatic2018]|
20
-|[CARD11](CARD11)|1|[Wu et al](papers/wuGeneticHeterogeneityPrimary2016)[@wuGeneticHeterogeneityPrimary2016]|[@yanBCRTLRSignaling2012a; @lenzOncogenicCARD11Mutations2008; @morinFrequentMutationHistonemodifying2011]|
21
-|[CCND1](CCND1)|1|[Bea et al](papers/beaLandscapeSomaticMutations2013)[@beaLandscapeSomaticMutations2013]||
22
-|[DAZAP1](DAZAP1)|1|[Pararajalingam et al](papers/pararajalingamCodingNoncodingDrivers2020)[@pararajalingamCodingNoncodingDrivers2020]||
23
-|[EWSR1](EWSR1)|1|[Pararajalingam et al](papers/pararajalingamCodingNoncodingDrivers2020)[@pararajalingamCodingNoncodingDrivers2020]||
24
-|[HNRNPH1](HNRNPH1)|1|[Pararajalingam et al](papers/pararajalingamCodingNoncodingDrivers2020)[@pararajalingamCodingNoncodingDrivers2020]||
25
-|[KMT2D](KMT2D)|1|[Bea et al](papers/beaLandscapeSomaticMutations2013)[@beaLandscapeSomaticMutations2013]|[@grandeGenomewideDiscoverySomatic2019; @rossiCodingGenomeSplenic2012c; @deschGenotypingCirculatingTumor2020; @morinFrequentMutationHistonemodifying2011]|
26
-|[MEF2B](MEF2B)|1|[Bea et al](papers/beaLandscapeSomaticMutations2013)[@beaLandscapeSomaticMutations2013]|[@morinFrequentMutationHistonemodifying2011]|
27
-|[NFKBIE](NFKBIE)|1|[Pararajalingam et al](papers/pararajalingamCodingNoncodingDrivers2020)[@pararajalingamCodingNoncodingDrivers2020]|[@mansouriFrequentNFKBIEDeletions2016; @morinGeneticLandscapesRelapsed2016]|
28
-|[NOTCH1](NOTCH1)|1|[Bea et al](papers/beaLandscapeSomaticMutations2013)[@beaLandscapeSomaticMutations2013]|[@loveGeneticLandscapeMutations2012; @pasqualucciAnalysisCodingGenome2011; @rossiCodingGenomeSplenic2012c]|
29
-|[NOTCH2](NOTCH2)|1|[Bea et al](papers/beaLandscapeSomaticMutations2013)[@beaLandscapeSomaticMutations2013]|[@zhangGeneticHeterogeneityDiffuse2013; @rossiCodingGenomeSplenic2012c]|
30
-|[NSD2](NSD2)|1|[Bea et al](papers/beaLandscapeSomaticMutations2013)[@beaLandscapeSomaticMutations2013]|[@zhangGeneticHeterogeneityDiffuse2013]|
31
-|[POT1](POT1)|1|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)[@zhangGenomicLandscapeMantle2014]||
32
-|[RB1](RB1)|1|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)[@zhangGenomicLandscapeMantle2014]|[@morinMutationalStructuralAnalysis2013]|
33
-|[S1PR1](S1PR1)|1|[Pararajalingam et al](papers/pararajalingamCodingNoncodingDrivers2020)[@pararajalingamCodingNoncodingDrivers2020]|[@lohrDiscoveryPrioritizationSomatic2012a]|
34
-|[SMARCA4](SMARCA4)|1|[Nadeu et al](papers/nadeuGenomicEpigenomicInsights2020b)[@nadeuGenomicEpigenomicInsights2020b]|[@richterRecurrentMutationID32012a; @lohrDiscoveryPrioritizationSomatic2012a; @krysiakRecurrentSomaticMutations2017b]|
35
-|[SP140](SP140)|1|[Bea et al](papers/beaLandscapeSomaticMutations2013)[@beaLandscapeSomaticMutations2013]||
36
-|[SYNE1](SYNE1)|1|[Nadeu et al](papers/nadeuGenomicEpigenomicInsights2020b)[@nadeuGenomicEpigenomicInsights2020b]||
37
-|[TERT](TERT)|1|[Nadeu et al](papers/nadeuGenomicEpigenomicInsights2020b)[@nadeuGenomicEpigenomicInsights2020b]||
38
-|[TLR2](TLR2)|1|[Bea et al](papers/beaLandscapeSomaticMutations2013)[@beaLandscapeSomaticMutations2013]|[@chapuyMolecularSubtypesDiffuse2018b]|
39
-|[TP53](TP53)|1|[Bea et al](papers/beaLandscapeSomaticMutations2013)[@beaLandscapeSomaticMutations2013]|[@tiacciPervasiveMutationsJAKSTAT2018b; @morinFrequentMutationHistonemodifying2011; @wildaInactivationARFMDM2p53Pathway2004; @rossiCodingGenomeSplenic2012c; @lohrDiscoveryPrioritizationSomatic2012a]|
40
-|[UBR5](UBR5)|1|[Pararajalingam et al](papers/pararajalingamCodingNoncodingDrivers2020)[@pararajalingamCodingNoncodingDrivers2020]|[@zhangGeneticHeterogeneityDiffuse2013]|
16
+|Gene|Summary| First MCL study | Other entities | QC result |
17
+|:-:|:--:|:-:|:-|:-|
18
+|[ATM](ATM)|Tier 1 GE[@beaLandscapeSomaticMutations2013], FE[@camachoATMGeneInactivation2002]|[Bea et al](papers/beaLandscapeSomaticMutations2013)|[@braggioGenomicAnalysisMarginal2012; @reddyGeneticFunctionalDrivers2017]||
19
+|[BIRC3](BIRC3)|Tier 1 GE[@beaLandscapeSomaticMutations2013], aSHM|[Bea et al](papers/beaLandscapeSomaticMutations2013)|[@arthurGenomewideDiscoverySomatic2018; @dunsCharacterizationDLBCLPMBL2021; @rossiAlterationBIRC3Multiple2011]||
20
+|[CARD11](CARD11)|Tier 1 GE[@wuGeneticHeterogeneityPrimary2016], FE[@lenzOncogenicCARD11Mutations2008]|[Wu et al](papers/wuGeneticHeterogeneityPrimary2016)|[@lenzOncogenicCARD11Mutations2008; @morinFrequentMutationHistonemodifying2011; @yanBCRTLRSignaling2012]||
21
+|[CCND1](CCND1)|Tier 1 GE[@beaLandscapeSomaticMutations2013]|[Bea et al](papers/beaLandscapeSomaticMutations2013)|||
22
+|[DAZAP1](DAZAP1)|Tier 1 GE[@pararajalingamCodingNoncodingDrivers2020]|[Pararajalingam et al](papers/pararajalingamCodingNoncodingDrivers2020)|||
23
+|[EWSR1](EWSR1)|Tier 1 GE[@pararajalingamCodingNoncodingDrivers2020]|[Pararajalingam et al](papers/pararajalingamCodingNoncodingDrivers2020)|||
24
+|[HNRNPH1](HNRNPH1)|Tier 1 GE[@pararajalingamCodingNoncodingDrivers2020]|[Pararajalingam et al](papers/pararajalingamCodingNoncodingDrivers2020)|||
25
+|[KMT2D](KMT2D)|Tier 1 GE[@beaLandscapeSomaticMutations2013], FE[@zhangDisruptionKMT2DPerturbs2015]|[Bea et al](papers/beaLandscapeSomaticMutations2013)|[@deschGenotypingCirculatingTumor2020; @grandeGenomewideDiscoverySomatic2019; @morinFrequentMutationHistonemodifying2011; @rossiCodingGenomeSplenic2012]||
26
+|[MEF2B](MEF2B)|Tier 1 GE[@beaLandscapeSomaticMutations2013], FE[@ponMEF2BMutationsNonHodgkin2015], aSHM|[Bea et al](papers/beaLandscapeSomaticMutations2013)|[@morinFrequentMutationHistonemodifying2011]||
27
+|[NFKBIE](NFKBIE)|Tier 1 GE[@pararajalingamCodingNoncodingDrivers2020], FE[@mansouriFunctionalLossIkBe2015]|[Pararajalingam et al](papers/pararajalingamCodingNoncodingDrivers2020)|[@mansouriFrequentNFKBIEDeletions2016; @morinGeneticLandscapesRelapsed2016]||
28
+|[NOTCH1](NOTCH1)|Tier 1 GE[@beaLandscapeSomaticMutations2013], FE[@ryanCellRegulomeLinks2017]|[Bea et al](papers/beaLandscapeSomaticMutations2013)|[@loveGeneticLandscapeMutations2012; @pasqualucciAnalysisCodingGenome2011; @rossiCodingGenomeSplenic2012]||
29
+|[NOTCH2](NOTCH2)|Tier 1 GE[@beaLandscapeSomaticMutations2013], FE[@leeGainoffunctionMutationsCopy2009]|[Bea et al](papers/beaLandscapeSomaticMutations2013)|[@rossiCodingGenomeSplenic2012; @zhangGeneticHeterogeneityDiffuse2013]||
30
+|[NSD2](NSD2)|Tier 1 GE[@beaLandscapeSomaticMutations2013]|[Bea et al](papers/beaLandscapeSomaticMutations2013)|[@zhangGeneticHeterogeneityDiffuse2013]||
31
+|[POT1](POT1)|Tier 1 GE[@zhangGenomicLandscapeMantle2014]|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)|||
32
+|[RB1](RB1)|Tier 1 GE[@zhangGenomicLandscapeMantle2014], FE[@pinyolInactivationRB1Mantlecell2007]|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)|[@morinMutationalStructuralAnalysis2013]||
33
+|[S1PR1](S1PR1)|Tier 1 GE[@pararajalingamCodingNoncodingDrivers2020]|[Pararajalingam et al](papers/pararajalingamCodingNoncodingDrivers2020)|[@lohrDiscoveryPrioritizationSomatic2012]||
34
+|[SMARCA4](SMARCA4)|Tier 1 GE[@nadeuGenomicEpigenomicInsights2020b], FE[@fernandoFunctionalCharacterizationSMARCA42020]|[Nadeu et al](papers/nadeuGenomicEpigenomicInsights2020b)|[@krysiakRecurrentSomaticMutations2017; @reddyGeneticFunctionalDrivers2017; @richterRecurrentMutationID32012]||
35
+|[SP140](SP140)|Tier 1 GE[@beaLandscapeSomaticMutations2013]|[Bea et al](papers/beaLandscapeSomaticMutations2013)|||
36
+|[SYNE1](SYNE1)|Tier 1 GE[@nadeuGenomicEpigenomicInsights2020b]|[Nadeu et al](papers/nadeuGenomicEpigenomicInsights2020b)|||
37
+|[TERT](TERT)|Tier 1 GE[@nadeuGenomicEpigenomicInsights2020b]|[Nadeu et al](papers/nadeuGenomicEpigenomicInsights2020b)|||
38
+|[TLR2](TLR2)|Tier 1 GE[@beaLandscapeSomaticMutations2013]|[Bea et al](papers/beaLandscapeSomaticMutations2013)|[@chapuyMolecularSubtypesDiffuse2018]||
39
+|[TP53](TP53)|Tier 1 GE[@beaLandscapeSomaticMutations2013], FE[@katoUnderstandingFunctionstructureFunctionmutation2003]|[Bea et al](papers/beaLandscapeSomaticMutations2013)|[@morinFrequentMutationHistonemodifying2011; @rossiCodingGenomeSplenic2012; @tiacciPervasiveMutationsJAKSTAT2018; @wildaInactivationARFMDM2p53Pathway2004]||
40
+|[UBR5](UBR5)|Tier 1 GE[@pararajalingamCodingNoncodingDrivers2020]|[Pararajalingam et al](papers/pararajalingamCodingNoncodingDrivers2020)|[@albuquerqueEnhancingKnowledgeDiscovery2017]||
41 41
42
-## Tier 2 MCL genes
42
+## Tier 2, low-confidence MCL genes
43 43
44 44
### *46 total*
45 45
46
-|Gene|Tier| First MCL evidence | Other entities |
47
-|:-:|:-:|:--|:-|
48
-|[ABCA3](ABCA3)|2|[Bea et al](papers/beaLandscapeSomaticMutations2013)[@beaLandscapeSomaticMutations2013]|[@zhangGeneticHeterogeneityDiffuse2013]|
49
-|[ABCC9](ABCC9)|2|[Bea et al](papers/beaLandscapeSomaticMutations2013)[@beaLandscapeSomaticMutations2013]||
50
-|[ANK2](ANK2)|2|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)[@zhangGenomicLandscapeMantle2014]|[@zhangGeneticHeterogeneityDiffuse2013]|
51
-|[ARID1B](ARID1B)|2||[@reddyGeneticFunctionalDrivers2017]|
52
-|[ATP11C](ATP11C)|2|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)[@zhangGenomicLandscapeMantle2014]||
53
-|[B2M](B2M)|2|[Pararajalingam et al](papers/pararajalingamCodingNoncodingDrivers2020)[@pararajalingamCodingNoncodingDrivers2020]|[@morinFrequentMutationHistonemodifying2011; @reichelFlowSortingExome2015a]|
54
-|[BCOR](BCOR)|2|[Nadeu et al](papers/nadeuGenomicEpigenomicInsights2020b)[@nadeuGenomicEpigenomicInsights2020b]|[@jalladesExomeSequencingIdentifies2017]|
55
-|[CDH8](CDH8)|2|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)[@zhangGenomicLandscapeMantle2014]|[@reddyGeneticFunctionalDrivers2017]|
56
-|[CHMP4C](CHMP4C)|2|[Bea et al](papers/beaLandscapeSomaticMutations2013)[@beaLandscapeSomaticMutations2013]||
57
-|[COL11A1](COL11A1)|2|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)[@zhangGenomicLandscapeMantle2014]||
58
-|[COL16A1](COL16A1)|2|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)[@zhangGenomicLandscapeMantle2014]||
59
-|[CRYBG3](CRYBG3)|2|[Bea et al](papers/beaLandscapeSomaticMutations2013)[@beaLandscapeSomaticMutations2013]||
60
-|[CTNNA2](CTNNA2)|2|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)[@zhangGenomicLandscapeMantle2014]||
61
-|[DCP1B](DCP1B)|2|[Bea et al](papers/beaLandscapeSomaticMutations2013)[@beaLandscapeSomaticMutations2013]||
62
-|[DHDH](DHDH)|2|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)[@zhangGenomicLandscapeMantle2014]||
63
-|[DLC1](DLC1)|2|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)[@zhangGenomicLandscapeMantle2014]||
64
-|[DLGAP2](DLGAP2)|2|[Bea et al](papers/beaLandscapeSomaticMutations2013)[@beaLandscapeSomaticMutations2013]||
65
-|[DNAJC6](DNAJC6)|2|[Bea et al](papers/beaLandscapeSomaticMutations2013)[@beaLandscapeSomaticMutations2013]||
66
-|[EIF2AK4](EIF2AK4)|2|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)[@zhangGenomicLandscapeMantle2014]||
67
-|[ESX1](ESX1)|2|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)[@zhangGenomicLandscapeMantle2014]||
68
-|[FAT4](FAT4)|2|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)[@zhangGenomicLandscapeMantle2014]|[@morinMutationalStructuralAnalysis2013; @parryWholeExomeSequencing2013]|
69
-|[GRIN2A](GRIN2A)|2|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)[@zhangGenomicLandscapeMantle2014]||
70
-|[HEPH](HEPH)|2|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)[@zhangGenomicLandscapeMantle2014]||
71
-|[KCNC2](KCNC2)|2|[Bea et al](papers/beaLandscapeSomaticMutations2013)[@beaLandscapeSomaticMutations2013]||
72
-|[KIAA1671](KIAA1671)|2|[Bea et al](papers/beaLandscapeSomaticMutations2013)[@beaLandscapeSomaticMutations2013]||
73
-|[KMT2C](KMT2C)|2|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)[@zhangGenomicLandscapeMantle2014]|[@sarkozyMutationalLandscapeGray2021a; @zhangGeneticHeterogeneityDiffuse2013; @zhouSporadicEndemicBurkitt2019]|
74
-|[LUZP4](LUZP4)|2|[Bea et al](papers/beaLandscapeSomaticMutations2013)[@beaLandscapeSomaticMutations2013]||
75
-|[MRGPRF](MRGPRF)|2|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)[@zhangGenomicLandscapeMantle2014]||
76
-|[NIN](NIN)|2|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)[@zhangGenomicLandscapeMantle2014]||
77
-|[OGDHL](OGDHL)|2|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)[@zhangGenomicLandscapeMantle2014]||
78
-|[PCDHB2](PCDHB2)|2|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)[@zhangGenomicLandscapeMantle2014]||
79
-|[PCSK2](PCSK2)|2|[Bea et al](papers/beaLandscapeSomaticMutations2013)[@beaLandscapeSomaticMutations2013]||
80
-|[PDLIM3](PDLIM3)|2|[Bea et al](papers/beaLandscapeSomaticMutations2013)[@beaLandscapeSomaticMutations2013]||
81
-|[PLXNB3](PLXNB3)|2|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)[@zhangGenomicLandscapeMantle2014]|[@spinaGeneticsNodalMarginal2016b]|
82
-|[RGS4](RGS4)|2|[Bea et al](papers/beaLandscapeSomaticMutations2013)[@beaLandscapeSomaticMutations2013]||
83
-|[ROBO2](ROBO2)|2|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)[@zhangGenomicLandscapeMantle2014]||
84
-|[SALL3](SALL3)|2|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)[@zhangGenomicLandscapeMantle2014]|[@loveGeneticLandscapeMutations2012]|
85
-|[SI](SI)|2|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)[@zhangGenomicLandscapeMantle2014]||
86
-|[SLC17A6](SLC17A6)|2|[Bea et al](papers/beaLandscapeSomaticMutations2013)[@beaLandscapeSomaticMutations2013]||
87
-|[SMARCB1](SMARCB1)|2|[Nadeu et al](papers/nadeuGenomicEpigenomicInsights2020b)[@nadeuGenomicEpigenomicInsights2020b]||
88
-|[SMC1A](SMC1A)|2|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)[@zhangGenomicLandscapeMantle2014]||
89
-|[TBC1D26](TBC1D26)|2|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)[@zhangGenomicLandscapeMantle2014]||
90
-|[TNRC6B](TNRC6B)|2|[Bea et al](papers/beaLandscapeSomaticMutations2013)[@beaLandscapeSomaticMutations2013]||
91
-|[TRPM6](TRPM6)|2|[Bea et al](papers/beaLandscapeSomaticMutations2013)[@beaLandscapeSomaticMutations2013]||
92
-|[ZNF117](ZNF117)|2|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)[@zhangGenomicLandscapeMantle2014]||
93
-|[ZNF296](ZNF296)|2|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)[@zhangGenomicLandscapeMantle2014]||
46
+|Gene|Summary| First MCL study | Other entities | QC result |
47
+|:-:|:--:|:-:|:-|:-|
48
+|[ABCA3](ABCA3)|Tier 2 GE[@beaLandscapeSomaticMutations2013]|[Bea et al](papers/beaLandscapeSomaticMutations2013)|[@zhangGeneticHeterogeneityDiffuse2013]||
49
+|[ABCC9](ABCC9)|Tier 2 GE[@beaLandscapeSomaticMutations2013]|[Bea et al](papers/beaLandscapeSomaticMutations2013)|||
50
+|[ANK2](ANK2)|Tier 2 GE[@zhangGenomicLandscapeMantle2014]|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)|[@zhangGeneticHeterogeneityDiffuse2013]||
51
+|[ARID1B](ARID1B)|Tier 2 GE||[@reddyGeneticFunctionalDrivers2017]||
52
+|[ATP11C](ATP11C)|Tier 2 GE[@zhangGenomicLandscapeMantle2014]|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)|||
53
+|[B2M](B2M)|Tier 2 GE[@pararajalingamCodingNoncodingDrivers2020], FE[@challa-malladiCombinedGeneticInactivation2011]|[Pararajalingam et al](papers/pararajalingamCodingNoncodingDrivers2020)|[@morinFrequentMutationHistonemodifying2011; @reichelFlowSortingExome2015]||
54
+|[BCOR](BCOR)|Tier 2 GE[@nadeuGenomicEpigenomicInsights2020b]|[Nadeu et al](papers/nadeuGenomicEpigenomicInsights2020b)|[@jalladesExomeSequencingIdentifies2017]||
55
+|[CDH8](CDH8)|Tier 2 GE[@zhangGenomicLandscapeMantle2014]|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)|[@reddyGeneticFunctionalDrivers2017]||
56
+|[CHMP4C](CHMP4C)|Tier 2 GE[@beaLandscapeSomaticMutations2013]|[Bea et al](papers/beaLandscapeSomaticMutations2013)|||
57
+|[COL11A1](COL11A1)|Tier 2 GE[@zhangGenomicLandscapeMantle2014]|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)|||
58
+|[COL16A1](COL16A1)|Tier 2 GE[@zhangGenomicLandscapeMantle2014]|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)|||
59
+|[CRYBG3](CRYBG3)|Tier 2 GE[@beaLandscapeSomaticMutations2013]|[Bea et al](papers/beaLandscapeSomaticMutations2013)|||
60
+|[CTNNA2](CTNNA2)|Tier 2 GE[@zhangGenomicLandscapeMantle2014]|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)|||
61
+|[DCP1B](DCP1B)|Tier 2 GE[@beaLandscapeSomaticMutations2013]|[Bea et al](papers/beaLandscapeSomaticMutations2013)|||
62
+|[DHDH](DHDH)|Tier 2 GE[@zhangGenomicLandscapeMantle2014]|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)|||
63
+|[DLC1](DLC1)|Tier 2 GE[@zhangGenomicLandscapeMantle2014]|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)|||
64
+|[DLGAP2](DLGAP2)|Tier 2 GE[@beaLandscapeSomaticMutations2013]|[Bea et al](papers/beaLandscapeSomaticMutations2013)|||
65
+|[DNAJC6](DNAJC6)|Tier 2 GE[@beaLandscapeSomaticMutations2013]|[Bea et al](papers/beaLandscapeSomaticMutations2013)|||
66
+|[EIF2AK4](EIF2AK4)|Tier 2 GE[@zhangGenomicLandscapeMantle2014]|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)|||
67
+|[ESX1](ESX1)|Tier 2 GE[@zhangGenomicLandscapeMantle2014]|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)|||
68
+|[FAT4](FAT4)|Tier 2 GE[@zhangGenomicLandscapeMantle2014]|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)|[@morinMutationalStructuralAnalysis2013; @parryWholeExomeSequencing2013]||
69
+|[GRIN2A](GRIN2A)|Tier 2 GE[@zhangGenomicLandscapeMantle2014]|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)|||
70
+|[HEPH](HEPH)|Tier 2 GE[@zhangGenomicLandscapeMantle2014]|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)|||
71
+|[KCNC2](KCNC2)|Tier 2 GE[@beaLandscapeSomaticMutations2013]|[Bea et al](papers/beaLandscapeSomaticMutations2013)|||
72
+|[KIAA1671](KIAA1671)|Tier 2 GE[@beaLandscapeSomaticMutations2013]|[Bea et al](papers/beaLandscapeSomaticMutations2013)|||
73
+|[KMT2C](KMT2C)|Tier 2 GE[@zhangGenomicLandscapeMantle2014]|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)|[@sarkozyMutationalLandscapeGray2021; @zhangGeneticHeterogeneityDiffuse2013; @zhouSporadicEndemicBurkitt2019]||
74
+|[LUZP4](LUZP4)|Tier 2 GE[@beaLandscapeSomaticMutations2013]|[Bea et al](papers/beaLandscapeSomaticMutations2013)|||
75
+|[MRGPRF](MRGPRF)|Tier 2 GE[@zhangGenomicLandscapeMantle2014]|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)|||
76
+|[NIN](NIN)|Tier 2 GE[@zhangGenomicLandscapeMantle2014]|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)|||
77
+|[OGDHL](OGDHL)|Tier 2 GE[@zhangGenomicLandscapeMantle2014]|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)|||
78
+|[PCDHB2](PCDHB2)|Tier 2 GE[@zhangGenomicLandscapeMantle2014]|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)|||
79
+|[PCSK2](PCSK2)|Tier 2 GE[@beaLandscapeSomaticMutations2013]|[Bea et al](papers/beaLandscapeSomaticMutations2013)|||
80
+|[PDLIM3](PDLIM3)|Tier 2 GE[@beaLandscapeSomaticMutations2013]|[Bea et al](papers/beaLandscapeSomaticMutations2013)|||
81
+|[PLXNB3](PLXNB3)|Tier 2 GE[@zhangGenomicLandscapeMantle2014]|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)|[@spinaGeneticsNodalMarginal2016]||
82
+|[RGS4](RGS4)|Tier 2 GE[@beaLandscapeSomaticMutations2013]|[Bea et al](papers/beaLandscapeSomaticMutations2013)|||
83
+|[ROBO2](ROBO2)|Tier 2 GE[@zhangGenomicLandscapeMantle2014]|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)|||
84
+|[SALL3](SALL3)|Tier 2 GE[@zhangGenomicLandscapeMantle2014]|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)|[@loveGeneticLandscapeMutations2012]||
85
+|[SI](SI)|Tier 2 GE[@zhangGenomicLandscapeMantle2014]|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)|||
86
+|[SLC17A6](SLC17A6)|Tier 2 GE[@beaLandscapeSomaticMutations2013]|[Bea et al](papers/beaLandscapeSomaticMutations2013)|||
87
+|[SMARCB1](SMARCB1)|Tier 2 GE[@nadeuGenomicEpigenomicInsights2020b]|[Nadeu et al](papers/nadeuGenomicEpigenomicInsights2020b)|||
88
+|[SMC1A](SMC1A)|Tier 2 GE[@zhangGenomicLandscapeMantle2014]|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)|||
89
+|[TBC1D26](TBC1D26)|Tier 2 GE[@zhangGenomicLandscapeMantle2014]|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)|||
90
+|[TNRC6B](TNRC6B)|Tier 2 GE[@beaLandscapeSomaticMutations2013]|[Bea et al](papers/beaLandscapeSomaticMutations2013)|||
91
+|[TRPM6](TRPM6)|Tier 2 GE[@beaLandscapeSomaticMutations2013]|[Bea et al](papers/beaLandscapeSomaticMutations2013)|||
92
+|[ZNF117](ZNF117)|Tier 2 GE[@zhangGenomicLandscapeMantle2014]|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)|||
93
+|[ZNF296](ZNF296)|Tier 2 GE[@zhangGenomicLandscapeMantle2014]|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)|||
94 94
95
-## Tier 3 MCL genes
95
+## Tier 3, retired MCL genes
96 96
97 97
### *0 total*
98 98
99
-|Gene|Tier| First MCL evidence | Other entities |
100
-|:-:|:-:|:--|:-|
99
+|Gene|Summary| First MCL study | Other entities | QC result |
100
+|:-:|:--:|:-:|:-|:-|
101 101
102 102
103 103
# References
MCL_sankey1-1.svg
... ...
@@ -0,0 +1 @@
1
+<svg aria-roledescription="sankey" role="graphics-document document" viewBox="0 0 800 750" height="750" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg" width="800" id="my-svg" style="background-color: white;"><style>#my-svg{font-family:"trebuchet ms",verdana,arial,sans-serif;font-size:16px;fill:#333;}#my-svg .error-icon{fill:#552222;}#my-svg .error-text{fill:#552222;stroke:#552222;}#my-svg .edge-thickness-normal{stroke-width:2px;}#my-svg .edge-thickness-thick{stroke-width:3.5px;}#my-svg .edge-pattern-solid{stroke-dasharray:0;}#my-svg .edge-pattern-dashed{stroke-dasharray:3;}#my-svg .edge-pattern-dotted{stroke-dasharray:2;}#my-svg .marker{fill:#333333;stroke:#333333;}#my-svg .marker.cross{stroke:#333333;}#my-svg svg{font-family:"trebuchet ms",verdana,arial,sans-serif;font-size:16px;}#my-svg :root{--mermaid-font-family:"trebuchet ms",verdana,arial,sans-serif;}</style><g/><g class="nodes"><g y="0" x="526.6666666666666" transform="translate(526.6666666666666,0)" id="node-1" class="node"><rect fill="#4e79a7" width="10" height="290.14925373134344"/></g><g y="0" x="790" transform="translate(790,0)" id="node-2" class="node"><rect fill="#f28e2c" width="10" height="236.4179104477612"/></g><g y="246.4179104477612" x="790" transform="translate(790,246.4179104477612)" id="node-3" class="node"><rect fill="#e15759" width="10" height="483.58208955223904"/></g><g y="385.3731343283583" x="526.6666666666666" transform="translate(526.6666666666666,385.3731343283583)" id="node-4" class="node"><rect fill="#76b7b2" width="10" height="53.73134328358208"/></g><g y="300.14925373134344" x="526.6666666666666" transform="translate(526.6666666666666,300.14925373134344)" id="node-5" class="node"><rect fill="#59a14f" width="10" height="75.22388059701484"/></g><g y="449.10447761194035" x="526.6666666666666" transform="translate(526.6666666666666,449.10447761194035)" id="node-6" class="node"><rect fill="#edc949" width="10" height="300.8955223880599"/></g><g y="11.45970900089457" x="0" transform="translate(0,11.45970900089457)" id="node-7" class="node"><rect fill="#af7aa1" width="10" height="720"/></g><g y="0" x="263.3333333333333" transform="translate(263.3333333333333,0)" id="node-8" class="node"><rect fill="#ff9da7" width="10" height="365.3731343283582"/></g><g y="445.7059008265178" x="263.3333333333333" transform="translate(263.3333333333333,445.7059008265178)" id="node-9" class="node"><rect fill="#9c755f" width="10" height="300.8955223880596"/></g><g y="381.9745575429357" x="263.3333333333333" transform="translate(263.3333333333333,381.9745575429357)" id="node-10" class="node"><rect fill="#bab0ab" width="10" height="53.73134328358219"/></g></g><g font-size="14" font-family="sans-serif" class="node-labels"><text text-anchor="end" dy="0.35em" y="145.07462686567172" x="520.6666666666666">Bea 2013</text><text text-anchor="end" dy="0.35em" y="118.2089552238806" x="784">Tier 1</text><text text-anchor="end" dy="0.35em" y="488.2089552238807" x="784">Tier 2</text><text text-anchor="end" dy="0.35em" y="412.2388059701493" x="520.6666666666666">Nadeu 2020</text><text text-anchor="end" dy="0.35em" y="337.76119402985086" x="520.6666666666666">Pararajalingam 2020</text><text text-anchor="end" dy="0.35em" y="599.5522388059703" x="520.6666666666666">Zhang 2014</text><text text-anchor="start" dy="0.35em" y="371.4597090008946" x="16">MCL genes</text><text text-anchor="start" dy="0.35em" y="182.6865671641791" x="279.3333333333333">MCL-WGS/exome</text><text text-anchor="start" dy="0.35em" y="596.1536620205476" x="279.3333333333333">MCL-exome</text><text text-anchor="start" dy="0.35em" y="408.8402291847268" x="279.3333333333333">MCL-</text></g><g stroke-opacity="0.5" fill="none" class="links"><g style="mix-blend-mode: multiply;" class="link"><path stroke-width="118.20895522388061" stroke="#f28e2c" 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... ...
\ No newline at end of file
MZL_genes.md
... ...
@@ -7,144 +7,144 @@ link-citations: true
7 7
8 8
## Origins of MZL genes
9 9
10
-![](MZL_sankey-1.svg)
10
+![](MZL_sankey1-1.svg)
11 11
12
-## Tier 1 MZL genes
12
+## Tier 1, high-confidence MZL genes
13 13
14 14
### *42 total*
15 15
16
-|Gene|Tier| First MZL evidence | Other entities |
17
-|:-:|:-:|:--|:-|
18
-|[ACTB](ACTB)|1||[@wienandGenomicAnalysesFlowsorted2019b; @lohrDiscoveryPrioritizationSomatic2012a]|
19
-|[ARID1A](ARID1A)|1|[Rossi et al](papers/rossiCodingGenomeSplenic2012c)[@rossiCodingGenomeSplenic2012c]|[@krysiakRecurrentSomaticMutations2017b; @loveGeneticLandscapeMutations2012; @zhangGeneticHeterogeneityDiffuse2013; @wienandGenomicAnalysesFlowsorted2019b]|
20
-|[ATM](ATM)|1|[Braggio et al](papers/braggioGenomicAnalysisMarginal2012)[@braggioGenomicAnalysisMarginal2012]|[@reddyGeneticFunctionalDrivers2017; @beaLandscapeSomaticMutations2013]|
21
-|[BCL10](BCL10)|1|[Spina et al](papers/spinaGeneticsNodalMarginal2016b)[@spinaGeneticsNodalMarginal2016b]|[@russler-germainMutationsAssociatedProgression2023b; @morinFrequentMutationHistonemodifying2011]|
22
-|[BCL7A](BCL7A)|1||[@krysiakRecurrentSomaticMutations2017b; @zhangGeneticHeterogeneityDiffuse2013; @grandeGenomewideDiscoverySomatic2019; @reichelFlowSortingExome2015a]|
23
-|[BIRC3](BIRC3)|1|[Rossi et al](papers/rossiAlterationBIRC3Multiple2011a)[@rossiAlterationBIRC3Multiple2011a]|[@dunsCharacterizationDLBCLPMBL2021b; @beaLandscapeSomaticMutations2013; @arthurGenomewideDiscoverySomatic2018]|
24
-|[BRAF](BRAF)|1||[@loveGeneticLandscapeMutations2012; @tiacciBRAFMutationsHairycell2011a]|
25
-|[BTG1](BTG1)|1||[@morinFrequentMutationHistonemodifying2011; @burkhardtClinicalRelevanceMolecular2022b; @sarkozyMutationalLandscapeGray2021a]|
26
-|[CARD11](CARD11)|1|[Yan et al](papers/yanBCRTLRSignaling2012a)[@yanBCRTLRSignaling2012a]|[@wuGeneticHeterogeneityPrimary2016; @morinFrequentMutationHistonemodifying2011; @lenzOncogenicCARD11Mutations2008]|
27
-|[CCND3](CCND3)|1|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)[@jalladesExomeSequencingIdentifies2017]|[@morinFrequentMutationHistonemodifying2011; @deschGenotypingCirculatingTumor2020; @richterRecurrentMutationID32012a]|
28
-|[CXCR4](CXCR4)|1||[@khodabakhshiRecurrentTargetsAberrant2012; @paneaWholeGenomeLandscape2019; @krysiakRecurrentSomaticMutations2017b]|
29
-|[DTX1](DTX1)|1|[Rossi et al](papers/rossiCodingGenomeSplenic2012c)[@rossiCodingGenomeSplenic2012c]|[@gomezUltraDeepSequencingReveals2023; @zhangGeneticHeterogeneityDiffuse2013; @loveGeneticLandscapeMutations2012]|
30
-|[EP300](EP300)|1|[Rossi et al](papers/rossiCodingGenomeSplenic2012c)[@rossiCodingGenomeSplenic2012c]|[@pasqualucciInactivatingMutationsAcetyltransferase2011a]|
31
-|[EZH2](EZH2)|1||[@loveGeneticLandscapeMutations2012; @morinSomaticMutationsAltering2010a; @mottokIntegrativeGenomicAnalysis2019b]|
32
-|[FAS](FAS)|1|[Spina et al](papers/spinaGeneticsNodalMarginal2016b)[@spinaGeneticsNodalMarginal2016b]|[@schollMutationsRegionFAS2007]|
33
-|[FAT1](FAT1)|1|[Spina et al](papers/spinaGeneticsNodalMarginal2016b)[@spinaGeneticsNodalMarginal2016b]||
34
-|[FOXO1](FOXO1)|1||[@schmitzBurkittLymphomaPathogenesis2012; @morinFrequentMutationHistonemodifying2011; @dunsCharacterizationDLBCLPMBL2021b]|
35
-|[H1-4](H1-4)|1|||
36
-|[H1-5](H1-5)|1|||
37
-|[ID3](ID3)|1|[Spina et al](papers/spinaGeneticsNodalMarginal2016b)[@spinaGeneticsNodalMarginal2016b]|[@schmitzBurkittLymphomaPathogenesis2012; @richterRecurrentMutationID32012a]|
38
-|[KLF2](KLF2)|1|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)[@jalladesExomeSequencingIdentifies2017]|[@pasqualucciAnalysisCodingGenome2011; @deschGenotypingCirculatingTumor2020]|
39
-|[KLHL6](KLHL6)|1|[Ganapathi et al](papers/ganapathiGeneticLandscapeDural2016)[@ganapathiGeneticLandscapeDural2016]|[@morinFrequentMutationHistonemodifying2011]|
40
-|[KMT2D](KMT2D)|1|[Rossi et al](papers/rossiCodingGenomeSplenic2012c)[@rossiCodingGenomeSplenic2012c]|[@beaLandscapeSomaticMutations2013; @grandeGenomewideDiscoverySomatic2019; @morinFrequentMutationHistonemodifying2011; @deschGenotypingCirculatingTumor2020]|
41
-|[MAP3K14](MAP3K14)|1|[Rossi et al](papers/rossiAlterationBIRC3Multiple2011a)[@rossiAlterationBIRC3Multiple2011a]|[@ottoGeneticLesionsTRAF32012a]|
42
-|[MPEG1](MPEG1)|1||[@morinMutationalStructuralAnalysis2013]|
43
-|[MYD88](MYD88)|1|[Yan et al](papers/yanBCRTLRSignaling2012a)[@yanBCRTLRSignaling2012a]|[@ngoOncogenicallyActiveMYD882011a]|
44
-|[NCOR2](NCOR2)|1|[Spina et al](papers/spinaGeneticsNodalMarginal2016b)[@spinaGeneticsNodalMarginal2016b]|[@schmitzBurkittLymphomaPathogenesis2012; @sarkozyMutationalLandscapeGray2021a]|
45
-|[NOL9](NOL9)|1|[Spina et al](papers/spinaGeneticsNodalMarginal2016b)[@spinaGeneticsNodalMarginal2016b]|[@schmitzGeneticsPathogenesisDiffuse2018a]|
46
-|[NOTCH1](NOTCH1)|1|[Rossi et al](papers/rossiCodingGenomeSplenic2012c)[@rossiCodingGenomeSplenic2012c]|[@beaLandscapeSomaticMutations2013; @pasqualucciAnalysisCodingGenome2011; @loveGeneticLandscapeMutations2012]|
47
-|[NOTCH2](NOTCH2)|1|[Rossi et al](papers/rossiCodingGenomeSplenic2012c)[@rossiCodingGenomeSplenic2012c]|[@beaLandscapeSomaticMutations2013; @zhangGeneticHeterogeneityDiffuse2013]|
48
-|[PCLO](PCLO)|1||[@lohrDiscoveryPrioritizationSomatic2012a]|
49
-|[POU2AF1](POU2AF1)|1||[@chapuyMolecularSubtypesDiffuse2018b; @krysiakRecurrentSomaticMutations2017b]|
50
-|[PTPRD](PTPRD)|1|[Spina et al](papers/spinaGeneticsNodalMarginal2016b)[@spinaGeneticsNodalMarginal2016b]||
51
-|[SIN3A](SIN3A)|1|[Rossi et al](papers/rossiCodingGenomeSplenic2012c)[@rossiCodingGenomeSplenic2012c]|[@chapuyMolecularSubtypesDiffuse2018b; @grandeGenomewideDiscoverySomatic2019]|
52
-|[SOCS1](SOCS1)|1||[@wenigerMutationsTumorSuppressor2006a; @morinFrequentMutationHistonemodifying2011]|
53
-|[SPEN](SPEN)|1|[Rossi et al](papers/rossiCodingGenomeSplenic2012c)[@rossiCodingGenomeSplenic2012c]|[@sarkozyMutationalLandscapeGray2021a; @albuquerqueEnhancingKnowledgeDiscovery2017a]|
54
-|[STAT6](STAT6)|1||[@ritzRecurrentMutationsSTAT62009a; @yildizActivatingSTAT6Mutations2015c]|
55
-|[TBL1XR1](TBL1XR1)|1|[Rossi et al](papers/rossiCodingGenomeSplenic2012c)[@rossiCodingGenomeSplenic2012c]|[@lohrDiscoveryPrioritizationSomatic2012a]|
56
-|[TNFAIP3](TNFAIP3)|1|[Rossi et al](papers/rossiAlterationBIRC3Multiple2011a)[@rossiAlterationBIRC3Multiple2011a]|[@schmitzTNFAIP3A20Tumor2009a; @compagnoMutationsMultipleGenes2009a]|
57
-|[TNFRSF14](TNFRSF14)|1|[Spina et al](papers/spinaGeneticsNodalMarginal2016b)[@spinaGeneticsNodalMarginal2016b]|[@morinFrequentMutationHistonemodifying2011; @cheungAcquiredTNFRSF14Mutations2010a]|
58
-|[TP53](TP53)|1|[Rossi et al](papers/rossiCodingGenomeSplenic2012c)[@rossiCodingGenomeSplenic2012c]|[@morinFrequentMutationHistonemodifying2011; @tiacciPervasiveMutationsJAKSTAT2018b; @lohrDiscoveryPrioritizationSomatic2012a; @wildaInactivationARFMDM2p53Pathway2004; @beaLandscapeSomaticMutations2013]|
59
-|[TRAF3](TRAF3)|1|[Rossi et al](papers/rossiAlterationBIRC3Multiple2011a)[@rossiAlterationBIRC3Multiple2011a]|[@pasqualucciAnalysisCodingGenome2011; @ottoGeneticLesionsTRAF32012a]|
16
+|Gene|Summary| First MZL study | Other entities | QC result |
17
+|:-:|:--:|:-:|:-|:-|
18
+|[ACTB](ACTB)|Tier 1 GE, aSHM||[@drevalGeneticSubdivisionsFollicular2023; @lohrDiscoveryPrioritizationSomatic2012; @wienandGenomicAnalysesFlowsorted2019]||
19
+|[ARID1A](ARID1A)|Tier 1 GE[@rossiCodingGenomeSplenic2012], FE[@barisicARID1AOrchestratesSWI2024]|[Rossi et al](papers/rossiCodingGenomeSplenic2012)|[@krysiakRecurrentSomaticMutations2017; @loveGeneticLandscapeMutations2012; @wienandGenomicAnalysesFlowsorted2019; @zhangGeneticHeterogeneityDiffuse2013]||
20
+|[ATM](ATM)|Tier 1 GE[@braggioGenomicAnalysisMarginal2012], FE[@camachoATMGeneInactivation2002]|[Braggio et al](papers/braggioGenomicAnalysisMarginal2012)|[@beaLandscapeSomaticMutations2013; @reddyGeneticFunctionalDrivers2017]||
21
+|[BCL10](BCL10)|Tier 1 GE[@spinaGeneticsNodalMarginal2016], FE[@xiaBCL10MutationsDefine2022]|[Spina et al](papers/spinaGeneticsNodalMarginal2016)|[@morinFrequentMutationHistonemodifying2011; @russler-germainMutationsAssociatedProgression2023]||
22
+|[BCL7A](BCL7A)|Tier 1 GE, FE[@balinas-gaviraFrequentMutationsAminoterminal2020], aSHM||[@grandeGenomewideDiscoverySomatic2019; @krysiakRecurrentSomaticMutations2017; @morinFrequentMutationHistonemodifying2011; @reichelFlowSortingExome2015]||
23
+|[BIRC3](BIRC3)|Tier 1 GE[@rossiAlterationBIRC3Multiple2011], aSHM|[Rossi et al](papers/rossiAlterationBIRC3Multiple2011)|[@arthurGenomewideDiscoverySomatic2018; @beaLandscapeSomaticMutations2013; @dunsCharacterizationDLBCLPMBL2021]||
24
+|[BRAF](BRAF)|Tier 1 GE, FE[@wanMechanismActivationRAFERK2004]||[@loveGeneticLandscapeMutations2012; @tiacciBRAFMutationsHairycell2011]||
25
+|[BTG1](BTG1)|Tier 1 GE, FE[@almasmoumFrequentLossBTG12021], aSHM||[@burkhardtClinicalRelevanceMolecular2022; @drevalGeneticSubdivisionsFollicular2023; @morinFrequentMutationHistonemodifying2011; @sarkozyMutationalLandscapeGray2021]||
26
+|[CARD11](CARD11)|Tier 1 GE[@yanBCRTLRSignaling2012], FE[@lenzOncogenicCARD11Mutations2008]|[Yan et al](papers/yanBCRTLRSignaling2012)|[@lenzOncogenicCARD11Mutations2008; @morinFrequentMutationHistonemodifying2011; @wuGeneticHeterogeneityPrimary2016]||
27
+|[CCND3](CCND3)|Tier 1 GE[@jalladesExomeSequencingIdentifies2017], FE[@schmitzBurkittLymphomaPathogenesis2012]|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)|[@deschGenotypingCirculatingTumor2020; @morinFrequentMutationHistonemodifying2011; @richterRecurrentMutationID32012]||
28
+|[CXCR4](CXCR4)|Tier 1 GE, FE[@zmajkovicovaGenotypephenotypeCorrelationsWHIM2022], aSHM||[@khodabakhshiRecurrentTargetsAberrant2012; @krysiakRecurrentSomaticMutations2017; @paneaWholeGenomeLandscape2019]||
29
+|[DTX1](DTX1)|Tier 1 GE[@rossiCodingGenomeSplenic2012], aSHM|[Rossi et al](papers/rossiCodingGenomeSplenic2012)|[@gomezUltraDeepSequencingReveals2023; @loveGeneticLandscapeMutations2012; @zhangGeneticHeterogeneityDiffuse2013]||
30
+|[EP300](EP300)|Tier 1 GE[@rossiCodingGenomeSplenic2012], FE[@pasqualucciInactivatingMutationsAcetyltransferase2011]|[Rossi et al](papers/rossiCodingGenomeSplenic2012)|[@pasqualucciInactivatingMutationsAcetyltransferase2011]||
31
+|[EZH2](EZH2)|Tier 1 GE, FE[@sneeringerCoordinatedActivitiesWildtype2010]||[@loveGeneticLandscapeMutations2012; @morinSomaticMutationsAltering2010; @mottokIntegrativeGenomicAnalysis2019]||
32
+|[FAS](FAS)|Tier 1 GE[@spinaGeneticsNodalMarginal2016], FE[@wangFasFADDDeathDomain2010]|[Spina et al](papers/spinaGeneticsNodalMarginal2016)|[@morinFrequentMutationHistonemodifying2011; @schollMutationsRegionFAS2007]||
33
+|[FAT1](FAT1)|Tier 1 GE[@spinaGeneticsNodalMarginal2016]|[Spina et al](papers/spinaGeneticsNodalMarginal2016)|||
34
+|[FOXO1](FOXO1)|Tier 1 GE, FE[@trinhAnalysisFOXO1Mutations]||[@dunsCharacterizationDLBCLPMBL2021; @morinFrequentMutationHistonemodifying2011; @schmitzBurkittLymphomaPathogenesis2012]||
35
+|[H1-4](H1-4)|Tier 1 GE||||
36
+|[H1-5](H1-5)|Tier 1 GE||||
37
+|[ID3](ID3)|Tier 1 GE[@spinaGeneticsNodalMarginal2016]|[Spina et al](papers/spinaGeneticsNodalMarginal2016)|[@richterRecurrentMutationID32012; @schmitzGeneticsPathogenesisDiffuse2018]||
38
+|[KLF2](KLF2)|Tier 1 GE[@jalladesExomeSequencingIdentifies2017], aSHM|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)|[@deschGenotypingCirculatingTumor2020; @drevalGeneticSubdivisionsFollicular2023; @pasqualucciAnalysisCodingGenome2011]||
39
+|[KLHL6](KLHL6)|Tier 1 GE[@ganapathiGeneticLandscapeDural2016], FE[@choiLossKLHL6Promotes2018], aSHM|[Ganapathi et al](papers/ganapathiGeneticLandscapeDural2016)|[@morinFrequentMutationHistonemodifying2011]||
40
+|[KMT2D](KMT2D)|Tier 1 GE[@rossiCodingGenomeSplenic2012], FE[@zhangDisruptionKMT2DPerturbs2015]|[Rossi et al](papers/rossiCodingGenomeSplenic2012)|[@beaLandscapeSomaticMutations2013; @deschGenotypingCirculatingTumor2020; @grandeGenomewideDiscoverySomatic2019; @morinFrequentMutationHistonemodifying2011]||
41
+|[MAP3K14](MAP3K14)|Tier 1 GE[@rossiAlterationBIRC3Multiple2011]|[Rossi et al](papers/rossiAlterationBIRC3Multiple2011)|[@ottoGeneticLesionsTRAF32012]||
42
+|[MPEG1](MPEG1)|Tier 1 GE||[@morinMutationalStructuralAnalysis2013]||
43
+|[MYD88](MYD88)|Tier 1 GE[@yanBCRTLRSignaling2012], FE[@ngoOncogenicallyActiveMYD882011]|[Yan et al](papers/yanBCRTLRSignaling2012)|[@drevalGeneticSubdivisionsFollicular2023; @ngoOncogenicallyActiveMYD882011]||
44
+|[NCOR2](NCOR2)|Tier 1 GE[@spinaGeneticsNodalMarginal2016]|[Spina et al](papers/spinaGeneticsNodalMarginal2016)|[@sarkozyMutationalLandscapeGray2021; @schmitzBurkittLymphomaPathogenesis2012]||
45
+|[NOL9](NOL9)|Tier 1 GE[@spinaGeneticsNodalMarginal2016]|[Spina et al](papers/spinaGeneticsNodalMarginal2016)|[@schmitzGeneticsPathogenesisDiffuse2018]||
46
+|[NOTCH1](NOTCH1)|Tier 1 GE[@rossiCodingGenomeSplenic2012], FE[@ryanCellRegulomeLinks2017]|[Rossi et al](papers/rossiCodingGenomeSplenic2012)|[@beaLandscapeSomaticMutations2013; @loveGeneticLandscapeMutations2012; @pasqualucciAnalysisCodingGenome2011]||
47
+|[NOTCH2](NOTCH2)|Tier 1 GE[@rossiCodingGenomeSplenic2012], FE[@leeGainoffunctionMutationsCopy2009]|[Rossi et al](papers/rossiCodingGenomeSplenic2012)|[@beaLandscapeSomaticMutations2013; @zhangGeneticHeterogeneityDiffuse2013]||
48
+|[PCLO](PCLO)|Tier 1 GE||[@lohrDiscoveryPrioritizationSomatic2012]||
49
+|[POU2AF1](POU2AF1)|Tier 1 GE, FE[@gonzalez-rinconUnravelingTransformationFollicular2019], aSHM||[@chapuyMolecularSubtypesDiffuse2018; @krysiakRecurrentSomaticMutations2017]||
50
+|[PTPRD](PTPRD)|Tier 1 GE[@spinaGeneticsNodalMarginal2016]|[Spina et al](papers/spinaGeneticsNodalMarginal2016)|[@drevalGeneticSubdivisionsFollicular2023]||
51
+|[SIN3A](SIN3A)|Tier 1 GE[@rossiCodingGenomeSplenic2012]|[Rossi et al](papers/rossiCodingGenomeSplenic2012)|[@chapuyMolecularSubtypesDiffuse2018; @grandeGenomewideDiscoverySomatic2019]||
52
+|[SOCS1](SOCS1)|Tier 1 GE, FE[@melznerBiallelicMutationSOCS12005], aSHM||[@drevalGeneticSubdivisionsFollicular2023; @morinFrequentMutationHistonemodifying2011; @wenigerMutationsTumorSuppressor2006]||
53
+|[SPEN](SPEN)|Tier 1 GE[@rossiCodingGenomeSplenic2012]|[Rossi et al](papers/rossiCodingGenomeSplenic2012)|[@albuquerqueEnhancingKnowledgeDiscovery2017; @sarkozyMutationalLandscapeGray2021]||
54
+|[STAT6](STAT6)|Tier 1 GE, FE[@mentzPARP14NovelTarget2022]||[@ritzRecurrentMutationsSTAT62009; @yildizActivatingSTAT6Mutations2015]||
55
+|[TBL1XR1](TBL1XR1)|Tier 1 GE[@rossiCodingGenomeSplenic2012], FE[@venturuttiTBL1XR1MutationsDrive2020]|[Rossi et al](papers/rossiCodingGenomeSplenic2012)|[@drevalGeneticSubdivisionsFollicular2023; @lohrDiscoveryPrioritizationSomatic2012]||
56
+|[TNFAIP3](TNFAIP3)|Tier 1 GE[@rossiAlterationBIRC3Multiple2011], FE[@compagnoMutationsMultipleGenes2009]|[Rossi et al](papers/rossiAlterationBIRC3Multiple2011)|[@compagnoMutationsMultipleGenes2009; @drevalGeneticSubdivisionsFollicular2023; @schmitzTNFAIP3A20Tumor2009]||
57
+|[TNFRSF14](TNFRSF14)|Tier 1 GE[@spinaGeneticsNodalMarginal2016], FE[@]|[Spina et al](papers/spinaGeneticsNodalMarginal2016)|[@cheungAcquiredTNFRSF14Mutations2010; @morinFrequentMutationHistonemodifying2011]||
58
+|[TP53](TP53)|Tier 1 GE[@rossiCodingGenomeSplenic2012], FE[@katoUnderstandingFunctionstructureFunctionmutation2003]|[Rossi et al](papers/rossiCodingGenomeSplenic2012)|[@beaLandscapeSomaticMutations2013; @morinFrequentMutationHistonemodifying2011; @tiacciPervasiveMutationsJAKSTAT2018; @wildaInactivationARFMDM2p53Pathway2004]||
59
+|[TRAF3](TRAF3)|Tier 1 GE[@rossiAlterationBIRC3Multiple2011]|[Rossi et al](papers/rossiAlterationBIRC3Multiple2011)|[@ottoGeneticLesionsTRAF32012; @pasqualucciAnalysisCodingGenome2011]||
60 60
61
-## Tier 2 MZL genes
61
+## Tier 2, low-confidence MZL genes
62 62
63 63
### *74 total*
64 64
65
-|Gene|Tier| First MZL evidence | Other entities |
66
-|:-:|:-:|:--|:-|
67
-|[ABCA13](ABCA13)|2|[Spina et al](papers/spinaGeneticsNodalMarginal2016b)[@spinaGeneticsNodalMarginal2016b]|[@sarkozyMutationalLandscapeGray2021a]|
68
-|[ACTG1](ACTG1)|2|[Spina et al](papers/spinaGeneticsNodalMarginal2016b)[@spinaGeneticsNodalMarginal2016b]|[@hubschmannMutationalMechanismsShaping2021b; @deschGenotypingCirculatingTumor2020]|
69
-|[ADD2](ADD2)|2|[Spina et al](papers/spinaGeneticsNodalMarginal2016b)[@spinaGeneticsNodalMarginal2016b]||
70
-|[AMN](AMN)|2|[Spina et al](papers/spinaGeneticsNodalMarginal2016b)[@spinaGeneticsNodalMarginal2016b]||
71
-|[AMOTL1](AMOTL1)|2|[Parry et al](papers/parryWholeExomeSequencing2013)[@parryWholeExomeSequencing2013]||
72
-|[AOC2](AOC2)|2|[Spina et al](papers/spinaGeneticsNodalMarginal2016b)[@spinaGeneticsNodalMarginal2016b]||
73
-|[ARHGAP20](ARHGAP20)|2|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)[@jalladesExomeSequencingIdentifies2017]||
74
-|[ARHGEF15](ARHGEF15)|2|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)[@jalladesExomeSequencingIdentifies2017]||
75
-|[ARHGEF17](ARHGEF17)|2|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)[@jalladesExomeSequencingIdentifies2017]||
76
-|[BCOR](BCOR)|2|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)[@jalladesExomeSequencingIdentifies2017]|[@nadeuGenomicEpigenomicInsights2020b]|
77
-|[C6orf103](C6orf103)|2|[Spina et al](papers/spinaGeneticsNodalMarginal2016b)[@spinaGeneticsNodalMarginal2016b]||
78
-|[CBFA2T3](CBFA2T3)|2|[Parry et al](papers/parryWholeExomeSequencing2013)[@parryWholeExomeSequencing2013]||
79
-|[CD79A](CD79A)|2|[Rossi et al](papers/rossiCodingGenomeSplenic2012c)[@rossiCodingGenomeSplenic2012c]|[@burkhardtClinicalRelevanceMolecular2022b]|
80
-|[CD9B](CD9B)|2|[Vandenbrand et al](papers/vandenbrandRecurrentMutationsGenes2017)[@vandenbrandRecurrentMutationsGenes2017]||
81
-|[CDC42BPB](CDC42BPB)|2|[Spina et al](papers/spinaGeneticsNodalMarginal2016b)[@spinaGeneticsNodalMarginal2016b]|[@hubschmannMutationalMechanismsShaping2021b]|
82
-|[CDKN2A](CDKN2A)|2|[Spina et al](papers/spinaGeneticsNodalMarginal2016b)[@spinaGeneticsNodalMarginal2016b]|[@morinMutationalStructuralAnalysis2013; @grandeGenomewideDiscoverySomatic2019]|
83
-|[CLGN](CLGN)|2|[Spina et al](papers/spinaGeneticsNodalMarginal2016b)[@spinaGeneticsNodalMarginal2016b]||
84
-|[CNBP](CNBP)|2|[Spina et al](papers/spinaGeneticsNodalMarginal2016b)[@spinaGeneticsNodalMarginal2016b]||
85
-|[CNKSR2](CNKSR2)|2|[Spina et al](papers/spinaGeneticsNodalMarginal2016b)[@spinaGeneticsNodalMarginal2016b]||
86
-|[CREBBP](CREBBP)|2|[Parry et al](papers/parryWholeExomeSequencing2013)[@parryWholeExomeSequencing2013]|[@dunsCharacterizationDLBCLPMBL2021b; @pasqualucciInactivatingMutationsAcetyltransferase2011a; @loveGeneticLandscapeMutations2012]|
87
-|[DNAH5](DNAH5)|2|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)[@jalladesExomeSequencingIdentifies2017]|[@morinMutationalStructuralAnalysis2013]|
88
-|[DNAH7](DNAH7)|2|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)[@jalladesExomeSequencingIdentifies2017]||
89
-|[DNAI1](DNAI1)|2|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)[@jalladesExomeSequencingIdentifies2017]||
90
-|[DOCK6](DOCK6)|2|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)[@jalladesExomeSequencingIdentifies2017]||
91
-|[DSP](DSP)|2||[@zhangGeneticHeterogeneityDiffuse2013]|
92
-|[DTNB](DTNB)|2|||
93
-|[DTX3L](DTX3L)|2|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)[@jalladesExomeSequencingIdentifies2017]||
94
-|[EGR1](EGR1)|2|[Rossi et al](papers/rossiCodingGenomeSplenic2012c)[@rossiCodingGenomeSplenic2012c]|[@reichelFlowSortingExome2015a; @krysiakRecurrentSomaticMutations2017b]|
95
-|[EGR2](EGR2)|2|[Rossi et al](papers/rossiCodingGenomeSplenic2012c)[@rossiCodingGenomeSplenic2012c]||
96
-|[EZH1](EZH1)|2|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)[@jalladesExomeSequencingIdentifies2017]||
97
-|[FAT4](FAT4)|2|[Parry et al](papers/parryWholeExomeSequencing2013)[@parryWholeExomeSequencing2013]|[@morinMutationalStructuralAnalysis2013; @zhangGenomicLandscapeMantle2014]|
98
-|[FBXO11](FBXO11)|2|[Parry et al](papers/parryWholeExomeSequencing2013)[@parryWholeExomeSequencing2013]|[@richterRecurrentMutationID32012a; @hubschmannMutationalMechanismsShaping2021b]|
99
-|[GPR98](GPR98)|2|[Spina et al](papers/spinaGeneticsNodalMarginal2016b)[@spinaGeneticsNodalMarginal2016b]||
100
-|[GPS2](GPS2)|2|[Rossi et al](papers/rossiCodingGenomeSplenic2012c)[@rossiCodingGenomeSplenic2012c]||
101
-|[HIST1H1D](HIST1H1D)|2|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)[@jalladesExomeSequencingIdentifies2017]|[@krysiakRecurrentSomaticMutations2017b; @morinMutationalStructuralAnalysis2013]|
102
-|[HIST1H2AD](HIST1H2AD)|2|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)[@jalladesExomeSequencingIdentifies2017]||
103
-|[HIST1H2AG](HIST1H2AG)|2|[Rossi et al](papers/rossiCodingGenomeSplenic2012c)[@rossiCodingGenomeSplenic2012c]|[@krysiakRecurrentSomaticMutations2017b; @paneaWholeGenomeLandscape2019; @morinMutationalStructuralAnalysis2013]|
104
-|[HIST1H2BK](HIST1H2BK)|2|[Rossi et al](papers/rossiCodingGenomeSplenic2012c)[@rossiCodingGenomeSplenic2012c]|[@paneaWholeGenomeLandscape2019; @zhangGeneticHeterogeneityDiffuse2013]|
105
-|[HIST4H4](HIST4H4)|2|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)[@jalladesExomeSequencingIdentifies2017]||
106
-|[HRAS](HRAS)|2|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)[@jalladesExomeSequencingIdentifies2017]|[@reddyGeneticFunctionalDrivers2017]|
107
-|[IKBKB](IKBKB)|2|[Rossi et al](papers/rossiAlterationBIRC3Multiple2011a)[@rossiAlterationBIRC3Multiple2011a]|[@wienandGenomicAnalysesFlowsorted2019b; @reddyGeneticFunctionalDrivers2017]|
108
-|[KAT6A](KAT6A)|2|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)[@jalladesExomeSequencingIdentifies2017]||
109
-|[KDM6A](KDM6A)|2|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)[@jalladesExomeSequencingIdentifies2017]||
110
-|[KIF26A](KIF26A)|2|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)[@jalladesExomeSequencingIdentifies2017]||
111
-|[LRP1B](LRP1B)|2|[Spina et al](papers/spinaGeneticsNodalMarginal2016b)[@spinaGeneticsNodalMarginal2016b]|[@zhangGeneticHeterogeneityDiffuse2013]|
112
-|[MCRS1](MCRS1)|2|[Rossi et al](papers/rossiCodingGenomeSplenic2012c)[@rossiCodingGenomeSplenic2012c]||
113
-|[MGA](MGA)|2|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)[@jalladesExomeSequencingIdentifies2017]|[@zhangGeneticHeterogeneityDiffuse2013]|
114
-|[MSL2](MSL2)|2|[Rossi et al](papers/rossiCodingGenomeSplenic2012c)[@rossiCodingGenomeSplenic2012c]||
115
-|[MYC](MYC)|2|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)[@jalladesExomeSequencingIdentifies2017]|[@johnstonCmycHypermutationBurkitt1992; @pasqualucciHypermutationMultipleProtooncogenes2001a; @dunsCharacterizationDLBCLPMBL2021b]|
116
-|[MYLK](MYLK)|2|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)[@jalladesExomeSequencingIdentifies2017]||
117
-|[NCOA6](NCOA6)|2|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)[@jalladesExomeSequencingIdentifies2017]||
118
-|[NRAS](NRAS)|2|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)[@jalladesExomeSequencingIdentifies2017]||
119
-|[PACRG](PACRG)|2|[Spina et al](papers/spinaGeneticsNodalMarginal2016b)[@spinaGeneticsNodalMarginal2016b]||
120
-|[PARK2](PARK2)|2|[Spina et al](papers/spinaGeneticsNodalMarginal2016b)[@spinaGeneticsNodalMarginal2016b]||
121
-|[PLA2G4D](PLA2G4D)|2|[Parry et al](papers/parryWholeExomeSequencing2013)[@parryWholeExomeSequencing2013]||
122
-|[PLXNB3](PLXNB3)|2|[Spina et al](papers/spinaGeneticsNodalMarginal2016b)[@spinaGeneticsNodalMarginal2016b]|[@zhangGenomicLandscapeMantle2014]|
123
-|[RAF1](RAF1)|2|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)[@jalladesExomeSequencingIdentifies2017]|[@fanComprehensiveCharacterizationDriver2020b]|
124
-|[RAPGEF2](RAPGEF2)|2||[@zhangGeneticHeterogeneityDiffuse2013]|
125
-|[RCOR1](RCOR1)|2|[Spina et al](papers/spinaGeneticsNodalMarginal2016b)[@spinaGeneticsNodalMarginal2016b]||
126
-|[RFTN1](RFTN1)|2||[@arthurGenomewideDiscoverySomatic2018; @dunsCharacterizationDLBCLPMBL2021b]|
127
-|[ROCK1](ROCK1)|2|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)[@jalladesExomeSequencingIdentifies2017]||
128
-|[RPL1L](RPL1L)|2|[Spina et al](papers/spinaGeneticsNodalMarginal2016b)[@spinaGeneticsNodalMarginal2016b]||
129
-|[SAMD5](SAMD5)|2|[Spina et al](papers/spinaGeneticsNodalMarginal2016b)[@spinaGeneticsNodalMarginal2016b]||
130
-|[SCG3](SCG3)|2|[Spina et al](papers/spinaGeneticsNodalMarginal2016b)[@spinaGeneticsNodalMarginal2016b]||
131
-|[STXBP5](STXBP5)|2|[Spina et al](papers/spinaGeneticsNodalMarginal2016b)[@spinaGeneticsNodalMarginal2016b]||
132
-|[SWAP70](SWAP70)|2|[Rossi et al](papers/rossiCodingGenomeSplenic2012c)[@rossiCodingGenomeSplenic2012c]||
133
-|[TAF1](TAF1)|2|[Spina et al](papers/spinaGeneticsNodalMarginal2016b)[@spinaGeneticsNodalMarginal2016b]|[@morinMutationalStructuralAnalysis2013]|
134
-|[TBK1](TBK1)|2|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)[@jalladesExomeSequencingIdentifies2017]||
135
-|[TCTN2](TCTN2)|2|[Spina et al](papers/spinaGeneticsNodalMarginal2016b)[@spinaGeneticsNodalMarginal2016b]||
136
-|[TNIP2](TNIP2)|2|[Vandenbrand et al](papers/vandenbrandRecurrentMutationsGenes2017)[@vandenbrandRecurrentMutationsGenes2017]||
137
-|[TRRAP](TRRAP)|2|[Rossi et al](papers/rossiCodingGenomeSplenic2012c)[@rossiCodingGenomeSplenic2012c]|[@zhangGeneticHeterogeneityDiffuse2013]|
138
-|[USH2A](USH2A)|2|[Parry et al](papers/parryWholeExomeSequencing2013)[@parryWholeExomeSequencing2013]||
139
-|[WAC](WAC)|2|[Rossi et al](papers/rossiCodingGenomeSplenic2012c)[@rossiCodingGenomeSplenic2012c]|[@reddyGeneticFunctionalDrivers2017]|
140
-|[WNK1](WNK1)|2|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)[@jalladesExomeSequencingIdentifies2017]|[@thomasGeneticSubgroupsInform2023; @hubschmannMutationalMechanismsShaping2021b]|
65
+|Gene|Summary| First MZL study | Other entities | QC result |
66
+|:-:|:--:|:-:|:-|:-|
67
+|[ABCA13](ABCA13)|Tier 2 GE[@spinaGeneticsNodalMarginal2016]|[Spina et al](papers/spinaGeneticsNodalMarginal2016)|[@sarkozyMutationalLandscapeGray2021]||
68
+|[ACTG1](ACTG1)|Tier 2 GE[@spinaGeneticsNodalMarginal2016], aSHM|[Spina et al](papers/spinaGeneticsNodalMarginal2016)|[@deschGenotypingCirculatingTumor2020; @fanComprehensiveCharacterizationDriver2020; @hubschmannMutationalMechanismsShaping2021]||
69
+|[ADD2](ADD2)|Tier 2 GE[@spinaGeneticsNodalMarginal2016]|[Spina et al](papers/spinaGeneticsNodalMarginal2016)|||
70
+|[AMN](AMN)|Tier 2 GE[@spinaGeneticsNodalMarginal2016]|[Spina et al](papers/spinaGeneticsNodalMarginal2016)|||
71
+|[AMOTL1](AMOTL1)|Tier 2 GE[@parryWholeExomeSequencing2013]|[Parry et al](papers/parryWholeExomeSequencing2013)|||
72
+|[AOC2](AOC2)|Tier 2 GE[@spinaGeneticsNodalMarginal2016]|[Spina et al](papers/spinaGeneticsNodalMarginal2016)|||
73
+|[ARHGAP20](ARHGAP20)|Tier 2 GE[@jalladesExomeSequencingIdentifies2017]|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)|||
74
+|[ARHGEF15](ARHGEF15)|Tier 2 GE[@jalladesExomeSequencingIdentifies2017]|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)|||
75
+|[ARHGEF17](ARHGEF17)|Tier 2 GE[@jalladesExomeSequencingIdentifies2017]|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)|||
76
+|[BCOR](BCOR)|Tier 2 GE[@jalladesExomeSequencingIdentifies2017]|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)|[@nadeuGenomicEpigenomicInsights2020b]||
77
+|[C6orf103](C6orf103)|Tier 2 GE[@spinaGeneticsNodalMarginal2016]|[Spina et al](papers/spinaGeneticsNodalMarginal2016)|||
78
+|[CBFA2T3](CBFA2T3)|Tier 2 GE[@parryWholeExomeSequencing2013]|[Parry et al](papers/parryWholeExomeSequencing2013)|||
79
+|[CD79A](CD79A)|Tier 2 GE[@rossiCodingGenomeSplenic2012]|[Rossi et al](papers/rossiCodingGenomeSplenic2012)|[@burkhardtClinicalRelevanceMolecular2022]||
80
+|[CD9B](CD9B)|Tier 2 GE[@vandenbrandRecurrentMutationsGenes2017]|[Vandenbrand et al](papers/vandenbrandRecurrentMutationsGenes2017)|||
81
+|[CDC42BPB](CDC42BPB)|Tier 2 GE[@spinaGeneticsNodalMarginal2016]|[Spina et al](papers/spinaGeneticsNodalMarginal2016)|[@hubschmannMutationalMechanismsShaping2021]||
82
+|[CDKN2A](CDKN2A)|Tier 2 GE[@spinaGeneticsNodalMarginal2016], FE[@kannengiesserFunctionalStructuralGenetic2009]|[Spina et al](papers/spinaGeneticsNodalMarginal2016)|[@grandeGenomewideDiscoverySomatic2019; @morinMutationalStructuralAnalysis2013]||
83
+|[CLGN](CLGN)|Tier 2 GE[@spinaGeneticsNodalMarginal2016]|[Spina et al](papers/spinaGeneticsNodalMarginal2016)|||
84
+|[CNBP](CNBP)|Tier 2 GE[@spinaGeneticsNodalMarginal2016]|[Spina et al](papers/spinaGeneticsNodalMarginal2016)|||
85
+|[CNKSR2](CNKSR2)|Tier 2 GE[@spinaGeneticsNodalMarginal2016]|[Spina et al](papers/spinaGeneticsNodalMarginal2016)|||
86
+|[CREBBP](CREBBP)|Tier 2 GE[@parryWholeExomeSequencing2013], FE[@pasqualucciInactivatingMutationsAcetyltransferase2011]|[Parry et al](papers/parryWholeExomeSequencing2013)|[@dunsCharacterizationDLBCLPMBL2021; @loveGeneticLandscapeMutations2012; @pasqualucciInactivatingMutationsAcetyltransferase2011]||
87
+|[DNAH5](DNAH5)|Tier 2 GE[@jalladesExomeSequencingIdentifies2017]|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)|[@morinMutationalStructuralAnalysis2013]||
88
+|[DNAH7](DNAH7)|Tier 2 GE[@jalladesExomeSequencingIdentifies2017]|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)|||
89
+|[DNAI1](DNAI1)|Tier 2 GE[@jalladesExomeSequencingIdentifies2017]|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)|||
90
+|[DOCK6](DOCK6)|Tier 2 GE[@jalladesExomeSequencingIdentifies2017]|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)|||
91
+|[DSP](DSP)|Tier 2 GE||[@zhangGeneticHeterogeneityDiffuse2013]||
92
+|[DTNB](DTNB)|Tier 2 GE||||
93
+|[DTX3L](DTX3L)|Tier 2 GE[@jalladesExomeSequencingIdentifies2017]|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)|||
94
+|[EGR1](EGR1)|Tier 2 GE[@rossiCodingGenomeSplenic2012]|[Rossi et al](papers/rossiCodingGenomeSplenic2012)|[@krysiakRecurrentSomaticMutations2017; @reichelFlowSortingExome2015]||
95
+|[EGR2](EGR2)|Tier 2 GE[@rossiCodingGenomeSplenic2012]|[Rossi et al](papers/rossiCodingGenomeSplenic2012)|||
96
+|[EZH1](EZH1)|Tier 2 GE[@jalladesExomeSequencingIdentifies2017]|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)|||
97
+|[FAT4](FAT4)|Tier 2 GE[@parryWholeExomeSequencing2013]|[Parry et al](papers/parryWholeExomeSequencing2013)|[@morinMutationalStructuralAnalysis2013; @zhangGenomicLandscapeMantle2014]||
98
+|[FBXO11](FBXO11)|Tier 2 GE[@parryWholeExomeSequencing2013], FE[@duanFBXO11TargetsBCL62011]|[Parry et al](papers/parryWholeExomeSequencing2013)|[@arthurGenomewideDiscoverySomatic2018; @richterRecurrentMutationID32012]||
99
+|[GPR98](GPR98)|Tier 2 GE[@spinaGeneticsNodalMarginal2016]|[Spina et al](papers/spinaGeneticsNodalMarginal2016)|||
100
+|[GPS2](GPS2)|Tier 2 GE[@rossiCodingGenomeSplenic2012]|[Rossi et al](papers/rossiCodingGenomeSplenic2012)|||
101
+|[HIST1H1D](HIST1H1D)|Tier 2 GE[@jalladesExomeSequencingIdentifies2017], aSHM|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)|[@krysiakRecurrentSomaticMutations2017; @morinMutationalStructuralAnalysis2013]||
102
+|[HIST1H2AD](HIST1H2AD)|Tier 2 GE[@jalladesExomeSequencingIdentifies2017]|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)|||
103
+|[HIST1H2AG](HIST1H2AG)|Tier 2 GE[@rossiCodingGenomeSplenic2012]|[Rossi et al](papers/rossiCodingGenomeSplenic2012)|[@krysiakRecurrentSomaticMutations2017; @morinMutationalStructuralAnalysis2013; @paneaWholeGenomeLandscape2019]||
104
+|[HIST1H2BK](HIST1H2BK)|Tier 2 GE[@rossiCodingGenomeSplenic2012], aSHM|[Rossi et al](papers/rossiCodingGenomeSplenic2012)|[@paneaWholeGenomeLandscape2019; @zhangGeneticHeterogeneityDiffuse2013]||
105
+|[HIST4H4](HIST4H4)|Tier 2 GE[@jalladesExomeSequencingIdentifies2017]|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)|||
106
+|[HRAS](HRAS)|Tier 2 GE[@jalladesExomeSequencingIdentifies2017]|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)|[@reddyGeneticFunctionalDrivers2017]||
107
+|[IKBKB](IKBKB)|Tier 2 GE[@rossiAlterationBIRC3Multiple2011]|[Rossi et al](papers/rossiAlterationBIRC3Multiple2011)|[@reddyGeneticFunctionalDrivers2017; @wienandGenomicAnalysesFlowsorted2019]||
108
+|[KAT6A](KAT6A)|Tier 2 GE[@jalladesExomeSequencingIdentifies2017]|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)|||
109
+|[KDM6A](KDM6A)|Tier 2 GE[@jalladesExomeSequencingIdentifies2017]|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)|||
110
+|[KIF26A](KIF26A)|Tier 2 GE[@jalladesExomeSequencingIdentifies2017]|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)|||
111
+|[LRP1B](LRP1B)|Tier 2 GE[@spinaGeneticsNodalMarginal2016]|[Spina et al](papers/spinaGeneticsNodalMarginal2016)|[@zhangGeneticHeterogeneityDiffuse2013]||
112
+|[MCRS1](MCRS1)|Tier 2 GE[@rossiCodingGenomeSplenic2012]|[Rossi et al](papers/rossiCodingGenomeSplenic2012)|||
113
+|[MGA](MGA)|Tier 2 GE[@jalladesExomeSequencingIdentifies2017], FE[@depaoliMGASuppressorMYC2013]|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)|[@reddyGeneticFunctionalDrivers2017]||
114
+|[MSL2](MSL2)|Tier 2 GE[@rossiCodingGenomeSplenic2012]|[Rossi et al](papers/rossiCodingGenomeSplenic2012)|||
115
+|[MYC](MYC)|Tier 2 GE[@jalladesExomeSequencingIdentifies2017], FE[@freieGermlinePointMutation2024], aSHM|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)|[@dunsCharacterizationDLBCLPMBL2021; @johnstonCmycHypermutationBurkitt1992; @pasqualucciHypermutationMultipleProtooncogenes2001]||
116
+|[MYLK](MYLK)|Tier 2 GE[@jalladesExomeSequencingIdentifies2017]|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)|||
117
+|[NCOA6](NCOA6)|Tier 2 GE[@jalladesExomeSequencingIdentifies2017]|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)|||
118
+|[NRAS](NRAS)|Tier 2 GE[@jalladesExomeSequencingIdentifies2017]|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)|||
119
+|[PACRG](PACRG)|Tier 2 GE[@spinaGeneticsNodalMarginal2016]|[Spina et al](papers/spinaGeneticsNodalMarginal2016)|||
120
+|[PARK2](PARK2)|Tier 2 GE[@spinaGeneticsNodalMarginal2016]|[Spina et al](papers/spinaGeneticsNodalMarginal2016)|||
121
+|[PLA2G4D](PLA2G4D)|Tier 2 GE[@parryWholeExomeSequencing2013]|[Parry et al](papers/parryWholeExomeSequencing2013)|||
122
+|[PLXNB3](PLXNB3)|Tier 2 GE[@spinaGeneticsNodalMarginal2016]|[Spina et al](papers/spinaGeneticsNodalMarginal2016)|[@zhangGenomicLandscapeMantle2014]||
123
+|[RAF1](RAF1)|Tier 2 GE[@jalladesExomeSequencingIdentifies2017]|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)|[@fanComprehensiveCharacterizationDriver2020]||
124
+|[RAPGEF2](RAPGEF2)|Tier 2 GE||[@zhangGeneticHeterogeneityDiffuse2013]||
125
+|[RCOR1](RCOR1)|Tier 2 GE[@spinaGeneticsNodalMarginal2016]|[Spina et al](papers/spinaGeneticsNodalMarginal2016)|||
126
+|[RFTN1](RFTN1)|Tier 2 GE, aSHM||[@arthurGenomewideDiscoverySomatic2018; @dunsCharacterizationDLBCLPMBL2021]||
127
+|[ROCK1](ROCK1)|Tier 2 GE[@jalladesExomeSequencingIdentifies2017]|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)|||
128
+|[RPL1L](RPL1L)|Tier 2 GE[@spinaGeneticsNodalMarginal2016]|[Spina et al](papers/spinaGeneticsNodalMarginal2016)|||
129
+|[SAMD5](SAMD5)|Tier 2 GE[@spinaGeneticsNodalMarginal2016]|[Spina et al](papers/spinaGeneticsNodalMarginal2016)|||
130
+|[SCG3](SCG3)|Tier 2 GE[@spinaGeneticsNodalMarginal2016]|[Spina et al](papers/spinaGeneticsNodalMarginal2016)|||
131
+|[STXBP5](STXBP5)|Tier 2 GE[@spinaGeneticsNodalMarginal2016]|[Spina et al](papers/spinaGeneticsNodalMarginal2016)|||
132
+|[SWAP70](SWAP70)|Tier 2 GE[@rossiCodingGenomeSplenic2012]|[Rossi et al](papers/rossiCodingGenomeSplenic2012)|||
133
+|[TAF1](TAF1)|Tier 2 GE[@spinaGeneticsNodalMarginal2016]|[Spina et al](papers/spinaGeneticsNodalMarginal2016)|[@morinMutationalStructuralAnalysis2013]||
134
+|[TBK1](TBK1)|Tier 2 GE[@jalladesExomeSequencingIdentifies2017]|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)|||
135
+|[TCTN2](TCTN2)|Tier 2 GE[@spinaGeneticsNodalMarginal2016]|[Spina et al](papers/spinaGeneticsNodalMarginal2016)|||
136
+|[TNIP2](TNIP2)|Tier 2 GE[@vandenbrandRecurrentMutationsGenes2017]|[Vandenbrand et al](papers/vandenbrandRecurrentMutationsGenes2017)|||
137
+|[TRRAP](TRRAP)|Tier 2 GE[@rossiCodingGenomeSplenic2012]|[Rossi et al](papers/rossiCodingGenomeSplenic2012)|[@zhangGeneticHeterogeneityDiffuse2013]||
138
+|[USH2A](USH2A)|Tier 2 GE[@parryWholeExomeSequencing2013]|[Parry et al](papers/parryWholeExomeSequencing2013)|||
139
+|[WAC](WAC)|Tier 2 GE[@rossiCodingGenomeSplenic2012]|[Rossi et al](papers/rossiCodingGenomeSplenic2012)|[@reddyGeneticFunctionalDrivers2017]||
140
+|[WNK1](WNK1)|Tier 2 GE[@jalladesExomeSequencingIdentifies2017]|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)|[@hubschmannMutationalMechanismsShaping2021; @thomasGeneticSubgroupsInform2023]||
141 141
142
-## Tier 3 MZL genes
142
+## Tier 3, retired MZL genes
143 143
144 144
### *0 total*
145 145
146
-|Gene|Tier| First MZL evidence | Other entities |
147
-|:-:|:-:|:--|:-|
146
+|Gene|Summary| First MZL study | Other entities | QC result |
147
+|:-:|:--:|:-:|:-|:-|
148 148
149 149
150 150
# References
MZL_sankey1-1.svg
... ...
@@ -0,0 +1 @@
1
+<svg aria-roledescription="sankey" role="graphics-document document" viewBox="0 0 800 750.7125244140625" height="750.7125244140625" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg" width="800" id="my-svg" style="background-color: white;"><style>#my-svg{font-family:"trebuchet ms",verdana,arial,sans-serif;font-size:16px;fill:#333;}#my-svg .error-icon{fill:#552222;}#my-svg .error-text{fill:#552222;stroke:#552222;}#my-svg .edge-thickness-normal{stroke-width:2px;}#my-svg .edge-thickness-thick{stroke-width:3.5px;}#my-svg .edge-pattern-solid{stroke-dasharray:0;}#my-svg .edge-pattern-dashed{stroke-dasharray:3;}#my-svg .edge-pattern-dotted{stroke-dasharray:2;}#my-svg .marker{fill:#333333;stroke:#333333;}#my-svg .marker.cross{stroke:#333333;}#my-svg svg{font-family:"trebuchet ms",verdana,arial,sans-serif;font-size:16px;}#my-svg :root{--mermaid-font-family:"trebuchet ms",verdana,arial,sans-serif;}</style><g/><g class="nodes"><g y="0" x="526.6666666666666" transform="translate(526.6666666666666,0)" id="node-1" class="node"><rect fill="#4e79a7" width="10" height="50.312499999999986"/></g><g y="0" x="790" transform="translate(790,0)" id="node-2" class="node"><rect fill="#f28e2c" width="10" height="503.1249999999999"/></g><g y="689.6874999999998" x="526.6666666666666" transform="translate(526.6666666666666,689.6874999999998)" id="node-3" class="node"><rect fill="#e15759" width="10" height="35.9375"/></g><g y="513.1249999999999" x="790" transform="translate(790,513.1249999999999)" id="node-4" class="node"><rect fill="#76b7b2" width="10" height="186.875"/></g><g y="735.6249999999998" x="526.6666666666666" transform="translate(526.6666666666666,735.6249999999998)" id="node-5" class="node"><rect fill="#59a14f" width="10" height="14.375"/></g><g y="60.312499999999986" x="526.6666666666666" transform="translate(526.6666666666666,60.312499999999986)" id="node-6" class="node"><rect fill="#edc949" width="10" height="201.25"/></g><g y="665.3124999999998" x="526.6666666666666" transform="translate(526.6666666666666,665.3124999999998)" id="node-7" class="node"><rect fill="#af7aa1" width="10" height="14.375"/></g><g y="432.4999999999998" x="526.6666666666666" transform="translate(526.6666666666666,432.4999999999998)" id="node-8" class="node"><rect fill="#ff9da7" width="10" height="222.8125"/></g><g y="271.5625" x="526.6666666666666" transform="translate(526.6666666666666,271.5625)" id="node-9" class="node"><rect fill="#9c755f" width="10" height="150.93749999999977"/></g><g y="13.940293062507234" x="0" transform="translate(0,13.940293062507234)" id="node-10" class="node"><rect fill="#bab0ab" width="10" height="690"/></g><g y="0" x="263.3333333333333" transform="translate(263.3333333333333,0)" id="node-11" class="node"><rect fill="#4e79a7" width="10" height="402.50000000000017"/></g><g y="674.3489565267026" x="263.3333333333333" transform="translate(263.3333333333333,674.3489565267026)" id="node-12" class="node"><rect fill="#f28e2c" width="10" height="35.9375"/></g><g y="720.2864565267026" x="263.3333333333333" transform="translate(263.3333333333333,720.2864565267026)" id="node-13" class="node"><rect fill="#e15759" width="10" height="14.375"/></g><g y="649.9739565267026" x="263.3333333333333" transform="translate(263.3333333333333,649.9739565267026)" id="node-14" class="node"><rect fill="#76b7b2" width="10" height="14.375"/></g><g y="417.1614565267027" x="263.3333333333333" transform="translate(263.3333333333333,417.1614565267027)" id="node-15" class="node"><rect fill="#59a14f" width="10" height="222.81249999999972"/></g></g><g font-size="14" font-family="sans-serif" class="node-labels"><text text-anchor="end" dy="0.35em" y="25.156249999999993" x="520.6666666666666">Parry 2013</text><text text-anchor="end" dy="0.35em" y="251.56249999999994" x="784">Tier 2</text><text text-anchor="end" dy="0.35em" y="707.6562499999998" x="520.6666666666666">Rossi 2011</text><text text-anchor="end" dy="0.35em" y="606.5624999999999" x="784">Tier 1</text><text text-anchor="end" dy="0.35em" y="742.8124999999998" x="520.6666666666666">Yan 2012</text><text text-anchor="end" dy="0.35em" y="160.9375" x="520.6666666666666">Jallades 2017</text><text text-anchor="end" dy="0.35em" y="672.4999999999998" x="520.6666666666666">Vandenbrand 2017</text><text text-anchor="end" dy="0.35em" y="543.9062499999998" x="520.6666666666666">Spina 2016</text><text text-anchor="end" dy="0.35em" y="347.0312499999999" x="520.6666666666666">Rossi 2012</text><text text-anchor="start" dy="0.35em" y="358.9402930625072" x="16">MZL genes</text><text text-anchor="start" dy="0.35em" y="201.25000000000009" x="279.3333333333333">MZL-exome</text><text text-anchor="start" dy="0.35em" y="692.3177065267026" x="279.3333333333333">MZL-Sanger</text><text text-anchor="start" dy="0.35em" y="727.4739565267026" x="279.3333333333333">MZL-Panel</text><text text-anchor="start" dy="0.35em" y="657.1614565267026" x="279.3333333333333">MZL-panel</text><text text-anchor="start" dy="0.35em" y="528.5677065267025" x="279.3333333333333">MZL-exome/panel</text></g><g stroke-opacity="0.5" fill="none" class="links"><g style="mix-blend-mode: multiply;" class="link"><path stroke-width="50.3125" stroke="#f28e2c" d="M536.6666666666666,25.15625C663.3333333333333,25.15625,663.3333333333333,25.15625,790,25.15625"/></g><g style="mix-blend-mode: multiply;" class="link"><path stroke-width="28.75" stroke="#76b7b2" d="M536.6666666666666,711.2499999999998C663.3333333333333,711.2499999999998,663.3333333333333,671.2499999999999,790,671.2499999999999"/></g><g style="mix-blend-mode: multiply;" class="link"><path stroke-width="7.1875" stroke="#f28e2c" d="M536.6666666666666,693.2812499999998C663.3333333333333,693.2812499999998,663.3333333333333,499.53125,790,499.53125"/></g><g style="mix-blend-mode: multiply;" class="link"><path stroke-width="14.375" stroke="#76b7b2" 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... ...
\ No newline at end of file
PMBL_genes.md
... ...
@@ -7,186 +7,186 @@ link-citations: true
7 7
8 8
## Origins of PMBL genes
9 9
10
-![](PMBL_sankey-1.svg)
10
+![](PMBL_sankey1-1.svg)
11 11
12
-## Tier 1 PMBL genes
12
+## Tier 1, high-confidence PMBL genes
13 13
14
-### *76 total*
14
+### *46 total*
15 15
16
-|Gene|Tier| First PMBL evidence | Other entities |
17
-|:-:|:-:|:--|:-|
18
-|[ACTB](ACTB)|1|[Wienand et al](papers/wienandGenomicAnalysesFlowsorted2019b)[@wienandGenomicAnalysesFlowsorted2019b]|[@lohrDiscoveryPrioritizationSomatic2012a]|
19
-|[ARID1A](ARID1A)|1|[Wienand et al](papers/wienandGenomicAnalysesFlowsorted2019b)[@wienandGenomicAnalysesFlowsorted2019b]|[@rossiCodingGenomeSplenic2012c; @zhangGeneticHeterogeneityDiffuse2013; @loveGeneticLandscapeMutations2012; @krysiakRecurrentSomaticMutations2017b]|
20
-|[ARID5B](ARID5B)|1|[Gomez et al](papers/gomezUltraDeepSequencingReveals2023)[@gomezUltraDeepSequencingReveals2023]|[@reddyGeneticFunctionalDrivers2017]|
21
-|[B2M](B2M)|1|[Reichel et al](papers/reichelFlowSortingExome2015a)[@reichelFlowSortingExome2015a]|[@pararajalingamCodingNoncodingDrivers2020; @morinFrequentMutationHistonemodifying2011]|
22
-|[BIRC6](BIRC6)|1|[Sarkozy et al](papers/sarkozyMutationalLandscapeGray2021a)[@sarkozyMutationalLandscapeGray2021a]|[@reddyGeneticFunctionalDrivers2017]|
23
-|[BTG1](BTG1)|1|[Sarkozy et al](papers/sarkozyMutationalLandscapeGray2021a)[@sarkozyMutationalLandscapeGray2021a]|[@burkhardtClinicalRelevanceMolecular2022b; @morinFrequentMutationHistonemodifying2011]|
24
-|[CD58](CD58)|1|[Schneider et al](papers/schneiderAlterationsCD58Gene2015a)[@schneiderAlterationsCD58Gene2015a]|[@morinFrequentMutationHistonemodifying2011]|
25
-|[CD83](CD83)|1|[Duns et al](papers/dunsCharacterizationDLBCLPMBL2021b)[@dunsCharacterizationDLBCLPMBL2021b]|[@paneaWholeGenomeLandscape2019; @russler-germainMutationsAssociatedProgression2023b; @morinMutationalStructuralAnalysis2013]|
26
-|[CDKN2A](CDKN2A)|1||[@spinaGeneticsNodalMarginal2016b; @morinMutationalStructuralAnalysis2013; @grandeGenomewideDiscoverySomatic2019]|
27
-|[CHD8](CHD8)|1||[@grandeGenomewideDiscoverySomatic2019]|
28
-|[CIITA](CIITA)|1|[Mottok et al](papers/mottokGenomicAlterationsCIITA2015b)[@mottokGenomicAlterationsCIITA2015b]|[@morinFrequentMutationHistonemodifying2011]|
29
-|[CISH](CISH)|1|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019b)[@mottokIntegrativeGenomicAnalysis2019b]||
30
-|[CREBBP](CREBBP)|1|[Duns et al](papers/dunsCharacterizationDLBCLPMBL2021b)[@dunsCharacterizationDLBCLPMBL2021b]|[@parryWholeExomeSequencing2013; @pasqualucciInactivatingMutationsAcetyltransferase2011a; @loveGeneticLandscapeMutations2012]|
31
-|[CSF2RB](CSF2RB)|1|[Reichel et al](papers/reichelFlowSortingExome2015a)[@reichelFlowSortingExome2015a]||
32
-|[DDX3X](DDX3X)|1|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019b)[@mottokIntegrativeGenomicAnalysis2019b]|[@schmitzBurkittLymphomaPathogenesis2012; @reddyGeneticFunctionalDrivers2017]|
33
-|[DTX1](DTX1)|1|[Gomez et al](papers/gomezUltraDeepSequencingReveals2023)[@gomezUltraDeepSequencingReveals2023]|[@loveGeneticLandscapeMutations2012; @rossiCodingGenomeSplenic2012c; @zhangGeneticHeterogeneityDiffuse2013]|
34
-|[DUSP2](DUSP2)|1|[Duns et al](papers/dunsCharacterizationDLBCLPMBL2021b)[@dunsCharacterizationDLBCLPMBL2021b]|[@lohrDiscoveryPrioritizationSomatic2012a]|
35
-|[EBF1](EBF1)|1|[Reichel et al](papers/reichelFlowSortingExome2015a)[@reichelFlowSortingExome2015a]|[@thomasGeneticSubgroupsInform2023; @bohleRoleEarlyBcell2013]|
36
-|[EEF1A1](EEF1A1)|1|[Reichel et al](papers/reichelFlowSortingExome2015a)[@reichelFlowSortingExome2015a]|[@hubschmannMutationalMechanismsShaping2021b]|
37
-|[ETS1](ETS1)|1||[@paneaWholeGenomeLandscape2019; @morinFrequentMutationHistonemodifying2011]|
38
-|[EWSR1](EWSR1)|1||[@pararajalingamCodingNoncodingDrivers2020]|
39
-|[EZH2](EZH2)|1|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019b)[@mottokIntegrativeGenomicAnalysis2019b]|[@morinSomaticMutationsAltering2010a; @loveGeneticLandscapeMutations2012]|
40
-|[FAS](FAS)|1||[@spinaGeneticsNodalMarginal2016b; @schollMutationsRegionFAS2007]|
41
-|[FAT1](FAT1)|1||[@spinaGeneticsNodalMarginal2016b]|
42
-|[FAT4](FAT4)|1||[@morinMutationalStructuralAnalysis2013; @zhangGenomicLandscapeMantle2014; @parryWholeExomeSequencing2013]|
43
-|[GNA13](GNA13)|1|[Reichel et al](papers/reichelFlowSortingExome2015a)[@reichelFlowSortingExome2015a]|[@morinFrequentMutationHistonemodifying2011; @loveGeneticLandscapeMutations2012]|
44
-|[HIST1H1B](HIST1H1B)|1|[Sarkozy et al](papers/sarkozyMutationalLandscapeGray2021a)[@sarkozyMutationalLandscapeGray2021a]|[@chapuyMolecularSubtypesDiffuse2018b; @krysiakRecurrentSomaticMutations2017b]|
45
-|[HIST1H1C](HIST1H1C)|1||[@paneaWholeGenomeLandscape2019; @morinFrequentMutationHistonemodifying2011]|
46
-|[HIST1H1D](HIST1H1D)|1||[@morinMutationalStructuralAnalysis2013; @jalladesExomeSequencingIdentifies2017; @krysiakRecurrentSomaticMutations2017b]|
47
-|[HIST1H1E](HIST1H1E)|1|[Reichel et al](papers/reichelFlowSortingExome2015a)[@reichelFlowSortingExome2015a]|[@krysiakRecurrentSomaticMutations2017b; @grandeGenomewideDiscoverySomatic2019; @lohrDiscoveryPrioritizationSomatic2012a]|
48
-|[HLA-B](HLA-B)|1|[Wienand et al](papers/wienandGenomicAnalysesFlowsorted2019b)[@wienandGenomicAnalysesFlowsorted2019b]|[@lohrDiscoveryPrioritizationSomatic2012a]|
49
-|[IL4R](IL4R)|1|[Vigano et al](papers/viganoSomaticIL4RMutations2018b)[@viganoSomaticIL4RMutations2018b]|[@dunsCharacterizationDLBCLPMBL2021b]|
50
-|[IRF8](IRF8)|1|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019b)[@mottokIntegrativeGenomicAnalysis2019b]|[@morinFrequentMutationHistonemodifying2011; @paneaWholeGenomeLandscape2019]|
51
-|[ITPKB](ITPKB)|1|[Reichel et al](papers/reichelFlowSortingExome2015a)[@reichelFlowSortingExome2015a]|[@schmitzGeneticsPathogenesisDiffuse2018a]|
52
-|[JAK1](JAK1)|1|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019b)[@mottokIntegrativeGenomicAnalysis2019b]|[@zhangGeneticHeterogeneityDiffuse2013]|
53
-|[KMT2C](KMT2C)|1|[Sarkozy et al](papers/sarkozyMutationalLandscapeGray2021a)[@sarkozyMutationalLandscapeGray2021a]|[@zhangGenomicLandscapeMantle2014; @zhouSporadicEndemicBurkitt2019; @zhangGeneticHeterogeneityDiffuse2013]|
54
-|[LTB](LTB)|1|[Desch et al](papers/deschGenotypingCirculatingTumor2020)[@deschGenotypingCirculatingTumor2020]|[@chapuyMolecularSubtypesDiffuse2018b]|
55
-|[MAP3K14](MAP3K14)|1|[Otto et al](papers/ottoGeneticLesionsTRAF32012a)[@ottoGeneticLesionsTRAF32012a]|[@rossiAlterationBIRC3Multiple2011a]|
56
-|[MS4A1](MS4A1)|1|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019b)[@mottokIntegrativeGenomicAnalysis2019b]|[@rushtonGeneticEvolutionaryPatterns2020]|
57
-|[NFKBIA](NFKBIA)|1|[Wienand et al](papers/wienandGenomicAnalysesFlowsorted2019b)[@wienandGenomicAnalysesFlowsorted2019b]|[@lakeMutationsNFKBIAEncoding2009; @russler-germainMutationsAssociatedProgression2023b]|
58
-|[NFKBIE](NFKBIE)|1|[Mansouri et al](papers/mansouriFrequentNFKBIEDeletions2016)[@mansouriFrequentNFKBIEDeletions2016]|[@morinGeneticLandscapesRelapsed2016; @pararajalingamCodingNoncodingDrivers2020]|
59
-|[OSBPL10](OSBPL10)|1||[@zhangGeneticHeterogeneityDiffuse2013]|
60
-|[P2RY8](P2RY8)|1||[@muppidiLossSignalingGa132014b; @lohrDiscoveryPrioritizationSomatic2012a]|
61
-|[PCLO](PCLO)|1||[@lohrDiscoveryPrioritizationSomatic2012a]|
62
-|[PHIP](PHIP)|1|||
63
-|[PIM1](PIM1)|1|[Duns et al](papers/dunsCharacterizationDLBCLPMBL2021b)[@dunsCharacterizationDLBCLPMBL2021b]|[@burkhardtClinicalRelevanceMolecular2022b; @pasqualucciHypermutationMultipleProtooncogenes2001a]|
64
-|[PIM2](PIM2)|1|[Reichel et al](papers/reichelFlowSortingExome2015a)[@reichelFlowSortingExome2015a]|[@arthurGenomewideDiscoverySomatic2018]|
65
-|[PRKDC](PRKDC)|1||[@hubschmannMutationalMechanismsShaping2021b; @schmitzGeneticsPathogenesisDiffuse2018a]|
66
-|[PTPN1](PTPN1)|1|[Gunawardana et al](papers/gunawardanaRecurrentSomaticMutations2014c)[@gunawardanaRecurrentSomaticMutations2014c]||
67
-|[PTPRD](PTPRD)|1||[@spinaGeneticsNodalMarginal2016b]|
68
-|[RHOA](RHOA)|1||[@richterRecurrentMutationID32012a; @zhangGeneticHeterogeneityDiffuse2013]|
69
-|[S1PR2](S1PR2)|1||[@muppidiLossSignalingGa132014b; @morinFrequentMutationHistonemodifying2011]|
70
-|[SGK1](SGK1)|1|[Duns et al](papers/dunsCharacterizationDLBCLPMBL2021b)[@dunsCharacterizationDLBCLPMBL2021b]|[@morinFrequentMutationHistonemodifying2011]|
71
-|[SIN3A](SIN3A)|1||[@chapuyMolecularSubtypesDiffuse2018b; @grandeGenomewideDiscoverySomatic2019; @rossiCodingGenomeSplenic2012c]|
72
-|[SMARCA2](SMARCA2)|1|||
73
-|[SMARCA4](SMARCA4)|1||[@lohrDiscoveryPrioritizationSomatic2012a; @nadeuGenomicEpigenomicInsights2020b; @krysiakRecurrentSomaticMutations2017b; @richterRecurrentMutationID32012a]|
74
-|[SOCS1](SOCS1)|1|[Weniger et al](papers/wenigerMutationsTumorSuppressor2006a)[@wenigerMutationsTumorSuppressor2006a]|[@morinFrequentMutationHistonemodifying2011]|
75
-|[SPEN](SPEN)|1|[Sarkozy et al](papers/sarkozyMutationalLandscapeGray2021a)[@sarkozyMutationalLandscapeGray2021a]|[@albuquerqueEnhancingKnowledgeDiscovery2017a; @rossiCodingGenomeSplenic2012c]|
76
-|[STAT3](STAT3)|1||[@lohrDiscoveryPrioritizationSomatic2012a]|
77
-|[STAT6](STAT6)|1|[Ritz et al](papers/ritzRecurrentMutationsSTAT62009a)[@ritzRecurrentMutationsSTAT62009a]|[@yildizActivatingSTAT6Mutations2015c]|
78
-|[TAP1](TAP1)|1||[@schmitzGeneticsPathogenesisDiffuse2018a]|
79
-|[TBL1XR1](TBL1XR1)|1||[@rossiCodingGenomeSplenic2012c; @lohrDiscoveryPrioritizationSomatic2012a]|
80
-|[TCF3](TCF3)|1||[@schmitzBurkittLymphomaPathogenesis2012]|
81
-|[TET3](TET3)|1|||
82
-|[TMSB4X](TMSB4X)|1||[@albuquerqueEnhancingKnowledgeDiscovery2017a]|
83
-|[TNFAIP3](TNFAIP3)|1|[Schmitz et al](papers/schmitzTNFAIP3A20Tumor2009a)[@schmitzTNFAIP3A20Tumor2009a]|[@compagnoMutationsMultipleGenes2009a; @rossiAlterationBIRC3Multiple2011a]|
84
-|[TNFRSF1B](TNFRSF1B)|1|||
85
-|[TP53](TP53)|1|[Tiacci et al](papers/tiacciPervasiveMutationsJAKSTAT2018b)[@tiacciPervasiveMutationsJAKSTAT2018b]|[@beaLandscapeSomaticMutations2013; @lohrDiscoveryPrioritizationSomatic2012a; @rossiCodingGenomeSplenic2012c; @wildaInactivationARFMDM2p53Pathway2004; @morinFrequentMutationHistonemodifying2011]|
86
-|[TRAF3](TRAF3)|1|[Otto et al](papers/ottoGeneticLesionsTRAF32012a)[@ottoGeneticLesionsTRAF32012a]|[@pasqualucciAnalysisCodingGenome2011; @rossiAlterationBIRC3Multiple2011a]|
87
-|[UBE2A](UBE2A)|1|[Reichel et al](papers/reichelFlowSortingExome2015a)[@reichelFlowSortingExome2015a]|[@lohrDiscoveryPrioritizationSomatic2012a]|
88
-|[UBR5](UBR5)|1||[@zhangGeneticHeterogeneityDiffuse2013; @pararajalingamCodingNoncodingDrivers2020]|
89
-|[UNC5C](UNC5C)|1||[@lohrDiscoveryPrioritizationSomatic2012a]|
90
-|[VPS13B](VPS13B)|1||[@lohrDiscoveryPrioritizationSomatic2012a]|
91
-|[WEE1](WEE1)|1|[Reichel et al](papers/reichelFlowSortingExome2015a)[@reichelFlowSortingExome2015a]|[@schmitzGeneticsPathogenesisDiffuse2018a]|
92
-|[XPO1](XPO1)|1|[Jardin et al](papers/jardinRecurrentMutationsExportin2016a)[@jardinRecurrentMutationsExportin2016a]|[@mareschalWholeExomeSequencing2016]|
93
-|[ZFP36L1](ZFP36L1)|1|[Reichel et al](papers/reichelFlowSortingExome2015a)[@reichelFlowSortingExome2015a]|[@paneaWholeGenomeLandscape2019; @morinFrequentMutationHistonemodifying2011]|
16
+|Gene|Summary| First PMBL study | Other entities | QC result |
17
+|:-:|:--:|:-:|:-|:-|
18
+|[ACTB](ACTB)|Tier 1 GE[@wienandGenomicAnalysesFlowsorted2019], aSHM|[Wienand et al](papers/wienandGenomicAnalysesFlowsorted2019)|[@drevalGeneticSubdivisionsFollicular2023; @lohrDiscoveryPrioritizationSomatic2012]||
19
+|[ARID1A](ARID1A)|Tier 1 GE[@wienandGenomicAnalysesFlowsorted2019], FE[@barisicARID1AOrchestratesSWI2024]|[Wienand et al](papers/wienandGenomicAnalysesFlowsorted2019)|[@krysiakRecurrentSomaticMutations2017; @loveGeneticLandscapeMutations2012; @rossiCodingGenomeSplenic2012; @zhangGeneticHeterogeneityDiffuse2013]||
20
+|[ARID5B](ARID5B)|Tier 1 GE[@gomezUltraDeepSequencingReveals2023]|[Gomez et al](papers/gomezUltraDeepSequencingReveals2023)|[@reddyGeneticFunctionalDrivers2017]||
21
+|[B2M](B2M)|Tier 1 GE[@reichelFlowSortingExome2015], FE[@challa-malladiCombinedGeneticInactivation2011]|[Reichel et al](papers/reichelFlowSortingExome2015)|[@morinFrequentMutationHistonemodifying2011; @pararajalingamCodingNoncodingDrivers2020]||
22
+|[BIRC6](BIRC6)|Tier 1 GE[@sarkozyMutationalLandscapeGray2021]|[Sarkozy et al](papers/sarkozyMutationalLandscapeGray2021)|[@reddyGeneticFunctionalDrivers2017]||
23
+|[BTG1](BTG1)|Tier 1 GE[@sarkozyMutationalLandscapeGray2021], FE[@almasmoumFrequentLossBTG12021], aSHM|[Sarkozy et al](papers/sarkozyMutationalLandscapeGray2021)|[@burkhardtClinicalRelevanceMolecular2022; @drevalGeneticSubdivisionsFollicular2023; @morinFrequentMutationHistonemodifying2011]||
24
+|[CD58](CD58)|Tier 1 GE[@schneiderAlterationsCD58Gene2015], FE[@challa-malladiCombinedGeneticInactivation2011]|[Schneider et al](papers/schneiderAlterationsCD58Gene2015)|[@morinFrequentMutationHistonemodifying2011]||
25
+|[CD83](CD83)|Tier 1 GE[@dunsCharacterizationDLBCLPMBL2021], aSHM|[Duns et al](papers/dunsCharacterizationDLBCLPMBL2021)|[@morinMutationalStructuralAnalysis2013; @paneaWholeGenomeLandscape2019; @russler-germainMutationsAssociatedProgression2023]||
26
+|[CIITA](CIITA)|Tier 1 GE[@mottokGenomicAlterationsCIITA2015], FE[@mottokGenomicAlterationsCIITA2015], aSHM|[Mottok et al](papers/mottokGenomicAlterationsCIITA2015)|[@morinFrequentMutationHistonemodifying2011]||
27
+|[CISH](CISH)|Tier 1 GE[@mottokIntegrativeGenomicAnalysis2019]|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019)|||
28
+|[CREBBP](CREBBP)|Tier 1 GE[@dunsCharacterizationDLBCLPMBL2021], FE[@pasqualucciInactivatingMutationsAcetyltransferase2011]|[Duns et al](papers/dunsCharacterizationDLBCLPMBL2021)|[@loveGeneticLandscapeMutations2012; @parryWholeExomeSequencing2013; @pasqualucciInactivatingMutationsAcetyltransferase2011]||
29
+|[CSF2RB](CSF2RB)|Tier 1 GE[@reichelFlowSortingExome2015]|[Reichel et al](papers/reichelFlowSortingExome2015)|||
30
+|[DDX3X](DDX3X)|Tier 1 GE[@mottokIntegrativeGenomicAnalysis2019], FE[@gongSequentialInverseDysregulation2021]|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019)|[@reddyGeneticFunctionalDrivers2017; @schmitzBurkittLymphomaPathogenesis2012]||
31
+|[DTX1](DTX1)|Tier 1 GE[@gomezUltraDeepSequencingReveals2023], aSHM|[Gomez et al](papers/gomezUltraDeepSequencingReveals2023)|[@loveGeneticLandscapeMutations2012; @rossiCodingGenomeSplenic2012; @zhangGeneticHeterogeneityDiffuse2013]||
32
+|[DUSP2](DUSP2)|Tier 1 GE[@dunsCharacterizationDLBCLPMBL2021], aSHM|[Duns et al](papers/dunsCharacterizationDLBCLPMBL2021)|[@drevalGeneticSubdivisionsFollicular2023; @lohrDiscoveryPrioritizationSomatic2012]||
33
+|[EBF1](EBF1)|Tier 1 GE[@reichelFlowSortingExome2015], FE[@ramirez-komoSpontaneousLossLineage2017], aSHM|[Reichel et al](papers/reichelFlowSortingExome2015)|[@bohleRoleEarlyBcell2013; @drevalGeneticSubdivisionsFollicular2023; @thomasGeneticSubgroupsInform2023]||
34
+|[EEF1A1](EEF1A1)|Tier 1 GE[@reichelFlowSortingExome2015]|[Reichel et al](papers/reichelFlowSortingExome2015)|[@chapuyMolecularSubtypesDiffuse2018; @hubschmannMutationalMechanismsShaping2021]||
35
+|[EZH2](EZH2)|Tier 1 GE[@mottokIntegrativeGenomicAnalysis2019], FE[@sneeringerCoordinatedActivitiesWildtype2010]|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019)|[@loveGeneticLandscapeMutations2012; @morinSomaticMutationsAltering2010]||
36
+|[GNA13](GNA13)|Tier 1 GE[@reichelFlowSortingExome2015], FE[@muppidiLossSignalingGa132014]|[Reichel et al](papers/reichelFlowSortingExome2015)|[@loveGeneticLandscapeMutations2012; @morinFrequentMutationHistonemodifying2011]||
37
+|[HIST1H1B](HIST1H1B)|Tier 1 GE[@sarkozyMutationalLandscapeGray2021], aSHM|[Sarkozy et al](papers/sarkozyMutationalLandscapeGray2021)|[@chapuyMolecularSubtypesDiffuse2018; @krysiakRecurrentSomaticMutations2017]||
38
+|[HIST1H1E](HIST1H1E)|Tier 1 GE[@reichelFlowSortingExome2015], aSHM|[Reichel et al](papers/reichelFlowSortingExome2015)|[@grandeGenomewideDiscoverySomatic2019; @krysiakRecurrentSomaticMutations2017; @lohrDiscoveryPrioritizationSomatic2012]||
39
+|[HLA-B](HLA-B)|Tier 1 GE[@wienandGenomicAnalysesFlowsorted2019], FE[@fangazioGeneticMechanismsHLAI2021]|[Wienand et al](papers/wienandGenomicAnalysesFlowsorted2019)|[@lohrDiscoveryPrioritizationSomatic2012]||
40
+|[IL4R](IL4R)|Tier 1 GE[@viganoSomaticIL4RMutations2018], FE[@viganoSomaticIL4RMutations2018], aSHM|[Vigano et al](papers/viganoSomaticIL4RMutations2018)|[@dunsCharacterizationDLBCLPMBL2021]||
41
+|[IRF8](IRF8)|Tier 1 GE[@mottokIntegrativeGenomicAnalysis2019], FE[@qiuIRF8mutantCellLymphoma2024], aSHM|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019)|[@morinFrequentMutationHistonemodifying2011; @paneaWholeGenomeLandscape2019]||
42
+|[ITPKB](ITPKB)|Tier 1 GE[@reichelFlowSortingExome2015], FE[@tiacciPervasiveMutationsJAKSTAT2018], aSHM|[Reichel et al](papers/reichelFlowSortingExome2015)|[@drevalGeneticSubdivisionsFollicular2023; @schmitzGeneticsPathogenesisDiffuse2018]||
43
+|[JAK1](JAK1)|Tier 1 GE[@mottokIntegrativeGenomicAnalysis2019]|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019)|[@reddyGeneticFunctionalDrivers2017]||
44
+|[KMT2C](KMT2C)|Tier 1 GE[@sarkozyMutationalLandscapeGray2021]|[Sarkozy et al](papers/sarkozyMutationalLandscapeGray2021)|[@zhangGeneticHeterogeneityDiffuse2013; @zhangGenomicLandscapeMantle2014; @zhouSporadicEndemicBurkitt2019]||
45
+|[LTB](LTB)|Tier 1 GE[@deschGenotypingCirculatingTumor2020], aSHM|[Desch et al](papers/deschGenotypingCirculatingTumor2020)|[@chapuyMolecularSubtypesDiffuse2018; @drevalGeneticSubdivisionsFollicular2023]||
46
+|[MAP3K14](MAP3K14)|Tier 1 GE[@ottoGeneticLesionsTRAF32012]|[Otto et al](papers/ottoGeneticLesionsTRAF32012)|[@rossiAlterationBIRC3Multiple2011]||
47
+|[MS4A1](MS4A1)|Tier 1 GE[@mottokIntegrativeGenomicAnalysis2019], FE[@rushtonGeneticEvolutionaryPatterns2020], aSHM|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019)|[@rushtonGeneticEvolutionaryPatterns2020]||
48
+|[NFKBIA](NFKBIA)|Tier 1 GE[@wienandGenomicAnalysesFlowsorted2019], FE[@jungnickelClonalDeleteriousMutations2000]|[Wienand et al](papers/wienandGenomicAnalysesFlowsorted2019)|[@russler-germainMutationsAssociatedProgression2023; @thomasMutationalAnalysisIkappaBalpha2004]||
49
+|[NFKBIE](NFKBIE)|Tier 1 GE[@mansouriFrequentNFKBIEDeletions2016], FE[@mansouriFunctionalLossIkBe2015]|[Mansouri et al](papers/mansouriFrequentNFKBIEDeletions2016)|[@morinGeneticLandscapesRelapsed2016; @pararajalingamCodingNoncodingDrivers2020]||
50
+|[PIM1](PIM1)|Tier 1 GE[@dunsCharacterizationDLBCLPMBL2021], FE[@kuoRolePIM1Ibrutinibresistant2016], aSHM|[Duns et al](papers/dunsCharacterizationDLBCLPMBL2021)|[@burkhardtClinicalRelevanceMolecular2022; @drevalGeneticSubdivisionsFollicular2023; @pasqualucciHypermutationMultipleProtooncogenes2001]||
51
+|[PIM2](PIM2)|Tier 1 GE[@reichelFlowSortingExome2015], aSHM|[Reichel et al](papers/reichelFlowSortingExome2015)|[@reddyGeneticFunctionalDrivers2017]||
52
+|[PTPN1](PTPN1)|Tier 1 GE[@gunawardanaRecurrentSomaticMutations2014]|[Gunawardana et al](papers/gunawardanaRecurrentSomaticMutations2014)|||
53
+|[SGK1](SGK1)|Tier 1 GE[@dunsCharacterizationDLBCLPMBL2021], FE[@gaoSGK1MutationsDLBCL2021], aSHM|[Duns et al](papers/dunsCharacterizationDLBCLPMBL2021)|[@morinFrequentMutationHistonemodifying2011]||
54
+|[SOCS1](SOCS1)|Tier 1 GE[@wenigerMutationsTumorSuppressor2006], FE[@melznerBiallelicMutationSOCS12005], aSHM|[Weniger et al](papers/wenigerMutationsTumorSuppressor2006)|[@drevalGeneticSubdivisionsFollicular2023; @morinFrequentMutationHistonemodifying2011]||
55
+|[SPEN](SPEN)|Tier 1 GE[@sarkozyMutationalLandscapeGray2021]|[Sarkozy et al](papers/sarkozyMutationalLandscapeGray2021)|[@albuquerqueEnhancingKnowledgeDiscovery2017; @rossiCodingGenomeSplenic2012]||
56
+|[STAT6](STAT6)|Tier 1 GE[@ritzRecurrentMutationsSTAT62009], FE[@mentzPARP14NovelTarget2022]|[Ritz et al](papers/ritzRecurrentMutationsSTAT62009)|[@yildizActivatingSTAT6Mutations2015]||
57
+|[TNFAIP3](TNFAIP3)|Tier 1 GE[@schmitzTNFAIP3A20Tumor2009], FE[@compagnoMutationsMultipleGenes2009]|[Schmitz et al](papers/schmitzTNFAIP3A20Tumor2009)|[@compagnoMutationsMultipleGenes2009; @drevalGeneticSubdivisionsFollicular2023; @rossiAlterationBIRC3Multiple2011]||
58
+|[TP53](TP53)|Tier 1 GE[@tiacciPervasiveMutationsJAKSTAT2018], FE[@katoUnderstandingFunctionstructureFunctionmutation2003]|[Tiacci et al](papers/tiacciPervasiveMutationsJAKSTAT2018)|[@beaLandscapeSomaticMutations2013; @morinFrequentMutationHistonemodifying2011; @rossiCodingGenomeSplenic2012; @wildaInactivationARFMDM2p53Pathway2004]||
59
+|[TRAF3](TRAF3)|Tier 1 GE[@ottoGeneticLesionsTRAF32012]|[Otto et al](papers/ottoGeneticLesionsTRAF32012)|[@pasqualucciAnalysisCodingGenome2011; @rossiAlterationBIRC3Multiple2011]||
60
+|[UBE2A](UBE2A)|Tier 1 GE[@reichelFlowSortingExome2015]|[Reichel et al](papers/reichelFlowSortingExome2015)|[@lohrDiscoveryPrioritizationSomatic2012]||
61
+|[WEE1](WEE1)|Tier 1 GE[@reichelFlowSortingExome2015]|[Reichel et al](papers/reichelFlowSortingExome2015)|[@schmitzGeneticsPathogenesisDiffuse2018]||
62
+|[XPO1](XPO1)|Tier 1 GE[@jardinRecurrentMutationsExportin2016], FE[@miloudiXPO1E571KMutationModifies2020]|[Jardin et al](papers/jardinRecurrentMutationsExportin2016)|[@mareschalWholeExomeSequencing2016]||
63
+|[ZFP36L1](ZFP36L1)|Tier 1 GE[@reichelFlowSortingExome2015], aSHM|[Reichel et al](papers/reichelFlowSortingExome2015)|[@morinFrequentMutationHistonemodifying2011; @paneaWholeGenomeLandscape2019]||
94 64
95
-## Tier 2 PMBL genes
65
+## Tier 2, low-confidence PMBL genes
96 66
97
-### *82 total*
67
+### *112 total*
98 68
99
-|Gene|Tier| First PMBL evidence | Other entities |
100
-|:-:|:-:|:--|:-|
101
-|[ABCA13](ABCA13)|2|[Sarkozy et al](papers/sarkozyMutationalLandscapeGray2021a)[@sarkozyMutationalLandscapeGray2021a]|[@spinaGeneticsNodalMarginal2016b]|
102
-|[ACTG1](ACTG1)|2|[Desch et al](papers/deschGenotypingCirculatingTumor2020)[@deschGenotypingCirculatingTumor2020]|[@spinaGeneticsNodalMarginal2016b; @hubschmannMutationalMechanismsShaping2021b]|
103
-|[AKAP6](AKAP6)|2|[Tiacci et al](papers/tiacciPervasiveMutationsJAKSTAT2018b)[@tiacciPervasiveMutationsJAKSTAT2018b]||
104
-|[ARIH2](ARIH2)|2|[Reichel et al](papers/reichelFlowSortingExome2015a)[@reichelFlowSortingExome2015a]||
105
-|[AXDND1](AXDND1)|2|[Gomez et al](papers/gomezUltraDeepSequencingReveals2023)[@gomezUltraDeepSequencingReveals2023]||
106
-|[BCL2](BCL2)|2|[Sarkozy et al](papers/sarkozyMutationalLandscapeGray2021a)[@sarkozyMutationalLandscapeGray2021a]|[@tanakaFrequentIncidenceSomatic1992; @burkhardtClinicalRelevanceMolecular2022b; @morinFrequentMutationHistonemodifying2011]|
107
-|[BCL7A](BCL7A)|2|[Reichel et al](papers/reichelFlowSortingExome2015a)[@reichelFlowSortingExome2015a]|[@krysiakRecurrentSomaticMutations2017b; @grandeGenomewideDiscoverySomatic2019; @zhangGeneticHeterogeneityDiffuse2013]|
108
-|[BIRC3](BIRC3)|2|[Duns et al](papers/dunsCharacterizationDLBCLPMBL2021b)[@dunsCharacterizationDLBCLPMBL2021b]|[@rossiAlterationBIRC3Multiple2011a; @beaLandscapeSomaticMutations2013; @arthurGenomewideDiscoverySomatic2018]|
109
-|[CCND3](CCND3)|2|[Desch et al](papers/deschGenotypingCirculatingTumor2020)[@deschGenotypingCirculatingTumor2020]|[@morinFrequentMutationHistonemodifying2011; @jalladesExomeSequencingIdentifies2017; @richterRecurrentMutationID32012a]|
110
-|[CDH2](CDH2)|2|[Desch et al](papers/deschGenotypingCirculatingTumor2020)[@deschGenotypingCirculatingTumor2020]||
111
-|[CDH5](CDH5)|2|[Gomez et al](papers/gomezUltraDeepSequencingReveals2023)[@gomezUltraDeepSequencingReveals2023]||
112
-|[CXCR5](CXCR5)|2|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019b)[@mottokIntegrativeGenomicAnalysis2019b]|[@schmitzGeneticsPathogenesisDiffuse2018a]|
113
-|[DGKB](DGKB)|2|[Tiacci et al](papers/tiacciPervasiveMutationsJAKSTAT2018b)[@tiacciPervasiveMutationsJAKSTAT2018b]||
114
-|[DMD](DMD)|2|[Reichel et al](papers/reichelFlowSortingExome2015a)[@reichelFlowSortingExome2015a]||
115
-|[DNAH12](DNAH12)|2|[Wienand et al](papers/wienandGenomicAnalysesFlowsorted2019b)[@wienandGenomicAnalysesFlowsorted2019b]||
116
-|[EGR1](EGR1)|2|[Reichel et al](papers/reichelFlowSortingExome2015a)[@reichelFlowSortingExome2015a]|[@rossiCodingGenomeSplenic2012c; @krysiakRecurrentSomaticMutations2017b]|
117
-|[EPHA7](EPHA7)|2|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019b)[@mottokIntegrativeGenomicAnalysis2019b]|[@zhangGeneticHeterogeneityDiffuse2013]|
118
-|[EZR](EZR)|2|[Desch et al](papers/deschGenotypingCirculatingTumor2020)[@deschGenotypingCirculatingTumor2020]||
119
-|[FOXO1](FOXO1)|2|[Duns et al](papers/dunsCharacterizationDLBCLPMBL2021b)[@dunsCharacterizationDLBCLPMBL2021b]|[@schmitzBurkittLymphomaPathogenesis2012; @morinFrequentMutationHistonemodifying2011]|
120
-|[GCSAM](GCSAM)|2|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019b)[@mottokIntegrativeGenomicAnalysis2019b]||
121
-|[GPR126](GPR126)|2|[Weniger et al](papers/wenigerMutationsTumorSuppressor2006a)[@wenigerMutationsTumorSuppressor2006a]||
122
-|[HECW2](HECW2)|2|[Reichel et al](papers/reichelFlowSortingExome2015a)[@reichelFlowSortingExome2015a]||
123
-|[HELLS](HELLS)|2|[Reichel et al](papers/reichelFlowSortingExome2015a)[@reichelFlowSortingExome2015a]||
124
-|[HIST1H2BC](HIST1H2BC)|2|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019b)[@mottokIntegrativeGenomicAnalysis2019b]|[@krysiakRecurrentSomaticMutations2017b; @lohrDiscoveryPrioritizationSomatic2012a]|
125
-|[HIST1H3B](HIST1H3B)|2|[Reichel et al](papers/reichelFlowSortingExome2015a)[@reichelFlowSortingExome2015a]|[@lohrDiscoveryPrioritizationSomatic2012a]|
126
-|[HIST1H4C](HIST1H4C)|2|[Reichel et al](papers/reichelFlowSortingExome2015a)[@reichelFlowSortingExome2015a]||
127
-|[HIST1H4E](HIST1H4E)|2|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019b)[@mottokIntegrativeGenomicAnalysis2019b]||
128
-|[HIST1H4J](HIST1H4J)|2|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019b)[@mottokIntegrativeGenomicAnalysis2019b]|[@paneaWholeGenomeLandscape2019]|
129
-|[HLA-A](HLA-A)|2|[Desch et al](papers/deschGenotypingCirculatingTumor2020)[@deschGenotypingCirculatingTumor2020]|[@lohrDiscoveryPrioritizationSomatic2012a]|
130
-|[HLA-C](HLA-C)|2|[Gomez et al](papers/gomezUltraDeepSequencingReveals2023)[@gomezUltraDeepSequencingReveals2023]|[@chapuyMolecularSubtypesDiffuse2018b]|
131
-|[HRNR](HRNR)|2|[Duns et al](papers/dunsCharacterizationDLBCLPMBL2021b)[@dunsCharacterizationDLBCLPMBL2021b]||
132
-|[IGLL5](IGLL5)|2|[Desch et al](papers/deschGenotypingCirculatingTumor2020)[@deschGenotypingCirculatingTumor2020]|[@paneaWholeGenomeLandscape2019; @russler-germainMutationsAssociatedProgression2023b; @chapuyMolecularSubtypesDiffuse2018b]|
133
-|[IKBKB](IKBKB)|2|[Wienand et al](papers/wienandGenomicAnalysesFlowsorted2019b)[@wienandGenomicAnalysesFlowsorted2019b]|[@reddyGeneticFunctionalDrivers2017; @rossiAlterationBIRC3Multiple2011a]|
134
-|[IL13RA1](IL13RA1)|2|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019b)[@mottokIntegrativeGenomicAnalysis2019b]||
135
-|[IL1RAPL2](IL1RAPL2)|2|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019b)[@mottokIntegrativeGenomicAnalysis2019b]||
136
-|[IRF2BP2](IRF2BP2)|2|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019b)[@mottokIntegrativeGenomicAnalysis2019b]||
137
-|[IRF4](IRF4)|2|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019b)[@mottokIntegrativeGenomicAnalysis2019b]|[@morinFrequentMutationHistonemodifying2011]|
138
-|[ITGB2](ITGB2)|2|||
139
-|[ITPR3](ITPR3)|2|[Tiacci et al](papers/tiacciPervasiveMutationsJAKSTAT2018b)[@tiacciPervasiveMutationsJAKSTAT2018b]|[@loveGeneticLandscapeMutations2012]|
140
-|[JUNB](JUNB)|2|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019b)[@mottokIntegrativeGenomicAnalysis2019b]|[@reddyGeneticFunctionalDrivers2017]|
141
-|[KLF2](KLF2)|2|[Desch et al](papers/deschGenotypingCirculatingTumor2020)[@deschGenotypingCirculatingTumor2020]|[@pasqualucciAnalysisCodingGenome2011; @jalladesExomeSequencingIdentifies2017]|
142
-|[KMT2D](KMT2D)|2|[Desch et al](papers/deschGenotypingCirculatingTumor2020)[@deschGenotypingCirculatingTumor2020]|[@beaLandscapeSomaticMutations2013; @morinFrequentMutationHistonemodifying2011; @rossiCodingGenomeSplenic2012c; @grandeGenomewideDiscoverySomatic2019]|
143
-|[LIMD2](LIMD2)|2|[Gomez et al](papers/gomezUltraDeepSequencingReveals2023)[@gomezUltraDeepSequencingReveals2023]||
144
-|[LPHN3](LPHN3)|2|[Duns et al](papers/dunsCharacterizationDLBCLPMBL2021b)[@dunsCharacterizationDLBCLPMBL2021b]||
145
-|[LRRN3](LRRN3)|2|[Sarkozy et al](papers/sarkozyMutationalLandscapeGray2021a)[@sarkozyMutationalLandscapeGray2021a]|[@zhangGeneticHeterogeneityDiffuse2013]|
146
-|[MAGEC2](MAGEC2)|2|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019b)[@mottokIntegrativeGenomicAnalysis2019b]||
147
-|[MCL1](MCL1)|2|[Duns et al](papers/dunsCharacterizationDLBCLPMBL2021b)[@dunsCharacterizationDLBCLPMBL2021b]|[@reddyGeneticFunctionalDrivers2017; @paneaWholeGenomeLandscape2019]|
148
-|[MFHAS1](MFHAS1)|2|[Sarkozy et al](papers/sarkozyMutationalLandscapeGray2021a)[@sarkozyMutationalLandscapeGray2021a]||
149
-|[MPDZ](MPDZ)|2|[Reichel et al](papers/reichelFlowSortingExome2015a)[@reichelFlowSortingExome2015a]|[@morinMutationalStructuralAnalysis2013]|
150
-|[MYB](MYB)|2|[Desch et al](papers/deschGenotypingCirculatingTumor2020)[@deschGenotypingCirculatingTumor2020]|[@reddyGeneticFunctionalDrivers2017]|
151
-|[MYC](MYC)|2|[Duns et al](papers/dunsCharacterizationDLBCLPMBL2021b)[@dunsCharacterizationDLBCLPMBL2021b]|[@pasqualucciHypermutationMultipleProtooncogenes2001a; @johnstonCmycHypermutationBurkitt1992; @jalladesExomeSequencingIdentifies2017]|
152
-|[NCOR2](NCOR2)|2|[Sarkozy et al](papers/sarkozyMutationalLandscapeGray2021a)[@sarkozyMutationalLandscapeGray2021a]|[@schmitzBurkittLymphomaPathogenesis2012; @spinaGeneticsNodalMarginal2016b]|
153
-|[NEK1](NEK1)|2|[Reichel et al](papers/reichelFlowSortingExome2015a)[@reichelFlowSortingExome2015a]||
154
-|[NFKB2](NFKB2)|2|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019b)[@mottokIntegrativeGenomicAnalysis2019b]|[@reddyGeneticFunctionalDrivers2017]|
155
-|[NSD2](NSD2)|2||[@zhangGeneticHeterogeneityDiffuse2013; @beaLandscapeSomaticMutations2013]|
156
-|[NUP214](NUP214)|2|[Tiacci et al](papers/tiacciPervasiveMutationsJAKSTAT2018b)[@tiacciPervasiveMutationsJAKSTAT2018b]||
157
-|[OR13C2](OR13C2)|2|[Gomez et al](papers/gomezUltraDeepSequencingReveals2023)[@gomezUltraDeepSequencingReveals2023]||
158
-|[PCBP1](PCBP1)|2||[@schmitzBurkittLymphomaPathogenesis2012]|
159
-|[PCDH7](PCDH7)|2||[@zhangGeneticHeterogeneityDiffuse2013]|
160
-|[PRUNE2](PRUNE2)|2|[Tiacci et al](papers/tiacciPervasiveMutationsJAKSTAT2018b)[@tiacciPervasiveMutationsJAKSTAT2018b]||
161
-|[RANBP2](RANBP2)|2|[Reichel et al](papers/reichelFlowSortingExome2015a)[@reichelFlowSortingExome2015a]||
162
-|[RBM38](RBM38)|2|[Wienand et al](papers/wienandGenomicAnalysesFlowsorted2019b)[@wienandGenomicAnalysesFlowsorted2019b]||
163
-|[RDH12](RDH12)|2|||
164
-|[RELN](RELN)|2|[Sarkozy et al](papers/sarkozyMutationalLandscapeGray2021a)[@sarkozyMutationalLandscapeGray2021a]|[@zhangGeneticHeterogeneityDiffuse2013]|
165
-|[RFTN1](RFTN1)|2|[Duns et al](papers/dunsCharacterizationDLBCLPMBL2021b)[@dunsCharacterizationDLBCLPMBL2021b]|[@arthurGenomewideDiscoverySomatic2018]|
166
-|[RGS1](RGS1)|2|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019b)[@mottokIntegrativeGenomicAnalysis2019b]|[@zhangGeneticHeterogeneityDiffuse2013]|
167
-|[SCN9A](SCN9A)|2|||
168
-|[SENP7](SENP7)|2|[Reichel et al](papers/reichelFlowSortingExome2015a)[@reichelFlowSortingExome2015a]||
169
-|[SETD5](SETD5)|2|[Tiacci et al](papers/tiacciPervasiveMutationsJAKSTAT2018b)[@tiacciPervasiveMutationsJAKSTAT2018b]|[@reddyGeneticFunctionalDrivers2017]|
170
-|[SETDB1](SETDB1)|2|[Reichel et al](papers/reichelFlowSortingExome2015a)[@reichelFlowSortingExome2015a]||
171
-|[SIAH2](SIAH2)|2|[Reichel et al](papers/reichelFlowSortingExome2015a)[@reichelFlowSortingExome2015a]|[@hubschmannMutationalMechanismsShaping2021b]|
172
-|[SMAD3](SMAD3)|2|||
173
-|[STAT5B](STAT5B)|2|[Tiacci et al](papers/tiacciPervasiveMutationsJAKSTAT2018b)[@tiacciPervasiveMutationsJAKSTAT2018b]|[@zhangGeneticHeterogeneityDiffuse2013]|
174
-|[STRAP](STRAP)|2|||
175
-|[TBC1D15](TBC1D15)|2|[Reichel et al](papers/reichelFlowSortingExome2015a)[@reichelFlowSortingExome2015a]||
176
-|[TICRR](TICRR)|2|[Reichel et al](papers/reichelFlowSortingExome2015a)[@reichelFlowSortingExome2015a]||
177
-|[TNIP1](TNIP1)|2|[Tiacci et al](papers/tiacciPervasiveMutationsJAKSTAT2018b)[@tiacciPervasiveMutationsJAKSTAT2018b]||
178
-|[TRIP11](TRIP11)|2|[Reichel et al](papers/reichelFlowSortingExome2015a)[@reichelFlowSortingExome2015a]|[@zhangGeneticHeterogeneityDiffuse2013]|
179
-|[VMP1](VMP1)|2|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019b)[@mottokIntegrativeGenomicAnalysis2019b]||
180
-|[WDR87](WDR87)|2|[Duns et al](papers/dunsCharacterizationDLBCLPMBL2021b)[@dunsCharacterizationDLBCLPMBL2021b]||
181
-|[ZCCHC11](ZCCHC11)|2|[Tiacci et al](papers/tiacciPervasiveMutationsJAKSTAT2018b)[@tiacciPervasiveMutationsJAKSTAT2018b]||
182
-|[ZNF217](ZNF217)|2|[Reichel et al](papers/reichelFlowSortingExome2015a)[@reichelFlowSortingExome2015a]|[@hubschmannMutationalMechanismsShaping2021b]|
69
+|Gene|Summary| First PMBL study | Other entities | QC result |
70
+|:-:|:--:|:-:|:-|:-|
71
+|[ABCA13](ABCA13)|Tier 2 GE[@sarkozyMutationalLandscapeGray2021]|[Sarkozy et al](papers/sarkozyMutationalLandscapeGray2021)|[@spinaGeneticsNodalMarginal2016]||
72
+|[ACTG1](ACTG1)|Tier 2 GE[@deschGenotypingCirculatingTumor2020], aSHM|[Desch et al](papers/deschGenotypingCirculatingTumor2020)|[@fanComprehensiveCharacterizationDriver2020; @hubschmannMutationalMechanismsShaping2021; @spinaGeneticsNodalMarginal2016]||
73
+|[AKAP6](AKAP6)|Tier 2 GE[@tiacciPervasiveMutationsJAKSTAT2018]|[Tiacci et al](papers/tiacciPervasiveMutationsJAKSTAT2018)|||
74
+|[ARIH2](ARIH2)|Tier 2 GE[@reichelFlowSortingExome2015]|[Reichel et al](papers/reichelFlowSortingExome2015)|||
75
+|[AXDND1](AXDND1)|Tier 2 GE[@gomezUltraDeepSequencingReveals2023]|[Gomez et al](papers/gomezUltraDeepSequencingReveals2023)|||
76
+|[BCL2](BCL2)|Tier 2 GE[@sarkozyMutationalLandscapeGray2021], aSHM|[Sarkozy et al](papers/sarkozyMutationalLandscapeGray2021)|[@burkhardtClinicalRelevanceMolecular2022; @morinFrequentMutationHistonemodifying2011; @tanakaFrequentIncidenceSomatic1992]||
77
+|[BCL7A](BCL7A)|Tier 2 GE[@reichelFlowSortingExome2015], FE[@balinas-gaviraFrequentMutationsAminoterminal2020], aSHM|[Reichel et al](papers/reichelFlowSortingExome2015)|[@grandeGenomewideDiscoverySomatic2019; @krysiakRecurrentSomaticMutations2017; @morinFrequentMutationHistonemodifying2011]||
78
+|[BIRC3](BIRC3)|Tier 2 GE[@dunsCharacterizationDLBCLPMBL2021], aSHM|[Duns et al](papers/dunsCharacterizationDLBCLPMBL2021)|[@arthurGenomewideDiscoverySomatic2018; @beaLandscapeSomaticMutations2013; @rossiAlterationBIRC3Multiple2011]||
79
+|[CCND3](CCND3)|Tier 2 GE[@deschGenotypingCirculatingTumor2020], FE[@schmitzBurkittLymphomaPathogenesis2012]|[Desch et al](papers/deschGenotypingCirculatingTumor2020)|[@jalladesExomeSequencingIdentifies2017; @morinFrequentMutationHistonemodifying2011; @richterRecurrentMutationID32012]||
80
+|[CDH2](CDH2)|Tier 2 GE[@deschGenotypingCirculatingTumor2020]|[Desch et al](papers/deschGenotypingCirculatingTumor2020)|||
81
+|[CDH5](CDH5)|Tier 2 GE[@gomezUltraDeepSequencingReveals2023]|[Gomez et al](papers/gomezUltraDeepSequencingReveals2023)|||
82
+|[CDKN2A](CDKN2A)|Tier 2 GE, FE[@kannengiesserFunctionalStructuralGenetic2009]||[@grandeGenomewideDiscoverySomatic2019; @morinMutationalStructuralAnalysis2013; @spinaGeneticsNodalMarginal2016]||
83
+|[CHD8](CHD8)|Tier 2 GE||[@grandeGenomewideDiscoverySomatic2019]||
84
+|[CXCR5](CXCR5)|Tier 2 GE[@mottokIntegrativeGenomicAnalysis2019]|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019)|[@schmitzGeneticsPathogenesisDiffuse2018]||
85
+|[DGKB](DGKB)|Tier 2 GE[@tiacciPervasiveMutationsJAKSTAT2018]|[Tiacci et al](papers/tiacciPervasiveMutationsJAKSTAT2018)|||
86
+|[DMD](DMD)|Tier 2 GE[@reichelFlowSortingExome2015]|[Reichel et al](papers/reichelFlowSortingExome2015)|||
87
+|[DNAH12](DNAH12)|Tier 2 GE[@wienandGenomicAnalysesFlowsorted2019]|[Wienand et al](papers/wienandGenomicAnalysesFlowsorted2019)|||
88
+|[EGR1](EGR1)|Tier 2 GE[@reichelFlowSortingExome2015]|[Reichel et al](papers/reichelFlowSortingExome2015)|[@krysiakRecurrentSomaticMutations2017; @rossiCodingGenomeSplenic2012]||
89
+|[EPHA7](EPHA7)|Tier 2 GE[@mottokIntegrativeGenomicAnalysis2019]|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019)|[@zhangGeneticHeterogeneityDiffuse2013]||
90
+|[ETS1](ETS1)|Tier 2 GE, aSHM||[@morinFrequentMutationHistonemodifying2011; @paneaWholeGenomeLandscape2019]||
91
+|[EWSR1](EWSR1)|Tier 2 GE||[@pararajalingamCodingNoncodingDrivers2020]||
92
+|[EZR](EZR)|Tier 2 GE[@deschGenotypingCirculatingTumor2020], aSHM|[Desch et al](papers/deschGenotypingCirculatingTumor2020)|||
93
+|[FAS](FAS)|Tier 2 GE, FE[@wangFasFADDDeathDomain2010]||[@morinFrequentMutationHistonemodifying2011; @schollMutationsRegionFAS2007; @spinaGeneticsNodalMarginal2016]||
94
+|[FAT1](FAT1)|Tier 2 GE||[@spinaGeneticsNodalMarginal2016]||
95
+|[FAT4](FAT4)|Tier 2 GE||[@morinMutationalStructuralAnalysis2013; @parryWholeExomeSequencing2013; @zhangGenomicLandscapeMantle2014]||
96
+|[FOXO1](FOXO1)|Tier 2 GE[@dunsCharacterizationDLBCLPMBL2021], FE[@trinhAnalysisFOXO1Mutations]|[Duns et al](papers/dunsCharacterizationDLBCLPMBL2021)|[@morinFrequentMutationHistonemodifying2011; @schmitzBurkittLymphomaPathogenesis2012]||
97
+|[GCSAM](GCSAM)|Tier 2 GE[@mottokIntegrativeGenomicAnalysis2019]|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019)|||
98
+|[GPR126](GPR126)|Tier 2 GE[@wenigerMutationsTumorSuppressor2006]|[Weniger et al](papers/wenigerMutationsTumorSuppressor2006)|||
99
+|[HECW2](HECW2)|Tier 2 GE[@reichelFlowSortingExome2015]|[Reichel et al](papers/reichelFlowSortingExome2015)|||
100
+|[HELLS](HELLS)|Tier 2 GE[@reichelFlowSortingExome2015]|[Reichel et al](papers/reichelFlowSortingExome2015)|||
101
+|[HIST1H1C](HIST1H1C)|Tier 2 GE, aSHM||[@morinFrequentMutationHistonemodifying2011; @paneaWholeGenomeLandscape2019]||
102
+|[HIST1H1D](HIST1H1D)|Tier 2 GE, aSHM||[@jalladesExomeSequencingIdentifies2017; @krysiakRecurrentSomaticMutations2017; @morinMutationalStructuralAnalysis2013]||
103
+|[HIST1H2BC](HIST1H2BC)|Tier 2 GE[@mottokIntegrativeGenomicAnalysis2019], aSHM|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019)|[@krysiakRecurrentSomaticMutations2017; @lohrDiscoveryPrioritizationSomatic2012]||
104
+|[HIST1H3B](HIST1H3B)|Tier 2 GE[@reichelFlowSortingExome2015], aSHM|[Reichel et al](papers/reichelFlowSortingExome2015)|[@lohrDiscoveryPrioritizationSomatic2012]||
105
+|[HIST1H4C](HIST1H4C)|Tier 2 GE[@reichelFlowSortingExome2015]|[Reichel et al](papers/reichelFlowSortingExome2015)|||
106
+|[HIST1H4E](HIST1H4E)|Tier 2 GE[@mottokIntegrativeGenomicAnalysis2019]|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019)|||
107
+|[HIST1H4J](HIST1H4J)|Tier 2 GE[@mottokIntegrativeGenomicAnalysis2019]|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019)|[@paneaWholeGenomeLandscape2019]||
108
+|[HLA-A](HLA-A)|Tier 2 GE[@deschGenotypingCirculatingTumor2020], FE[@fangazioGeneticMechanismsHLAI2021]|[Desch et al](papers/deschGenotypingCirculatingTumor2020)|[@lohrDiscoveryPrioritizationSomatic2012]||
109
+|[HLA-C](HLA-C)|Tier 2 GE[@gomezUltraDeepSequencingReveals2023], FE[@fangazioGeneticMechanismsHLAI2021]|[Gomez et al](papers/gomezUltraDeepSequencingReveals2023)|[@chapuyMolecularSubtypesDiffuse2018]||
110
+|[HRNR](HRNR)|Tier 2 GE[@dunsCharacterizationDLBCLPMBL2021]|[Duns et al](papers/dunsCharacterizationDLBCLPMBL2021)|||
111
+|[IGLL5](IGLL5)|Tier 2 GE[@deschGenotypingCirculatingTumor2020], aSHM|[Desch et al](papers/deschGenotypingCirculatingTumor2020)|[@chapuyMolecularSubtypesDiffuse2018; @paneaWholeGenomeLandscape2019; @russler-germainMutationsAssociatedProgression2023]||
112
+|[IKBKB](IKBKB)|Tier 2 GE[@wienandGenomicAnalysesFlowsorted2019]|[Wienand et al](papers/wienandGenomicAnalysesFlowsorted2019)|[@reddyGeneticFunctionalDrivers2017; @rossiAlterationBIRC3Multiple2011]||
113
+|[IL13RA1](IL13RA1)|Tier 2 GE[@mottokIntegrativeGenomicAnalysis2019]|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019)|||
114
+|[IL1RAPL2](IL1RAPL2)|Tier 2 GE[@mottokIntegrativeGenomicAnalysis2019]|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019)|||
115
+|[IRF2BP2](IRF2BP2)|Tier 2 GE[@mottokIntegrativeGenomicAnalysis2019]|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019)|||
116
+|[IRF4](IRF4)|Tier 2 GE[@mottokIntegrativeGenomicAnalysis2019], aSHM|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019)|[@drevalGeneticSubdivisionsFollicular2023; @morinFrequentMutationHistonemodifying2011]||
117
+|[ITGB2](ITGB2)|Tier 2 GE||||
118
+|[ITPR3](ITPR3)|Tier 2 GE[@tiacciPervasiveMutationsJAKSTAT2018]|[Tiacci et al](papers/tiacciPervasiveMutationsJAKSTAT2018)|[@loveGeneticLandscapeMutations2012]||
119
+|[JUNB](JUNB)|Tier 2 GE[@mottokIntegrativeGenomicAnalysis2019]|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019)|[@lohrDiscoveryPrioritizationSomatic2012]||
120
+|[KLF2](KLF2)|Tier 2 GE[@deschGenotypingCirculatingTumor2020], aSHM|[Desch et al](papers/deschGenotypingCirculatingTumor2020)|[@drevalGeneticSubdivisionsFollicular2023; @jalladesExomeSequencingIdentifies2017; @pasqualucciAnalysisCodingGenome2011]||
121
+|[KMT2D](KMT2D)|Tier 2 GE[@deschGenotypingCirculatingTumor2020], FE[@zhangDisruptionKMT2DPerturbs2015]|[Desch et al](papers/deschGenotypingCirculatingTumor2020)|[@beaLandscapeSomaticMutations2013; @grandeGenomewideDiscoverySomatic2019; @morinFrequentMutationHistonemodifying2011; @rossiCodingGenomeSplenic2012]||
122
+|[LIMD2](LIMD2)|Tier 2 GE[@gomezUltraDeepSequencingReveals2023]|[Gomez et al](papers/gomezUltraDeepSequencingReveals2023)|||
123
+|[LPHN3](LPHN3)|Tier 2 GE[@dunsCharacterizationDLBCLPMBL2021]|[Duns et al](papers/dunsCharacterizationDLBCLPMBL2021)|||
124
+|[LRRN3](LRRN3)|Tier 2 GE[@sarkozyMutationalLandscapeGray2021]|[Sarkozy et al](papers/sarkozyMutationalLandscapeGray2021)|[@zhangGeneticHeterogeneityDiffuse2013]||
125
+|[MAGEC2](MAGEC2)|Tier 2 GE[@mottokIntegrativeGenomicAnalysis2019]|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019)|||
126
+|[MCL1](MCL1)|Tier 2 GE[@dunsCharacterizationDLBCLPMBL2021]|[Duns et al](papers/dunsCharacterizationDLBCLPMBL2021)|[@paneaWholeGenomeLandscape2019; @reddyGeneticFunctionalDrivers2017]||
127
+|[MFHAS1](MFHAS1)|Tier 2 GE[@sarkozyMutationalLandscapeGray2021]|[Sarkozy et al](papers/sarkozyMutationalLandscapeGray2021)|||
128
+|[MPDZ](MPDZ)|Tier 2 GE[@reichelFlowSortingExome2015]|[Reichel et al](papers/reichelFlowSortingExome2015)|[@morinMutationalStructuralAnalysis2013]||
129
+|[MYB](MYB)|Tier 2 GE[@deschGenotypingCirculatingTumor2020]|[Desch et al](papers/deschGenotypingCirculatingTumor2020)|[@reddyGeneticFunctionalDrivers2017]||
130
+|[MYC](MYC)|Tier 2 GE[@dunsCharacterizationDLBCLPMBL2021], FE[@freieGermlinePointMutation2024], aSHM|[Duns et al](papers/dunsCharacterizationDLBCLPMBL2021)|[@jalladesExomeSequencingIdentifies2017; @johnstonCmycHypermutationBurkitt1992; @pasqualucciHypermutationMultipleProtooncogenes2001]||
131
+|[NCOR2](NCOR2)|Tier 2 GE[@sarkozyMutationalLandscapeGray2021]|[Sarkozy et al](papers/sarkozyMutationalLandscapeGray2021)|[@schmitzBurkittLymphomaPathogenesis2012; @spinaGeneticsNodalMarginal2016]||
132
+|[NEK1](NEK1)|Tier 2 GE[@reichelFlowSortingExome2015]|[Reichel et al](papers/reichelFlowSortingExome2015)|||
133
+|[NFKB2](NFKB2)|Tier 2 GE[@mottokIntegrativeGenomicAnalysis2019]|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019)|[@reddyGeneticFunctionalDrivers2017]||
134
+|[NSD2](NSD2)|Tier 2 GE||[@beaLandscapeSomaticMutations2013; @zhangGeneticHeterogeneityDiffuse2013]||
135
+|[NUP214](NUP214)|Tier 2 GE[@tiacciPervasiveMutationsJAKSTAT2018]|[Tiacci et al](papers/tiacciPervasiveMutationsJAKSTAT2018)|||
136
+|[OR13C2](OR13C2)|Tier 2 GE[@gomezUltraDeepSequencingReveals2023]|[Gomez et al](papers/gomezUltraDeepSequencingReveals2023)|||
137
+|[OSBPL10](OSBPL10)|Tier 2 GE, aSHM||[@zhangGeneticHeterogeneityDiffuse2013]||
138
+|[P2RY8](P2RY8)|Tier 2 GE, FE[@muppidiLossSignalingGa132014]||[@drevalGeneticSubdivisionsFollicular2023; @lohrDiscoveryPrioritizationSomatic2012; @muppidiLossSignalingGa132014]||
139
+|[PCBP1](PCBP1)|Tier 2 GE||[@schmitzBurkittLymphomaPathogenesis2012]||
140
+|[PCDH7](PCDH7)|Tier 2 GE[@gomezUltraDeepSequencingReveals2023]|[Gomez et al](papers/gomezUltraDeepSequencingReveals2023)|[@zhangGeneticHeterogeneityDiffuse2013]||
141
+|[PCLO](PCLO)|Tier 2 GE||[@lohrDiscoveryPrioritizationSomatic2012]||
142
+|[PHIP](PHIP)|Tier 2 GE||||
143
+|[PRKDC](PRKDC)|Tier 2 GE||[@hubschmannMutationalMechanismsShaping2021; @schmitzGeneticsPathogenesisDiffuse2018]||
144
+|[PRUNE2](PRUNE2)|Tier 2 GE[@tiacciPervasiveMutationsJAKSTAT2018]|[Tiacci et al](papers/tiacciPervasiveMutationsJAKSTAT2018)|||
145
+|[PTPRD](PTPRD)|Tier 2 GE||[@drevalGeneticSubdivisionsFollicular2023; @spinaGeneticsNodalMarginal2016]||
146
+|[RANBP2](RANBP2)|Tier 2 GE[@reichelFlowSortingExome2015]|[Reichel et al](papers/reichelFlowSortingExome2015)|||
147
+|[RBM38](RBM38)|Tier 2 GE[@wienandGenomicAnalysesFlowsorted2019]|[Wienand et al](papers/wienandGenomicAnalysesFlowsorted2019)|||
148
+|[RDH12](RDH12)|Tier 2 GE[@gomezUltraDeepSequencingReveals2023]|[Gomez et al](papers/gomezUltraDeepSequencingReveals2023)|||
149
+|[RELN](RELN)|Tier 2 GE[@sarkozyMutationalLandscapeGray2021]|[Sarkozy et al](papers/sarkozyMutationalLandscapeGray2021)|[@zhangGeneticHeterogeneityDiffuse2013]||
150
+|[RFTN1](RFTN1)|Tier 2 GE[@dunsCharacterizationDLBCLPMBL2021], aSHM|[Duns et al](papers/dunsCharacterizationDLBCLPMBL2021)|[@arthurGenomewideDiscoverySomatic2018]||
151
+|[RGS1](RGS1)|Tier 2 GE[@mottokIntegrativeGenomicAnalysis2019]|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019)|[@zhangGeneticHeterogeneityDiffuse2013]||
152
+|[RHOA](RHOA)|Tier 2 GE, FE[@ohayreInactivatingMutationsGNA132016]||[@richterRecurrentMutationID32012; @zhangGeneticHeterogeneityDiffuse2013]||
153
+|[S1PR2](S1PR2)|Tier 2 GE, FE[@muppidiLossSignalingGa132014], aSHM||[@drevalGeneticSubdivisionsFollicular2023; @morinFrequentMutationHistonemodifying2011; @muppidiLossSignalingGa132014]||
154
+|[SCN9A](SCN9A)|Tier 2 GE[@gomezUltraDeepSequencingReveals2023]|[Gomez et al](papers/gomezUltraDeepSequencingReveals2023)|||
155
+|[SENP7](SENP7)|Tier 2 GE[@reichelFlowSortingExome2015]|[Reichel et al](papers/reichelFlowSortingExome2015)|||
156
+|[SETD5](SETD5)|Tier 2 GE[@tiacciPervasiveMutationsJAKSTAT2018]|[Tiacci et al](papers/tiacciPervasiveMutationsJAKSTAT2018)|[@reddyGeneticFunctionalDrivers2017]||
157
+|[SETDB1](SETDB1)|Tier 2 GE[@reichelFlowSortingExome2015]|[Reichel et al](papers/reichelFlowSortingExome2015)|||
158
+|[SIAH2](SIAH2)|Tier 2 GE[@reichelFlowSortingExome2015]|[Reichel et al](papers/reichelFlowSortingExome2015)|[@hubschmannMutationalMechanismsShaping2021]||
159
+|[SIN3A](SIN3A)|Tier 2 GE||[@chapuyMolecularSubtypesDiffuse2018; @grandeGenomewideDiscoverySomatic2019; @rossiCodingGenomeSplenic2012]||
160
+|[SMAD3](SMAD3)|Tier 2 GE||||
161
+|[SMARCA2](SMARCA2)|Tier 2 GE||||
162
+|[SMARCA4](SMARCA4)|Tier 2 GE, FE[@fernandoFunctionalCharacterizationSMARCA42020]||[@krysiakRecurrentSomaticMutations2017; @nadeuGenomicEpigenomicInsights2020b; @reddyGeneticFunctionalDrivers2017; @richterRecurrentMutationID32012]||
163
+|[STAT3](STAT3)|Tier 2 GE, FE[@huNovelMissenseM206K2013]||[@morinFrequentMutationHistonemodifying2011]||
164
+|[STAT5B](STAT5B)|Tier 2 GE[@tiacciPervasiveMutationsJAKSTAT2018]|[Tiacci et al](papers/tiacciPervasiveMutationsJAKSTAT2018)|[@reddyGeneticFunctionalDrivers2017]||
165
+|[STRAP](STRAP)|Tier 2 GE[@gomezUltraDeepSequencingReveals2023]|[Gomez et al](papers/gomezUltraDeepSequencingReveals2023)|||
166
+|[TAP1](TAP1)|Tier 2 GE||[@schmitzGeneticsPathogenesisDiffuse2018]||
167
+|[TBC1D15](TBC1D15)|Tier 2 GE[@reichelFlowSortingExome2015]|[Reichel et al](papers/reichelFlowSortingExome2015)|||
168
+|[TBL1XR1](TBL1XR1)|Tier 2 GE, FE[@venturuttiTBL1XR1MutationsDrive2020]||[@drevalGeneticSubdivisionsFollicular2023; @lohrDiscoveryPrioritizationSomatic2012; @rossiCodingGenomeSplenic2012]||
169
+|[TCF3](TCF3)|Tier 2 GE||[@schmitzBurkittLymphomaPathogenesis2012]||
170
+|[TET3](TET3)|Tier 2 GE||||
171
+|[TICRR](TICRR)|Tier 2 GE[@reichelFlowSortingExome2015]|[Reichel et al](papers/reichelFlowSortingExome2015)|||
172
+|[TMSB4X](TMSB4X)|Tier 2 GE, aSHM||[@drevalGeneticSubdivisionsFollicular2023; @reddyGeneticFunctionalDrivers2017]||
173
+|[TNFRSF1B](TNFRSF1B)|Tier 2 GE||||
174
+|[TNIP1](TNIP1)|Tier 2 GE[@tiacciPervasiveMutationsJAKSTAT2018]|[Tiacci et al](papers/tiacciPervasiveMutationsJAKSTAT2018)|||
175
+|[TRIP11](TRIP11)|Tier 2 GE[@reichelFlowSortingExome2015]|[Reichel et al](papers/reichelFlowSortingExome2015)|[@zhangGeneticHeterogeneityDiffuse2013]||
176
+|[UBR5](UBR5)|Tier 2 GE||[@albuquerqueEnhancingKnowledgeDiscovery2017; @pararajalingamCodingNoncodingDrivers2020]||
177
+|[UNC5C](UNC5C)|Tier 2 GE||[@lohrDiscoveryPrioritizationSomatic2012]||
178
+|[VMP1](VMP1)|Tier 2 GE[@mottokIntegrativeGenomicAnalysis2019]|[Mottok et al](papers/mottokIntegrativeGenomicAnalysis2019)|||
179
+|[VPS13B](VPS13B)|Tier 2 GE||||
180
+|[WDR87](WDR87)|Tier 2 GE[@dunsCharacterizationDLBCLPMBL2021]|[Duns et al](papers/dunsCharacterizationDLBCLPMBL2021)|||
181
+|[ZCCHC11](ZCCHC11)|Tier 2 GE[@tiacciPervasiveMutationsJAKSTAT2018]|[Tiacci et al](papers/tiacciPervasiveMutationsJAKSTAT2018)|||
182
+|[ZNF217](ZNF217)|Tier 2 GE[@reichelFlowSortingExome2015]|[Reichel et al](papers/reichelFlowSortingExome2015)|[@hubschmannMutationalMechanismsShaping2021]||
183 183
184
-## Tier 3 PMBL genes
184
+## Tier 3, retired PMBL genes
185 185
186 186
### *0 total*
187 187
188
-|Gene|Tier| First PMBL evidence | Other entities |
189
-|:-:|:-:|:--|:-|
188
+|Gene|Summary| First PMBL study | Other entities | QC result |
189
+|:-:|:--:|:-:|:-|:-|
190 190
191 191
192 192
# References
PMBL_sankey1-1.svg
... ...
@@ -0,0 +1 @@
1
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transform="translate(526.6666666666666,650.3448275862067)" id="node-1" class="node"><rect fill="#4e79a7" width="10" height="11.379310344827445"/></g><g y="0" x="790" transform="translate(790,0)" id="node-2" class="node"><rect fill="#f28e2c" width="10" height="216.20689655172427"/></g><g y="693.1034482758619" x="526.6666666666666" transform="translate(526.6666666666666,693.1034482758619)" id="node-3" class="node"><rect fill="#e15759" width="10" height="56.89655172413791"/></g><g y="226.20689655172427" x="790" transform="translate(790,226.20689655172427)" id="node-4" class="node"><rect fill="#76b7b2" width="10" height="443.79310344827593"/></g><g y="175" x="526.6666666666666" transform="translate(526.6666666666666,175)" id="node-5" class="node"><rect fill="#59a14f" width="10" height="62.58620689655169"/></g><g y="0" x="526.6666666666666" transform="translate(526.6666666666666,0)" id="node-6" class="node"><rect fill="#edc949" width="10" height="165"/></g><g y="671.7241379310342" x="526.6666666666666" transform="translate(526.6666666666666,671.7241379310342)" id="node-7" class="node"><rect fill="#af7aa1" width="10" height="11.379310344827672"/></g><g y="247.5862068965517" x="526.6666666666666" transform="translate(526.6666666666666,247.5862068965517)" id="node-8" class="node"><rect fill="#ff9da7" width="10" height="39.82758620689651"/></g><g y="297.4137931034482" x="526.6666666666666" transform="translate(526.6666666666666,297.4137931034482)" id="node-9" class="node"><rect fill="#9c755f" width="10" height="73.96551724137925"/></g><g y="381.37931034482745" x="526.6666666666666" transform="translate(526.6666666666666,381.37931034482745)" id="node-10" class="node"><rect fill="#bab0ab" width="10" height="119.48275862068965"/></g><g y="510.8620689655171" x="526.6666666666666" transform="translate(526.6666666666666,510.8620689655171)" id="node-11" class="node"><rect fill="#4e79a7" width="10" height="62.58620689655186"/></g><g y="583.448275862069" x="526.6666666666666" transform="translate(526.6666666666666,583.448275862069)" id="node-12" class="node"><rect fill="#f28e2c" width="10" height="56.896551724137794"/></g><g y="0" x="0" transform="translate(0,0)" id="node-13" class="node"><rect fill="#e15759" width="10" height="659.9999999999999"/></g><g y="0" x="263.3333333333333" transform="translate(263.3333333333333,0)" id="node-14" class="node"><rect fill="#76b7b2" width="10" height="580.3448275862067"/></g><g y="625.9889886795344" x="263.3333333333333" transform="translate(263.3333333333333,625.9889886795344)" id="node-15" class="node"><rect fill="#59a14f" width="10" height="11.379310344827445"/></g><g y="650.126964418254" x="263.3333333333333" transform="translate(263.3333333333333,650.126964418254)" id="node-16" class="node"><rect fill="#edc949" width="10" height="56.89655172413791"/></g><g y="604.6096783347068" x="263.3333333333333" transform="translate(263.3333333333333,604.6096783347068)" id="node-17" class="node"><rect fill="#af7aa1" width="10" height="11.379310344827445"/></g></g><g font-size="14" font-family="sans-serif" class="node-labels"><text text-anchor="end" dy="0.35em" y="656.0344827586205" x="520.6666666666666">Otto 2012</text><text text-anchor="end" dy="0.35em" y="108.10344827586214" x="784">Tier 1</text><text text-anchor="end" dy="0.35em" y="721.5517241379308" x="520.6666666666666">Desch 2020</text><text text-anchor="end" dy="0.35em" y="448.10344827586226" x="784">Tier 2</text><text text-anchor="end" dy="0.35em" y="206.29310344827584" x="520.6666666666666">Sarkozy 2021</text><text text-anchor="end" dy="0.35em" y="82.5" x="520.6666666666666">Reichel 2015</text><text text-anchor="end" dy="0.35em" y="677.413793103448" x="520.6666666666666">Weniger 2006</text><text text-anchor="end" dy="0.35em" y="267.49999999999994" x="520.6666666666666">Wienand 2019</text><text text-anchor="end" dy="0.35em" y="334.3965517241378" x="520.6666666666666">Duns 2021</text><text text-anchor="end" dy="0.35em" y="441.12068965517227" x="520.6666666666666">Mottok 2019</text><text text-anchor="end" dy="0.35em" y="542.155172413793" x="520.6666666666666">Gomez 2023</text><text text-anchor="end" dy="0.35em" y="611.8965517241379" x="520.6666666666666">Tiacci 2018</text><text text-anchor="start" dy="0.35em" y="329.99999999999994" x="16">PMBL genes</text><text text-anchor="start" dy="0.35em" y="290.1724137931034" x="279.3333333333333">PMBL-exome</text><text text-anchor="start" dy="0.35em" y="631.6786438519481" x="279.3333333333333">PMBL-Sanger</text><text text-anchor="start" dy="0.35em" y="678.575240280323" x="279.3333333333333">PMBL-panel</text><text text-anchor="start" dy="0.35em" y="610.2993335071205" x="279.3333333333333">PMBL-Array/Sanger</text></g><g stroke-opacity="0.5" fill="none" class="links"><g style="mix-blend-mode: multiply;" class="link"><path stroke-width="11.379310344827585" stroke="#f28e2c" 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SETD1B.md
... ...
@@ -19,7 +19,7 @@ timeline
19 19
20 20
|Entity|Tier|Description |
21 21
|:------:|:----:|--------------------------|
22
-|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene[@albuquerqueEnhancingKnowledgeDiscovery2017a; @reddyGeneticFunctionalDrivers2017; @schmitzGeneticsPathogenesisDiffuse2018a]|
22
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene[@albuquerqueEnhancingKnowledgeDiscovery2017; @reddyGeneticFunctionalDrivers2017; @schmitzGeneticsPathogenesisDiffuse2018]|
23 23
24 24
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
25 25
morinlab.bib
... ...
@@ -1,4 +1,777 @@
1
-@article{hodsonRegulationNormalBcell2016a,
1
+@article{miloudiXPO1E571KMutationModifies2020,
2
+ title = {{{XPO1E571K Mutation Modifies Exportin}} 1 {{Localisation}} and {{Interactome}} in {{B-cell Lymphoma}}},
3
+ author = {Miloudi, Hadjer and Bohers, Élodie and Guillonneau, François and Taly, Antoine and Gibouin, Vincent Cabaud and Viailly, Pierre-Julien and Jego, Gaëtan and Grumolato, Luca and Jardin, Fabrice and Sola, Brigitte},
4
+ date = {2020-09-30},
5
+ journaltitle = {Cancers},
6
+ shortjournal = {Cancers (Basel)},
7
+ volume = {12},
8
+ number = {10},
9
+ eprint = {33007990},
10
+ eprinttype = {pmid},
11
+ pages = {2829},
12
+ issn = {2072-6694},
13
+ doi = {10.3390/cancers12102829},
14
+ abstract = {The XPO1 gene encodes exportin 1 (XPO1) that controls the nuclear export of cargo proteins and RNAs. Almost 25\% of primary mediastinal B-cell lymphoma (PMBL) and classical Hodgkin lymphoma (cHL) cases harboured a recurrent XPO1 point mutation (NM\_003400, chr2:g61718472C{$>$}T) resulting in the E571K substitution within the hydrophobic groove of the protein, the site of cargo binding. We investigated the impact of the XPO1E571K mutation using PMBL/cHL cells having various XPO1 statuses and CRISPR-Cas9-edited cells in which the E571K mutation was either introduced or knocked-out. We first confirmed that the mutation was present in both XPO1 mRNA and protein. We observed that the mutation did not modify the export capacity but rather the subcellular localisation of XPO1 itself. In particular, mutant XPO1 bound to importin β1 modified the nuclear export/import dynamics of relevant cargoes.},
15
+ langid = {english},
16
+ pmcid = {PMC7600770},
17
+ keywords = {B-cell lymphoma,CRISPR–Cas9,importin β1,indirect immunofluorescence,nuclear export,nuclear import,proteomics,proximity ligation assay,XPO1/CRM1},
18
+ file = {/Users/rmorin/Zotero/storage/IQBJHDK5/Miloudi et al. - 2020 - XPO1E571K Mutation Modifies Exportin 1 Localisatio.pdf}
19
+}
20
+
21
+@article{asmarGenomewideProfilingIdentifies2013,
22
+ title = {Genome-Wide Profiling Identifies a {{DNA}} Methylation Signature That Associates with {{TET2}} Mutations in Diffuse Large {{B-cell}} Lymphoma},
23
+ author = {Asmar, Fazila and Punj, Vasu and Christensen, Jesper and Pedersen, Marianne T. and Pedersen, Anja and Nielsen, Anders B. and Hother, Christoffer and Ralfkiaer, Ulrik and Brown, Peter and Ralfkiaer, Elisabeth and Helin, Kristian and Grønbæk, Kirsten},
24
+ date = {2013-12},
25
+ journaltitle = {Haematologica},
26
+ shortjournal = {Haematologica},
27
+ volume = {98},
28
+ number = {12},
29
+ eprint = {23831920},
30
+ eprinttype = {pmid},
31
+ pages = {1912--1920},
32
+ issn = {1592-8721},
33
+ doi = {10.3324/haematol.2013.088740},
34
+ abstract = {The discovery that the Ten-Eleven Translocation (TET) hydroxylases cause DNA demethylation has fundamentally changed the notion of how DNA methylation is regulated. Clonal analysis of the hematopoetic stem cell compartment suggests that TET2 mutations can be early events in hematologic cancers and recent investigations have shown TET2 mutations in diffuse large B-cell lymphoma. However, the detection rates and the types of TET2 mutations vary, and the relation to global methylation patterns has not been investigated. Here, we show TET2 mutations in 12 of 100 diffuse large B-cell lymphomas with 7\% carrying loss-of-function and 5\% carrying missense mutations. Genome-wide methylation profiling using 450K Illumina arrays identified 315 differentially methylated genes between TET2 mutated and TET2 wild-type cases. TET2 mutations are primarily associated with hypermethylation within CpG islands (70\%; P{$<$}0.0001), and at CpG-rich promoters (60\%; P{$<$}0.0001) of genes involved in hematopoietic differentiation and cellular development. Hypermethylated loci in TET2 mutated samples overlap with the bivalent (H3K27me3/H3K4me3) silencing mark in human embryonic stem cells (P=1.5×10(-30)). Surprisingly, gene expression profiling showed that only 11\% of the hypermethylated genes were down-regulated, among which there were several genes previously suggested to be tumor suppressors. A meta-analysis suggested that the 35 hypermethylated and down-regulated genes are associated with the activated B-cell-like type of diffuse large B-cell lymphoma in other studies. In conclusion, our data suggest that TET2 mutations may cause aberrant methylation mainly of genes involved in hematopoietic development, which are silenced but poised for activation in human embryonic stem cells.},
35
+ langid = {english},
36
+ pmcid = {PMC3856967},
37
+ keywords = {Aged,Dioxygenases,DNA Methylation,DNA-Binding Proteins,Female,Gene Expression Profiling,Genome-Wide Association Study,Humans,Lymphoma Large B-Cell Diffuse,Male,Middle Aged,Mutation,Proto-Oncogene Proteins},
38
+ file = {/Users/rmorin/Zotero/storage/AIIBGXFW/Asmar et al. - 2013 - Genome-wide profiling identifies a DNA methylation.pdf}
39
+}
40
+
41
+@article{mentzPARP14NovelTarget2022,
42
+ title = {{{PARP14}} Is a Novel Target in {{STAT6}} Mutant Follicular Lymphoma},
43
+ author = {Mentz, Michael and Keay, William and Strobl, Carolin Dorothea and Antoniolli, Martina and Adolph, Louisa and Heide, Michael and Lechner, Axel and Haebe, Sarah and Osterode, Elisa and Kridel, Robert and Ziegenhain, Christoph and Wange, Lucas Esteban and Hildebrand, Johannes Adrian and Shree, Tanaya and Silkenstedt, Elisabeth and Staiger, Annette M. and Ott, German and Horn, Heike and Szczepanowski, Monika and Richter, Julia and Levy, Ronald and Rosenwald, Andreas and Enard, Wolfgang and Zimber-Strobl, Ursula and family=Bergwelt-Baildon, given=Michael, prefix=von, useprefix=true and Hiddemann, Wolfgang and Klapper, Wolfram and Schmidt-Supprian, Marc and Rudelius, Martina and Bararia, Deepak and Passerini, Verena and Weigert, Oliver},
44
+ date = {2022-09},
45
+ journaltitle = {Leukemia},
46
+ shortjournal = {Leukemia},
47
+ volume = {36},
48
+ number = {9},
49
+ eprint = {35851155},
50
+ eprinttype = {pmid},
51
+ pages = {2281--2292},
52
+ issn = {1476-5551},
53
+ doi = {10.1038/s41375-022-01641-x},
54
+ abstract = {The variable clinical course of follicular lymphoma (FL) is determined by the molecular heterogeneity of tumor cells and complex interactions within the tumor microenvironment (TME). IL-4 producing follicular helper T cells (TFH) are critical components of the FL TME. Binding of IL-4 to IL-4R on FL cells activates JAK/STAT signaling. We identified STAT6 mutations (STAT6MUT) in 13\% of FL (N\,=\,33/258), all clustered within the DNA binding domain. Gene expression data and immunohistochemistry showed upregulation of IL-4/STAT6 target genes in STAT6MUT FL, including CCL17, CCL22, and FCER2 (CD23). Functionally, STAT6MUT was gain-of-function by serial replating phenotype in pre-B CFU assays. Expression of STAT6MUT enhanced IL-4 induced FCER2/CD23, CCL17 and CCL22 expression and was associated with nuclear accumulation of pSTAT6. RNA sequencing identified PARP14 -a transcriptional switch and co-activator of STAT6- among the top differentially upregulated genes in IL-4 stimulated STAT6MUT lymphoma cells and in STAT6MUT primary FL cells. Quantitative chromatin immunoprecipitation (qChIP) demonstrated binding of STAT6MUT but not STAT6WT to the PARP14 promotor. Reporter assays showed increased IL-4 induced transactivation activity of STAT6MUT at the PARP14 promotor, suggesting a self-reinforcing regulatory circuit. Knock-down of PARP14 or PARP-inhibition abrogated the STAT6MUT gain-of-function phenotype. Thus, our results identify PARP14 as a novel therapeutic target in STAT6MUT FL.},
55
+ langid = {english},
56
+ pmcid = {PMC9417990},
57
+ keywords = {Humans,Immunohistochemistry,Interleukin-4,Lymphoma B-Cell,Lymphoma Follicular,Poly(ADP-ribose) Polymerases,STAT6 Transcription Factor,Transcriptional Activation,Tumor Microenvironment},
58
+ file = {/Users/rmorin/Zotero/storage/YQKA9DY3/Mentz et al. - 2022 - PARP14 is a novel target in STAT6 mutant follicula.pdf}
59
+}
60
+
61
+
62
+@article{cazzolaBiologicClinicalSignificance2013,
63
+ title = {Biologic and Clinical Significance of Somatic Mutations of {{SF3B1}} in Myeloid and Lymphoid Neoplasms},
64
+ author = {Cazzola, Mario and Rossi, Marianna and Malcovati, Luca and {Associazione Italiana per la Ricerca sul Cancro Gruppo Italiano Malattie Mieloproliferative}},
65
+ date = {2013-01-10},
66
+ journaltitle = {Blood},
67
+ shortjournal = {Blood},
68
+ volume = {121},
69
+ number = {2},
70
+ eprint = {23160465},
71
+ eprinttype = {pmid},
72
+ pages = {260--269},
73
+ issn = {1528-0020},
74
+ doi = {10.1182/blood-2012-09-399725},
75
+ abstract = {Precursor mRNA splicing is catalyzed by the spliceosome, a macromolecule composed of small nuclear RNAs associated with proteins. The SF3B1 gene encodes subunit 1 of the splicing factor 3b, which is important for anchoring the spliceosome to precursor mRNA. In 2011, whole-exome sequencing studies showed recurrent somatic mutations of SF3B1 and other genes of the RNA splicing machinery in patients with myelodysplastic syndrome or myelodysplastic/myeloproliferative neoplasm. SF3B1 mutations had a particularly high frequency among conditions characterized by ring sideroblasts, which is consistent with a causal relationship. SF3B1 mutants were also detected at a lower frequency in a variety of other tumor types. In chronic lymphocytic leukemia, SF3B1 was found to be the second most frequently mutated gene. In myelodysplastic syndromes, SF3B1 mutations appear to be founding genetic lesions and are associated with a low risk of leukemic evolution. In contrast, SF3B1 mutations have a lower incidence in early stages of chronic lymphocytic leukemia, are more common in advanced disease, and tend to be associated with poor prognosis, suggesting that they occur during clonal evolution of the disease. The assessment of SF3B1 mutation status may become innovative diagnostic and prognostic tools and the availability of spliceosome modulators opens novel therapeutic prospects.},
76
+ langid = {english},
77
+ pmcid = {PMC3790951},
78
+ keywords = {Humans,Mutation,Myelodysplastic-Myeloproliferative Diseases,Phosphoproteins,Ribonucleoprotein U2 Small Nuclear,RNA Splicing,RNA Splicing Factors},
79
+ file = {/Users/rmorin/Zotero/storage/GQCK6NWZ/Cazzola et al. - 2013 - Biologic and clinical significance of somatic muta.pdf}
80
+}
81
+
82
+@article{fernandoFunctionalCharacterizationSMARCA42020,
83
+ title = {Functional Characterization of {{SMARCA4}} Variants Identified by Targeted Exome-Sequencing of 131,668 Cancer Patients},
84
+ author = {Fernando, Tharu M. and Piskol, Robert and Bainer, Russell and Sokol, Ethan S. and Trabucco, Sally E. and Zhang, Qing and Trinh, Huong and Maund, Sophia and Kschonsak, Marc and Chaudhuri, Subhra and Modrusan, Zora and Januario, Thomas and Yauch, Robert L.},
85
+ date = {2020-11-03},
86
+ journaltitle = {Nature Communications},
87
+ shortjournal = {Nat Commun},
88
+ volume = {11},
89
+ number = {1},
90
+ eprint = {33144586},
91
+ eprinttype = {pmid},
92
+ pages = {5551},
93
+ issn = {2041-1723},
94
+ doi = {10.1038/s41467-020-19402-8},
95
+ abstract = {Genomic studies performed in cancer patients and tumor-derived cell lines have identified a high frequency of alterations in components of the mammalian switch/sucrose non-fermentable (mSWI/SNF or BAF) chromatin remodeling complex, including its core catalytic subunit, SMARCA4. Cells exhibiting loss of SMARCA4 rely on its paralog, SMARCA2, making SMARCA2 an attractive therapeutic target. Here we report the genomic profiling of solid tumors from 131,668 cancer patients, identifying 9434 patients with one or more SMARCA4 gene alterations. Homozygous SMARCA4 mutations were highly prevalent in certain tumor types, notably non-small cell lung cancer (NSCLC), and associated with reduced survival. The large sample size revealed previously uncharacterized hotspot missense mutations within the SMARCA4 helicase domain. Functional characterization of these mutations demonstrated markedly reduced remodeling activity. Surprisingly, a few SMARCA4 missense variants partially or fully rescued paralog dependency, underscoring that careful selection criteria must be employed to identify patients with inactivating, homozygous SMARCA4 missense mutations who may benefit from SMARCA2-targeted therapy.},
96
+ langid = {english},
97
+ pmcid = {PMC7609548},
98
+ keywords = {Carcinogenesis,Cell Line Tumor,Cell Proliferation,Chromatin,Cohort Studies,DNA Helicases,Exome Sequencing,Gene Expression Regulation Neoplastic,Homozygote,Humans,Mutation,Mutation Missense,Neoplasms,Nuclear Proteins,Nucleosomes,Protein Domains,Transcription Factors},
99
+ file = {/Users/rmorin/Zotero/storage/B9PHK4HX/Fernando et al. - 2020 - Functional characterization of SMARCA4 variants id.pdf}
100
+}
101
+
102
+@article{weberPiggyBacTransposonTools2019,
103
+ title = {{{PiggyBac}} Transposon Tools for Recessive Screening Identify {{B-cell}} Lymphoma Drivers in Mice},
104
+ author = {Weber, Julia and family=Rosa, given=Jorge, prefix=de la, useprefix=true and Grove, Carolyn S. and Schick, Markus and Rad, Lena and Baranov, Olga and Strong, Alexander and Pfaus, Anja and Friedrich, Mathias J. and Engleitner, Thomas and Lersch, Robert and Öllinger, Rupert and Grau, Michael and Menendez, Irene Gonzalez and Martella, Manuela and Kohlhofer, Ursula and Banerjee, Ruby and Turchaninova, Maria A. and Scherger, Anna and Hoffman, Gary J. and Hess, Julia and Kuhn, Laura B. and Ammon, Tim and Kim, Johnny and Schneider, Günter and Unger, Kristian and Zimber-Strobl, Ursula and Heikenwälder, Mathias and Schmidt-Supprian, Marc and Yang, Fengtang and Saur, Dieter and Liu, Pentao and Steiger, Katja and Chudakov, Dmitriy M. and Lenz, Georg and Quintanilla-Martinez, Leticia and Keller, Ulrich and Vassiliou, George S. and Cadiñanos, Juan and Bradley, Allan and Rad, Roland},
105
+ date = {2019-03-29},
106
+ journaltitle = {Nature Communications},
107
+ shortjournal = {Nat Commun},
108
+ volume = {10},
109
+ number = {1},
110
+ eprint = {30926791},
111
+ eprinttype = {pmid},
112
+ pages = {1415},
113
+ issn = {2041-1723},
114
+ doi = {10.1038/s41467-019-09180-3},
115
+ abstract = {B-cell lymphoma (BCL) is the most common hematologic malignancy. While sequencing studies gave insights into BCL genetics, identification of non-mutated cancer genes remains challenging. Here, we describe PiggyBac transposon tools and mouse models for recessive screening and show their application to study clonal B-cell lymphomagenesis. In a genome-wide screen, we discover BCL genes related to diverse molecular processes, including signaling, transcriptional regulation, chromatin regulation, or RNA metabolism. Cross-species analyses show the efficiency of the screen to pinpoint human cancer drivers altered by non-genetic mechanisms, including clinically relevant genes dysregulated epigenetically, transcriptionally, or post-transcriptionally in human BCL. We also describe a CRISPR/Cas9-based in vivo platform for BCL functional genomics, and validate discovered genes, such as Rfx7, a transcription factor, and Phip, a chromatin regulator, which suppress lymphomagenesis in mice. Our study gives comprehensive insights into the molecular landscapes of BCL and underlines the power of genome-scale screening to inform biology.},
116
+ langid = {english},
117
+ pmcid = {PMC6440946},
118
+ keywords = {Animals,Clone Cells,CRISPR-Cas Systems,DNA Transposable Elements,Gene Dosage,Gene Expression Regulation Neoplastic,Genes Neoplasm,Genes Tumor Suppressor,Genetic Association Studies,Genetic Testing,Humans,Loss of Heterozygosity,Lymphoma B-Cell,Mice Inbred C57BL,Mice Transgenic,Receptors Antigen B-Cell,Reproducibility of Results},
119
+ file = {/Users/rmorin/Zotero/storage/3HPDTVR9/Weber et al. - 2019 - PiggyBac transposon tools for recessive screening .pdf}
120
+}
121
+
122
+@article{pinyolInactivationRB1Mantlecell2007,
123
+ title = {Inactivation of {{RB1}} in Mantle-Cell Lymphoma Detected by Nonsense-Mediated {{mRNA}} Decay Pathway Inhibition and Microarray Analysis},
124
+ author = {Pinyol, Magda and Bea, Silvia and Plà, Laura and Ribrag, Vincent and Bosq, Jacques and Rosenwald, Andreas and Campo, Elias and Jares, Pedro},
125
+ date = {2007-06-15},
126
+ journaltitle = {Blood},
127
+ shortjournal = {Blood},
128
+ volume = {109},
129
+ number = {12},
130
+ eprint = {17332242},
131
+ eprinttype = {pmid},
132
+ pages = {5422--5429},
133
+ issn = {0006-4971},
134
+ doi = {10.1182/blood-2006-11-057208},
135
+ abstract = {Mantle-cell lymphoma (MCL) is genetically characterized by the translocation t(11;14)(q13;q32) and a high number of secondary chromosomal abnormalities. To identify genes inactivated in this lymphoma, we examined 5 MCL cell lines following a strategy previously described in tumors with microsatellite instability that is based on the combined inhibition of the nonsense-mediated mRNA decay pathway and gene-expression profiling. This approach, together with the design of a conservative algorithm for analysis of the results, allowed the identification of 3 genes carrying premature stop codons. These genes were p53 with a mutation previously described in JEKO-1, the leukocyte-derived arginine aminopeptidase (LRAP) gene in REC-1 that showed a new splicing isoform generating a premature stop codon, and RB1 in UPN-1 that contained an intragenic homozygous deletion resulting in a truncated transcript and total loss of protein expression. The new LRAP isoform was detected also in 2 primary MCLs, whereas inactivating intragenic deletions of RB1 were found in the primary tumor from which UPN-1 was derived and 1 additional blastoid MCL. These tumors carried a concomitant inactivation of p53, whereas p16INK4a was wild type. These results indicate for the first time that RB1 may be inactivated in aggressive MCL by intragenic deletions.},
136
+ langid = {english},
137
+ keywords = {Algorithms,Cell Line Tumor,Codon Nonsense,Dental Enamel Proteins,Gene Expression Profiling,Gene Silencing,Humans,Lymphoma Mantle-Cell,Microarray Analysis,Protein Isoforms,Retinoblastoma Protein,RNA Messenger,Tumor Suppressor Protein p53},
138
+ file = {/Users/rmorin/Zotero/storage/AVNQXD5P/Pinyol et al. - 2007 - Inactivation of RB1 in mantle-cell lymphoma detect.pdf}
139
+}
140
+
141
+@article{freieGermlinePointMutation2024,
142
+ title = {A Germline Point Mutation in the {{MYC-FBW7}} Phosphodegron Initiates Hematopoietic Malignancies},
143
+ author = {Freie, Brian and Carroll, Patrick A. and Varnum-Finney, Barbara J. and Ramsey, Erin L. and Ramani, Vijay and Bernstein, Irwin and Eisenman, Robert N.},
144
+ date = {2024-04-17},
145
+ journaltitle = {Genes \& Development},
146
+ shortjournal = {Genes Dev},
147
+ volume = {38},
148
+ number = {5-6},
149
+ eprint = {38565249},
150
+ eprinttype = {pmid},
151
+ pages = {253--272},
152
+ issn = {1549-5477},
153
+ doi = {10.1101/gad.351292.123},
154
+ abstract = {Oncogenic activation of MYC in cancers predominantly involves increased transcription rather than coding region mutations. However, MYC-dependent lymphomas frequently acquire point mutations in the MYC phosphodegron, including at threonine 58 (T58), where phosphorylation permits binding via the FBW7 ubiquitin ligase triggering MYC degradation. To understand how T58 phosphorylation functions in normal cell physiology, we introduced an alanine mutation at T58 (T58A) into the endogenous c-Myc locus in the mouse germline. While MYC-T58A mice develop normally, lymphomas and myeloid leukemias emerge in ∼60\% of adult homozygous T58A mice. We found that primitive hematopoietic progenitor cells from MYC-T58A mice exhibit aberrant self-renewal normally associated with hematopoietic stem cells (HSCs) and up-regulate a subset of MYC target genes important in maintaining stem/progenitor cell balance. In lymphocytes, genomic occupancy by MYC-T58A was increased at all promoters compared with WT MYC, while genes differentially expressed in a T58A-dependent manner were significantly more proximal to MYC-bound enhancers. MYC-T58A lymphocyte progenitors exhibited metabolic alterations and decreased activation of inflammatory and apoptotic pathways. Our data demonstrate that a single point mutation stabilizing MYC is sufficient to skew target gene expression, producing a profound gain of function in multipotential hematopoietic progenitors associated with self-renewal and initiation of lymphomas and leukemias.},
155
+ langid = {english},
156
+ pmcid = {PMC11065175},
157
+ keywords = {Animals,F-Box-WD Repeat-Containing Protein 7,FBW7,Germ Cells,Hematologic Neoplasms,hematopoiesis,Hematopoietic Stem Cells,leukemia,lymphoma,Lymphoma,Mice,MYC,Point Mutation,progenitor cells,protein stability,Proto-Oncogene Proteins c-myc,self-renewal},
158
+ file = {/Users/rmorin/Zotero/storage/5ZEIGWRU/Freie et al. - 2024 - A germline point mutation in the MYC-FBW7 phosphod.pdf}
159
+}
160
+
161
+@article{demosthenousLossFunctionMutations2015,
162
+ title = {Loss of Function Mutations in {{PTPN6}} Promote {{STAT3}} Deregulation via {{JAK3}} Kinase in Diffuse Large {{B-cell}} Lymphoma},
163
+ author = {Demosthenous, Christos and Han, Jing Jing and Hu, Guangzhen and Stenson, Mary and Gupta, Mamta},
164
+ date = {2015-12-29},
165
+ journaltitle = {Oncotarget},
166
+ shortjournal = {Oncotarget},
167
+ volume = {6},
168
+ number = {42},
169
+ eprint = {26565811},
170
+ eprinttype = {pmid},
171
+ pages = {44703--44713},
172
+ issn = {1949-2553},
173
+ doi = {10.18632/oncotarget.6300},
174
+ abstract = {PTPN6 (SHP1) is a tyrosine phosphatase that negatively controls the activity of multiple signaling pathways including STAT signaling, however role of mutated PTPN6 is not much known. Here we investigated whether PTPN6 might also be a potential target for diffuse large B cell lymphoma (DLBCL) and performed Sanger sequencing of the PTPN6 gene. We have identified missense mutations within PTPN6 (N225K and A550V) in 5\% (2/38) of DLBCL tumors. Site directed mutagenesis was performed to mutate wild type (WT) PTPN6 and stable cell lines were generated by lentiviral transduction of PTPN6(WT), PTPN6(N225K) and PTPN6(A550V) constructs, and effects of WT or mutated PTPN6 on STAT3 signaling were analyzed. WT PTPN6 dephosphorylated STAT3, but had no effect on STAT1, STAT5 or STAT6 phosphorylation. Both PTPN6 mutants were unable to inhibit constitutive, as well as cytokines induced STAT3 activation. Both PTPN6 mutants also demonstrated reduced tyrosine phosphatase activity and exhibited enhanced STAT3 transactivation activity. Intriguingly, a lack of direct binding between STAT3 and WT or mutated PTPN6 was observed. However, compared to WT PTPN6, cells expressing PTPN6 mutants exhibited increased binding between JAK3 and PTPN6 suggesting a more dynamic interaction of PTPN6 with upstream regulators of STAT3. Consistent with this notion, both the mutants demonstrated increased resistance to JAK3 inhibitor, WHIP-154 relative to WT PTPN6. Overall, this is the first study, which demonstrates that N225K and A550V PTPN6 mutations cause loss-of-function leading to JAK3 mediated deregulation of STAT3 pathway and uncovers a mechanism that tumor cells can use to control PTPN6 substrate specificity.},
175
+ langid = {english},
176
+ pmcid = {PMC4792586},
177
+ keywords = {Antineoplastic Agents,DLBCL,Drug Resistance Neoplasm,Gene Expression Regulation Enzymologic,Gene Expression Regulation Neoplastic,HEK293 Cells,Humans,JAK kinases,Janus Kinase 3,Lymphoma Large B-Cell Diffuse,Mutagenesis Site-Directed,Mutation Missense,Phosphorylation,Protein Binding,Protein Kinase Inhibitors,Protein Tyrosine Phosphatase Non-Receptor Type 6,PTPN6 mutations,Signal Transduction,STAT3,STAT3 Transcription Factor,Substrate Specificity,Transfection},
178
+ file = {/Users/rmorin/Zotero/storage/3T2BAVY4/Demosthenous et al. - 2015 - Loss of function mutations in PTPN6 promote STAT3 .pdf}
179
+}
180
+
181
+@article{grabinerDiverseArrayCancerassociated2014,
182
+ title = {A Diverse Array of Cancer-Associated {{MTOR}} Mutations Are Hyperactivating and Can Predict Rapamycin Sensitivity},
183
+ author = {Grabiner, Brian C. and Nardi, Valentina and Birsoy, Kıvanc and Possemato, Richard and Shen, Kuang and Sinha, Sumi and Jordan, Alexander and Beck, Andrew H. and Sabatini, David M.},
184
+ date = {2014-05},
185
+ journaltitle = {Cancer Discovery},
186
+ shortjournal = {Cancer Discov},
187
+ volume = {4},
188
+ number = {5},
189
+ eprint = {24631838},
190
+ eprinttype = {pmid},
191
+ pages = {554--563},
192
+ issn = {2159-8290},
193
+ doi = {10.1158/2159-8290.CD-13-0929},
194
+ abstract = {Genes encoding components of the PI3K-AKT-mTOR signaling axis are frequently mutated in cancer, but few mutations have been characterized in MTOR, the gene encoding the mTOR kinase. Using publicly available tumor genome sequencing data, we generated a comprehensive catalog of mTOR pathway mutations in cancer, identifying 33 MTOR mutations that confer pathway hyperactivation. The mutations cluster in six distinct regions in the C-terminal half of mTOR and occur in multiple cancer types, with one cluster particularly prominent in kidney cancer. The activating mutations do not affect mTOR complex assembly, but a subset reduces binding to the mTOR inhibitor DEPTOR. mTOR complex 1 (mTORC1) signaling in cells expressing various activating mutations remains sensitive to pharmacologic mTOR inhibition, but is partially resistant to nutrient deprivation. Finally, cancer cell lines with hyperactivating MTOR mutations display heightened sensitivity to rapamycin both in culture and in vivo xenografts, suggesting that such mutations confer mTOR pathway dependency.},
195
+ langid = {english},
196
+ pmcid = {PMC4012430},
197
+ keywords = {Animals,Antibiotics Antineoplastic,Cell Line Tumor,Databases Factual,HEK293 Cells,HeLa Cells,Humans,MAP Kinase Signaling System,MCF-7 Cells,Mechanistic Target of Rapamycin Complex 1,Mechanistic Target of Rapamycin Complex 2,Mice,Mice Nude,Multiprotein Complexes,Mutation,Neoplasms,Neoplasms Experimental,Protein Kinase Inhibitors,Sirolimus,TOR Serine-Threonine Kinases,Xenograft Model Antitumor Assays},
198
+ file = {/Users/rmorin/Zotero/storage/9XHKLA8X/Grabiner et al. - 2014 - A diverse array of cancer-associated MTOR mutation.pdf}
199
+}
200
+
201
+@article{trissalMIR142LossofFunctionMutations2018,
202
+ title = {{{MIR142 Loss-of-Function Mutations Derepress ASH1L}} to {{Increase HOXA Gene Expression}} and {{Promote Leukemogenesis}}},
203
+ author = {Trissal, Maria C. and Wong, Terrence N. and Yao, Juo-Chin and Ramaswamy, Rahul and Kuo, Iris and Baty, Jack and Sun, Yaping and Jih, Gloria and Parikh, Nishi and Berrien-Elliott, Melissa M. and Fehniger, Todd A. and Ley, Timothy J. and Maillard, Ivan and Reddy, Pavan R. and Link, Daniel C.},
204
+ date = {2018-07-01},
205
+ journaltitle = {Cancer Research},
206
+ shortjournal = {Cancer Res},
207
+ volume = {78},
208
+ number = {13},
209
+ eprint = {29724719},
210
+ eprinttype = {pmid},
211
+ pages = {3510--3521},
212
+ issn = {1538-7445},
213
+ doi = {10.1158/0008-5472.CAN-17-3592},
214
+ abstract = {Point mutations in the seed sequence of miR-142-3p are present in a subset of acute myelogenous leukemia (AML) and in several subtypes of B-cell lymphoma. Here, we show that mutations associated with AML result both in loss of miR-142-3p function and in decreased miR-142-5p expression. Mir142 loss altered the hematopoietic differentiation of multipotent hematopoietic progenitors, enhancing their myeloid potential while suppressing their lymphoid potential. During hematopoietic maturation, loss of Mir142 increased ASH1L protein expression and consequently resulted in the aberrant maintenance of Hoxa gene expression in myeloid-committed hematopoietic progenitors. Mir142 loss also enhanced the disease-initiating activity of IDH2-mutant hematopoietic cells in mice. Together these data suggest a novel model in which miR-142, through repression of ASH1L activity, plays a key role in suppressing HOXA9/A10 expression during normal myeloid differentiation. AML-associated loss-of-function mutations of MIR142 disrupt this negative signaling pathway, resulting in sustained HOXA9/A10 expression in myeloid progenitors/myeloblasts and ultimately contributing to leukemic transformation.Significance: These findings provide mechanistic insights into the role of miRNAs in leukemogenesis and hematopoietic stem cell function. Cancer Res; 78(13); 3510-21. ©2018 AACR.},
215
+ langid = {english},
216
+ pmcid = {PMC6030481},
217
+ keywords = {Animals,Bone Marrow,Carcinogenesis,Disease Models Animal,DNA-Binding Proteins,Gene Expression Regulation Leukemic,HEK293 Cells,Hematopoietic Stem Cells,Histone-Lysine N-Methyltransferase,Homeobox A10 Proteins,Homeodomain Proteins,Humans,Isocitrate Dehydrogenase,Leukemia Myeloid Acute,Loss of Function Mutation,Mice,Mice Inbred C57BL,Mice Knockout,MicroRNAs,Point Mutation,Receptor EphB2,Signal Transduction,Transcription Factors},
218
+ file = {/Users/rmorin/Zotero/storage/IZCJQVV3/Trissal et al. - 2018 - MIR142 Loss-of-Function Mutations Derepress ASH1L .pdf}
219
+}
220
+
221
+@article{depaoliMGASuppressorMYC2013,
222
+ title = {{{MGA}}, a Suppressor of {{MYC}}, Is Recurrently Inactivated in High Risk Chronic Lymphocytic Leukemia},
223
+ author = {De Paoli, Lorenzo and Cerri, Michaela and Monti, Sara and Rasi, Silvia and Spina, Valeria and Bruscaggin, Alessio and Greco, Mariangela and Ciardullo, Carmela and Famà, Rosella and Cresta, Stefania and Maffei, Rossana and Ladetto, Marco and Martini, Maurizio and Laurenti, Luca and Forconi, Francesco and Marasca, Roberto and Larocca, Luigi M. and Bertoni, Francesco and Gaidano, Gianluca and Rossi, Davide},
224
+ date = {2013-05},
225
+ journaltitle = {Leukemia \& Lymphoma},
226
+ shortjournal = {Leuk Lymphoma},
227
+ volume = {54},
228
+ number = {5},
229
+ eprint = {23039309},
230
+ eprinttype = {pmid},
231
+ pages = {1087--1090},
232
+ issn = {1029-2403},
233
+ doi = {10.3109/10428194.2012.723706},
234
+ langid = {english},
235
+ keywords = {Base Sequence,Basic Helix-Loop-Helix Transcription Factors,Gene Deletion,Humans,Leukemia Lymphocytic Chronic B-Cell,Mutation,Proto-Oncogene Proteins c-myc}
236
+}
237
+
238
+@article{scheffzekRasRasGAPComplexStructural1997,
239
+ title = {The {{Ras-RasGAP}} Complex: Structural Basis for {{GTPase}} Activation and Its Loss in Oncogenic {{Ras}} Mutants},
240
+ shorttitle = {The {{Ras-RasGAP}} Complex},
241
+ author = {Scheffzek, K. and Ahmadian, M. R. and Kabsch, W. and Wiesmüller, L. and Lautwein, A. and Schmitz, F. and Wittinghofer, A.},
242
+ date = {1997-07-18},
243
+ journaltitle = {Science (New York, N.Y.)},
244
+ shortjournal = {Science},
245
+ volume = {277},
246
+ number = {5324},
247
+ eprint = {9219684},
248
+ eprinttype = {pmid},
249
+ pages = {333--338},
250
+ issn = {0036-8075},
251
+ doi = {10.1126/science.277.5324.333},
252
+ abstract = {The three-dimensional structure of the complex between human H-Ras bound to guanosine diphosphate and the guanosine triphosphatase (GTPase)-activating domain of the human GTPase-activating protein p120GAP (GAP-334) in the presence of aluminum fluoride was solved at a resolution of 2.5 angstroms. The structure shows the partly hydrophilic and partly hydrophobic nature of the communication between the two molecules, which explains the sensitivity of the interaction toward both salts and lipids. An arginine side chain (arginine-789) of GAP-334 is supplied into the active site of Ras to neutralize developing charges in the transition state. The switch II region of Ras is stabilized by GAP-334, thus allowing glutamine-61 of Ras, mutation of which activates the oncogenic potential, to participate in catalysis. The structural arrangement in the active site is consistent with a mostly associative mechanism of phosphoryl transfer and provides an explanation for the activation of Ras by glycine-12 and glutamine-61 mutations. Glycine-12 in the transition state mimic is within van der Waals distance of both arginine-789 of GAP-334 and glutamine-61 of Ras, and even its mutation to alanine would disturb the arrangements of residues in the transition state.},
253
+ langid = {english},
254
+ keywords = {Aluminum Compounds,Amino Acid Sequence,Binding Sites,Catalysis,Cell Transformation Neoplastic,Crystallography X-Ray,Enzyme Activation,Fluorides,GTP Phosphohydrolases,GTP-Binding Proteins,GTPase-Activating Proteins,Guanosine Diphosphate,Guanosine Triphosphate,Humans,Models Molecular,Molecular Sequence Data,Mutation,Protein Conformation,Protein Structure Secondary,Proteins,ras GTPase-Activating Proteins,ras Proteins,Signal Transduction}
255
+}
256
+
257
+@article{pfeiferPTENLossDefines2013,
258
+ title = {{{PTEN}} Loss Defines a {{PI3K}}/{{AKT}} Pathway-Dependent Germinal Center Subtype of Diffuse Large {{B-cell}} Lymphoma},
259
+ author = {Pfeifer, Matthias and Grau, Michael and Lenze, Dido and Wenzel, Sören-Sebastian and Wolf, Annette and Wollert-Wulf, Brigitte and Dietze, Kerstin and Nogai, Hendrik and Storek, Benjamin and Madle, Hannelore and Dörken, Bernd and Janz, Martin and Dirnhofer, Stephan and Lenz, Peter and Hummel, Michael and Tzankov, Alexandar and Lenz, Georg},
260
+ date = {2013-07-23},
261
+ journaltitle = {Proceedings of the National Academy of Sciences of the United States of America},
262
+ shortjournal = {Proc Natl Acad Sci U S A},
263
+ volume = {110},
264
+ number = {30},
265
+ eprint = {23840064},
266
+ eprinttype = {pmid},
267
+ pages = {12420--12425},
268
+ issn = {1091-6490},
269
+ doi = {10.1073/pnas.1305656110},
270
+ abstract = {Diffuse large B-cell lymphoma (DLBCL) represents a heterogeneous diagnostic category with distinct molecular subtypes that can be defined by gene expression profiling. However, even within these defined subtypes, heterogeneity prevails. To further elucidate the pathogenesis of these entities, we determined the expression of the tumor suppressor phosphatase and tensin homolog (PTEN) in 248 primary DLBCL patient samples. These analyses revealed that loss of PTEN was detectable in 55\% of germinal center B-cell-like (GCB) DLBCLs, whereas this abnormality was found in only 14\% of non-GCB DLBCL patient samples. In GCB DLBCL, the PTEN status was inversely correlated with activation of the oncogenic PI3K/protein kinase B (AKT) pathway in both DLBCL cell lines and primary patient samples. Reexpression of PTEN induced cytotoxicity in PTEN-deficient GCB DLBCL cell line models by inhibiting PI3K/AKT signaling, indicating an addiction to this pathway in this subset of GCB DLBCLs. PI3K/AKT inhibition induced down-regulation of the transcription factor MYC. Reexpression of MYC rescued GCB DLBCL cells from PTEN-induced toxicity, identifying a regulatory mechanism of MYC expression in DLBCL. Finally, pharmacologic PI3K inhibition resulted in toxicity selectively in PTEN-deficient GCB DLBCL lines. Collectively, our results indicate that PTEN loss defines a PI3K/AKT-dependent GCB DLBCL subtype that is addicted to PI3K and MYC signaling and suggest that pharmacologic inhibition of PI3K might represent a promising therapeutic approach in these lymphomas.},
271
+ langid = {english},
272
+ pmcid = {PMC3725065},
273
+ keywords = {Cohort Studies,Humans,Lymphoma Large B-Cell Diffuse,lymphopedia,p38 Mitogen-Activated Protein Kinases,Phosphatidylinositol 3-Kinases,PTEN Phosphohydrolase,Signal Transduction},
274
+ file = {/Users/rmorin/Zotero/storage/XALB6YM6/Pfeifer et al. - 2013 - PTEN loss defines a PI3KAKT pathway-dependent ger.pdf}
275
+}
276
+
277
+@article{hodsonRegulationNormalBcell2016,
278
+ title = {Regulation of Normal {{B-cell}} Differentiation and Malignant {{B-cell}} Survival by {{OCT2}}},
279
+ author = {Hodson, Daniel J. and Shaffer, Arthur L. and Xiao, Wenming and Wright, George W. and Schmitz, Roland and Phelan, James D. and Yang, Yandan and Webster, Daniel E. and Rui, Lixin and Kohlhammer, Holger and Nakagawa, Masao and Waldmann, Thomas A. and Staudt, Louis M.},
280
+ date = {2016-04-05},
281
+ journaltitle = {Proceedings of the National Academy of Sciences of the United States of America},
282
+ shortjournal = {Proc Natl Acad Sci U S A},
283
+ volume = {113},
284
+ number = {14},
285
+ eprint = {26993806},
286
+ eprinttype = {pmid},
287
+ pages = {E2039-2046},
288
+ issn = {1091-6490},
289
+ doi = {10.1073/pnas.1600557113},
290
+ abstract = {The requirement for the B-cell transcription factor OCT2 (octamer-binding protein 2, encoded by Pou2f2) in germinal center B cells has proved controversial. Here, we report that germinal center B cells are formed normally after depletion of OCT2 in a conditional knockout mouse, but their proliferation is reduced and in vivo differentiation to antibody-secreting plasma cells is blocked. This finding led us to examine the role of OCT2 in germinal center-derived lymphomas. shRNA knockdown showed that almost all diffuse large B-cell lymphoma (DLBCL) cell lines are addicted to the expression of OCT2 and its coactivator OCA-B. Genome-wide chromatin immunoprecipitation (ChIP) analysis and gene-expression profiling revealed the broad transcriptional program regulated by OCT2 that includes the expression of STAT3, IL-10, ELL2, XBP1, MYC, TERT, and ADA. Importantly, genetic alteration of OCT2 is not a requirement for cellular addiction in DLBCL. However, we detected amplifications of the POU2F2 locus in DLBCL tumor biopsies and a recurrent mutation of threonine 223 in the DNA-binding domain of OCT2. This neomorphic mutation subtly alters the DNA-binding preference of OCT2, leading to the transactivation of noncanonical target genes including HIF1a and FCRL3 Finally, by introducing mutations designed to disrupt the OCT2-OCA-B interface, we reveal a requirement for this protein-protein interface that ultimately might be exploited therapeutically. Our findings, combined with the predominantly B-cell-restricted expression of OCT2 and the absence of a systemic phenotype in our knockout mice, suggest that an OCT2-targeted therapeutic strategy would be efficacious in both major subtypes of DLBCL while avoiding systemic toxicity.},
291
+ langid = {english},
292
+ pmcid = {PMC4833274},
293
+ keywords = {Animals,B-Lymphocytes,cancer biology,Cell Differentiation,Cell Line Tumor,Cell Survival,germinal center,lymphoma,Lymphoma Large B-Cell Diffuse,lymphopedia,Mice,Mice Knockout,Organic Cation Transport Proteins,Organic Cation Transporter 2},
294
+ file = {/Users/rmorin/Zotero/storage/IMDHB5EC/Hodson et al. - 2016 - Regulation of normal B-cell differentiation and ma.pdf;/Users/rmorin/Zotero/storage/YQRVND4V/Hodson et al. - 2016 - Regulation of normal B-cell differentiation and ma.pdf}
295
+}
296
+
297
+@article{gaoSGK1MutationsDLBCL2021,
298
+ title = {{{SGK1}} Mutations in {{DLBCL}} Generate Hyperstable Protein Neoisoforms That Promote {{AKT}} Independence},
299
+ author = {Gao, Jie and Sidiropoulou, Eirini and Walker, Ieuan and Krupka, Joanna A. and Mizielinski, Karol and Usheva, Zelvera and Samarajiwa, Shamith A. and Hodson, Daniel J.},
300
+ date = {2021-09-16},
301
+ journaltitle = {Blood},
302
+ shortjournal = {Blood},
303
+ volume = {138},
304
+ number = {11},
305
+ eprint = {33988691},
306
+ eprinttype = {pmid},
307
+ pages = {959--964},
308
+ issn = {1528-0020},
309
+ doi = {10.1182/blood.2020010432},
310
+ abstract = {Serum and glucocorticoid-regulated kinase 1 (SGK1) is one of the most frequently mutated genes in diffuse large B-cell lymphoma (DLBCL). However, little is known about its function or the consequence of its mutation. The frequent finding of truncating mutations has led to the widespread assumption that these represent loss-of-function variants and, accordingly, that SGK1 must act as a tumor suppressor. In this study, instead, the most common SGK1 mutations led to production of aberrantly spliced messenger RNA neoisoforms in which translation is initiated from downstream methionines. The resulting N-terminal truncated protein isoforms showed increased expression related to the exclusion of an N-terminal degradation domain. However, they retained a functional kinase domain, the overexpression of which rendered cells resistant to AKT inhibition, in part because of increased phosphorylation of GSK3B. These findings challenge the prevailing assumption that SGK1 is a tumor-suppressor gene in DLBCL and provide the impetus to explore further the pharmacological inhibition of SGK1 as a therapeutic strategy for DLBCL.},
311
+ langid = {english},
312
+ pmcid = {PMC8701626},
313
+ keywords = {Cells Cultured,Enzyme Stability,Humans,Immediate-Early Proteins,Lymphoma Large B-Cell Diffuse,lymphopedia,Phosphorylation,Protein Domains,Protein Isoforms,Protein Serine-Threonine Kinases,Proto-Oncogene Proteins c-akt},
314
+ file = {/Users/rmorin/Zotero/storage/J9ETHUL6/Gao et al. - 2021 - SGK1 mutations in DLBCL generate hyperstable prote.pdf;/Users/rmorin/Zotero/storage/TXGZRW9Y/Gao et al. - 2021 - SGK1 mutations in DLBCL generate hyperstable prote.pdf}
315
+}
316
+
317
+@article{gonzalez-rinconUnravelingTransformationFollicular2019,
318
+ title = {Unraveling Transformation of Follicular Lymphoma to Diffuse Large {{B-cell}} Lymphoma},
319
+ author = {González-Rincón, Julia and Méndez, Miriam and Gómez, Sagrario and García, Juan F. and Martín, Paloma and Bellas, Carmen and Pedrosa, Lucía and Rodríguez-Pinilla, Socorro M. and Camacho, Francisca I. and Quero, Cristina and Pérez-Callejo, David and Rueda, Antonio and Llanos, Marta and Gómez-Codina, José and Piris, Miguel A. and Montes-Moreno, Santiago and Bárcena, Carmen and Rodríguez-Abreu, Delvys and Menárguez, Javier and family=Cruz-Merino, given=Luis, prefix=de la, useprefix=true and Monsalvo, Silvia and Parejo, Consuelo and Royuela, Ana and Kwee, Ivo and Cascione, Luciano and Arribas, Alberto and Bertoni, Francesco and Mollejo, Manuela and Provencio, Mariano and Sánchez-Beato, Margarita},
320
+ date = {2019},
321
+ journaltitle = {PloS One},
322
+ shortjournal = {PLoS One},
323
+ volume = {14},
324
+ number = {2},
325
+ eprint = {30802265},
326
+ eprinttype = {pmid},
327
+ pages = {e0212813},
328
+ issn = {1932-6203},
329
+ doi = {10.1371/journal.pone.0212813},
330
+ abstract = {Follicular lymphoma (FL) is an indolent but largely incurable disease. Some patients suffer histological transformation to a more aggressive subtype with poorer prognosis. This study aimed to improve our understanding of the genetics underlying FL histological transformation, and to identify genetic drivers or promoters of the transformation by elucidating the differences between FL samples from patients who did and did not transform. We conducted targeted massive parallel sequencing of 22 pre-transformed FL/transformed diffuse large B-cell lymphoma pairs and 20 diagnostic samples from non-transformed FL patients. Additionally, 22 matched samples from 11 transformed FL patients (pre-transformed FL and diffuse large B-cell lymphoma) and 9 non-transformed FLs were studied for copy number variation using SNP arrays. We identified recurrently mutated genes that were enriched at transformation, most notably LRP1B, GNA13 and POU2AF1, which have roles in B-cell differentiation, GC architecture and migration. Mutations in POU2AF1 might be associated with lower levels of expression, were more frequent in transformed FLs, and seemed to be specific to transformed- compared with de novo-diffuse large B-cell lymphomas. Pre-transformed FLs carried more mutations per sample and had greater subclonal heterogeneity than non-transformed FLs. Finally, we identified four mutated genes in FL samples that differed between patients who did and did not transform: NOTCH2, DTX1, UBE2A and HIST1H1E. The presence of mutations in these genes was associated with shorter time to transformation when mutated in the FL biopsies. This information might be useful for identifying patients at higher risk of transformation.},
331
+ langid = {english},
332
+ pmcid = {PMC6388933},
333
+ keywords = {Adult,Aged,B-Lymphocytes,Biopsy,Cell Differentiation,Cell Transformation Neoplastic,Female,Follow-Up Studies,Humans,Lymphoma Follicular,Lymphoma Large B-Cell Diffuse,Male,Middle Aged,Mutation,Neoplasm Proteins},
334
+ file = {/Users/rmorin/Zotero/storage/BBLFASN6/González-Rincón et al. - 2019 - Unraveling transformation of follicular lymphoma t.pdf}
335
+}
336
+
337
+@article{jungnickelClonalDeleteriousMutations2000,
338
+ title = {Clonal Deleterious Mutations in the {{IkappaBalpha}} Gene in the Malignant Cells in {{Hodgkin}}'s Lymphoma},
339
+ author = {Jungnickel, B. and Staratschek-Jox, A. and Bräuninger, A. and Spieker, T. and Wolf, J. and Diehl, V. and Hansmann, M. L. and Rajewsky, K. and Küppers, R.},
340
+ date = {2000-01-17},
341
+ journaltitle = {The Journal of Experimental Medicine},
342
+ shortjournal = {J Exp Med},
343
+ volume = {191},
344
+ number = {2},
345
+ eprint = {10637284},
346
+ eprinttype = {pmid},
347
+ pages = {395--402},
348
+ issn = {0022-1007},
349
+ doi = {10.1084/jem.191.2.395},
350
+ abstract = {Members of the nuclear factor (NF)-kappaB family of transcription factors play a crucial role in cellular activation, immune responses, and oncogenesis. In most cells, they are kept inactive in the cytosol by complex formation with members of the inhibitor of NF-kappaB (IkappaB) family, whose degradation activates NF-kappaB in response to diverse stimuli. In Hodgkin's lymphoma (HL), high constitutive nuclear activity of NF-kappaB is characteristic of the malignant Hodgkin and Reed-Sternberg (H/RS) cells, which occur at low number in a background of nonneoplastic inflammatory cells. In single H/RS cells micromanipulated from histological sections of HL, we detect clonal deleterious somatic mutations in the IkappaBalpha gene in two of three Epstein-Barr virus (EBV)-negative cases but not in two EBV-positive cases (in which a viral oncogene may account for NF-kappaB activation). There was no evidence for IkappaBalpha mutations in two non-HL entities or in normal germinal center B cells. This study establishes deleterious IkappaBalpha mutations as the first recurrent genetic defect found in H/RS cells, indicating a role of IkappaBalpha defects in the pathogenesis of HL and implying that IkappaBalpha is a tumor suppressor gene.},
351
+ langid = {english},
352
+ pmcid = {PMC2195754},
353
+ keywords = {Adult,Child,DNA-Binding Proteins,Female,Gene Deletion,Hodgkin Disease,Humans,I-kappa B Proteins,Male,NF-KappaB Inhibitor alpha,Tumor Cells Cultured},
354
+ file = {/Users/rmorin/Zotero/storage/CABELY4P/Jungnickel et al. - 2000 - Clonal deleterious mutations in the IkappaBalpha g.pdf}
355
+}
356
+
357
+@article{kuoRolePIM1Ibrutinibresistant2016,
358
+ title = {The Role of {{PIM1}} in the Ibrutinib-Resistant {{ABC}} Subtype of Diffuse Large {{B-cell}} Lymphoma},
359
+ author = {Kuo, Hsu-Ping and Ezell, Scott A. and Hsieh, Sidney and Schweighofer, Karl J. and Cheung, Leo Wk and Wu, Shiquan and Apatira, Mutiah and Sirisawad, Mint and Eckert, Karl and Liang, Yu and Hsu, Jeff and Chen, Chun-Te and Beaupre, Darrin and Chang, Betty Y.},
360
+ date = {2016},
361
+ journaltitle = {American Journal of Cancer Research},
362
+ shortjournal = {Am J Cancer Res},
363
+ volume = {6},
364
+ number = {11},
365
+ eprint = {27904766},
366
+ eprinttype = {pmid},
367
+ pages = {2489--2501},
368
+ issn = {2156-6976},
369
+ abstract = {Diffuse large B cell lymphoma (DLBCL) is a heterogeneous lymphoma and the most common subtype of non-Hodgkin lymphoma, accounting for roughly 30\% of newly diagnosed cases in the United States. DLBCL can be separated into the activated B cell-like (ABC) and germinal center B cell-like (GCB) subtypes, with distinct gene expression profiles, oncogenic aberrations, and clinical outcomes. ABC-DLBCL is characterized by chronically active B-cell receptor (BCR) signaling that can be modulated by Bruton's tyrosine kinase (BTK) activity. Thus, BTK serves as an attractive therapeutic target in this type of B-cell malignancy. Ibrutinib, a first-in-class, orally available covalent BTK inhibitor, has demonstrated clinical activity in several B-cell leukemias and lymphomas. A phase 1/2 clinical trial of single-agent ibrutinib in relapsed and refractory DLBCL patients revealed an overall response rate of 37\% in ABC-DLBCL patients. However, responses to kinase-directed therapies are often limited by emerging resistance mechanisms that bypass the therapeutic target. Here we report the discovery of point mutations within the kinase PIM1 that reduce sensitivity to ibrutinib in ABC-DLBCL. These mutations stabilize PIM1 and affect upstream regulators and downstream targets of NF-κB signaling. The introduction of mutant PIM1 into an ABC-DLBCL cell line, TMD8, increased colony formation and decreased sensitivity to ibrutinib. In addition, ibrutinib-resistant cell lines generated by prolonged ibrutinib exposure in vitro upregulated PIM1 expression, consistent with a role for PIM1 in antagonizing ibrutinib activity. The combination of a pan-PIM inhibitor with ibrutinib synergistically inhibited proliferation in vitro and tumor growth in vivo. Together, these data provide a rationale for combining BTK and PIM1 inhibition in the treatment of ABC-DLBCL.},
370
+ langid = {english},
371
+ pmcid = {PMC5126268},
372
+ keywords = {Bruton’s tyrosine kinase,DLBCL,ibrutinib,PIM1}
373
+}
374
+
375
+@article{ryanCellRegulomeLinks2017,
376
+ title = {A {{B Cell Regulome Links Notch}} to {{Downstream Oncogenic Pathways}} in {{Small B Cell Lymphomas}}},
377
+ author = {Ryan, Russell J. H. and Petrovic, Jelena and Rausch, Dylan M. and Zhou, Yeqiao and Lareau, Caleb A. and Kluk, Michael J. and Christie, Amanda L. and Lee, Winston Y. and Tarjan, Daniel R. and Guo, Bingqian and Donohue, Laura K. H. and Gillespie, Shawn M. and Nardi, Valentina and Hochberg, Ephraim P. and Blacklow, Stephen C. and Weinstock, David M. and Faryabi, Robert B. and Bernstein, Bradley E. and Aster, Jon C. and Pear, Warren S.},
378
+ date = {2017-10-17},
379
+ journaltitle = {Cell Reports},
380
+ shortjournal = {Cell Rep},
381
+ volume = {21},
382
+ number = {3},
383
+ eprint = {29045844},
384
+ eprinttype = {pmid},
385
+ pages = {784--797},
386
+ issn = {2211-1247},
387
+ doi = {10.1016/j.celrep.2017.09.066},
388
+ abstract = {Gain-of-function Notch mutations are recurrent in mature small B cell lymphomas such as mantle cell lymphoma (MCL) and chronic lymphocytic leukemia (CLL), but the Notch target genes that contribute to B cell oncogenesis are largely unknown. We performed integrative analysis of Notch-regulated transcripts, genomic binding of Notch transcription complexes, and genome conformation data to identify direct Notch target genes in MCL cell lines. This B~cell Notch regulome is largely controlled through Notch-bound distal enhancers and includes genes involved in B cell receptor and cytokine signaling and the oncogene MYC, which sustains proliferation of Notch-dependent MCL cell lines via a Notch-regulated lineage-restricted enhancer complex. Expression of direct Notch target genes is associated with Notch activity in an MCL xenograft model and in CLL lymph node biopsies. Our findings provide key insights into the role of Notch in MCL and other B~cell malignancies and have important implications for therapeutic targeting of Notch-dependent oncogenic pathways.},
389
+ langid = {english},
390
+ pmcid = {PMC5687286},
391
+ keywords = {Animals,B-Lymphocytes,Biopsy,Cell Differentiation,Cell Line Tumor,chronic lymphocytic leukemia,Enhancer Elements Genetic,Gene Expression Regulation Neoplastic,Gene Rearrangement,Humans,Lymph Nodes,lymphoma,Lymphoma B-Cell,mantle cell lymphoma,Mice,MYC,Notch signaling,Oncogenes,Proto-Oncogene Proteins c-myc,Receptors Notch,Signal Transduction,Tumor Microenvironment,Xenograft Model Antitumor Assays},
392
+ file = {/Users/rmorin/Zotero/storage/THJV7L2D/Ryan et al. - 2017 - A B Cell Regulome Links Notch to Downstream Oncoge.pdf}
393
+}
394
+
395
+@article{lazarianHotspotMutationTranscription2021,
396
+ title = {A Hotspot Mutation in Transcription Factor {{IKZF3}} Drives {{B}} Cell Neoplasia via Transcriptional Dysregulation},
397
+ author = {Lazarian, Gregory and Yin, Shanye and Ten Hacken, Elisa and Sewastianik, Tomasz and Uduman, Mohamed and Font-Tello, Alba and Gohil, Satyen H. and Li, Shuqiang and Kim, Ekaterina and Joyal, Heather and Billington, Leah and Witten, Elizabeth and Zheng, Mei and Huang, Teddy and Severgnini, Mariano and Lefebvre, Valerie and Rassenti, Laura Z. and Gutierrez, Catherine and Georgopoulos, Katia and Ott, Christopher J. and Wang, Lili and Kipps, Thomas J. and Burger, Jan A. and Livak, Kenneth J. and Neuberg, Donna S. and Baran-Marszak, Fanny and Cymbalista, Florence and Carrasco, Ruben D. and Wu, Catherine J.},
398
+ date = {2021-03-08},
399
+ journaltitle = {Cancer Cell},
400
+ shortjournal = {Cancer Cell},
401
+ volume = {39},
402
+ number = {3},
403
+ eprint = {33689703},
404
+ eprinttype = {pmid},
405
+ pages = {380-393.e8},
406
+ issn = {1878-3686},
407
+ doi = {10.1016/j.ccell.2021.02.003},
408
+ abstract = {Hotspot mutation of IKZF3 (IKZF3-L162R) has been identified as a putative driver of chronic lymphocytic leukemia (CLL), but its function remains unknown. Here, we demonstrate its driving role in CLL through a B cell-restricted conditional knockin mouse model. Mutant Ikzf3 alters DNA binding specificity and target selection, leading to hyperactivation of B cell receptor (BCR) signaling, overexpression of nuclear factor κB (NF-κB) target genes, and development of CLL-like disease in elderly mice with a penetrance of \textasciitilde 40\%. Human CLL carrying either IKZF3 mutation or high IKZF3 expression was associated with overexpression of BCR/NF-κB pathway members and reduced sensitivity to BCR signaling inhibition by ibrutinib. Our results thus highlight IKZF3 oncogenic function in CLL via transcriptional dysregulation and demonstrate that this pro-survival function can be achieved by either somatic mutation or overexpression of this CLL driver. This emphasizes the need for combinatorial approaches to overcome IKZF3-mediated BCR inhibitor resistance.},
409
+ langid = {english},
410
+ pmcid = {PMC8034546},
411
+ keywords = {Animals,B-Lymphocytes,BCR signaling,CLL,Humans,Ikaros Transcription Factor,IKZF3,Leukemia Lymphocytic Chronic B-Cell,Mice,Mice Inbred C57BL,Mice Inbred NOD,murine mode,Mutation,NF-kappa B,NF-κB,Receptors Antigen B-Cell,Signal Transduction,Transcription Genetic},
412
+ file = {/Users/rmorin/Zotero/storage/52PQRRWL/Lazarian et al. - 2021 - A hotspot mutation in transcription factor IKZF3 d.pdf}
413
+}
414
+
415
+@article{zhangDisruptionKMT2DPerturbs2015,
416
+ title = {Disruption of {{KMT2D}} Perturbs Germinal Center {{B}} Cell Development and Promotes Lymphomagenesis},
417
+ author = {Zhang, Jiyuan and Dominguez-Sola, David and Hussein, Shafinaz and Lee, Ji-Eun and Holmes, Antony B. and Bansal, Mukesh and Vlasevska, Sofija and Mo, Tongwei and Tang, Hongyan and Basso, Katia and Ge, Kai and Dalla-Favera, Riccardo and Pasqualucci, Laura},
418
+ date = {2015-10},
419
+ journaltitle = {Nature Medicine},
420
+ shortjournal = {Nat Med},
421
+ volume = {21},
422
+ number = {10},
423
+ eprint = {26366712},
424
+ eprinttype = {pmid},
425
+ pages = {1190--1198},
426
+ issn = {1546-170X},
427
+ doi = {10.1038/nm.3940},
428
+ abstract = {Mutations in the gene encoding the KMT2D (or MLL2) methyltransferase are highly recurrent and occur early during tumorigenesis in diffuse large B cell lymphoma (DLBCL) and follicular lymphoma (FL). However, the functional consequences of these mutations and their role in lymphomagenesis are unknown. Here we show that FL- and DLBCL-associated KMT2D mutations impair KMT2D enzymatic activity, leading to diminished global H3K4 methylation in germinal-center (GC) B cells and DLBCL cells. Conditional deletion of Kmt2d early during B cell development, but not after initiation of the GC reaction, results in an increase in GC B cells and enhances B cell proliferation in mice. Moreover, genetic ablation of Kmt2d in mice overexpressing Bcl2 increases the incidence of GC-derived lymphomas resembling human tumors. These findings suggest that KMT2D acts as a tumor suppressor gene whose early loss facilitates lymphomagenesis by remodeling the epigenetic landscape of the cancer precursor cells. Eradication of KMT2D-deficient cells may thus represent a rational therapeutic approach for targeting early tumorigenic events.},
429
+ langid = {english},
430
+ pmcid = {PMC5145002},
431
+ keywords = {Animals,B-Lymphocytes,Cell Proliferation,DNA Methylation,DNA-Binding Proteins,Epigenesis Genetic,Gene Silencing,Germinal Center,Humans,Lymphoma Large B-Cell Diffuse,Mice,Mutation Missense,Neoplasm Proteins,Transcription Genetic},
432
+ file = {/Users/rmorin/Zotero/storage/3WZ3HYIK/Zhang et al. - 2015 - Disruption of KMT2D perturbs germinal center B cel.pdf}
433
+}
434
+
435
+@article{choiLossKLHL6Promotes2018,
436
+ title = {Loss of {{KLHL6}} Promotes Diffuse Large {{B-cell}} Lymphoma Growth and Survival by Stabilizing the {{mRNA}} Decay Factor Roquin2},
437
+ author = {Choi, Jaewoo and Lee, Kyutae and Ingvarsdottir, Kristin and Bonasio, Roberto and Saraf, Anita and Florens, Laurence and Washburn, Michael P. and Tadros, Saber and Green, Michael R. and Busino, Luca},
438
+ date = {2018-05},
439
+ journaltitle = {Nature Cell Biology},
440
+ shortjournal = {Nat Cell Biol},
441
+ volume = {20},
442
+ number = {5},
443
+ eprint = {29695787},
444
+ eprinttype = {pmid},
445
+ pages = {586--596},
446
+ issn = {1476-4679},
447
+ doi = {10.1038/s41556-018-0084-5},
448
+ abstract = {Kelch-like protein 6 (KLHL6) is an uncharacterized gene mutated in diffuse large B-cell lymphoma (DLBCL). Here we report that KLHL6 assembles with cullin3 to form a functional cullin-RING ubiquitin ligase. Mutations in KLHL6 inhibit its ligase activity by disrupting the interaction with cullin3. Loss of KLHL6 favours DLBCL growth and survival both in vitro and in xenograft models. We further established that the mRNA decay factor roquin2 is a substrate of KLHL6. Degradation of roquin2 is dependent on B-cell receptor activation, and requires the integrity of the Tyr691 residue in roquin2 that is essential for its interaction with KLHL6. A non-degradable roquin2(Y691F) mutant requires its RNA-binding ability to phenocopy the effect of KLHL6 loss. Stabilization of roquin2 promotes mRNA decay of the tumour suppressor and NF-κB pathway inhibitor, tumour necrosis factor-α-inducible gene 3. Collectively, our findings uncover the tumour suppressing mechanism of KLHL6.},
449
+ langid = {english},
450
+ pmcid = {PMC5926793},
451
+ keywords = {Animals,Carrier Proteins,Cell Line Tumor,Cell Proliferation,Cell Survival,Gene Expression Regulation Enzymologic,Gene Expression Regulation Neoplastic,HEK293 Cells,Humans,Lymphoma Large B-Cell Diffuse,Mice Inbred NOD,Mice SCID,Mutation,NF-kappa B,Protein Stability,Proteolysis,Receptors Antigen B-Cell,Repressor Proteins,RNA Messenger,RNA Stability,Signal Transduction,Tumor Necrosis Factor alpha-Induced Protein 3,Tumor Suppressor Proteins,Tyrosine,Ubiquitination},
452
+}
453
+
454
+@article{mansouriFunctionalLossIkBe2015,
455
+ title = {Functional Loss of {{IκBε}} Leads to {{NF-κB}} Deregulation in Aggressive Chronic Lymphocytic Leukemia},
456
+ author = {Mansouri, Larry and Sutton, Lesley-Ann and Ljungström, Viktor and Bondza, Sina and Arngården, Linda and Bhoi, Sujata and Larsson, Jimmy and Cortese, Diego and Kalushkova, Antonia and Plevova, Karla and Young, Emma and Gunnarsson, Rebeqa and Falk-Sörqvist, Elin and Lönn, Peter and Muggen, Alice F. and Yan, Xiao-Jie and Sander, Birgitta and Enblad, Gunilla and Smedby, Karin E. and Juliusson, Gunnar and Belessi, Chrysoula and Rung, Johan and Chiorazzi, Nicholas and Strefford, Jonathan C. and Langerak, Anton W. and Pospisilova, Sarka and Davi, Frederic and Hellström, Mats and Jernberg-Wiklund, Helena and Ghia, Paolo and Söderberg, Ola and Stamatopoulos, Kostas and Nilsson, Mats and Rosenquist, Richard},
457
+ date = {2015-06-01},
458
+ journaltitle = {The Journal of Experimental Medicine},
459
+ shortjournal = {J Exp Med},
460
+ volume = {212},
461
+ number = {6},
462
+ eprint = {25987724},
463
+ eprinttype = {pmid},
464
+ pages = {833--843},
465
+ issn = {1540-9538},
466
+ doi = {10.1084/jem.20142009},
467
+ abstract = {NF-κB is constitutively activated in chronic lymphocytic leukemia (CLL); however, the implicated molecular mechanisms remain largely unknown. Thus, we performed targeted deep sequencing of 18 core complex genes within the NF-κB pathway in a discovery and validation CLL cohort totaling 315 cases. The most frequently mutated gene was NFKBIE (21/315 cases; 7\%), which encodes IκBε, a negative regulator of NF-κB in normal B cells. Strikingly, 13 of these cases carried an identical 4-bp frameshift deletion, resulting in a truncated protein. Screening of an additional 377 CLL cases revealed that NFKBIE aberrations predominated in poor-prognostic patients and were associated with inferior outcome. Minor subclones and/or clonal evolution were also observed, thus potentially linking this recurrent event to disease progression. Compared with wild-type patients, NFKBIE-deleted cases showed reduced IκBε protein levels and decreased p65 inhibition, along with increased phosphorylation and nuclear translocation of p65. Considering the central role of B cell receptor (BcR) signaling in CLL pathobiology, it is notable that IκBε loss was enriched in aggressive cases with distinctive stereotyped BcR, likely contributing to their poor prognosis, and leading to an altered response to BcR inhibitors. Because NFKBIE deletions were observed in several other B cell lymphomas, our findings suggest a novel common mechanism of NF-κB deregulation during lymphomagenesis.},
468
+ langid = {english},
469
+ pmcid = {PMC4451125},
470
+ keywords = {Cell Nucleus,Cell Survival,Chromosome Aberrations,Cohort Studies,Cytoplasm,DNA Mutational Analysis,Frameshift Mutation,Gene Deletion,Gene Expression Profiling,Gene Expression Regulation Leukemic,Humans,I-kappa B Kinase,Leukemia Lymphocytic Chronic B-Cell,Lymphoma B-Cell,Lymphoma B-Cell Marginal Zone,Lymphoma Mantle-Cell,NF-kappa B,Oligonucleotide Array Sequence Analysis,Receptors Antigen B-Cell,Signal Transduction,Treatment Outcome},
471
+ file = {/Users/rmorin/Zotero/storage/IFEN6256/Mansouri et al. - 2015 - Functional loss of IκBε leads to NF-κB deregulatio.pdf}
472
+}
473
+
474
+@article{saffieFBXW7TriggersDegradation2020,
475
+ title = {{{FBXW7 Triggers Degradation}} of {{KMT2D}} to {{Favor Growth}} of {{Diffuse Large B-cell Lymphoma Cells}}},
476
+ author = {Saffie, Rizwan and Zhou, Nan and Rolland, Delphine and Önder, Özlem and Basrur, Venkatesha and Campbell, Sydney and Wellen, Kathryn E. and Elenitoba-Johnson, Kojo S. J. and Capell, Brian C. and Busino, Luca},
477
+ date = {2020-06-15},
478
+ journaltitle = {Cancer Research},
479
+ shortjournal = {Cancer Res},
480
+ volume = {80},
481
+ number = {12},
482
+ eprint = {32350066},
483
+ eprinttype = {pmid},
484
+ pages = {2498--2511},
485
+ issn = {1538-7445},
486
+ doi = {10.1158/0008-5472.CAN-19-2247},
487
+ abstract = {Mature B-cell neoplasms are the fifth most common neoplasm. Due to significant heterogeneity at the clinical and genetic levels, current therapies for these cancers fail to provide long-term cures. The clinical success of proteasome inhibition for the treatment of multiple myeloma and B-cell lymphomas has made the ubiquitin pathway an important emerging therapeutic target. In this study, we assessed the role of the E3 ligase FBXW7 in mature B-cell neoplasms. FBXW7 targeted the frequently inactivated tumor suppressor KMT2D for protein degradation, subsequently regulating gene expression signatures related to oxidative phosphorylation (OxPhos). Loss of FBXW7 inhibited diffuse large B-cell lymphoma cell growth and further sensitized cells to OxPhos inhibition. These data elucidate a novel mechanism of regulation of KMT2D levels by the ubiquitin pathway and uncover a role of FBXW7 in regulating oxidative phosphorylation in B-cell malignancies. SIGNIFICANCE: These findings characterize FBXW7 as a prosurvival factor in B-cell lymphoma via degradation of the chromatin modifier KMT2D.},
488
+ langid = {english},
489
+ pmcid = {PMC7417195},
490
+ keywords = {Animals,Cell Line Tumor,Cell Proliferation,Chromatin,DNA-Binding Proteins,F-Box-WD Repeat-Containing Protein 7,Female,Gene Expression Regulation Neoplastic,Gene Knockout Techniques,HEK293 Cells,Humans,Lymphoma Large B-Cell Diffuse,Mice,Neoplasm Proteins,Oxidative Phosphorylation,Proteolysis,RNA Small Interfering,Signal Transduction,Ubiquitin,Xenograft Model Antitumor Assays},
491
+ file = {/Users/rmorin/Zotero/storage/5KJ466DP/Saffie et al. - 2020 - FBXW7 Triggers Degradation of KMT2D to Favor Growt.pdf;/Users/rmorin/Zotero/storage/RQSU3BV9/Saffie et al. - 2020 - FBXW7 Triggers Degradation of KMT2D to Favor Growt.pdf}
492
+}
493
+
494
+@article{katoUnderstandingFunctionstructureFunctionmutation2003,
495
+ title = {Understanding the Function-Structure and Function-Mutation Relationships of P53 Tumor Suppressor Protein by High-Resolution Missense Mutation Analysis},
496
+ author = {Kato, Shunsuke and Han, Shuang-Yin and Liu, Wen and Otsuka, Kazunori and Shibata, Hiroyuki and Kanamaru, Ryunosuke and Ishioka, Chikashi},
497
+ date = {2003-07-08},
498
+ journaltitle = {Proceedings of the National Academy of Sciences of the United States of America},
499
+ shortjournal = {Proc Natl Acad Sci U S A},
500
+ volume = {100},
501
+ number = {14},
502
+ eprint = {12826609},
503
+ eprinttype = {pmid},
504
+ pages = {8424--8429},
505
+ issn = {0027-8424},
506
+ doi = {10.1073/pnas.1431692100},
507
+ abstract = {Inactivation of the tumor suppressor p53 by missense mutations is the most frequent genetic alteration in human cancers. The common missense mutations in the TP53 gene disrupt the ability of p53 to bind to DNA and consequently to transactivate downstream genes. However, it is still not fully understood how a large number of the remaining mutations affect p53 structure and function. Here, we used a comprehensive site-directed mutagenesis technique and a yeast-based functional assay to construct, express, and evaluate 2,314 p53 mutants representing all possible amino acid substitutions caused by a point mutation throughout the protein (5.9 substitutions per residue), and correlated p53 function with structure- and tumor-derived mutations. This high-resolution mutation analysis allows evaluation of previous predictions and hypotheses through interrelation of function, structure and mutation.},
508
+ langid = {english},
509
+ pmcid = {PMC166245},
510
+ keywords = {Amino Acid Substitution,DNA Repair,Genes p53,Genes Reporter,Humans,Luciferases,Models Molecular,Mutagenesis Site-Directed,Mutation Missense,Point Mutation,Polymerase Chain Reaction,Protein Conformation,Protein Structure Tertiary,Recombinant Fusion Proteins,Saccharomyces cerevisiae,Structure-Activity Relationship,Transcriptional Activation,Tumor Suppressor Protein p53},
511
+ file = {/Users/rmorin/Zotero/storage/K7XZZIYN/Kato et al. - 2003 - Understanding the function-structure and function-.pdf}
512
+}
513
+
514
+@article{skalniakRegulatoryFeedbackLoop2009,
515
+ title = {Regulatory Feedback Loop between {{NF-kappaB}} and {{MCP-1-induced}} Protein 1 {{RNase}}},
516
+ author = {Skalniak, Lukasz and Mizgalska, Danuta and Zarebski, Adrian and Wyrzykowska, Paulina and Koj, Aleksander and Jura, Jolanta},
517
+ date = {2009-10},
518
+ journaltitle = {The FEBS journal},
519
+ shortjournal = {FEBS J},
520
+ volume = {276},
521
+ number = {20},
522
+ eprint = {19747262},
523
+ eprinttype = {pmid},
524
+ pages = {5892--5905},
525
+ issn = {1742-4658},
526
+ doi = {10.1111/j.1742-4658.2009.07273.x},
527
+ abstract = {A novel gene ZC3H12A, encoding MCP-1-induced protein 1 (MCPIP), was recently identified in human peripheral blood monocytes treated with monocyte chemotactic protein 1 (MCP-1) and in human monocyte-derived macrophages stimulated with interleukin (IL)-1beta. These experiments revealed that the gene undergoes rapid and potent transcription induction upon stimulation with proinflammatory molecules, such as MCP-1, IL-1beta, tumour necrosis factor alpha and lipopolysaccharide. Here we show that the induction of ZC3H12A by IL-1beta is predominantly NF-kappaB-dependent because inhibition of this signalling pathway results in the impairment of ZC3H12A transcription activation. Our results indicate the presence of an IL-1beta-responding region within the second intron of the ZC3H12A gene, which contains four functional NF-kappaB-binding sites. Therefore, we propose that this transcription enhancer transduces a ZC3H12A transcription-inducing signal after IL-1beta stimulation. Recent reports suggest that MCPIP acts as a negative regulator of inflammatory processes because it is engaged in the degradation of transcripts coding for certain proinflammatory cytokines. Our observations provide evidence for a novel negative feedback loop in the activation of NF-kappaB and point to potential significance of MCPIP in the treatment of various pathological states, such as diabetes or cancer that involve disturbances in the functioning of the NF-kappaB system.},
528
+ langid = {english},
529
+ keywords = {Base Sequence,Binding Sites,Blotting Western,Cell Line Tumor,Chromatin Immunoprecipitation,Electrophoretic Mobility Shift Assay,Humans,I-kappa B Proteins,Interleukin-1beta,Molecular Sequence Data,Mutagenesis Site-Directed,NF-kappa B,Polymerase Chain Reaction,Ribonucleases,Signal Transduction,Transcription Factors,Transcription Genetic,Transcription Initiation Site}
530
+}
531
+
532
+@article{wangFasFADDDeathDomain2010,
533
+ title = {The {{Fas-FADD}} Death Domain Complex Structure Reveals the Basis of {{DISC}} Assembly and Disease Mutations},
534
+ author = {Wang, Liwei and Yang, Jin Kuk and Kabaleeswaran, Venkataraman and Rice, Amanda J. and Cruz, Anthony C. and Park, Ah Young and Yin, Qian and Damko, Ermelinda and Jang, Se Bok and Raunser, Stefan and Robinson, Carol V. and Siegel, Richard M. and Walz, Thomas and Wu, Hao},
535
+ date = {2010-11},
536
+ journaltitle = {Nature Structural \& Molecular Biology},
537
+ shortjournal = {Nat Struct Mol Biol},
538
+ volume = {17},
539
+ number = {11},
540
+ eprint = {20935634},
541
+ eprinttype = {pmid},
542
+ pages = {1324--1329},
543
+ issn = {1545-9985},
544
+ doi = {10.1038/nsmb.1920},
545
+ abstract = {The death-inducing signaling complex (DISC) formed by the death receptor Fas, the adaptor protein FADD and caspase-8 mediates the extrinsic apoptotic program. Mutations in Fas that disrupt the DISC cause autoimmune lymphoproliferative syndrome (ALPS). Here we show that the Fas-FADD death domain (DD) complex forms an asymmetric oligomeric structure composed of 5-7 Fas DD and 5 FADD DD, whose interfaces harbor ALPS-associated mutations. Structure-based mutations disrupt the Fas-FADD interaction in vitro and in living cells; the severity of a mutation correlates with the number of occurrences of a particular interaction in the structure. The highly oligomeric structure explains the requirement for hexameric or membrane-bound FasL in Fas signaling. It also predicts strong dominant negative effects from Fas mutations, which are confirmed by signaling assays. The structure optimally positions the FADD death effector domain (DED) to interact with the caspase-8 DED for caspase recruitment and higher-order aggregation.},
546
+ langid = {english},
547
+ pmcid = {PMC2988912},
548
+ keywords = {Amino Acid Sequence,Animals,Apoptosis,Autoimmune Lymphoproliferative Syndrome,Caspase 8,Cell Line,fas Receptor,Fas-Associated Death Domain Protein,Humans,Mice,Models Molecular,Molecular Sequence Data,Mutation,Protein Structure Tertiary,Sequence Alignment,Spectrometry Mass Electrospray Ionization,Tandem Mass Spectrometry},
549
+}
550
+
551
+@article{zmajkovicovaGenotypephenotypeCorrelationsWHIM2022,
552
+ title = {Genotype-Phenotype Correlations in {{WHIM}} Syndrome: A Systematic Characterization of {{CXCR4WHIM}} Variants},
553
+ shorttitle = {Genotype-Phenotype Correlations in {{WHIM}} Syndrome},
554
+ author = {Zmajkovicova, Katarina and Pawar, Sumit and Maier-Munsa, Sabine and Maierhofer, Barbara and Wiest, Ivana and Skerlj, Renato and Taveras, Arthur G. and Badarau, Adriana},
555
+ date = {2022-09},
556
+ journaltitle = {Genes and Immunity},
557
+ shortjournal = {Genes Immun},
558
+ volume = {23},
559
+ number = {6},
560
+ eprint = {36089616},
561
+ eprinttype = {pmid},
562
+ pages = {196--204},
563
+ issn = {1476-5470},
564
+ doi = {10.1038/s41435-022-00181-9},
565
+ abstract = {Warts, hypogammaglobulinemia, infections, myelokathexis (WHIM) syndrome is a rare primary immunodeficiency predominantly caused by heterozygous gain-of-function mutations in CXCR4 C-terminus. We assessed genotype-phenotype correlations for known pathogenic CXCR4 variants and in vitro response of each variant to mavorixafor, an investigational CXCR4 antagonist. We used cell-based assays to analyze CXCL12-induced receptor trafficking and downstream signaling of 14 pathogenic CXCR4 variants previously identified in patients with WHIM syndrome. All CXCR4 variants displayed impaired receptor trafficking, hyperactive downstream signaling, and enhanced chemotaxis in response to CXCL12. Mavorixafor inhibited CXCL12-dependent signaling and hyperactivation in cells harboring CXCR4WHIM mutations. A strong correlation was found between CXCR4 internalization defect and severity of blood leukocytopenias and infection susceptibility, and between AKT activation and immunoglobulin A level and CD4+ T-cell counts. This study is the first to show WHIM syndrome clinical phenotype variability as a function of both CXCR4WHIM genotype diversity and associated functional dysregulation. Our findings suggest that CXCR4 internalization may be used to assess the pathogenicity of CXCR4 variants in vitro and also as a potential WHIM-related disease biomarker. The investigational CXCR4 antagonist mavorixafor inhibited CXCL12-dependent signaling in all tested CXCR4-variant cell lines at clinically relevant concentrations.},
566
+ langid = {english},
567
+ pmcid = {PMC9519442},
568
+ keywords = {Agammaglobulinemia,Aminoquinolines,Benzimidazoles,Biomarkers,Butylamines,Genetic Association Studies,Humans,Immunoglobulin A,Immunologic Deficiency Syndromes,Neutropenia,Primary Immunodeficiency Diseases,Proto-Oncogene Proteins c-akt,Receptors CXCR4,Warts},
569
+}
570
+
571
+@article{ramirez-komoSpontaneousLossLineage2017,
572
+ title = {Spontaneous Loss of {{B}} Lineage Transcription Factors Leads to Pre-{{B}} Leukemia in {{Ebf1}}+/-{{Bcl-xLTg}} Mice},
573
+ author = {Ramírez-Komo, J. A. and Delaney, M. A. and Straign, D. and Lukin, K. and Tsang, M. and Iritani, B. M. and Hagman, J.},
574
+ date = {2017-07-10},
575
+ journaltitle = {Oncogenesis},
576
+ shortjournal = {Oncogenesis},
577
+ volume = {6},
578
+ number = {7},
579
+ eprint = {28692033},
580
+ eprinttype = {pmid},
581
+ pages = {e355},
582
+ issn = {2157-9024},
583
+ doi = {10.1038/oncsis.2017.55},
584
+ abstract = {Early B-cell factor 1 (EBF1) plays a central role in B-cell lineage specification and commitment. Loss of this critical transcription factor is strongly associated with high-risk, relapsed and therapy-resistant B-cell-acute lymphoblastic leukemia, especially in children. However, Ebf1 haploinsufficient mice exhibit a normal lifespan. To determine whether prolonged survival of B cells would enable tumorigenesis in Ebf1 haploinsufficient animals, we generated Ebf1+/-Bcl-xLTg mice, which express the anti-apoptotic factor Bcl-xL in B cells. Approximately half of Ebf1+/-Bcl-xLTg mice develop aggressive oligoclonal leukemia as they age, which engrafts in congenic wild-type recipients without prior conditioning. The neoplastic cells display a pre-B phenotype and express early developmental- and natural killer cell/myeloid-markers inappropriately. In addition, we found tumor cell-specific loss of several transcription factors critical for maintaining differentiation: EBF1, TCF3 and RUNX1. However, in the majority of tumors, loss of Ebf1 expression was not due to loss of heterozygosity. This is the first spontaneous mouse model of pre-B leukemia to demonstrate inappropriate expression of non-B-cell-specific genes associated with loss of Ebf1, Tcf3 and Runx1 expression.},
585
+ langid = {english},
586
+ pmcid = {PMC5541707},
587
+}
588
+
589
+@article{wangETV6MutationCohort2014,
590
+ title = {{{ETV6}} Mutation in a Cohort of 970 Patients with Hematologic Malignancies},
591
+ author = {Wang, Qinrong and Dong, Shasha and Yao, Hong and Wen, Lijun and Qiu, Huiying and Qin, Llili and Ma, Liang and Chen, Suning},
592
+ date = {2014-10},
593
+ journaltitle = {Haematologica},
594
+ shortjournal = {Haematologica},
595
+ volume = {99},
596
+ number = {10},
597
+ eprint = {24997145},
598
+ eprinttype = {pmid},
599
+ pages = {e176-178},
600
+ issn = {1592-8721},
601
+ doi = {10.3324/haematol.2014.104406},
602
+ langid = {english},
603
+ pmcid = {PMC4181263},
604
+ keywords = {Cohort Studies,ETS Translocation Variant 6 Protein,ETV6,hematologic malignancies,Hematologic Neoplasms,Humans,Mutation,mutations,Proto-Oncogene Proteins c-ets,Repressor Proteins},
605
+}
606
+
607
+@article{sneeringerCoordinatedActivitiesWildtype2010,
608
+ title = {Coordinated Activities of Wild-Type plus Mutant {{EZH2}} Drive Tumor-Associated Hypertrimethylation of Lysine 27 on Histone {{H3}} ({{H3K27}}) in Human {{B-cell}} Lymphomas},
609
+ author = {Sneeringer, Christopher J. and Scott, Margaret Porter and Kuntz, Kevin W. and Knutson, Sarah K. and Pollock, Roy M. and Richon, Victoria M. and Copeland, Robert A.},
610
+ date = {2010-12-07},
611
+ journaltitle = {Proceedings of the National Academy of Sciences of the United States of America},
612
+ shortjournal = {Proc Natl Acad Sci U S A},
613
+ volume = {107},
614
+ number = {49},
615
+ eprint = {21078963},
616
+ eprinttype = {pmid},
617
+ pages = {20980--20985},
618
+ issn = {1091-6490},
619
+ doi = {10.1073/pnas.1012525107},
620
+ abstract = {EZH2, the catalytic subunit of the PRC2 complex, catalyzes the mono- through trimethylation of lysine 27 on histone H3 (H3K27). Histone H3K27 trimethylation is a mechanism for suppressing transcription of specific genes that are proximal to the site of histone modification. Point mutations of the EZH2 gene (Tyr641) have been reported to be linked to subsets of human B-cell lymphoma. The mutant allele is always found associated with a wild-type allele (heterozygous) in disease cells, and the mutations were reported to ablate the enzymatic activity of the PRC2 complex for methylating an unmodified peptide substrate. Here we demonstrate that the WT enzyme displays greatest catalytic efficiency (k(cat)/K) for the zero to monomethylation reaction of H3K27 and diminished efficiency for subsequent (mono- to di- and di- to trimethylation) reactions. In stark contrast, the disease-associated Y641 mutations display very limited ability to perform the first methylation reaction, but have enhanced catalytic efficiency for the subsequent reactions, relative to the WT enzyme. These results imply that the malignant phenotype of disease requires the combined activities of a H3K27 monomethylating enzyme (PRC2 containing WT EZH2 or EZH1) together with the mutant PRC2s for augmented conversion of H3K27 to the trimethylated form. To our knowledge, this is the first example of a human disease that is dependent on the coordinated activities of normal and disease-associated mutant enzymatic function.},
621
+ langid = {english},
622
+ pmcid = {PMC3000297},
623
+ file = {/Users/rmorin/Zotero/storage/QKW38HUB/Sneeringer et al. - 2010 - Coordinated activities of wild-type plus mutant EZ.pdf}
624
+}
625
+
626
+@article{fangazioGeneticMechanismsHLAI2021,
627
+ title = {Genetic Mechanisms of {{HLA-I}} Loss and Immune Escape in Diffuse Large {{B}} Cell Lymphoma},
628
+ author = {Fangazio, Marco and Ladewig, Erik and Gomez, Karen and Garcia-Ibanez, Laura and Kumar, Rahul and Teruya-Feldstein, Julie and Rossi, Davide and Filip, Ioan and Pan-Hammarström, Qiang and Inghirami, Giorgio and Boldorini, Renzo and Ott, German and Staiger, Annette M. and Chapuy, Björn and Gaidano, Gianluca and Bhagat, Govind and Basso, Katia and Rabadan, Raul and Pasqualucci, Laura and Dalla-Favera, Riccardo},
629
+ date = {2021-06-01},
630
+ journaltitle = {Proceedings of the National Academy of Sciences of the United States of America},
631
+ shortjournal = {Proc Natl Acad Sci U S A},
632
+ volume = {118},
633
+ number = {22},
634
+ eprint = {34050029},
635
+ eprinttype = {pmid},
636
+ pages = {e2104504118},
637
+ issn = {1091-6490},
638
+ doi = {10.1073/pnas.2104504118},
639
+ abstract = {Fifty percent of diffuse large B cell lymphoma (DLBCL) cases lack cell-surface expression of the class I major histocompatibility complex (MHC-I), thus escaping recognition by cytotoxic T cells. Here we show that, across B cell lymphomas, loss of MHC-I, but not MHC-II, is preferentially restricted to DLBCL. To identify the involved mechanisms, we performed whole exome and targeted HLA deep-sequencing in 74 DLBCL samples, and found somatic inactivation of B2M and the HLA-I loci in 80\% (34 of 42) of MHC-INEG tumors. Furthermore, 70\% (22 of 32) of MHC-IPOS DLBCLs harbored monoallelic HLA-I genetic alterations (MHC-IPOS/mono), indicating allele-specific inactivation. MHC-INEG and MHC-IPOS/mono cases harbored significantly higher mutational burden and inferred neoantigen load, suggesting potential coselection of HLA-I loss and sustained neoantigen production. Notably, the analysis of {$>$}500,000 individuals across different cancer types revealed common germline HLA-I homozygosity, preferentially in DLBCL. In mice, germinal-center B cells lacking HLA-I expression did not progress to lymphoma and were counterselected in the context of oncogene-driven lymphomagenesis, suggesting that additional events are needed to license immune evasion. These results suggest a multistep process of HLA-I loss in DLBCL development including both germline and somatic events, and have direct implications for the pathogenesis and immunotherapeutic targeting of this disease.},
640
+ langid = {english},
641
+ pmcid = {PMC8179151},
642
+ keywords = {beta 2-Microglobulin,Cell Line Tumor,Cell Transformation Neoplastic,Cytidine Deaminase,DLBCL,Gene Silencing,Histocompatibility Antigens Class I,HLA,Humans,immune evasion,Lymphoma Large B-Cell Diffuse,Proto-Oncogene Proteins c-bcl-6},
643
+}
644
+
645
+@article{kannengiesserFunctionalStructuralGenetic2009,
646
+ title = {Functional, Structural, and Genetic Evaluation of 20 {{CDKN2A}} Germ Line Mutations Identified in Melanoma-Prone Families or Patients},
647
+ author = {Kannengiesser, Caroline and Brookes, Sharon and family=Arroyo, given=Anna Gutierrez, prefix=del, useprefix=true and Pham, Danielle and Bombled, Johny and Barrois, Michel and Mauffret, Olivier and Avril, Marie-Françoise M. and Chompret, Agnès and Lenoir, Gilbert M. and Sarasin, Alain and {French Hereditary Melanoma Study Group} and Peters, Gordon and Bressac-de Paillerets, Brigitte},
648
+ date = {2009-04},
649
+ journaltitle = {Human Mutation},
650
+ shortjournal = {Hum Mutat},
651
+ volume = {30},
652
+ number = {4},
653
+ eprint = {19260062},
654
+ eprinttype = {pmid},
655
+ pages = {564--574},
656
+ issn = {1098-1004},
657
+ doi = {10.1002/humu.20845},
658
+ abstract = {Germline mutations of the CDKN2A gene are found in melanoma-prone families and individuals with multiple sporadic melanomas. The encoded protein, p16(INK4A), comprises four ankyrin-type repeats, and the mutations, most of which are missense and occur throughout the entire coding region, can disrupt the conformation of these structural motifs as well as the association of p16(INK4a) with its physiological targets, the cyclin-dependent kinases (CDKs) CDK4 and CDK6. Assessing pathogenicity of nonsynonymous mutations is critical to evaluate melanoma risk in carriers. In the current study, we investigate 20 CDKN2A germline mutations whose effects on p16(INK4A) structure and function have not been previously documented (Thr18\_Ala19dup, Gly23Asp, Arg24Gln, Gly35Ala, Gly35Val, Ala57Val, Ala60Val, Ala60Arg, Leu65dup, Gly67Arg, Gly67\_Asn71del, Glu69Gly, Asp74Tyr, Thr77Pro, Arg80Pro, Pro81Thr, Arg87Trp, Leu97Arg, Arg99Pro, and [Leu113Leu;Pro114Ser]). By considering genetic information, the predicted impact of each variant on the protein structure, its ability to interact with CDK4 and impede cell proliferation in experimental settings, we conclude that 18 of the 20 CDKN2A variants can be classed as loss of function mutations, whereas the results for two remain ambiguous. Discriminating between mutant and neutral variants of p16(INK4A) not only adds to our understanding of the functionally critical residues in the protein but provides information that can be used for melanoma risk prediction.},
659
+ langid = {english},
660
+ keywords = {Cell Line,Cell Proliferation,Cyclin-Dependent Kinase 4,Cyclin-Dependent Kinase Inhibitor p16,Family Health,Genetic Testing,Germ-Line Mutation,Humans,Melanoma,Models Molecular,Mutation Missense,Protein Binding,Protein Structure Tertiary},
661
+}
662
+
663
+@article{huFollicularLymphomaassociatedBTK2021,
664
+ title = {Follicular {{Lymphoma-associated BTK Mutations}} Are {{Inactivating Resulting}} in {{Augmented AKT Activation}}},
665
+ author = {Hu, Nan and Wang, Fangyang and Sun, Tianyu and Xu, Zhengfan and Zhang, Jing and Bernard, Denzil and Xu, Shilin and Wang, Shaomeng and Kaminski, Mark and Devata, Suma and Phillips, Tycel and Malek, Sami N.},
666
+ date = {2021-04-15},
667
+ journaltitle = {Clinical Cancer Research: An Official Journal of the American Association for Cancer Research},
668
+ shortjournal = {Clin Cancer Res},
669
+ volume = {27},
670
+ number = {8},
671
+ eprint = {33419778},
672
+ eprinttype = {pmid},
673
+ pages = {2301--2313},
674
+ issn = {1557-3265},
675
+ doi = {10.1158/1078-0432.CCR-20-3741},
676
+ abstract = {PURPOSE: On the basis of the recent discovery of mutations in Bruton tyrosine kinase (BTK) in follicular lymphoma, we studied their functional properties. EXPERIMENTAL DESIGN: We identified novel somatic BTK mutations in 7\% of a combined total of 139 follicular lymphoma and 11 transformed follicular lymphoma cases, none of which had received prior treatment with B-cell receptor (BCR) targeted drugs. We reconstituted wild-type (WT) and mutant BTK into various engineered lymphoma cell lines. We measured BCR-induced signal transduction events in engineered cell lines and primary human follicular lymphoma B cells. RESULTS: We uncovered that all BTK mutants destabilized the BTK protein and some created BTK kinase-dead mutants. The phospholipase C gamma 2 (PLCγ2) is a substrate of BTK but the BTK mutants did not alter PLCγ2 phosphorylation. Instead, we discovered that BTK mutants induced an exaggerated AKT phosphorylation phenotype in anti-Ig-treated recombinant lymphoma cell lines. The short hairpin RNA-mediated knockdown of BTK expression in primary human nonmalignant lymph node-derived B cells resulted in strong anti-Ig-induced AKT activation, as did the degradation of BTK protein in cell lines using ibrutinib-based proteolysis targeting chimera. Finally, through analyses of primary human follicular lymphoma B cells carrying WT or mutant BTK, we detected elevated AKT phosphorylation following surface Ig crosslinking in all follicular lymphoma B cells, including all BTK-mutant follicular lymphoma. The augmented AKT phosphorylation following BCR crosslinking could be abrogated by pretreatment with a PI3Kδ inhibitor. CONCLUSIONS: Altogether, our data uncover novel unexpected properties of follicular lymphoma-associated BTK mutations with direct implications for targeted therapy development in follicular lymphoma.See related commentary by Afaghani and Taylor, p. 2123.},
677
+ langid = {english},
678
+ pmcid = {PMC8046715},
679
+ keywords = {Agammaglobulinaemia Tyrosine Kinase,Cell Line Tumor,Class I Phosphatidylinositol 3-Kinases,DNA Mutational Analysis,Gene Knockdown Techniques,HEK293 Cells,Humans,Loss of Function Mutation,Lymphoma Follicular,Mutagenesis Site-Directed,Phospholipase C gamma,Phosphorylation,Primary Cell Culture,Protein Stability,Proto-Oncogene Proteins c-akt},
680
+}
681
+
682
+@article{almasmoumFrequentLossBTG12021,
683
+ title = {Frequent Loss of {{BTG1}} Activity and Impaired Interactions with the {{Caf1}} Subunit of the {{Ccr4-Not}} Deadenylase in Non-{{Hodgkin}} Lymphoma},
684
+ author = {Almasmoum, Hibah Ali and Airhihen, Blessing and Seedhouse, Claire and Winkler, Gerlof Sebastiaan},
685
+ date = {2021-02},
686
+ journaltitle = {Leukemia \& Lymphoma},
687
+ shortjournal = {Leuk Lymphoma},
688
+ volume = {62},
689
+ number = {2},
690
+ eprint = {33021411},
691
+ eprinttype = {pmid},
692
+ pages = {281--290},
693
+ issn = {1029-2403},
694
+ doi = {10.1080/10428194.2020.1827243},
695
+ abstract = {Mutations in the highly similar genes B-cell translocation gene 1 (BTG1) and BTG2 are identified in approximately 10-15\% of non-Hodgkin lymphoma cases, which may suggest a direct involvement of BTG1 and BTG2 in malignant transformation. However, it is unclear whether or how disease-associated mutations impair the function of these genes. Therefore, we selected 16 BTG1 variants based on in silico analysis. We then evaluated (i) the ability of these variants to interact with the known protein-binding partners CNOT7 and CNOT8, which encode the Caf1 catalytic subunit of the Ccr4-Not deadenylase complex; (ii) the activity of the variant proteins in cell cycle progression; (iii) translational repression; and (iv) mRNA degradation. Based on these analyses, we conclude that mutations in BTG1 may contribute to malignant transformation and tumor cell proliferation by interfering with its anti-proliferative activity and ability to interact with CNOT7 and CNOT8.},
696
+ langid = {english},
697
+ keywords = {BTG1,BTG2,Ccr4–Not,Cell Proliferation,Exoribonucleases,Humans,Immediate-Early Proteins,Lymphoma and Hodgkin disease,Lymphoma Non-Hodgkin,mRNA decay,Neoplasm Proteins,Protein Binding,Receptors CCR4,Repressor Proteins,Transcription Factors,Tumor Suppressor Proteins},
698
+}
699
+
700
+@article{wanMechanismActivationRAFERK2004,
701
+ title = {Mechanism of Activation of the {{RAF-ERK}} Signaling Pathway by Oncogenic Mutations of {{B-RAF}}},
702
+ author = {Wan, Paul T. C. and Garnett, Mathew J. and Roe, S. Mark and Lee, Sharlene and Niculescu-Duvaz, Dan and Good, Valerie M. and Jones, C. Michael and Marshall, Christopher J. and Springer, Caroline J. and Barford, David and Marais, Richard and {Cancer Genome Project}},
703
+ date = {2004-03-19},
704
+ journaltitle = {Cell},
705
+ shortjournal = {Cell},
706
+ volume = {116},
707
+ number = {6},
708
+ eprint = {15035987},
709
+ eprinttype = {pmid},
710
+ pages = {855--867},
711
+ issn = {0092-8674},
712
+ doi = {10.1016/s0092-8674(04)00215-6},
713
+ abstract = {Over 30 mutations of the B-RAF gene associated with human cancers have been identified, the majority of which are located within the kinase domain. Here we show that of 22 B-RAF mutants analyzed, 18 have elevated kinase activity and signal to ERK in vivo. Surprisingly, three mutants have reduced kinase activity towards MEK in vitro but, by activating C-RAF in vivo, signal to ERK in cells. The structures of wild type and oncogenic V599EB-RAF kinase domains in complex with the RAF inhibitor BAY43-9006 show that the activation segment is held in an inactive conformation by association with the P loop. The clustering of most mutations to these two regions suggests that disruption of this interaction converts B-RAF into its active conformation. The high activity mutants signal to ERK by directly phosphorylating MEK, whereas the impaired activity mutants stimulate MEK by activating endogenous C-RAF, possibly via an allosteric or transphosphorylation mechanism.},
714
+ langid = {english},
715
+ keywords = {Allosteric Regulation,Animals,Catalytic Domain,Cell Transformation Neoplastic,Enzyme Inhibitors,Gene Expression Regulation Enzymologic,MAP Kinase Kinase 1,MAP Kinase Signaling System,Mice,Mitogen-Activated Protein Kinase Kinases,Mitogen-Activated Protein Kinases,Models Molecular,Molecular Conformation,Mutation,Neoplasms,NIH 3T3 Cells,Oncogenes,Oocytes,Phosphorylation,Phosphotransferases,Proto-Oncogene Proteins B-raf,Proto-Oncogene Proteins c-raf,Up-Regulation,Xenopus},
716
+}
717
+
718
+@article{masclePointMutationsBCL62003,
719
+ title = {Point Mutations in {{BCL6 DNA-binding}} Domain Reveal Distinct Roles for the Six Zinc Fingers},
720
+ author = {Mascle, Xavier and Albagli, Olivier and Lemercier, Claudie},
721
+ date = {2003-01-10},
722
+ journaltitle = {Biochemical and Biophysical Research Communications},
723
+ shortjournal = {Biochem Biophys Res Commun},
724
+ volume = {300},
725
+ number = {2},
726
+ eprint = {12504096},
727
+ eprinttype = {pmid},
728
+ pages = {391--396},
729
+ issn = {0006-291X},
730
+ doi = {10.1016/s0006-291x(02)02873-5},
731
+ abstract = {The B-cell lymphoma 6 (BCL6) gene encodes a transcriptional repressor containing six C-terminal Krüppel-like zinc fingers. The zinc finger (ZF) cluster is necessary and sufficient for interaction with both DNA and several proteins and for nuclear targeting. However, the functional specificity of the six ZFs in these cellular roles is unknown. To characterize this domain, we mutated individually each ZF of BCL6. Our results reveal that mutation of the two N-terminal ZFs does not impair cognate DNA-binding, cellular localization of the protein nor the transcriptional repression capacity of BCL6. By contrast, mutation of any of the remaining ZFs abolishes the binding of BCL6 to DNA in vitro and the transrepressive function of the protein in vivo. Finally, none of the six mutations affect the interaction between BCL6 and class II histone deacetylases. Thus our experiments demonstrate that BCL6 uses each of the four C-terminus ZFs for binding to a target sequence while the two amino terminal fingers are likely engaged in other unknown function(s).},
732
+ langid = {english},
733
+ keywords = {Amino Acid Sequence,Binding Sites,DNA-Binding Proteins,Gene Expression Regulation,HeLa Cells,Histone Deacetylases,Humans,Molecular Sequence Data,Point Mutation,Protein Structure Tertiary,Proto-Oncogene Proteins,Proto-Oncogene Proteins c-bcl-6,Repressor Proteins,Sequence Alignment,Transcription Factors,Transcription Genetic,Zinc Fingers},
734
+}
735
+
736
+@article{camachoATMGeneInactivation2002,
737
+ title = {{{ATM}} Gene Inactivation in Mantle Cell Lymphoma Mainly Occurs by Truncating Mutations and Missense Mutations Involving the Phosphatidylinositol-3 Kinase Domain and Is Associated with Increasing Numbers of Chromosomal Imbalances},
738
+ author = {Camacho, Emma and Hernández, Luis and Hernández, Silvia and Tort, Frederic and Bellosillo, Beatriz and Beà, Silvia and Bosch, Francesc and Montserrat, Emili and Cardesa, Antonio and Fernández, Pedro L. and Campo, Elias},
739
+ date = {2002-01-01},
740
+ journaltitle = {Blood},
741
+ shortjournal = {Blood},
742
+ volume = {99},
743
+ number = {1},
744
+ eprint = {11756177},
745
+ eprinttype = {pmid},
746
+ pages = {238--244},
747
+ issn = {0006-4971},
748
+ doi = {10.1182/blood.v99.1.238},
749
+ abstract = {The ataxia-telangiectasia mutated (ATM) gene codifies for a protein critically involved in the cellular response to DNA damage. ATM alterations have been observed in some sporadic lymphoproliferative disorders. The recurrent 11q22-23 deletions found in mantle cell lymphoma (MCL) suggest that ATM could be inactivated in these lymphomas. In this study, ATM gene alterations and protein expression were examined in 20 and 17 MCL tumor specimens, respectively. Previously, these patients had been examined for p53 and p14(ARF) gene status and analyzed by comparative genomic hybridization. Nine patients had 11q22-23 losses. Eight ATM gene mutations were detected in 7 patients. These alterations were 3 missense mutations in the phosphatidylinositol-3 kinase (PI-3K) domain and 5 truncating mutations, including 3 frameshifts, a nonsense mutation, and a substitution of the initial methionine. All truncating mutations were associated with lack of protein expression. Somatic origin was demonstrated in 3 mutations, whereas one mutation was carried heterozygously in the patient germ line. Chromosomal imbalances were significantly higher in typical MCL with ATM inactivation (7.8 +/- 1.3) than in tumors with the wild-type gene (3 +/- 1.1) (P =.001). Moreover, tumors with bi-allelic ATM alteration were associated with 3q gains (P =.015) and frequent extranodal involvement (P =.049). ATM gene alterations were not related to the histologic variant of the tumors, p53/p14(ARF) gene status, survival, or other clinicopathologic features of the patients. These findings indicate that ATM gene mutations in MCL are mainly truncating or missense mutations involving the PI-3K domain, and that may play a role in the pathogenesis of a subset of these tumors with increased numbers of chromosomal imbalances.},
750
+ langid = {english},
751
+ keywords = {Alleles,Ataxia Telangiectasia Mutated Proteins,Blotting Western,Cell Cycle Proteins,Chromosome Aberrations,Chromosomes Human Pair 11,DNA Mutational Analysis,DNA-Binding Proteins,Gene Deletion,Gene Expression,Humans,Lymphoma Mantle-Cell,Mutation,Mutation Missense,Phosphatidylinositol 3-Kinases,Polymorphism Genetic,Protein Serine-Threonine Kinases,Tumor Suppressor Proteins},
752
+}
753
+
754
+@article{yusufovaHistoneH1Loss2021,
755
+ title = {Histone {{H1}} Loss Drives Lymphoma by Disrupting {{3D}} Chromatin Architecture},
756
+ author = {Yusufova, Nevin and Kloetgen, Andreas and Teater, Matt and Osunsade, Adewola and Camarillo, Jeannie M. and Chin, Christopher R. and Doane, Ashley S. and Venters, Bryan J. and Portillo-Ledesma, Stephanie and Conway, Joseph and Phillip, Jude M. and Elemento, Olivier and Scott, David W. and Béguelin, Wendy and Licht, Jonathan D. and Kelleher, Neil L. and Staudt, Louis M. and Skoultchi, Arthur I. and Keogh, Michael-Christopher and Apostolou, Effie and Mason, Christopher E. and Imielinski, Marcin and Schlick, Tamar and David, Yael and Tsirigos, Aristotelis and Allis, C. David and Soshnev, Alexey A. and Cesarman, Ethel and Melnick, Ari M.},
757
+ date = {2021-01},
758
+ journaltitle = {Nature},
759
+ shortjournal = {Nature},
760
+ volume = {589},
761
+ number = {7841},
762
+ eprint = {33299181},
763
+ eprinttype = {pmid},
764
+ pages = {299--305},
765
+ issn = {1476-4687},
766
+ doi = {10.1038/s41586-020-3017-y},
767
+ abstract = {Linker histone H1 proteins bind to nucleosomes and facilitate chromatin compaction1, although their biological functions are poorly understood. Mutations in the genes that encode H1 isoforms B-E (H1B, H1C, H1D and H1E; also known as H1-5, H1-2, H1-3 and H1-4, respectively) are highly recurrent in B~cell lymphomas, but the pathogenic relevance of these mutations to cancer and the mechanisms that are involved are unknown. Here we show that lymphoma-associated H1 alleles are genetic driver mutations in lymphomas. Disruption of H1 function results in a profound architectural remodelling of the genome, which is characterized by large-scale yet focal shifts of chromatin from a compacted to a relaxed state. This decompaction drives distinct changes in epigenetic states, primarily owing to a gain of histone H3 dimethylation at lysine 36 (H3K36me2) and/or loss of repressive H3 trimethylation at lysine 27 (H3K27me3). These changes unlock the expression of stem cell genes that are normally silenced during early development. In mice, loss of H1c and H1e (also known as H1f2 and H1f4, respectively) conferred germinal centre B~cells with enhanced fitness and self-renewal properties, ultimately leading to aggressive lymphomas with an increased repopulating potential. Collectively, our data indicate that H1 proteins are normally required to sequester early developmental genes into architecturally inaccessible genomic compartments. We also establish H1 as a bona fide tumour suppressor and show that mutations in H1 drive malignant transformation primarily through three-dimensional genome reorganization, which leads to epigenetic reprogramming and derepression of developmentally silenced genes.},
768
+ langid = {english},
769
+ pmcid = {PMC7855728},
770
+ keywords = {Alleles,Animals,B-Lymphocytes,Cell Self Renewal,Cell Transformation Neoplastic,Chromatin,Chromatin Assembly and Disassembly,Epigenesis Genetic,Gene Expression Regulation Neoplastic,Gene Silencing,Genes Tumor Suppressor,Germinal Center,Histones,Humans,Lymphoma,Mice,Mutation,Stem Cells},
771
+ file = {/Users/rmorin/Zotero/storage/GE6IPBBF/Yusufova et al. - 2021 - Histone H1 loss drives lymphoma by disrupting 3D c.pdf}
772
+}
773
+
774
+@article{hodsonRegulationNormalBcell2016,
2 775
title = {Regulation of Normal {{B-cell}} Differentiation and Malignant {{B-cell}} Survival by {{OCT2}}},
3 776
author = {Hodson, Daniel J. and Shaffer, Arthur L. and Xiao, Wenming and Wright, George W. and Schmitz, Roland and Phelan, James D. and Yang, Yandan and Webster, Daniel E. and Rui, Lixin and Kohlhammer, Holger and Nakagawa, Masao and Waldmann, Thomas A. and Staudt, Louis M.},
4 777
date = {2016-04-05},
... ...
@@ -17,7 +790,7 @@
17 790
keywords = {Animals,B-Lymphocytes,cancer biology,Cell Differentiation,Cell Line Tumor,Cell Survival,germinal center,lymphoma,Lymphoma Large B-Cell Diffuse,Mice,Mice Knockout,Organic Cation Transport Proteins,Organic Cation Transporter 2}
18 791
}
19 792
20
-@article{melznerBiallelicMutationSOCS12005a,
793
+@article{melznerBiallelicMutationSOCS12005,
21 794
title = {Biallelic Mutation of {{SOCS-1}} Impairs {{JAK2}} Degradation and Sustains Phospho-{{JAK2}} Action in the {{MedB-1}} Mediastinal Lymphoma Line},
22 795
author = {Melzner, Ingo and Bucur, Alexandra Juliana and Brüderlein, Silke and Dorsch, Karola and Hasel, Cornelia and Barth, Thomas F. E. and Leithäuser, Frank and Möller, Peter},
23 796
date = {2005-03-15},
... ...
@@ -53,7 +826,7 @@
53 826
keywords = {3T3 Cells,Animals,Autoimmune Lymphoproliferative Syndrome,B-Lymphocytes,Caspase 8,Cells Cultured,Chromosomal Instability,Down-Regulation,Genes p53,Genetic Predisposition to Disease,Lymphoma B-Cell,Mice,Mice Inbred C57BL,Mice Transgenic,Survival Analysis}
54 827
}
55 828
56
-@article{venturuttiTBL1XR1MutationsDrive2020b,
829
+@article{venturuttiTBL1XR1MutationsDrive2020,
57 830
title = {{{TBL1XR1 Mutations Drive Extranodal Lymphoma}} by {{Inducing}} a {{Pro-tumorigenic Memory Fate}}},
58 831
author = {Venturutti, Leandro and Teater, Matt and Zhai, Andrew and Chadburn, Amy and Babiker, Leena and Kim, Daleum and Béguelin, Wendy and Lee, Tak C. and Kim, Youngjun and Chin, Christopher R. and Yewdell, William T. and Raught, Brian and Phillip, Jude M. and Jiang, Yanwen and Staudt, Louis M. and Green, Michael R. and Chaudhuri, Jayanta and Elemento, Olivier and Farinha, Pedro and Weng, Andrew P. and Nissen, Michael D. and Steidl, Christian and Morin, Ryan D. and Scott, David W. and Privé, Gilbert G. and Melnick, Ari M.},
59 832
date = {2020-07-23},
... ...
@@ -72,7 +845,7 @@
72 845
keywords = {ABC-DLBCL,Animals,BACH2,Basic-Leucine Zipper Transcription Factors,BCL6,cell fate,cell of origin,Chromatin,extranodal lymphoma,germinal center,Germinal Center,Histone Deacetylases,Humans,Immunologic Memory,Lymphoma Large B-Cell Diffuse,memory B cells,Mice,Mice Inbred C57BL,Mice Knockout,Mutagenesis Site-Directed,Nuclear Proteins,Nuclear Receptor Co-Repressor 2,Precursor Cells B-Lymphoid,Protein Binding,Proto-Oncogene Proteins c-bcl-6,Receptors Cytoplasmic and Nuclear,Repressor Proteins,RNA Interference,RNA Small Interfering,TBL1XR1,Transcription Genetic}
73 846
}
74 847
75
-@article{huNovelMissenseM206K2013b,
848
+@article{huNovelMissenseM206K2013,
76 849
title = {A Novel Missense ({{M206K}}) {{STAT3}} Mutation in Diffuse Large {{B}} Cell Lymphoma Deregulates {{STAT3}} Signaling},
77 850
author = {Hu, Guangzhen and Witzig, Thomas E. and Gupta, Mamta},
78 851
date = {2013},
... ...
@@ -109,7 +882,7 @@
109 882
keywords = {Animals,Apoptosis,Cell Line Tumor,Chromatin Immunoprecipitation,Forkhead Transcription Factors,Gene Expression Profiling,Gene Expression Regulation Neoplastic,Germinal Center,GTP-Binding Protein alpha Subunits G12-G13,Heterografts,Humans,Kaplan-Meier Estimate,Lymphoma Large B-Cell Diffuse,Mice,Neoplasm Proteins,Neoplasm Transplantation,Prognosis,Proto-Oncogene Proteins c-akt,Receptors Lysosphingolipid,Repressor Proteins,RNA Interference,RNA Small Interfering,Signal Transduction,Sphingosine-1-Phosphate Receptors}
110 883
}
111 884
112
-@article{ortega-molinaOncogenicRagGTPase2019b,
885
+@article{ortega-molinaOncogenicRagGTPase2019,
113 886
title = {Oncogenic {{Rag GTPase}} Signaling Enhances {{B}} Cell Activation and Drives Follicular Lymphoma Sensitive to Pharmacological Inhibition of {{mTOR}}},
114 887
author = {Ortega-Molina, Ana and Deleyto-Seldas, Nerea and Carreras, Joaquim and Sanz, Alba and Lebrero-Fernández, Cristina and Menéndez, Camino and Vandenberg, Andrew and Fernández-Ruiz, Beatriz and Marín-Arraiza, Leyre and family=Calle Arregui, given=Celia, prefix=de la, useprefix=true and Belén Plata-Gómez, Ana and Caleiras, Eduardo and family=Martino, given=Alba, prefix=de, useprefix=true and Martínez-Martín, Nuria and Troulé, Kevin and Piñeiro-Yáñez, Elena and Nakamura, Naoya and Araf, Shamzah and Victora, Gabriel D. and Okosun, Jessica and Fitzgibbon, Jude and Efeyan, Alejo},
115 888
date = {2019-08},
... ...
@@ -259,7 +1032,7 @@
259 1032
keywords = {Animals,BAF complex,chromatin,chromatin remodeling,clonal precursor cells,DNA-Binding Proteins,epigenetics,Humans,humoral immunity,lymphoma,Lymphoma,Memory B Cells,Mice,Mutation,Nuclear Proteins,pioneer transcription factors,plasticity,precision therapy,Transcription Factors}
260 1033
}
261 1034
262
-@article{dobashiTP53OSBPL10Alterations2018b,
1035
+@article{dobashiTP53OSBPL10Alterations2018,
263 1036
title = {{{TP53}} and {{OSBPL10}} Alterations in Diffuse Large {{B-cell}} Lymphoma: Prognostic Markers Identified via Exome Analysis of Cases with Extreme Prognosis},
264 1037
shorttitle = {{{TP53}} and {{OSBPL10}} Alterations in Diffuse Large {{B-cell}} Lymphoma},
265 1038
author = {Dobashi, Akito and Togashi, Yuki and Tanaka, Norio and Yokoyama, Masahiro and Tsuyama, Naoko and Baba, Satoko and Mori, Seiichi and Hatake, Kiyohiko and Yamaguchi, Toshiharu and Noda, Tetsuo and Takeuchi, Kengo},
... ...
@@ -476,7 +1249,7 @@
476 1249
langid = {english}
477 1250
}
478 1251
479
-@article{ennishiTMEM30ALossoffunctionMutations2020b,
1252
+@article{ennishiTMEM30ALossoffunctionMutations2020,
480 1253
title = {{{TMEM30A}} Loss-of-Function Mutations Drive Lymphomagenesis and Confer Therapeutically Exploitable Vulnerability in {{B-cell}} Lymphoma},
481 1254
author = {Ennishi, Daisuke and Healy, Shannon and Bashashati, Ali and Saberi, Saeed and Hother, Christoffer and Mottok, Anja and Chan, Fong Chun and Chong, Lauren and Abraham, Libin and Kridel, Robert and Boyle, Merrill and Meissner, Barbara and Aoki, Tomohiro and Takata, Katsuyoshi and Woolcock, Bruce W. and Viganò, Elena and Gold, Michael and Molday, Laurie L. and Molday, Robert S. and Telenius, Adele and Li, Michael Y. and Wretham, Nicole and Dos Santos, Nancy and Wong, Mark and Viller, Natasja N. and Uger, Robert A. and Duns, Gerben and Baticados, Abigail and Madero, Angel and Bristow, Brianna N. and Farinha, Pedro and Slack, Graham W. and Ben-Neriah, Susana and Lai, Daniel and Zhang, Allen W. and Salehi, Sohrab and Shulha, Hennady P. and Chiu, Derek S. and Mostafavi, Sara and Gerrie, Alina S. and Huang, Da Wei and Rushton, Christopher and Villa, Diego and Sehn, Laurie H. and Savage, Kerry J. and Mungall, Andrew J. and Weng, Andrew P. and Bally, Marcel B. and Morin, Ryan D. and Cohen Freue, Gabriela V. and Staudt, Louis M. and Connors, Joseph M. and Marra, Marco A. and Shah, Sohrab P. and Gascoyne, Randy D. and Scott, David W. and Steidl, Christian},
482 1255
date = {2020-04},
... ...
@@ -568,7 +1341,7 @@
568 1341
keywords = {Adult,Aged,Biomarkers Tumor,DNA Mutational Analysis,Exons,Female,Humans,Lymphoma Large B-Cell Diffuse,Male,Middle Aged,Mutation,Neoplasm Grading,Neoplasm Staging,Prognosis,Proportional Hazards Models,Protein Domains,Ubiquitin-Protein Ligases}
569 1342
}
570 1343
571
-@article{jardinDiffuseLargeBcell2010a,
1344
+@article{jardinDiffuseLargeBcell2010,
572 1345
title = {Diffuse Large {{B-cell}} Lymphomas with {{CDKN2A}} Deletion Have a Distinct Gene Expression Signature and a Poor Prognosis under {{R-CHOP}} Treatment: A {{GELA}} Study},
573 1346
shorttitle = {Diffuse Large {{B-cell}} Lymphomas with {{CDKN2A}} Deletion Have a Distinct Gene Expression Signature and a Poor Prognosis under {{R-CHOP}} Treatment},
574 1347
author = {Jardin, Fabrice and Jais, Jean-Philippe and Molina, Thierry-Jo and Parmentier, Françoise and Picquenot, Jean-Michel and Ruminy, Philippe and Tilly, Hervé and Bastard, Christian and Salles, Gilles-André and Feugier, Pierre and Thieblemont, Catherine and Gisselbrecht, Christian and family=Reynies, given=Aurelien, prefix=de, useprefix=true and Coiffier, Bertrand and Haioun, Corinne and Leroy, Karen},
... ...
@@ -643,7 +1416,7 @@
643 1416
keywords = {Adenine,Animals,CD8-Positive T-Lymphocytes,Humans,Leukemia Lymphocytic Chronic B-Cell,Mice,Mutation,NF-kappa B,Piperidines,Pyrazoles,Pyrimidines,Tumor Escape,Tumor Microenvironment}
644 1417
}
645 1418
646
-@article{fanComprehensiveCharacterizationDriver2020b,
1419
+@article{fanComprehensiveCharacterizationDriver2020,
647 1420
title = {Comprehensive Characterization of Driver Genes in Diffuse Large {{B}} Cell Lymphoma},
648 1421
author = {Fan, Zheng and Pei, Renzhi and Sha, Keya and Chen, Lieguang and Wang, Tiantian and Lu, Ying},
649 1422
date = {2020-07},
... ...
@@ -662,7 +1435,7 @@
662 1435
keywords = {CNV,diffuse large B cell lymphoma,driver gene,driver pathway,overall survival rate,PPI network,WGCNA}
663 1436
}
664 1437
665
-@article{lunningMutationChromatinModifiers2015b,
1438
+@article{lunningMutationChromatinModifiers2015,
666 1439
title = {Mutation of Chromatin Modifiers; an Emerging Hallmark of Germinal Center {{B-cell}} Lymphomas},
667 1440
author = {Lunning, M. A. and Green, M. R.},
668 1441
date = {2015-10-16},
... ...
@@ -681,7 +1454,7 @@
681 1454
keywords = {Animals,Chromatin,Germinal Center,Histone Acetyltransferases,Histone Methyltransferases,Histone-Lysine N-Methyltransferase,Humans,Lymphoma Large B-Cell Diffuse,Mutation,Nuclear Proteins}
682 1455
}
683 1456
684
-@article{witjesPrevalenceCytoplasmicActin2020b,
1457
+@article{witjesPrevalenceCytoplasmicActin2020,
685 1458
title = {Prevalence of {{Cytoplasmic Actin Mutations}} in {{Diffuse Large B-Cell Lymphoma}} and {{Multiple Myeloma}}: {{A Functional Assessment Based}} on {{Actin Three-Dimensional Structures}}},
686 1459
shorttitle = {Prevalence of {{Cytoplasmic Actin Mutations}} in {{Diffuse Large B-Cell Lymphoma}} and {{Multiple Myeloma}}},
687 1460
author = {Witjes, Laura and Van Troys, Marleen and Verhasselt, Bruno and Ampe, Christophe},
... ...
@@ -701,7 +1474,7 @@
701 1474
keywords = {ACTB,ACTG1,actin mutations,Actins,Alleles,Biomarkers Tumor,cBioPortal,Cytoplasm,Databases Genetic,F-actin,Gene Amplification,Gene Deletion,Genetic Association Studies,Genetic Predisposition to Disease,Humans,lymphoid cancer,Lymphoma Large B-Cell Diffuse,meta-analysis of patient data,Models Molecular,Multiple Myeloma,Mutation,Mutation Rate,myosin,Organ Specificity,patient cancer data,plasma cell myeloma,Protein Conformation,Software,Structure-Activity Relationship}
702 1475
}
703 1476
704
-@article{delageBTG1InactivationDrives2023a,
1477
+@article{delageBTG1InactivationDrives2023,
705 1478
title = {{{BTG1}} Inactivation Drives Lymphomagenesis and Promotes Lymphoma Dissemination through Activation of {{BCAR1}}},
706 1479
author = {Delage, Lorric and Lambert, Mireille and Bardel, Émilie and Kundlacz, Cindy and Chartoire, Dimitri and Conchon, Axel and Peugnet, Anne-Laure and Gorka, Lucas and Auberger, Patrick and Jacquel, Arnaud and Soussain, Carole and Destaing, Olivier and Delecluse, Henri-Jacques and Delecluse, Susanne and Merabet, Samir and Traverse-Glehen, Alexandra and Salles, Gilles and Bachy, Emmanuel and Billaud, Marc and Ghesquières, Hervé and Genestier, Laurent and Rouault, Jean-Pierre and Sujobert, Pierre},
707 1480
date = {2023-03-09},
... ...
@@ -729,7 +1502,7 @@
729 1502
doi = {10.1126/science.abj7412}
730 1503
}
731 1504
732
-@article{balinas-gaviraFrequentMutationsAminoterminal2020b,
1505
+@article{balinas-gaviraFrequentMutationsAminoterminal2020,
733 1506
title = {Frequent Mutations in the Amino-Terminal Domain of {{BCL7A}} Impair Its Tumor Suppressor Role in {{DLBCL}}},
734 1507
author = {Baliñas-Gavira, Carlos and Rodríguez, M. I. and Andrades, Á and Cuadros, M. and Álvarez-Pérez, J. and Álvarez-Prado, Ángel F. and family=Yébenes, given=V. G., prefix=de, useprefix=false and Sanchez-Hernandez, S. and Fernández-Vigo, Elvira and Muñoz, Javier and Martín, F. and Ramiro, A. and Martinez-Climent, J. and Medina, P.},
735 1508
date = {2020},
... ...
@@ -796,11 +1569,23 @@
796 1569
keywords = {Animals,B-cell,BAF,Chromatin,DNA Helicases,epigenetics,germinal center,Haploinsufficiency,Humans,Hyperplasia,immunology,lymphoma,Lymphoma B-Cell,Mice,Nuclear Proteins,SMARCA4,SWI/SNF,transcription,Transcription Factors}
797 1570
}
798 1571
799
-@article{challa-malladiCombinedGeneticInactivationa,
800
- title = {Combined {{Genetic Inactivation}} of \&beta;2-{{Microglobulin}} and {{CD58 Reveals Frequent Escape}} from {{Immune Recognition}} in {{Diffuse Large B Cell Lymphoma}}},
801
- author = {Challa-Malladi, Madhavi and Lieu, Yen K and Califano, Olivia and Holmes, Antony B and Bhagat, Govind and Murty, Vundavalli V and Dominguez-Sola, David and Pasqualucci, Laura and Dalla-Favera, Riccardo},
1572
+@article{challa-malladiCombinedGeneticInactivation2011,
1573
+ title = {Combined Genetic Inactivation of Β2-{{Microglobulin}} and {{CD58}} Reveals Frequent Escape from Immune Recognition in Diffuse Large {{B}} Cell Lymphoma},
1574
+ author = {Challa-Malladi, Madhavi and Lieu, Yen K. and Califano, Olivia and Holmes, Antony B. and Bhagat, Govind and Murty, Vundavalli V. and Dominguez-Sola, David and Pasqualucci, Laura and Dalla-Favera, Riccardo},
1575
+ date = {2011-12-13},
802 1576
journaltitle = {Cancer Cell},
803
- pages = {1--13}
1577
+ shortjournal = {Cancer Cell},
1578
+ volume = {20},
1579
+ number = {6},
1580
+ eprint = {22137796},
1581
+ eprinttype = {pmid},
1582
+ pages = {728--740},
1583
+ issn = {1878-3686},
1584
+ doi = {10.1016/j.ccr.2011.11.006},
1585
+ abstract = {We report that diffuse large B cell lymphoma (DLBCL) commonly fails to express cell-surface molecules necessary for the recognition of tumor cells by immune-effector cells. In 29\% of cases, mutations and deletions inactivate the β2-Microglobulin gene, thus preventing the cell-surface expression of the HLA class-I (HLA-I) complex that is necessary for recognition by CD8(+) cytotoxic T~cells. In 21\% of cases, analogous lesions~involve the CD58 gene, which encodes a molecule involved in T and natural killer cell-mediated responses. In addition to gene inactivation, alternative mechanisms lead to aberrant expression of HLA-I and CD58 in {$>$}60\% of DLBCL. These two events are significantly associated in this disease, suggesting that they are coselected during lymphomagenesis for their combined role in escape from immune-surveillance.},
1586
+ langid = {english},
1587
+ pmcid = {PMC3660995},
1588
+ keywords = {beta 2-Microglobulin,CD58 Antigens,Cell Line Tumor,Coculture Techniques,Cytotoxicity Immunologic,DNA Copy Number Variations,DNA Mutational Analysis,Genetic Association Studies,Genotype,Histocompatibility Antigens Class I,Humans,Killer Cells Natural,Lymphoma Large B-Cell Diffuse,Mutation,Polymorphism Single Nucleotide,Protein Stability,Transcription Genetic},
804 1589
}
805 1590
806 1591
@article{nieGenomewideCRISPRScreens2021b,
... ...
@@ -961,7 +1746,7 @@
961 1746
issue = {5\_Supplement}
962 1747
}
963 1748
964
-@article{nieDualRoleCD702022b,
1749
+@article{nieDualRoleCD702022,
965 1750
title = {The Dual Role of {{CD70}} in {{B-cell}} Lymphomagenesis},
966 1751
author = {Nie, Man and Ren, Weicheng and Ye, Xiaofei and Berglund, Mattias and Wang, Xianhuo and Fjordén, Karin and Du, Likun and Giannoula, Yvonne and Lei, Dexin and Su, Wenjia and Li, Wei and Liu, Dongbing and Linderoth, Johan and Jiang, Chengyi and Bao, Huijing and Jiang, Wenqi and Huang, Huiqiang and Hou, Yong and Zhu, Shida and Enblad, Gunilla and Jerkeman, Mats and Wu, Kui and Zhang, Huilai and Amini, Rose-Marie and Li, Zhi-Ming and Pan-Hammarström, Qiang},
967 1752
date = {2022-12},
... ...
@@ -979,7 +1764,7 @@
979 1764
pmcid = {PMC9722974},
980 1765
keywords = {Animals,B-Lymphocytes,CD27 Ligand,CD70,CD8-Positive T-Lymphocytes,diffuse large B-cell lymphoma,Epstein-Barr Virus Infections,genetic aberration,HBV infection,Humans,immune evasion,Lymphoma Large B-Cell Diffuse,Mice,Tumor Microenvironment}
981 1766
}
982
-@article{abateDistinctViralMutational2015a,
1767
+@article{abateDistinctViralMutational2015,
983 1768
title = {Distinct {{Viral}} and {{Mutational Spectrum}} of {{Endemic Burkitt Lymphoma}}},
984 1769
author = {Abate, F. and Ambrosio, M. and Mundo, L. and Laginestra, M. and Fuligni, F. and Rossi, M. and Zairis, Sakellarios and Gazaneo, Sara and Falco, G. De and Lazzi, S. and Bellan, C. and Rocca, B. J. and Amato, T. and Marasco, E. and Etebari, Maryam and Ogwang, M. and Calbi, V. and Ndede, I. and Patel, K. and Chumba, D. and Piccaluga, P. and Pileri, S. and Leoncini, L. and Rabadán, R.},
985 1770
date = {2015},
... ...
@@ -1120,7 +1905,7 @@
1120 1905
langid = {english}
1121 1906
}
1122 1907
1123
-@article{albuquerqueEnhancingKnowledgeDiscovery2017a,
1908
+@article{albuquerqueEnhancingKnowledgeDiscovery2017,
1124 1909
title = {Enhancing Knowledge Discovery from Cancer Genomics Data with {{Galaxy}}},
1125 1910
author = {Albuquerque, Marco A. and Grande, Bruno M. and Ritch, Elie J. and Pararajalingam, Prasath and Jessa, Selin and Krzywinski, Martin and Grewal, Jasleen K. and Shah, Sohrab P. and Boutros, Paul C. and Morin, Ryan D.},
1126 1911
date = {2017-05-01},
... ...
@@ -1554,7 +2339,7 @@
1554 2339
keywords = {DNA methylation,Long non-coding RNAs,Reprogramming}
1555 2340
}
1556 2341
1557
-@article{barariaCathepsinAlterationsInduce2020c,
2342
+@article{barariaCathepsinAlterationsInduce2020,
1558 2343
title = {Cathepsin {{S Alterations Induce}} a {{Tumor-Promoting Immune Microenvironment}} in {{Follicular Lymphoma}}},
1559 2344
author = {Bararia, Deepak and Hildebrand, Johannes A. and Stolz, Sebastian and Haebe, Sarah and Alig, Stefan and Trevisani, Christopher P. and Osorio-Barrios, Francisco and Bartoschek, Michael D. and Mentz, Michael and Pastore, Alessandro and Gaitzsch, Erik and Heide, Michael and Jurinovic, Vindi and Rautter, Katharina and Gunawardana, Jay and Sabdia, Muhammed B. and Szczepanowski, Monika and Richter, Julia and Klapper, Wolfram and Louissaint, Abner and Ludwig, Christina and Bultmann, Sebastian and Leonhardt, Heinrich and Eustermann, Sebastian and Hopfner, Karl-Peter and Hiddemann, Wolfgang and family=Bergwelt-Baildon, given=Michael, prefix=von, useprefix=true and Steidl, Christian and Kridel, Robert and Tobin, Joshua W. D. and Gandhi, Maher K. and Weinstock, David M. and Schmidt-Supprian, Marc and Sárosi, Menyhárt B. and Rudelius, Martina and Passerini, Verena and Mautner, Josef and Weigert, Oliver},
1560 2345
date = {2020-05-05},
... ...
@@ -2056,7 +2841,7 @@
2056 2841
pmcid = {PMC4075446}
2057 2842
}
2058 2843
2059
-@article{burkhardtClinicalRelevanceMolecular2022b,
2844
+@article{burkhardtClinicalRelevanceMolecular2022,
2060 2845
title = {Clinical Relevance of Molecular Characteristics in {{Burkitt}} Lymphoma Differs According to Age},
2061 2846
author = {Burkhardt, Birgit and Michgehl, Ulf and Rohde, Jonas and Erdmann, Tabea and Berning, Philipp and Reutter, Katrin and Rohde, Marius and Borkhardt, Arndt and Burmeister, Thomas and Dave, Sandeep and Tzankov, Alexandar and Dugas, Martin and Sandmann, Sarah and Fend, Falko and Finger, Jasmin and Mueller, Stephanie and Gökbuget, Nicola and Haferlach, Torsten and Kern, Wolfgang and Hartmann, Wolfgang and Klapper, Wolfram and Oschlies, Ilske and Richter, Julia and Kontny, Udo and Lutz, Mathias and Maecker-Kolhoff, Britta and Ott, German and Rosenwald, Andreas and Siebert, Reiner and family=Stackelberg, given=Arend, prefix=von, useprefix=true and Strahm, Brigitte and Woessmann, Wilhelm and Zimmermann, Martin and Zapukhlyak, Myroslav and Grau, Michael and Lenz, Georg},
2062 2847
date = {2022-07-06},
... ...
@@ -2459,7 +3244,7 @@
2459 3244
pages = {777--790}
2460 3245
}
2461 3246
2462
-@article{chapuyGenomicAnalysesPMBL2019b,
3247
+@article{chapuyGenomicAnalysesPMBL2019,
2463 3248
title = {Genomic Analyses of {{PMBL}} Reveal New Drivers and Mechanisms of Sensitivity to {{PD-1}} Blockade},
2464 3249
author = {Chapuy, Bjoern and Stewart, Chip and Dunford, Andrew J. and Kim, Jaegil and Wienand, Kirsty and Kamburov, Atanas and Griffin, Gabriel K. and Chen, Pei-Hsuan and Lako, Ana and Redd, Robert A. and Cote, Claire M. and Ducar, Matthew D. and Thorner, Aaron R. and Rodig, Scott J. and Getz, Gad and Shipp, Margaret A.},
2465 3250
date = {2019-12-26},
... ...
@@ -2478,7 +3263,7 @@
2478 3263
keywords = {Adult,Antineoplastic Agents Immunological,Biomarkers Tumor,Cohort Studies,DNA Copy Number Variations,Female,Gene Expression Regulation Neoplastic,Genomics,Humans,Lymphoma Large B-Cell Diffuse,Male,Mediastinal Neoplasms,Mutation,Prognosis,Programmed Cell Death 1 Receptor,Trans-Activators}
2479 3264
}
2480 3265
2481
-@article{chapuyMolecularSubtypesDiffuse2018b,
3266
+@article{chapuyMolecularSubtypesDiffuse2018,
2482 3267
title = {Molecular Subtypes of Diffuse Large {{B}} Cell Lymphoma Are Associated with Distinct Pathogenic Mechanisms and Outcomes},
2483 3268
author = {Chapuy, Bjoern and Stewart, Chip and Dunford, Andrew J. and Kim, Jaegil and Kamburov, Atanas and Redd, Robert A. and Lawrence, Mike S. and Roemer, Margaretha G. M. and Li, Amy J. and Ziepert, Marita and Staiger, Annette M. and Wala, Jeremiah A. and Ducar, Matthew D. and Leshchiner, Ignaty and Rheinbay, Ester and Taylor-Weiner, Amaro and Coughlin, Caroline A. and Hess, Julian M. and Pedamallu, Chandra S. and Livitz, Dimitri and Rosebrock, Daniel and Rosenberg, Mara and Tracy, Adam A. and Horn, Heike and family=Hummelen, given=Paul, prefix=van, useprefix=true and Feldman, Andrew L. and Link, Brian K. and Novak, Anne J. and Cerhan, James R. and Habermann, Thomas M. and Siebert, Reiner and Rosenwald, Andreas and Thorner, Aaron R. and Meyerson, Matthew L. and Golub, Todd R. and Beroukhim, Rameen and Wulf, Gerald G. and Ott, German and Rodig, Scott J. and Monti, Stefano and Neuberg, Donna S. and Loeffler, Markus and Pfreundschuh, Michael and Trümper, Lorenz and Getz, Gad and Shipp, Margaret A.},
2484 3269
date = {2018-05},
... ...
@@ -2691,7 +3476,7 @@
2691 3476
pmcid = {PMC2376092}
2692 3477
}
2693 3478
2694
-@article{cheungAcquiredTNFRSF14Mutations2010a,
3479
+@article{cheungAcquiredTNFRSF14Mutations2010,
2695 3480
title = {Acquired {{TNFRSF14}} Mutations in Follicular Lymphoma Are Associated with Worse Prognosis},
2696 3481
author = {Cheung, K.-John J. and Johnson, Nathalie A. and Affleck, Joslynn G. and Severson, Tesa and Steidl, Christian and Ben-Neriah, Susana and Schein, Jacqueline and Morin, Ryan D. and Moore, Richard and Shah, Sohrab P. and Qian, Hong and Paul, Jessica E. and Telenius, Adele and Relander, Thomas and Lam, Wan and Savage, Kerry and Connors, Joseph M. and Brown, Carolyn and Marra, Marco A. and Gascoyne, Randy D. and Horsman, Douglas E.},
2697 3482
date = {2010-11-15},
... ...
@@ -2909,7 +3694,7 @@
2909 3694
langid = {english}
2910 3695
}
2911 3696
2912
-@article{compagnoMutationsMultipleGenes2009a,
3697
+@article{compagnoMutationsMultipleGenes2009,
2913 3698
title = {Mutations of Multiple Genes Cause Deregulation of {{NF-kappaB}} in Diffuse Large {{B-cell}} Lymphoma},
2914 3699
author = {Compagno, Mara and Lim, Wei Keat and Grunn, Adina and Nandula, Subhadra V. and Brahmachary, Manisha and Shen, Qiong and Bertoni, Francesco and Ponzoni, Maurilio and Scandurra, Marta and Califano, Andrea and Bhagat, Govind and Chadburn, Amy and Dalla-Favera, Riccardo and Pasqualucci, Laura},
2915 3700
date = {2009-06-04},
... ...
@@ -3438,7 +4223,7 @@
3438 4223
pages = {1061--1063}
3439 4224
}
3440 4225
3441
-@article{dunsCharacterizationDLBCLPMBL2021b,
4226
+@article{dunsCharacterizationDLBCLPMBL2021,
3442 4227
title = {Characterization of {{DLBCL}} with a {{PMBL}} Gene Expression Signature},
3443 4228
author = {Duns, Gerben and Viganò, Elena and Ennishi, Daisuke and Sarkozy, Clementine and Hung, Stacy S. and Chavez, Elizabeth and Takata, Katsuyoshi and Rushton, Christopher and Jiang, Aixiang and Ben-Neriah, Susana and Woolcock, Bruce W. and Slack, Graham W. and Hsi, Eric D. and Craig, Jeffrey W. and Hilton, Laura K. and Shah, Sohrab P. and Farinha, Pedro and Mottok, Anja and Gascoyne, Randy D. and Morin, Ryan D. and Savage, Kerry J. and Scott, David W. and Steidl, Christian},
3444 4229
date = {2021-07-15},
... ...
@@ -4443,7 +5228,7 @@
4443 5228
abstract = {Summary: Circular layout is an efficient way for the visualization of huge amounts of genomic information. Here we present the circlize package, which provides an implementation of circular layout generation in R as well as an enhancement of available software. The flexibility of this package is based on the usage of low-level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. Together with the seamless connection between the powerful computational and visual environment in R, circlize gives users more convenience and freedom to design figures for better understanding genomic patterns behind multi-dimensional data. Availability and implementation: ~circlize is available at the Comprehensive R Archive Network (CRAN): http://cran.r-project.org/web/packages/circlize/Contact: ~b.brors@dkfz.deSupplementary information: ~Supplementary data are available at Bioinformatics online.}
4444 5229
}
4445 5230
4446
-@article{gunawardanaRecurrentSomaticMutations2014c,
5231
+@article{gunawardanaRecurrentSomaticMutations2014,
4447 5232
title = {Recurrent Somatic Mutations of {{PTPN1}} in Primary Mediastinal {{B}} Cell Lymphoma and {{Hodgkin}} Lymphoma},
4448 5233
author = {Gunawardana, Jay and Chan, Fong Chun and Telenius, Adèle and Woolcock, Bruce and Kridel, Robert and Tan, King L. and Ben-Neriah, Susana and Mottok, Anja and Lim, Raymond S. and Boyle, Merrill and Rogic, Sanja and Rimsza, Lisa M. and Guiter, Chrystelle and Leroy, Karen and Gaulard, Philippe and Haioun, Corinne and Marra, Marco A. and Savage, Kerry J. and Connors, Joseph M. and Shah, Sohrab P. and Gascoyne, Randy D. and Steidl, Christian},
4449 5234
date = {2014-04},
... ...
@@ -5155,7 +5940,7 @@
5155 5940
keywords = {Alternative Splicing,Biomarkers Tumor,Carcinoma Hepatocellular,DNA-Binding Proteins,Gene Expression Profiling,Gene Expression Regulation Neoplastic,Humans,Liver Neoplasms,Neoplasm Metastasis,Prognosis,RNA Splicing Factors,RNA-Binding Proteins,Tumor Cells Cultured}
5156 5941
}
5157 5942
5158
-@article{hubschmannMutationalMechanismsShaping2021b,
5943
+@article{hubschmannMutationalMechanismsShaping2021,
5159 5944
title = {Mutational Mechanisms Shaping the Coding and Noncoding Genome of Germinal Center Derived {{B-cell}} Lymphomas},
5160 5945
author = {Hübschmann, Daniel and Kleinheinz, Kortine and Wagener, Rabea and Bernhart, Stephan H. and López, Cristina and Toprak, Umut H. and Sungalee, Stephanie and Ishaque, Naveed and Kretzmer, Helene and Kreuz, Markus and Waszak, Sebastian M. and Paramasivam, Nagarajan and Ammerpohl, Ole and Aukema, Sietse M. and Beekman, Renée and Bergmann, Anke K. and Bieg, Matthias and Binder, Hans and Borkhardt, Arndt and Borst, Christoph and Brors, Benedikt and Bruns, Philipp and Carrillo de Santa Pau, Enrique and Claviez, Alexander and Doose, Gero and Haake, Andrea and Karsch, Dennis and Haas, Siegfried and Hansmann, Martin-Leo and Hoell, Jessica I. and Hovestadt, Volker and Huang, Bingding and Hummel, Michael and Jäger-Schmidt, Christina and Kerssemakers, Jules N. A. and Korbel, Jan O. and Kube, Dieter and Lawerenz, Chris and Lenze, Dido and Martens, Joost H. A. and Ott, German and Radlwimmer, Bernhard and Reisinger, Eva and Richter, Julia and Rico, Daniel and Rosenstiel, Philip and Rosenwald, Andreas and Schillhabel, Markus and Stilgenbauer, Stephan and Stadler, Peter F. and Martín-Subero, José I. and Szczepanowski, Monika and Warsow, Gregor and Weniger, Marc A. and Zapatka, Marc and Valencia, Alfonso and Stunnenberg, Hendrik G. and Lichter, Peter and Möller, Peter and Loeffler, Markus and Eils, Roland and Klapper, Wolfram and Hoffmann, Steve and Trümper, Lorenz and {ICGC MMML-Seq consortium} and {ICGC DE-Mining consortium} and {BLUEPRINT consortium} and Küppers, Ralf and Schlesner, Matthias and Siebert, Reiner},
5161 5946
date = {2021-07},
... ...
@@ -5518,7 +6303,7 @@
5518 6303
pages = {1523--1531}
5519 6304
}
5520 6305
5521
-@article{jardinRecurrentMutationsExportin2016a,
6306
+@article{jardinRecurrentMutationsExportin2016,
5522 6307
title = {Recurrent Mutations of the Exportin 1 Gene ({{XPO1}}) and Their Impact on Selective Inhibitor of Nuclear Export Compounds Sensitivity in Primary Mediastinal {{B-cell}} Lymphoma},
5523 6308
author = {Jardin, Fabrice and Pujals, Anais and Pelletier, Laura and Bohers, Elodie and Camus, Vincent and Mareschal, Sylvain and Dubois, Sydney and Sola, Brigitte and Ochmann, Marlène and Lemonnier, François and Viailly, Pierre-Julien and Bertrand, Philippe and Maingonnat, Catherine and Traverse-Glehen, Alexandra and Gaulard, Philippe and Damotte, Diane and Delarue, Richard and Haioun, Corinne and Argueta, Christian and Landesman, Yosef and Salles, Gilles and Jais, Jean-Philippe and Figeac, Martin and Copie-Bergman, Christiane and Molina, Thierry Jo and Picquenot, Jean Michel and Cornic, Marie and Fest, Thierry and Milpied, Noel and Lemasle, Emilie and Stamatoullas, Aspasia and Moeller, Peter and Dyer, Martin J. S. and Sundstrom, Christer and Bastard, Christian and Tilly, Hervé and Leroy, Karen},
5524 6309
date = {2016-09},
... ...
@@ -6076,7 +6861,7 @@
6076 6861
keywords = {Adult,Aged,Aged 80 and over,Amyloid Precursor Protein Secretases,Apoptosis,Base Sequence,Benzodiazepinones,Cell Line Tumor,Cell Proliferation,Cyclin D1,Exons,Female,Gene Expression Profiling,Humans,Lymphoma Mantle-Cell,Male,Middle Aged,Mutation,Prognosis,Receptor Notch1,Sequence Analysis RNA,Signal Transduction,Survival Analysis,Transcriptome}
6077 6862
}
6078 6863
6079
-@article{krysiakRecurrentSomaticMutations2017b,
6864
+@article{krysiakRecurrentSomaticMutations2017,
6080 6865
title = {Recurrent Somatic Mutations Affecting {{B-cell}} Receptor Signaling Pathway Genes in Follicular Lymphoma},
6081 6866
author = {Krysiak, Kilannin and Gomez, Felicia and White, Brian S. and Matlock, Matthew and Miller, Christopher A. and Trani, Lee and Fronick, Catrina C. and Fulton, Robert S. and Kreisel, Friederike and Cashen, Amanda F. and Carson, Kenneth R. and Berrien-Elliott, Melissa M. and Bartlett, Nancy L. and Griffith, Malachi and Griffith, Obi L. and Fehniger, Todd A.},
6082 6867
date = {2017-01-26},
... ...
@@ -6209,7 +6994,7 @@
6209 6994
pmcid = {PMC6678222}
6210 6995
}
6211 6996
6212
-@article{kwanhianMicroRNA142Mutated202012b,
6997
+@article{kwanhianMicroRNA142Mutated202012,
6213 6998
title = {{{MicroRNA-142}} Is Mutated in about 20\% of Diffuse Large {{B-cell}} Lymphoma},
6214 6999
author = {Kwanhian, Wiyada and Lenze, Dido and Alles, Julia and Motsch, Natalie and Barth, Stephanie and Döll, Celina and Imig, Jochen and Hummel, Michael and Tinguely, Marianne and Trivedi, Pankaj and Lulitanond, Viraphong and Meister, Gunter and Renner, Christoph and Grässer, Friedrich A.},
6215 7000
date = {2012-10},
... ...
@@ -6922,7 +7707,7 @@
6922 7707
pages = {1458--1465}
6923 7708
}
6924 7709
6925
-@article{lohrDiscoveryPrioritizationSomatic2012a,
7710
+@article{lohrDiscoveryPrioritizationSomatic2012,
6926 7711
title = {Discovery and Prioritization of Somatic Mutations in Diffuse Large {{B-cell}} Lymphoma ({{DLBCL}}) by Whole-Exome Sequencing},
6927 7712
author = {Lohr, Jens G. and Stojanov, Petar and Lawrence, Michael S. and Auclair, Daniel and Chapuy, Bjoern and Sougnez, Carrie and Cruz-Gordillo, Peter and Knoechel, Birgit and Asmann, Yan W. and Slager, Susan L. and Novak, Anne J. and Dogan, Ahmet and Ansell, Stephen M. and Link, Brian K. and Zou, Lihua and Gould, Joshua and Saksena, Gordon and Stransky, Nicolas and Rangel-Escareño, Claudia and Fernandez-Lopez, Juan Carlos and Hidalgo-Miranda, Alfredo and Melendez-Zajgla, Jorge and Hernández-Lemus, Enrique and Schwarz-Cruz y Celis, Angela and Imaz-Rosshandler, Ivan and Ojesina, Akinyemi I. and Jung, Joonil and Pedamallu, Chandra S. and Lander, Eric S. and Habermann, Thomas M. and Cerhan, James R. and Shipp, Margaret A. and Getz, Gad and Golub, Todd R.},
6928 7713
date = {2012-03-06},
... ...
@@ -7016,7 +7801,7 @@ Subject\_term\_id: cancer-genomics;lymphocytes;lymphoid-tissues;oncology}
7016 7801
pages = {1828--1837}
7017 7802
}
7018 7803
7019
-@article{louissaintPediatrictypeNodalFollicular2016a,
7804
+@article{louissaintPediatrictypeNodalFollicular2016,
7020 7805
title = {Pediatric-Type Nodal Follicular Lymphoma: A Biologically Distinct Lymphoma with Frequent {{MAPK}} Pathway Mutations},
7021 7806
shorttitle = {Pediatric-Type Nodal Follicular Lymphoma},
7022 7807
author = {Louissaint, Abner and Schafernak, Kristian T. and Geyer, Julia T. and Kovach, Alexandra E. and Ghandi, Mahmoud and Gratzinger, Dita and Roth, Christine G. and Paxton, Christian N. and Kim, Sunhee and Namgyal, Chungdak and Morin, Ryan and Morgan, Elizabeth A. and Neuberg, Donna S. and South, Sarah T. and Harris, Marian H. and Hasserjian, Robert P. and Hochberg, Ephraim P. and Garraway, Levi A. and Harris, Nancy Lee and Weinstock, David M.},
... ...
@@ -7884,7 +8669,7 @@ Subject\_term\_id: cancer-genomics;lymphocytes;lymphoid-tissues;oncology}
7884 8669
keywords = {Biomarkers Tumor,DNA Copy Number Variations,Gene Expression Profiling,Genome Human,GTP-Binding Protein alpha Subunits G12-G13,High-Throughput Nucleotide Sequencing,Humans,Lymphoma Large B-Cell Diffuse,Mutation,Oligonucleotide Array Sequence Analysis,Real-Time Polymerase Chain Reaction,Reverse Transcriptase Polymerase Chain Reaction,RNA Messenger,Tumor Cells Cultured}
7885 8670
}
7886 8671
7887
-@article{morinSomaticMutationsAltering2010a,
8672
+@article{morinSomaticMutationsAltering2010,
7888 8673
title = {Somatic Mutations Altering {{EZH2}} ({{Tyr641}}) in Follicular and Diffuse Large {{B-cell}} Lymphomas of Germinal-Center Origin},
7889 8674
author = {Morin, Ryan D. and Johnson, Nathalie A. and Severson, Tesa M. and Mungall, Andrew J. and An, Jianghong and Goya, Rodrigo and Paul, Jessica E. and Boyle, Merrill and Woolcock, Bruce W. and Kuchenbauer, Florian and Yap, Damian and Humphries, R. Keith and Griffith, Obi L. and Shah, Sohrab and Zhu, Henry and Kimbara, Michelle and Shashkin, Pavel and Charlot, Jean F. and Tcherpakov, Marianna and Corbett, Richard and Tam, Angela and Varhol, Richard and Smailus, Duane and Moksa, Michelle and Zhao, Yongjun and Delaney, Allen and Qian, Hong and Birol, Inanc and Schein, Jacqueline and Moore, Richard and Holt, Robert and Horsman, Doug E. and Connors, Joseph M. and Jones, Steven and Aparicio, Samuel and Hirst, Martin and Gascoyne, Randy D. and Marra, Marco A.},
7890 8675
date = {2010-02},
... ...
@@ -7967,7 +8752,7 @@ Subject\_term\_id: cancer-genomics;lymphocytes;lymphoid-tissues;oncology}
7967 8752
pages = {7444--7451}
7968 8753
}
7969 8754
7970
-@article{mottokGenomicAlterationsCIITA2015b,
8755
+@article{mottokGenomicAlterationsCIITA2015,
7971 8756
title = {Genomic {{Alterations}} in {{CIITA Are Frequent}} in {{Primary Mediastinal Large B Cell Lymphoma}} and {{Are Associated}} with {{Diminished MHC Class II Expression}}},
7972 8757
author = {Mottok, Anja and Woolcock, Bruce and Chan, Fong Chun and Tong, King Mong and Chong, Lauren and Farinha, Pedro and Telenius, Adèle and Chavez, Elizabeth and Ramchandani, Suvan and Drake, Marie and Boyle, Merrill and Ben-Neriah, Susana and Scott, David W. and Rimsza, Lisa M. and Siebert, Reiner and Gascoyne, Randy D. and Steidl, Christian},
7973 8758
date = {2015-11-17},
... ...
@@ -7985,7 +8770,7 @@ Subject\_term\_id: cancer-genomics;lymphocytes;lymphoid-tissues;oncology}
7985 8770
keywords = {Cell Line,DNA Mutational Analysis,Gene Expression,Genetic Association Studies,Genetic Predisposition to Disease,Histocompatibility Antigens Class II,Humans,Introns,Lymphoma Large B-Cell Diffuse,Male,Mediastinal Neoplasms,Nuclear Proteins,Point Mutation,Sequence Deletion,Trans-Activators,Tumor Escape}
7986 8771
}
7987 8772
7988
-@article{mottokIntegrativeGenomicAnalysis2019b,
8773
+@article{mottokIntegrativeGenomicAnalysis2019,
7989 8774
title = {Integrative Genomic Analysis Identifies Key Pathogenic Mechanisms in Primary Mediastinal Large {{B-cell}} Lymphoma},
7990 8775
author = {Mottok, Anja and Hung, Stacy S. and Chavez, Elizabeth A. and Woolcock, Bruce and Telenius, Adèle and Chong, Lauren C. and Meissner, Barbara and Nakamura, Hisae and Rushton, Christopher and Viganò, Elena and Sarkozy, Clementine and Gascoyne, Randy D. and Connors, Joseph M. and Ben-Neriah, Susana and Mungall, Andrew and Marra, Marco A. and Siebert, Reiner and Scott, David W. and Savage, Kerry J. and Steidl, Christian},
7991 8776
date = {2019-09-05},
... ...
@@ -8084,7 +8869,7 @@ Subject\_term\_id: cancer-genomics;lymphocytes;lymphoid-tissues;oncology}
8084 8869
keywords = {Cancer drivers,Carcinogenesis,Computational Biology,Genome Human,Humans,Local functional mutations bias,Mutation,Neoplasms,Non-coding drivers,Non-coding regions,Open Reading Frames,Promoter Regions Genetic,RNA Long Noncoding,Software}
8085 8870
}
8086 8871
8087
-@article{muppidiLossSignalingGa132014b,
8872
+@article{muppidiLossSignalingGa132014,
8088 8873
title = {Loss of Signaling via {{Gα13}} in Germinal Center {{B}} Cell-Derived Lymphoma},
8089 8874
author = {Muppidi, J. and Schmitz, R. and Green, Jesse A. and Green, Jesse A. and Xiao, Wenming and Larsen, Adrien B. and Braun, S. and An, Jinping and Xu, Ying and Rosenwald, A. and Ott, G. and Gascoyne, R. and Rimsza, L. and Campo, E. and Jaffe, E. and Delabie, J. and Smeland, E. and Braziel, R. and Tubbs, R. and Cook, J. and Weisenburger, D. and Chan, W. and Vaidehi, N. and Staudt, L. and Cyster, J.},
8090 8875
date = {2014},
... ...
@@ -8261,7 +9046,7 @@ Subject\_term\_id: cancer-genomics;lymphocytes;lymphoid-tissues;oncology}
8261 9046
journaltitle = {Nature Medicine}
8262 9047
}
8263 9048
8264
-@article{ngoOncogenicallyActiveMYD882011a,
9049
+@article{ngoOncogenicallyActiveMYD882011,
8265 9050
title = {Oncogenically Active {{MYD88}} Mutations in Human Lymphoma},
8266 9051
author = {Ngo, Vu N. and Young, Ryan M. and Schmitz, Roland and Jhavar, Sameer and Xiao, Wenming and Lim, Kian-Huat and Kohlhammer, Holger and Xu, Weihong and Yang, Yandan and Zhao, Hong and Shaffer, Arthur L. and Romesser, Paul and Wright, George and Powell, John and Rosenwald, Andreas and Muller-Hermelink, Hans Konrad and Ott, German and Gascoyne, Randy D. and Connors, Joseph M. and Rimsza, Lisa M. and Campo, Elias and Jaffe, Elaine S. and Delabie, Jan and Smeland, Erlend B. and Fisher, Richard I. and Braziel, Rita M. and Tubbs, Raymond R. and Cook, J. R. and Weisenburger, Denny D. and Chan, Wing C. and Staudt, Louis M.},
8267 9052
date = {2011-02-03},
... ...
@@ -8496,7 +9281,7 @@ Subject\_term\_id: cancer-genomics;lymphocytes;lymphoid-tissues;oncology}
8496 9281
pages = {1381--1385}
8497 9282
}
8498 9283
8499
-@article{okosunRecurrentMTORC1activatingRRAGC2016a,
9284
+@article{okosunRecurrentMTORC1activatingRRAGC2016,
8500 9285
title = {Recurrent {{mTORC1-activating RRAGC}} Mutations in Follicular Lymphoma},
8501 9286
author = {Okosun, Jessica and Wolfson, Rachel L. and Wang, Jun and Araf, Shamzah and Wilkins, Lucy and Castellano, Brian M. and Escudero-Ibarz, Leire and Al Seraihi, Ahad Fahad and Richter, Julia and Bernhart, Stephan H. and Efeyan, Alejo and Iqbal, Sameena and Matthews, Janet and Clear, Andrew and Guerra-Assunção, José Afonso and Bödör, Csaba and Quentmeier, Hilmar and Mansbridge, Christopher and Johnson, Peter and Davies, Andrew and Strefford, Jonathan C. and Packham, Graham and Barrans, Sharon and Jack, Andrew and Du, Ming-Qing and Calaminici, Maria and Lister, T. Andrew and Auer, Rebecca and Montoto, Silvia and Gribben, John G. and Siebert, Reiner and Chelala, Claude and Zoncu, Roberto and Sabatini, David M. and Fitzgibbon, Jude},
8502 9287
date = {2016-02},
... ...
@@ -8623,7 +9408,7 @@ Subject\_term\_id: cancer-genomics;lymphocytes;lymphoid-tissues;oncology}
8623 9408
keywords = {Cell staining,Cytoplasm,Cytoplasmic staining,Metastasis,Renal cancer,Renal cell carcinoma,Small interfering RNA,Transfection}
8624 9409
}
8625 9410
8626
-@article{ottoGeneticLesionsTRAF32012a,
9411
+@article{ottoGeneticLesionsTRAF32012,
8627 9412
title = {Genetic Lesions of the {{TRAF3}} and {{MAP3K14}} Genes in Classical {{Hodgkin}} Lymphoma},
8628 9413
author = {Otto, Claudia and Giefing, Maciej and Massow, Anne and Vater, Inga and Gesk, Stefan and Schlesner, Matthias and Richter, Julia and Klapper, Wolfram and Hansmann, Martin-Leo and Siebert, Reiner and Küppers, Ralf},
8629 9414
date = {2012-06},
... ...
@@ -8798,7 +9583,7 @@ Subject\_term\_id: cancer-genomics;lymphocytes;lymphoid-tissues;oncology}
8798 9583
pages = {341--346}
8799 9584
}
8800 9585
8801
-@article{pasqualucciHypermutationMultipleProtooncogenes2001a,
9586
+@article{pasqualucciHypermutationMultipleProtooncogenes2001,
8802 9587
title = {Hypermutation of Multiple Proto-Oncogenes in {{B-cell}} Diffuse Large-Cell Lymphomas},
8803 9588
author = {Pasqualucci, L. and Neumeister, P. and Goossens, T. and Nanjangud, G. and Chaganti, R. S. and Küppers, R. and Dalla-Favera, R.},
8804 9589
date = {2001-07-19},
... ...
@@ -8816,7 +9601,7 @@ Subject\_term\_id: cancer-genomics;lymphocytes;lymphoid-tissues;oncology}
8816 9601
keywords = {B-Lymphocytes,DNA Mutational Analysis,DNA-Binding Proteins,Genes myc,Germinal Center,Humans,Lymphoma B-Cell,Lymphoma Large B-Cell Diffuse,Molecular Sequence Data,Mutation,PAX5 Transcription Factor,Proteins,Proto-Oncogenes,Transcription Factors}
8817 9602
}
8818 9603
8819
-@article{pasqualucciInactivatingMutationsAcetyltransferase2011a,
9604
+@article{pasqualucciInactivatingMutationsAcetyltransferase2011,
8820 9605
title = {Inactivating Mutations of Acetyltransferase Genes in {{B-cell}} Lymphoma},
8821 9606
author = {Pasqualucci, Laura and Dominguez-Sola, David and Chiarenza, Annalisa and Fabbri, Giulia and Grunn, Adina and Trifonov, Vladimir and Kasper, Lawryn H. and Lerach, Stephanie and Tang, Hongyan and Ma, Jing and Rossi, Davide and Chadburn, Amy and Murty, Vundavalli V. and Mullighan, Charles G. and Gaidano, Gianluca and Rabadan, Raul and Brindle, Paul K. and Dalla-Favera, Riccardo},
8822 9607
date = {2011-03-10},
... ...
@@ -8835,7 +9620,7 @@ Subject\_term\_id: cancer-genomics;lymphocytes;lymphoid-tissues;oncology}
8835 9620
keywords = {Acetyl Coenzyme A,Acetylation,Acetyltransferases,Animals,Base Sequence,Cells Cultured,CREB-Binding Protein,DNA-Binding Proteins,E1A-Associated p300 Protein,Gene Expression Regulation Neoplastic,HEK293 Cells,Histone Acetyltransferases,Humans,Lymphoma B-Cell,Lymphoma Follicular,Lymphoma Large B-Cell Diffuse,Mice,Mutation,Mutation Missense,Polymorphism Single Nucleotide,Protein Binding,Protein Structure Tertiary,Proto-Oncogene Proteins c-bcl-6,Recurrence,Sequence Deletion,Tumor Suppressor Protein p53}
8836 9621
}
8837 9622
8838
-@article{pasqualucciInactivationPRDM1BLIMP12006a,
9623
+@article{pasqualucciInactivationPRDM1BLIMP12006,
8839 9624
title = {Inactivation of the {{PRDM1}}/{{BLIMP1}} Gene in Diffuse Large {{B}} Cell Lymphoma.},
8840 9625
author = {Pasqualucci, Laura and Compagno, Mara and Houldsworth, Jane and Monti, Stefano and Grunn, Adina and Nandula, Subhadra V and Aster, Jon C and Murty, Vundavally V and Shipp, Margaret A and Dalla-Favera, Riccardo},
8841 9626
date = {2006-02},
... ...
@@ -9295,7 +10080,7 @@ Subject\_term\_id: genome-assembly-algorithms;transcriptomics}
9295 10080
abstract = {Rituximab, a type I anti-CD20 monoclonal antibody (mAb), induces incomplete B cell depletion in some patients with rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE), thus contributing to a poor clinical response. The mechanisms of this resistance remain elusive. The purpose of this study was to determine whether type II mAb are more efficient than type I mAb at depleting B cells from RA and SLE patients, whether internalization influences the efficiency of depletion, and whether Fcγ receptor type IIb (FcγRIIb) and the B cell receptor regulate this internalization process. We used an in vitro whole blood B cell–depletion assay to assess the efficiency of depletion, flow cytometry to study cell surface protein expression, and surface fluorescence–quenching assays to assess rituximab internalization, in samples from patients with RA and patients with SLE. Paired t-test or Mann-Whitney U test was used to compare groups, and Spearman's rank correlation test was used to assess correlation. We found that type II mAb internalized significantly less rituximab than type I mAb and depleted B cells from patients with RA and SLE at least 2-fold more efficiently than type I mAb. Internalization of rituximab was highly variable between patients, was regulated by FcγRIIb, and inversely correlated with cytotoxicity in whole blood B cell–depletion assays. The lowest levels of internalization were seen in IgD– B cells, including postswitched (IgD–CD27+) memory cells. Internalization of type I anti-CD20 mAb was also partially inhibited by anti-IgM stimulation. Variability in internalization of rituximab was observed and was correlated with impaired B cell depletion. Therefore, slower-internalizing type II mAb should be considered as alternative B cell–depleting agents for the treatment of RA and SLE.}
9296 10081
}
9297 10082
9298
-@article{reichelFlowSortingExome2015a,
10083
+@article{reichelFlowSortingExome2015,
9299 10084
title = {Flow Sorting and Exome Sequencing Reveal the Oncogenome of Primary {{Hodgkin}} and {{Reed-Sternberg}} Cells},
9300 10085
author = {Reichel, Jonathan and Chadburn, Amy and Rubinstein, Paul G. and Giulino-Roth, Lisa and Tam, Wayne and Liu, Yifang and Gaiolla, Rafael and Eng, Kenneth and Brody, Joshua and Inghirami, Giorgio and Carlo-Stella, Carmelo and Santoro, Armando and Rahal, Daoud and Totonchy, Jennifer and Elemento, Olivier and Cesarman, Ethel and Roshal, Mikhail},
9301 10086
date = {2015-02-12},
... ...
@@ -9323,7 +10108,7 @@ Subject\_term\_id: genome-assembly-algorithms;transcriptomics}
9323 10108
pages = {55--60}
9324 10109
}
9325 10110
9326
-@article{richterRecurrentMutationID32012a,
10111
+@article{richterRecurrentMutationID32012,
9327 10112
title = {Recurrent Mutation of the {{ID3}} Gene in {{Burkitt}} Lymphoma Identified by Integrated Genome, Exome and Transcriptome Sequencing},
9328 10113
author = {Richter, Julia and Schlesner, Matthias and Hoffmann, Steve and Kreuz, Markus and Leich, Ellen and Burkhardt, Birgit and Rosolowski, Maciej and Ammerpohl, Ole and Wagener, Rabea and Bernhart, Stephan H. and Lenze, Dido and Szczepanowski, Monika and Paulsen, Maren and Lipinski, Simone and Russell, Robert B. and Adam-Klages, Sabine and Apic, Gordana and Claviez, Alexander and Hasenclever, Dirk and Hovestadt, Volker and Hornig, Nadine and Korbel, Jan O. and Kube, Dieter and Langenberger, David and Lawerenz, Chris and Lisfeld, Jasmin and Meyer, Katharina and Picelli, Simone and Pischimarov, Jordan and Radlwimmer, Bernhard and Rausch, Tobias and Rohde, Marius and Schilhabel, Markus and Scholtysik, René and Spang, Rainer and Trautmann, Heiko and Zenz, Thorsten and Borkhardt, Arndt and Drexler, Hans G. and Möller, Peter and MacLeod, Roderick A. F. and Pott, Christiane and Schreiber, Stefan and Trümper, Lorenz and Loeffler, Markus and Stadler, Peter F. and Lichter, Peter and Eils, Roland and Küppers, Ralf and Hummel, Michael and Klapper, Wolfram and Rosenstiel, Philip and Rosenwald, Andreas and Brors, Benedikt and Siebert, Reiner and {ICGC MMML-Seq Project}},
9329 10114
date = {2012-12},
... ...
@@ -9392,7 +10177,7 @@ Subject\_term\_id: genome-assembly-algorithms;transcriptomics}
9392 10177
abstract = {limma is an R/Bioconductor software package that provides an integrated solution for analysing data from gene expression experiments. It contains rich features for handling complex experimental designs and for information borrowing to overcome the problem of small sample sizes. Over the past decade, limma has been a popular choice for gene discovery through differential expression analyses of microarray and high-throughput PCR data. The package contains particularly strong facilities for reading, normalizing and exploring such data. Recently, the capabilities of limma have been significantly expanded in two important directions. First, the package can now perform both differential expression and differential splicing analyses of RNA sequencing (RNA-seq) data. All the downstream analysis tools previously restricted to microarray data are now available for RNA-seq as well. These capabilities allow users to analyse both RNA-seq and microarray data with very similar pipelines. Second, the package is now able to go past the traditional gene-wise expression analyses in a variety of ways, analysing expression profiles in terms of co-regulated sets of genes or in terms of higher-order expression signatures. This provides enhanced possibilities for biological interpretation of gene expression differences. This article reviews the philosophy and design of the limma package, summarizing both new and historical features, with an emphasis on recent enhancements and features that have not been previously described.}
9393 10178
}
9394 10179
9395
-@article{ritzRecurrentMutationsSTAT62009a,
10180
+@article{ritzRecurrentMutationsSTAT62009,
9396 10181
title = {Recurrent Mutations of the {{STAT6 DNA}} Binding Domain in Primary Mediastinal {{B-cell}} Lymphoma},
9397 10182
author = {Ritz, Olga and Guiter, Chrystelle and Castellano, Flavia and Dorsch, Karola and Melzner, Julia and Jais, Jean-Philippe and Dubois, Gwendoline and Gaulard, Philippe and Möller, Peter and Leroy, Karen},
9398 10183
date = {2009-08-06},
... ...
@@ -9573,7 +10358,7 @@ Subject\_term\_id: genome-assembly-algorithms;transcriptomics}
9573 10358
pages = {1405--1409}
9574 10359
}
9575 10360
9576
-@article{rossiAlterationBIRC3Multiple2011a,
10361
+@article{rossiAlterationBIRC3Multiple2011,
9577 10362
title = {Alteration of {{BIRC3}} and Multiple Other {{NF-κB}} Pathway Genes in Splenic Marginal Zone Lymphoma},
9578 10363
author = {Rossi, Davide and Deaglio, Silvia and Dominguez-Sola, David and Rasi, Silvia and Vaisitti, Tiziana and Agostinelli, Claudio and Spina, Valeria and Bruscaggin, Alessio and Monti, Sara and Cerri, Michaela and Cresta, Stefania and Fangazio, Marco and Arcaini, Luca and Lucioni, Marco and Marasca, Roberto and Thieblemont, Catherine and Capello, Daniela and Facchetti, Fabio and Kwee, Ivo and Pileri, Stefano A. and Foà, Robin and Bertoni, Francesco and Dalla-Favera, Riccardo and Pasqualucci, Laura and Gaidano, Gianluca},
9579 10364
date = {2011-11-03},
... ...
@@ -9591,7 +10376,7 @@ Subject\_term\_id: genome-assembly-algorithms;transcriptomics}
9591 10376
keywords = {Baculoviral IAP Repeat-Containing 3 Protein,Case-Control Studies,Cluster Analysis,DNA Mutational Analysis,Gene Expression Profiling,Gene Expression Regulation Neoplastic,Humans,Inhibitor of Apoptosis Proteins,Lymphoma B-Cell Marginal Zone,Microarray Analysis,Models Biological,NF-kappa B,Signal Transduction,Splenic Neoplasms,Ubiquitin-Protein Ligases}
9592 10377
}
9593 10378
9594
-@article{rossiCodingGenomeSplenic2012c,
10379
+@article{rossiCodingGenomeSplenic2012,
9595 10380
title = {The Coding Genome of Splenic Marginal Zone Lymphoma: Activation of {{NOTCH2}} and Other Pathways Regulating Marginal Zone Development},
9596 10381
shorttitle = {The Coding Genome of Splenic Marginal Zone Lymphoma},
9597 10382
author = {Rossi, Davide and Trifonov, Vladimir and Fangazio, Marco and Bruscaggin, Alessio and Rasi, Silvia and Spina, Valeria and Monti, Sara and Vaisitti, Tiziana and Arruga, Francesca and Famà, Rosella and Ciardullo, Carmela and Greco, Mariangela and Cresta, Stefania and Piranda, Daniela and Holmes, Antony and Fabbri, Giulia and Messina, Monica and Rinaldi, Andrea and Wang, Jiguang and Agostinelli, Claudio and Piccaluga, Pier Paolo and Lucioni, Marco and Tabbò, Fabrizio and Serra, Roberto and Franceschetti, Silvia and Deambrogi, Clara and Daniele, Giulia and Gattei, Valter and Marasca, Roberto and Facchetti, Fabio and Arcaini, Luca and Inghirami, Giorgio and Bertoni, Francesco and Pileri, Stefano A. and Deaglio, Silvia and Foà, Robin and Dalla-Favera, Riccardo and Pasqualucci, Laura and Rabadan, Raul and Gaidano, Gianluca},
... ...
@@ -9701,7 +10486,7 @@ Subject\_term\_id: genome-assembly-algorithms;transcriptomics}
9701 10486
keywords = {Antibodies Monoclonal Murine-Derived,Antineoplastic Combined Chemotherapy Protocols,Humans,Lymphoma Large B-Cell Diffuse,Morinlab,Neoplasm Recurrence Local,Rituximab}
9702 10487
}
9703 10488
9704
-@article{russler-germainMutationsAssociatedProgression2023b,
10489
+@article{russler-germainMutationsAssociatedProgression2023,
9705 10490
title = {Mutations Associated with Progression in Follicular Lymphoma Predict Inferior Outcomes at Diagnosis: {{Alliance A151303}}},
9706 10491
author = {Russler-Germain, David A. and Krysiak, Kilannin and Ramirez, Cody A. and Mosior, Matthew and Watkins, Marcus P. and Gomez, Felicia and Skidmore, Zachary L. and Trani, L. and Gao, F. and Geyer, Susan and Cashen, A. and Mehta-Shah, N. and Kahl, B. and Bartlett, N. and Alderuccio, J. and Lossos, I. and Ondrejka, S. and Hsi, E. and Martin, P. and Leonard, J. and Griffith, M. and Griffith, O. and Fehniger, T.},
9707 10492
date = {2023},
... ...
@@ -9958,7 +10743,7 @@ Subject\_term\_id: genome-assembly-algorithms;transcriptomics}
9958 10743
pmcid = {PMC6154734}
9959 10744
}
9960 10745
9961
-@article{sarkozyMutationalLandscapeGray2021a,
10746
+@article{sarkozyMutationalLandscapeGray2021,
9962 10747
title = {Mutational Landscape of Gray Zone Lymphoma},
9963 10748
author = {Sarkozy, Clémentine and Hung, Stacy S. and Chavez, Elizabeth A. and Duns, Gerben and Takata, Katsuyoshi and Chong, Lauren C. and Aoki, Tomohiro and Jiang, Aixiang and Miyata-Takata, Tomoko and Telenius, Adèle and Slack, Graham W. and Molina, Thierry Jo and Ben-Neriah, Susana and Farinha, Pedro and Dartigues, Peggy and Damotte, Diane and Mottok, Anja and Salles, Gilles A. and Casasnovas, Rene-Olivier and Savage, Kerry J. and Laurent, Camille and Scott, David W. and Traverse-Glehen, Alexandra and Steidl, Christian},
9964 10749
date = {2021-04-01},
... ...
@@ -10145,7 +10930,7 @@ Subject\_term\_id: genome-assembly-algorithms;transcriptomics}
10145 10930
keywords = {Basic Helix-Loop-Helix Transcription Factors,Burkitt Lymphoma,Cell Cycle,Cyclin D3,Cyclin-Dependent Kinase 6,Genes myc,Genomics,High-Throughput Nucleotide Sequencing,Humans,Inhibitor of Differentiation Proteins,Molecular Targeted Therapy,Neoplasm Proteins,Phosphatidylinositol 3-Kinases,Receptors Antigen B-Cell,RNA Interference,Signal Transduction}
10146 10931
}
10147 10932
10148
-@article{schmitzGeneticsPathogenesisDiffuse2018a,
10933
+@article{schmitzGeneticsPathogenesisDiffuse2018,
10149 10934
title = {Genetics and {{Pathogenesis}} of {{Diffuse Large B-Cell Lymphoma}}},
10150 10935
author = {Schmitz, Roland and Wright, George W. and Huang, Da Wei and Johnson, Calvin A. and Phelan, James D. and Wang, James Q. and Roulland, Sandrine and Kasbekar, Monica and Young, Ryan M. and Shaffer, Arthur L. and Hodson, Daniel J. and Xiao, Wenming and Yu, Xin and Yang, Yandan and Zhao, Hong and Xu, Weihong and Liu, Xuelu and Zhou, Bin and Du, Wei and Chan, Wing C. and Jaffe, Elaine S. and Gascoyne, Randy D. and Connors, Joseph M. and Campo, Elias and Lopez-Guillermo, Armando and Rosenwald, Andreas and Ott, German and Delabie, Jan and Rimsza, Lisa M. and Tay Kuang Wei, Kevin and Zelenetz, Andrew D. and Leonard, John P. and Bartlett, Nancy L. and Tran, Bao and Shetty, Jyoti and Zhao, Yongmei and Soppet, Dan R. and Pittaluga, Stefania and Wilson, Wyndham H. and Staudt, Louis M.},
10151 10936
date = {2018-04-12},
... ...
@@ -10164,7 +10949,7 @@ Subject\_term\_id: genome-assembly-algorithms;transcriptomics}
10164 10949
keywords = {Antineoplastic Combined Chemotherapy Protocols,Biopsy,Epigenesis Genetic,Exome,Gene Expression Profiling,Genetic Heterogeneity,Genotype,Humans,Kaplan-Meier Estimate,Lymphoma Large B-Cell Diffuse,Mutation,Prognosis,Sequence Analysis DNA,Transcriptome}
10165 10950
}
10166 10951
10167
-@article{schmitzTNFAIP3A20Tumor2009a,
10952
+@article{schmitzTNFAIP3A20Tumor2009,
10168 10953
title = {{{TNFAIP3}} ({{A20}}) Is a Tumor Suppressor Gene in {{Hodgkin}} Lymphoma and Primary Mediastinal {{B}} Cell Lymphoma},
10169 10954
author = {Schmitz, Roland and Hansmann, Martin-Leo and Bohle, Verena and Martin-Subero, Jose Ignacio and Hartmann, Sylvia and Mechtersheimer, Gunhild and Klapper, Wolfram and Vater, Inga and Giefing, Maciej and Gesk, Stefan and Stanelle, Jens and Siebert, Reiner and Küppers, Ralf},
10170 10955
date = {2009-05-11},
... ...
@@ -10183,7 +10968,7 @@ Subject\_term\_id: genome-assembly-algorithms;transcriptomics}
10183 10968
keywords = {Cell Line Tumor,Chromosome Deletion,DNA Transposable Elements,DNA-Binding Proteins,Epstein-Barr Virus Infections,Frameshift Mutation,Genes Tumor Suppressor,Hodgkin Disease,Humans,Intracellular Signaling Peptides and Proteins,Lymphoma B-Cell,Mutation,Mutation Missense,Nuclear Proteins,Polymorphism Single Nucleotide,Transcription Genetic,Tumor Necrosis Factor alpha-Induced Protein 3}
10184 10969
}
10185 10970
10186
-@article{schneiderAlterationsCD58Gene2015a,
10971
+@article{schneiderAlterationsCD58Gene2015,
10187 10972
title = {Alterations of the {{CD58}} Gene in Classical {{Hodgkin}} Lymphoma},
10188 10973
author = {Schneider, Markus and Schneider, Stefanie and Zühlke-Jenisch, Reina and Klapper, Wolfram and Sundström, Christer and Hartmann, Sylvia and Hansmann, Martin-Leo and Siebert, Reiner and Küppers, Ralf and Giefing, Maciej},
10189 10974
date = {2015-10},
... ...
@@ -10719,7 +11504,7 @@ Subject\_term\_id: genome-assembly-algorithms;transcriptomics}
10719 11504
pages = {781--786}
10720 11505
}
10721 11506
10722
-@article{spinaGeneticsNodalMarginal2016b,
11507
+@article{spinaGeneticsNodalMarginal2016,
10723 11508
title = {The Genetics of Nodal Marginal Zone Lymphoma},
10724 11509
author = {Spina, Valeria and Khiabanian, Hossein and Messina, Monica and Monti, Sara and Cascione, Luciano and Bruscaggin, Alessio and Spaccarotella, Elisa and Holmes, Antony B. and Arcaini, Luca and Lucioni, Marco and Tabbò, Fabrizio and Zairis, Sakellarios and Diop, Fary and Cerri, Michaela and Chiaretti, Sabina and Marasca, Roberto and Ponzoni, Maurilio and Deaglio, Silvia and Ramponi, Antonio and Tiacci, Enrico and Pasqualucci, Laura and Paulli, Marco and Falini, Brunangelo and Inghirami, Giorgio and Bertoni, Francesco and Foà, Robin and Rabadan, Raul and Gaidano, Gianluca and Rossi, Davide},
10725 11510
date = {2016-09-08},
... ...
@@ -11251,7 +12036,7 @@ Subject\_term\_id: genome-assembly-algorithms;transcriptomics}
11251 12036
keywords = {Morinlab}
11252 12037
}
11253 12038
11254
-@article{tiacciAnalyzingPrimaryHodgkin2012a,
12039
+@article{tiacciAnalyzingPrimaryHodgkin2012,
11255 12040
title = {Analyzing Primary {{Hodgkin}} and {{Reed-Sternberg}} Cells to Capture the Molecular and Cellular Pathogenesis of Classical {{Hodgkin}} Lymphoma},
11256 12041
author = {Tiacci, Enrico and Döring, Claudia and Brune, Verena and family=Noesel, given=Carel J. M., prefix=van, useprefix=true and Klapper, Wolfram and Mechtersheimer, Gunhild and Falini, Brunangelo and Küppers, Ralf and Hansmann, Martin-Leo},
11257 12042
date = {2012-11-29},
... ...
@@ -11269,7 +12054,7 @@ Subject\_term\_id: genome-assembly-algorithms;transcriptomics}
11269 12054
keywords = {Adult,Apoptosis Regulatory Proteins,B-Lymphocytes,Cell Line Tumor,Cells Cultured,Cluster Analysis,Gene Expression Profiling,Gene Expression Regulation Neoplastic,Hodgkin Disease,Humans,Immunohistochemistry,Inositol Polyphosphate 5-Phosphatases,Lymphoma B-Cell,Membrane Proteins,Mitochondrial Proteins,Oligonucleotide Array Sequence Analysis,Phosphatidylinositol-345-Trisphosphate 5-Phosphatases,Phosphoric Monoester Hydrolases,Reed-Sternberg Cells,Tumor Cells Cultured,Tumor Microenvironment}
11270 12055
}
11271 12056
11272
-@article{tiacciBRAFMutationsHairycell2011a,
12057
+@article{tiacciBRAFMutationsHairycell2011,
11273 12058
title = {{{BRAF}} Mutations in Hairy-Cell Leukemia},
11274 12059
author = {Tiacci, Enrico and Trifonov, Vladimir and Schiavoni, Gianluca and Holmes, Antony and Kern, Wolfgang and Martelli, Maria Paola and Pucciarini, Alessandra and Bigerna, Barbara and Pacini, Roberta and Wells, Victoria A. and Sportoletti, Paolo and Pettirossi, Valentina and Mannucci, Roberta and Elliott, Oliver and Liso, Arcangelo and Ambrosetti, Achille and Pulsoni, Alessandro and Forconi, Francesco and Trentin, Livio and Semenzato, Gianpietro and Inghirami, Giorgio and Capponi, Monia and Di Raimondo, Francesco and Patti, Caterina and Arcaini, Luca and Musto, Pellegrino and Pileri, Stefano and Haferlach, Claudia and Schnittger, Susanne and Pizzolo, Giovanni and Foà, Robin and Farinelli, Laurent and Haferlach, Torsten and Pasqualucci, Laura and Rabadan, Raul and Falini, Brunangelo},
11275 12060
date = {2011-06-16},
... ...
@@ -11288,7 +12073,7 @@ Subject\_term\_id: genome-assembly-algorithms;transcriptomics}
11288 12073
keywords = {Adult,Aged,Extracellular Signal-Regulated MAP Kinases,Female,Humans,Leukemia Hairy Cell,Lymphoma B-Cell,Male,MAP Kinase Kinase Kinases,Middle Aged,Mutation,Proto-Oncogene Proteins B-raf,Sequence Analysis DNA}
11289 12074
}
11290 12075
11291
-@article{tiacciPervasiveMutationsJAKSTAT2018b,
12076
+@article{tiacciPervasiveMutationsJAKSTAT2018,
11292 12077
title = {Pervasive Mutations of {{JAK-STAT}} Pathway Genes in Classical {{Hodgkin}} Lymphoma},
11293 12078
author = {Tiacci, Enrico and Ladewig, Erik and Schiavoni, Gianluca and Penson, Alex and Fortini, Elisabetta and Pettirossi, Valentina and Wang, Yuchun and Rosseto, Ariele and Venanzi, Alessandra and Vlasevska, Sofija and Pacini, Roberta and Piattoni, Simonetta and Tabarrini, Alessia and Pucciarini, Alessandra and Bigerna, Barbara and Santi, Alessia and Gianni, Alessandro M. and Viviani, Simonetta and Cabras, Antonello and Ascani, Stefano and Crescenzi, Barbara and Mecucci, Cristina and Pasqualucci, Laura and Rabadan, Raul and Falini, Brunangelo},
11294 12079
date = {2018-05-31},
... ...
@@ -11616,7 +12401,7 @@ Subject\_term\_id: genome-assembly-algorithms;transcriptomics}
11616 12401
urldate = {2022-10-03}
11617 12402
}
11618 12403
11619
-@article{viganoSomaticIL4RMutations2018b,
12404
+@article{viganoSomaticIL4RMutations2018,
11620 12405
title = {Somatic {{IL4R}} Mutations in Primary Mediastinal Large {{B-cell}} Lymphoma Lead to Constitutive {{JAK-STAT}} Signaling Activation},
11621 12406
author = {Viganò, Elena and Gunawardana, Jay and Mottok, Anja and Van Tol, Tessa and Mak, Katina and Chan, Fong Chun and Chong, Lauren and Chavez, Elizabeth and Woolcock, Bruce and Takata, Katsuyoshi and Twa, David and Shulha, Hennady P. and Telenius, Adèle and Kutovaya, Olga and Hung, Stacy S. and Healy, Shannon and Ben-Neriah, Susana and Leroy, Karen and Gaulard, Philippe and Diepstra, Arjan and Kridel, Robert and Savage, Kerry J. and Rimsza, Lisa and Gascoyne, Randy and Steidl, Christian},
11622 12407
date = {2018-05-03},
... ...
@@ -11975,7 +12760,7 @@ Subject\_term\_id: genome-assembly-algorithms;transcriptomics}
11975 12760
langid = {english}
11976 12761
}
11977 12762
11978
-@article{wenigerMutationsTumorSuppressor2006a,
12763
+@article{wenigerMutationsTumorSuppressor2006,
11979 12764
title = {Mutations of the Tumor Suppressor Gene {{SOCS-1}} in Classical {{Hodgkin}} Lymphoma Are Frequent and Associated with Nuclear Phospho-{{STAT5}} Accumulation},
11980 12765
author = {Weniger, M. A. and Melzner, I. and Menz, C. K. and Wegener, S. and Bucur, A. J. and Dorsch, K. and Mattfeldt, T. and Barth, T. F. E. and Möller, P.},
11981 12766
date = {2006-04-27},
... ...
@@ -12033,7 +12818,7 @@ Subject\_term\_id: genome-assembly-algorithms;transcriptomics}
12033 12818
keywords = {Cancer genomics,DNA sequencing,Research data}
12034 12819
}
12035 12820
12036
-@article{wienandGenomicAnalysesFlowsorted2019b,
12821
+@article{wienandGenomicAnalysesFlowsorted2019,
12037 12822
title = {Genomic Analyses of Flow-Sorted {{Hodgkin Reed-Sternberg}} Cells Reveal Complementary Mechanisms of Immune Evasion},
12038 12823
author = {Wienand, Kirsty and Chapuy, Bjoern and Stewart, Chip and Dunford, Andrew J. and Wu, David and Kim, Jaegil and Kamburov, Atanas and Wood, Timothy R. and Cader, Fathima Zumla and Ducar, Matthew D. and Thorner, Aaron R. and Nag, Anwesha and Heubeck, Alexander T. and Buonopane, Michael J. and Redd, Robert A. and Bojarczuk, Kamil and Lawton, Lee N. and Armand, Philippe and Rodig, Scott J. and Fromm, Jonathan R. and Getz, Gad and Shipp, Margaret A.},
12039 12824
date = {2019-12-10},
... ...
@@ -12392,7 +13177,7 @@ Subject\_term\_id: genome-assembly-algorithms;transcriptomics}
12392 13177
pages = {1678--1687}
12393 13178
}
12394 13179
12395
-@article{yanBCRTLRSignaling2012a,
13180
+@article{yanBCRTLRSignaling2012,
12396 13181
title = {{{BCR}} and {{TLR}} Signaling Pathways Are Recurrently Targeted by Genetic Changes in Splenic Marginal Zone Lymphomas},
12397 13182
author = {Yan, Qingguo and Huang, Yuanxue and Watkins, A. James and Kocialkowski, Sylvia and Zeng, Naiyan and Hamoudi, Rifat A. and Isaacson, Peter G. and family=Leval, given=Laurence, prefix=de, useprefix=true and Wotherspoon, Andrew and Du, Ming-Qing},
12398 13183
date = {2012-04},
... ...
@@ -12501,7 +13286,7 @@ Subject\_term\_id: genome-assembly-algorithms;transcriptomics}
12501 13286
keywords = {C-myc,Cancer,CDC4,Cyclin E,FBXW7,HTLV,Jun,mcl-1,mTOR,Notch}
12502 13287
}
12503 13288
12504
-@article{yildizActivatingSTAT6Mutations2015c,
13289
+@article{yildizActivatingSTAT6Mutations2015,
12505 13290
title = {Activating {{STAT6}} Mutations in Follicular Lymphoma},
12506 13291
author = {Yildiz, Mehmet and Li, Hongxiu and Bernard, Denzil and Amin, Nisar A. and Ouillette, Peter and Jones, Siân and Saiya-Cork, Kamlai and Parkin, Brian and Jacobi, Kathryn and Shedden, Kerby and Wang, Shaomeng and Chang, Alfred E. and Kaminski, Mark S. and Malek, Sami N.},
12507 13292
date = {2015-01-22},
papers/abateDistinctViralMutational2015.md
... ...
@@ -0,0 +1,43 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @abateDistinctViralMutational2015
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|BL|0|1|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 0
26
+New Tier 1, BL Tier 1, 0
27
+This study, New Tier 2, 1
28
+New Tier 2, BL Tier 2, 1
29
+This study, New Tier 3, 0
30
+New Tier 3, BL Tier 3, 0
31
+All other BL studies, BL Tier 1, 32
32
+All other BL studies, BL Tier 2, 71
33
+All other BL studies, BL Tier 3, 70
34
+```
35
+
36
+### Tier 2
37
+|New gene|BL tier|
38
+|:-|:-:|
39
+|[CCNF](../CCNF)|2 |
40
+
41
+
42
+# Details
43
+
papers/abateDistinctViralMutational2015a.md
... ...
@@ -1,40 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @abateDistinctViralMutational2015a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|BL|0|1|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 0
26
-New Tier 1, BL Tier 1, 0
27
-This study, New Tier 2, 1
28
-New Tier 2, BL Tier 2, 1
29
-All other BL studies, BL Tier 1, 29
30
-All other BL studies, BL Tier 2, 156
31
-```
32
-
33
-### Tier 2
34
-|New gene|BL tier|
35
-|:-|:-:|
36
-|[CCNF](../CCNF)|2 |
37
-
38
-
39
-# Details
40
-
papers/albuquerqueEnhancingKnowledgeDiscovery2017.md
... ...
@@ -0,0 +1,58 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @albuquerqueEnhancingKnowledgeDiscovery2017
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|4|6|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 4
26
+New Tier 1, DLBCL Tier 1, 4
27
+This study, New Tier 2, 6
28
+New Tier 2, DLBCL Tier 2, 6
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
31
+All other DLBCL studies, DLBCL Tier 1, 121
32
+All other DLBCL studies, DLBCL Tier 2, 204
33
+All other DLBCL studies, DLBCL Tier 3, 387
34
+```
35
+
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|DLBCL tier|
40
+|:-|:-:|
41
+|[BTK](../BTK)|1 |
42
+|[SETD1B](../SETD1B)|1 |
43
+|[SPEN](../SPEN)|1 |
44
+|[TET2](../TET2)|1 |
45
+
46
+### Tier 2
47
+|New gene|DLBCL tier|
48
+|:-|:-:|
49
+|[ASXL3](../ASXL3)|2 |
50
+|[CEP164](../CEP164)|2 |
51
+|[DNMT3B](../DNMT3B)|2 |
52
+|[ERAP2](../ERAP2)|2 |
53
+|[UBR5](../UBR5)|2 |
54
+|[UHRF1BP1](../UHRF1BP1)|2 |
55
+
56
+
57
+# Details
58
+
papers/albuquerqueEnhancingKnowledgeDiscovery2017a.md
... ...
@@ -1,44 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @albuquerqueEnhancingKnowledgeDiscovery2017a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|3|0|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 3
26
-New Tier 1, DLBCL Tier 1, 3
27
-This study, New Tier 2, 0
28
-New Tier 2, DLBCL Tier 2, 0
29
-All other DLBCL studies, DLBCL Tier 1, 125
30
-All other DLBCL studies, DLBCL Tier 2, 198
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|DLBCL tier|
37
-|:-|:-:|
38
-|[BTK](../BTK)|1 |
39
-|[TET2](../TET2)|1 |
40
-|[TMSB4X](../TMSB4X)|1 |
41
-
42
-
43
-# Details
44
-
papers/arthurGenomewideDiscoverySomatic2018.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @arthurGenomewideDiscoverySomatic2018
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|8|12|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|2|14|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -22,12 +22,15 @@ config:
22 22
suffix: ' genes)'
23 23
---
24 24
sankey-beta
25
-This study, New Tier 1, 8
26
-New Tier 1, DLBCL Tier 1, 8
27
-This study, New Tier 2, 12
28
-New Tier 2, DLBCL Tier 2, 12
29
-All other DLBCL studies, DLBCL Tier 1, 120
30
-All other DLBCL studies, DLBCL Tier 2, 186
25
+This study, New Tier 1, 2
26
+New Tier 1, DLBCL Tier 1, 2
27
+This study, New Tier 2, 14
28
+New Tier 2, DLBCL Tier 2, 14
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
31
+All other DLBCL studies, DLBCL Tier 1, 123
32
+All other DLBCL studies, DLBCL Tier 2, 196
33
+All other DLBCL studies, DLBCL Tier 3, 387
31 34
```
32 35
33 36
## Novel genes reported in this study
... ...
@@ -35,14 +38,8 @@ All other DLBCL studies, DLBCL Tier 2, 186
35 38
### Tier 1
36 39
|New gene|DLBCL tier|
37 40
|:-|:-:|
38
-|[BCL7A](../BCL7A)|1 |
39
-|[ETV6](../ETV6)|1 |
40
-|[GRHPR](../GRHPR)|1 |
41
-|[LCOR](../LCOR)|1 |
42
-|[MEF2C](../MEF2C)|1 |
43
-|[OSBPL10](../OSBPL10)|1 |
44
-|[PIM2](../PIM2)|1 |
45
-|[ZC3H12A](../ZC3H12A)|1 |
41
+|[FBXO11](../FBXO11)|1 |
42
+|[RFX7](../RFX7)|1 |
46 43
47 44
### Tier 2
48 45
|New gene|DLBCL tier|
... ...
@@ -55,21 +52,13 @@ All other DLBCL studies, DLBCL Tier 2, 186
55 52
|[MALAT1](../MALAT1)|2 |
56 53
|[NEAT1](../NEAT1)|2 |
57 54
|[RFTN1](../RFTN1)|2 |
55
+|[RHEX](../RHEX)|2 |
58 56
|[SERPINA9](../SERPINA9)|2 |
59 57
|[ST6GAL1](../ST6GAL1)|2 |
60 58
|[TBC1D4](../TBC1D4)|2 |
59
+|[USP7](../USP7)|2 |
61 60
|[ZCCHC7](../ZCCHC7)|2 |
62 61
63 62
64
-## Data Availability
65
-
66
-|**Repository**|**Accession**|
67
-|-|-|
68
-|[dbGAP](https://www.ncbi.nlm.nih.gov/gap/)| phs000532.v18.p6 |
69
-|[EGA](https://ega-archive.org/)|EGAD00001003783|
70
-|[EGA](https://ega-archive.org/)|EGAD00001004142|
71
-
72
-
73
-
74 63
# Details
75 64
papers/barariaCathepsinAlterationsInduce2020.md
... ...
@@ -0,0 +1,45 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @barariaCathepsinAlterationsInduce2020
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|FL|1|0|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 1
26
+New Tier 1, FL Tier 1, 1
27
+This study, New Tier 2, 0
28
+New Tier 2, FL Tier 2, 0
29
+This study, New Tier 3, 0
30
+New Tier 3, FL Tier 3, 0
31
+All other FL studies, FL Tier 1, 53
32
+All other FL studies, FL Tier 2, 59
33
+All other FL studies, FL Tier 3, 0
34
+```
35
+
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|FL tier|
40
+|:-|:-:|
41
+|[CTSS](../CTSS)|1 |
42
+
43
+
44
+# Details
45
+
papers/barariaCathepsinAlterationsInduce2020c.md
... ...
@@ -1,42 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @barariaCathepsinAlterationsInduce2020c
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|FL|1|0|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 1
26
-New Tier 1, FL Tier 1, 1
27
-This study, New Tier 2, 0
28
-New Tier 2, FL Tier 2, 0
29
-All other FL studies, FL Tier 1, 65
30
-All other FL studies, FL Tier 2, 50
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|FL tier|
37
-|:-|:-:|
38
-|[CTSS](../CTSS)|1 |
39
-
40
-
41
-# Details
42
-
papers/beaLandscapeSomaticMutations2013.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @beaLandscapeSomaticMutations2013
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|MCL|11|16|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|MCL|11|16|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 11
26 26
New Tier 1, MCL Tier 1, 11
27 27
This study, New Tier 2, 16
28 28
New Tier 2, MCL Tier 2, 16
29
+This study, New Tier 3, 0
30
+New Tier 3, MCL Tier 3, 0
29 31
All other MCL studies, MCL Tier 1, 12
30 32
All other MCL studies, MCL Tier 2, 30
33
+All other MCL studies, MCL Tier 3, 0
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/bohleRoleEarlyBcell2013.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @bohleRoleEarlyBcell2013
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|1|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|1|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, DLBCL Tier 1, 1
27 27
This study, New Tier 2, 0
28 28
New Tier 2, DLBCL Tier 2, 0
29
-All other DLBCL studies, DLBCL Tier 1, 127
30
-All other DLBCL studies, DLBCL Tier 2, 198
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
31
+All other DLBCL studies, DLBCL Tier 1, 124
32
+All other DLBCL studies, DLBCL Tier 2, 210
33
+All other DLBCL studies, DLBCL Tier 3, 387
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/braggioGenomicAnalysisMarginal2012.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @braggioGenomicAnalysisMarginal2012
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|MZL|1|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|MZL|1|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, MZL Tier 1, 1
27 27
This study, New Tier 2, 0
28 28
New Tier 2, MZL Tier 2, 0
29
+This study, New Tier 3, 0
30
+New Tier 3, MZL Tier 3, 0
29 31
All other MZL studies, MZL Tier 1, 41
30 32
All other MZL studies, MZL Tier 2, 74
33
+All other MZL studies, MZL Tier 3, 0
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/burkhardtClinicalRelevanceMolecular2022.md
... ...
@@ -0,0 +1,67 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @burkhardtClinicalRelevanceMolecular2022
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|BL|0|25|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 0
26
+New Tier 1, BL Tier 1, 0
27
+This study, New Tier 2, 25
28
+New Tier 2, BL Tier 2, 25
29
+This study, New Tier 3, 0
30
+New Tier 3, BL Tier 3, 0
31
+All other BL studies, BL Tier 1, 32
32
+All other BL studies, BL Tier 2, 47
33
+All other BL studies, BL Tier 3, 70
34
+```
35
+
36
+### Tier 2
37
+|New gene|BL tier|
38
+|:-|:-:|
39
+|[ADAMTS5](../ADAMTS5)|2 |
40
+|[ADNP](../ADNP)|2 |
41
+|[AGO4](../AGO4)|2 |
42
+|[BCL2](../BCL2)|2 |
43
+|[BTG1](../BTG1)|2 |
44
+|[CD79A](../CD79A)|2 |
45
+|[CHD4](../CHD4)|2 |
46
+|[CPXM2](../CPXM2)|2 |
47
+|[E2F2](../E2F2)|2 |
48
+|[EDNRB](../EDNRB)|2 |
49
+|[ERAP1](../ERAP1)|2 |
50
+|[HLA-DQB1](../HLA-DQB1)|2 |
51
+|[KLHL26](../KLHL26)|2 |
52
+|[NOA1](../NOA1)|2 |
53
+|[PIM1](../PIM1)|2 |
54
+|[PPP6R2](../PPP6R2)|2 |
55
+|[PREX1](../PREX1)|2 |
56
+|[REV3L](../REV3L)|2 |
57
+|[RPL10](../RPL10)|2 |
58
+|[SAL3](../SAL3)|2 |
59
+|[TTN](../TTN)|2 |
60
+|[VWA7](../VWA7)|2 |
61
+|[ZAN](../ZAN)|2 |
62
+|[ZBTB7A](../ZBTB7A)|2 |
63
+|[ZNF85](../ZNF85)|2 |
64
+
65
+
66
+# Details
67
+
papers/burkhardtClinicalRelevanceMolecular2022b.md
... ...
@@ -1,64 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @burkhardtClinicalRelevanceMolecular2022b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|BL|0|25|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 0
26
-New Tier 1, BL Tier 1, 0
27
-This study, New Tier 2, 25
28
-New Tier 2, BL Tier 2, 25
29
-All other BL studies, BL Tier 1, 29
30
-All other BL studies, BL Tier 2, 132
31
-```
32
-
33
-### Tier 2
34
-|New gene|BL tier|
35
-|:-|:-:|
36
-|[ADAMTS5](../ADAMTS5)|2 |
37
-|[ADNP](../ADNP)|2 |
38
-|[AGO4](../AGO4)|2 |
39
-|[BCL2](../BCL2)|2 |
40
-|[BTG1](../BTG1)|2 |
41
-|[CD79A](../CD79A)|2 |
42
-|[CHD4](../CHD4)|2 |
43
-|[CPXM2](../CPXM2)|2 |
44
-|[E2F2](../E2F2)|2 |
45
-|[EDNRB](../EDNRB)|2 |
46
-|[ERAP1](../ERAP1)|2 |
47
-|[HLA-DQB1](../HLA-DQB1)|2 |
48
-|[KLHL26](../KLHL26)|2 |
49
-|[NOA1](../NOA1)|2 |
50
-|[PIM1](../PIM1)|2 |
51
-|[PPP6R2](../PPP6R2)|2 |
52
-|[PREX1](../PREX1)|2 |
53
-|[REV3L](../REV3L)|2 |
54
-|[RPL10](../RPL10)|2 |
55
-|[SAL3](../SAL3)|2 |
56
-|[TTN](../TTN)|2 |
57
-|[VWA7](../VWA7)|2 |
58
-|[ZAN](../ZAN)|2 |
59
-|[ZBTB7A](../ZBTB7A)|2 |
60
-|[ZNF85](../ZNF85)|2 |
61
-
62
-
63
-# Details
64
-
papers/chapuyMolecularSubtypesDiffuse2018.md
... ...
@@ -0,0 +1,81 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @chapuyMolecularSubtypesDiffuse2018
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|10|13|6|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 10
26
+New Tier 1, DLBCL Tier 1, 10
27
+This study, New Tier 2, 13
28
+New Tier 2, DLBCL Tier 2, 13
29
+This study, New Tier 3, 6
30
+New Tier 3, DLBCL Tier 3, 6
31
+All other DLBCL studies, DLBCL Tier 1, 115
32
+All other DLBCL studies, DLBCL Tier 2, 197
33
+All other DLBCL studies, DLBCL Tier 3, 381
34
+```
35
+
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|DLBCL tier| Average variant quality | QC outcome |
40
+|:-|:-:|:-:|:-:|
41
+|[EEF1A1](../EEF1A1)|1 || |
42
+|[HIST1H1B](../HIST1H1B)|1 || |
43
+|[HIST1H2AM](../HIST1H2AM)|1 || |
44
+|[HIST2H2BE](../HIST2H2BE)|1 || |
45
+|[HLA-C](../HLA-C)|1 || |
46
+|[HVCN1](../HVCN1)|1 || |
47
+|[LTB](../LTB)|1 || |
48
+|[POU2AF1](../POU2AF1)|1 || |
49
+|[SIN3A](../SIN3A)|1 || |
50
+|[ZC3H12A](../ZC3H12A)|1 || |
51
+
52
+### Tier 2
53
+|New gene|DLBCL tier| Average variant quality | QC outcome |
54
+|:-|:-:|:-:|:-:|
55
+|[BCL11A](../BCL11A)|2 || |
56
+|[COQ7](../COQ7)|2 |&starf; &starf; &starf; &star; &star; |PASS |
57
+|[CRIP1](../CRIP1)|2 |&starf; &starf; &starf; &star; &star; |PASS |
58
+|[DOCK1](../DOCK1)|2 |&starf; &starf; &starf; &star; &star; |PASS |
59
+|[GABRA2](../GABRA2)|2 || |
60
+|[HLA-DMA](../HLA-DMA)|2 || |
61
+|[IGLL5](../IGLL5)|2 || |
62
+|[IL6](../IL6)|2 |&starf; &starf; &starf; &star; &star; |PASS |
63
+|[LYN](../LYN)|2 |&starf; &starf; &starf; &starf; &star; |PASS |
64
+|[NAV1](../NAV1)|2 || |
65
+|[PRPS1](../PRPS1)|2 |&starf; &starf; &starf; &starf; &star; |PASS |
66
+|[TLR2](../TLR2)|2 |&starf; &starf; &starf; &starf; &star; |PASS |
67
+|[ZNF423](../ZNF423)|2 |&starf; &starf; &starf; &star; &star; |PASS |
68
+
69
+### Tier 3
70
+|New gene|DLBCL tier| Average variant quality | QC outcome |
71
+|:-|:-:|:-:|:-:|
72
+|[CCL4](../CCL4)|3 |&star; &star; &star; &star; &star; |FAIL |
73
+|[FUT5](../FUT5)|3 |&starf; &star; &star; &star; &star; |FAIL |
74
+|[NANOG](../NANOG)|3 |&star; &star; &star; &star; &star; |FAIL |
75
+|[NLRP8](../NLRP8)|3 |&starf; &starf; &star; &star; &star; |FAIL |
76
+|[PDE4DIP](../PDE4DIP)|3 |&starf; &starf; &star; &star; &star; |FAIL |
77
+|[RAD9A](../RAD9A)|3 |&star; &star; &star; &star; &star; |FAIL |
78
+
79
+
80
+# Details
81
+
papers/chapuyMolecularSubtypesDiffuse2018b.md
... ...
@@ -1,71 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @chapuyMolecularSubtypesDiffuse2018b
7
-## Summary of novel genes
8
-
9
-|Entity| Total| Tier 1| Tier 2| Tier 2 Pass| Tier 2 Fail| Fail Rate|
10
-|:-:|:-:|:-:|:-:|:-:|:-:|:-:|
11
-|DLBCL|19|2|17| 10\* | 7 | 41% |
12
-
13
-
14
-```mermaid
15
----
16
-config:
17
- sankey:
18
- showValues: true
19
- linkColor: target
20
- width: 600
21
- height: 300
22
- nodeAlignment: right
23
- prefix: '('
24
- suffix: ' genes)'
25
----
26
-sankey-beta
27
-New to this study, DLBCL Tier 1, 2
28
-New to this study, DLBCL Tier 2, 17
29
-DLBCL Tier 2, Pass QC, 10
30
-DLBCL Tier 2, Fail QC, 7
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|DLBCL tier|
37
-|:-|:-:|
38
-|[HIST1H1B](../HIST1H1B)|1 |
39
-|[LTB](../LTB)|1 |
40
-
41
-### Tier 2
42
-|Novel Gene|DLBCL tier|Average variant quality|QC outcome|
43
-|:-|:-:|:-:|:-:|
44
-|[GABRA2](../GABRA2)|2 |TBD|TBD|
45
-|[COQ7](../COQ7)|2 |&starf; &starf; &starf; &star; &star; |**Pass**|
46
-|[CRIP1](../CRIP1)|2 |&starf; &starf; &starf; &star; &star; |**Pass**|
47
-|[DOCK1](../DOCK1)|2 |&starf; &starf; &starf; &star; &star; |**Pass**|
48
-|[NAV1](../NAV1)|2 |TBD|TBD|
49
-|[IL6](../IL6)|2 |&starf; &starf; &starf; &star; &star; |**Pass**|
50
-|[LYN](../LYN)|2 |&starf; &starf; &starf; &starf; &star; |**Pass**|
51
-|[PRPS1](../PRPS1)|2 |&starf; &starf; &starf; &starf; &star; |**Pass**|
52
-|[TLR2](../TLR2)|2 |&starf; &starf; &starf; &starf; &star; |**Pass**|
53
-|[ZNF423](../ZNF423)|2 |&starf; &starf; &starf; &star; &star; |**Pass**|
54
-|[FUT5](../FUT5)|2 |&starf; &star; &star; &star; &star; |**Fail**|
55
-|[RAD9A](../RAD9A)|2 |*No variants reported*|**Fail**|
56
-|[CCL4](../CCL4)|2 |*No variants reported*|**Fail**|
57
-|[SMEK1](../SMEK1)|2 |*No variants in paired samples*|**Fail**|
58
-|[NANOG](../NANOG)|2 |*No variants reported*|**Fail**|
59
-|[NLRP8](../NLRP8)|2 |&starf; &starf; &star; &star; &star; |**Fail**|
60
-|[PDE4DIP](../PDE4DIP)|2 |&starf; &starf; &star; &star; &star; |**Fail**|
61
-
62
-
63
-## Data Availability
64
-
65
-|**Repository**|**Accession**|
66
-|-|-|
67
-|[dbGAP](https://www.ncbi.nlm.nih.gov/gap/)| phs000450.v1.p1|
68
-|[dbGAP](https://www.ncbi.nlm.nih.gov/gap/)| phs000450.v3.p1|
69
-
70
-# Details
71
-
papers/cheungAcquiredTNFRSF14Mutations2010.md
... ...
@@ -0,0 +1,45 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @cheungAcquiredTNFRSF14Mutations2010
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|FL|1|0|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 1
26
+New Tier 1, FL Tier 1, 1
27
+This study, New Tier 2, 0
28
+New Tier 2, FL Tier 2, 0
29
+This study, New Tier 3, 0
30
+New Tier 3, FL Tier 3, 0
31
+All other FL studies, FL Tier 1, 53
32
+All other FL studies, FL Tier 2, 59
33
+All other FL studies, FL Tier 3, 0
34
+```
35
+
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|FL tier|
40
+|:-|:-:|
41
+|[TNFRSF14](../TNFRSF14)|1 |
42
+
43
+
44
+# Details
45
+
papers/cheungAcquiredTNFRSF14Mutations2010a.md
... ...
@@ -1,43 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @cheungAcquiredTNFRSF14Mutations2010a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|FL|1|0|
12
-|DLBCL|1|0|
13
-```mermaid
14
----
15
-config:
16
- sankey:
17
- showValues: true
18
- linkColor: target
19
- width: 600
20
- height: 300
21
- nodeAlignment: right
22
- prefix: '('
23
- suffix: ' genes)'
24
----
25
-sankey-beta
26
-This study, New Tier 1, 1
27
-New Tier 1, DLBCL Tier 1, 1
28
-This study, New Tier 2, 0
29
-New Tier 2, DLBCL Tier 2, 0
30
-All other DLBCL studies, DLBCL Tier 1, 127
31
-All other DLBCL studies, DLBCL Tier 2, 198
32
-```
33
-
34
-## Novel genes reported in this study
35
-
36
-### Tier 1
37
-|New gene|FL tier|DLBCL tier|
38
-|:-|:-:|:-:|
39
-|[TNFRSF14](../TNFRSF14)|1 |1 |
40
-
41
-
42
-# Details
43
-
papers/compagnoMutationsMultipleGenes2009.md
... ...
@@ -0,0 +1,45 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @compagnoMutationsMultipleGenes2009
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|1|0|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 1
26
+New Tier 1, DLBCL Tier 1, 1
27
+This study, New Tier 2, 0
28
+New Tier 2, DLBCL Tier 2, 0
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
31
+All other DLBCL studies, DLBCL Tier 1, 124
32
+All other DLBCL studies, DLBCL Tier 2, 210
33
+All other DLBCL studies, DLBCL Tier 3, 387
34
+```
35
+
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|DLBCL tier|
40
+|:-|:-:|
41
+|[TNFAIP3](../TNFAIP3)|1 |
42
+
43
+
44
+# Details
45
+
papers/compagnoMutationsMultipleGenes2009a.md
... ...
@@ -1,42 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @compagnoMutationsMultipleGenes2009a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|1|0|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 1
26
-New Tier 1, DLBCL Tier 1, 1
27
-This study, New Tier 2, 0
28
-New Tier 2, DLBCL Tier 2, 0
29
-All other DLBCL studies, DLBCL Tier 1, 127
30
-All other DLBCL studies, DLBCL Tier 2, 198
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|DLBCL tier|
37
-|:-|:-:|
38
-|[TNFAIP3](../TNFAIP3)|1 |
39
-
40
-
41
-# Details
42
-
papers/davisChronicActiveBcellreceptor2010.md
... ...
@@ -0,0 +1,45 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @davisChronicActiveBcellreceptor2010
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|1|0|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 1
26
+New Tier 1, DLBCL Tier 1, 1
27
+This study, New Tier 2, 0
28
+New Tier 2, DLBCL Tier 2, 0
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
31
+All other DLBCL studies, DLBCL Tier 1, 124
32
+All other DLBCL studies, DLBCL Tier 2, 210
33
+All other DLBCL studies, DLBCL Tier 3, 387
34
+```
35
+
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|DLBCL tier|
40
+|:-|:-:|
41
+|[CD79B](../CD79B)|1 |
42
+
43
+
44
+# Details
45
+
papers/deschGenotypingCirculatingTumor2020.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @deschGenotypingCirculatingTumor2020
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|1|9|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|PMBL|1|9|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, PMBL Tier 1, 1
27 27
This study, New Tier 2, 9
28 28
New Tier 2, PMBL Tier 2, 9
29
-All other PMBL studies, PMBL Tier 1, 75
30
-All other PMBL studies, PMBL Tier 2, 73
29
+This study, New Tier 3, 0
30
+New Tier 3, PMBL Tier 3, 0
31
+All other PMBL studies, PMBL Tier 1, 45
32
+All other PMBL studies, PMBL Tier 2, 103
33
+All other PMBL studies, PMBL Tier 3, 0
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/drevalGeneticSubdivisionsFollicular2023.md
... ...
@@ -0,0 +1,70 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @drevalGeneticSubdivisionsFollicular2023
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|FL|10|11|0|
12
+|DLBCL|20|1|0|
13
+```mermaid
14
+---
15
+config:
16
+ sankey:
17
+ showValues: true
18
+ linkColor: target
19
+ width: 600
20
+ height: 300
21
+ nodeAlignment: right
22
+ prefix: '('
23
+ suffix: ' genes)'
24
+---
25
+sankey-beta
26
+This study, New Tier 1, 10
27
+New Tier 1, FL Tier 1, 10
28
+This study, New Tier 2, 11
29
+New Tier 2, FL Tier 2, 11
30
+This study, New Tier 3, 0
31
+New Tier 3, FL Tier 3, 0
32
+All other FL studies, FL Tier 1, 44
33
+All other FL studies, FL Tier 2, 48
34
+All other FL studies, FL Tier 3, 0
35
+```
36
+
37
+## Novel genes reported in this study
38
+
39
+### Tier 1
40
+|New gene|FL tier|DLBCL tier|
41
+|:-|:-:|:-:|
42
+|[ACTB](../ACTB)|1 |1 |
43
+|[BCL6](../BCL6)|1 |1 |
44
+|[BTG1](../BTG1)|2 |1 |
45
+|[BTG2](../BTG2)|2 |1 |
46
+|[CD79B](../CD79B)|2 |1 |
47
+|[DUSP2](../DUSP2)|2 |1 |
48
+|[EBF1](../EBF1)|1 |1 |
49
+|[GNAI2](../GNAI2)|1 |1 |
50
+|[IRF4](../IRF4)|1 |1 |
51
+|[ITPKB](../ITPKB)|2 |1 |
52
+|[KLF2](../KLF2)|2 |1 |
53
+|[LTB](../LTB)|2 |1 |
54
+|[MYD88](../MYD88)|2 |1 |
55
+|[P2RY8](../P2RY8)|2 |1 |
56
+|[PIM1](../PIM1)|1 |1 |
57
+|[S1PR2](../S1PR2)|2 |1 |
58
+|[SOCS1](../SOCS1)|1 |1 |
59
+|[TBL1XR1](../TBL1XR1)|1 |1 |
60
+|[TMSB4X](../TMSB4X)|1 |1 |
61
+|[TNFAIP3](../TNFAIP3)|1 |1 |
62
+
63
+### Tier 2
64
+|New gene|FL tier|DLBCL tier|
65
+|:-|:-:|:-:|
66
+|[PTPRD](../PTPRD)|2 |2 |
67
+
68
+
69
+# Details
70
+
papers/dunsCharacterizationDLBCLPMBL2021.md
... ...
@@ -0,0 +1,63 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @dunsCharacterizationDLBCLPMBL2021
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|8|3|0|
12
+|PMBL|6|8|0|
13
+```mermaid
14
+---
15
+config:
16
+ sankey:
17
+ showValues: true
18
+ linkColor: target
19
+ width: 600
20
+ height: 300
21
+ nodeAlignment: right
22
+ prefix: '('
23
+ suffix: ' genes)'
24
+---
25
+sankey-beta
26
+This study, New Tier 1, 6
27
+New Tier 1, PMBL Tier 1, 6
28
+This study, New Tier 2, 8
29
+New Tier 2, PMBL Tier 2, 8
30
+This study, New Tier 3, 0
31
+New Tier 3, PMBL Tier 3, 0
32
+All other PMBL studies, PMBL Tier 1, 40
33
+All other PMBL studies, PMBL Tier 2, 104
34
+All other PMBL studies, PMBL Tier 3, 0
35
+```
36
+
37
+## Novel genes reported in this study
38
+
39
+### Tier 1
40
+|New gene|DLBCL tier|PMBL tier| Average variant quality | QC outcome |
41
+|:-|:-:|:-:|:-:|:-:|
42
+|[CD83](../CD83)|1 |1 || |
43
+|[CREBBP](../CREBBP)|1 |1 || |
44
+|[DUSP2](../DUSP2)|1 |1 || |
45
+|[FOXO1](../FOXO1)|1 |2 || |
46
+|[IL4R](../IL4R)|1 |1 || |
47
+|[MYC](../MYC)|1 |2 || |
48
+|[PIM1](../PIM1)|1 |1 || |
49
+|[SGK1](../SGK1)|1 |1 || |
50
+
51
+### Tier 2
52
+|New gene|DLBCL tier|PMBL tier| Average variant quality | QC outcome |
53
+|:-|:-:|:-:|:-:|:-:|
54
+|[BIRC3](../BIRC3)|2 |2 || |
55
+|[HRNR](../HRNR)| |2 || |
56
+|[LPHN3](../LPHN3)| |2 || |
57
+|[MCL1](../MCL1)|2 |2 |&starf; &starf; &starf; &star; &star; |PASS |
58
+|[RFTN1](../RFTN1)|2 |2 || |
59
+|[WDR87](../WDR87)| |2 || |
60
+
61
+
62
+# Details
63
+
papers/dunsCharacterizationDLBCLPMBL2021b.md
... ...
@@ -1,60 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @dunsCharacterizationDLBCLPMBL2021b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|6|8|
12
-|DLBCL|8|3|
13
-```mermaid
14
----
15
-config:
16
- sankey:
17
- showValues: true
18
- linkColor: target
19
- width: 600
20
- height: 300
21
- nodeAlignment: right
22
- prefix: '('
23
- suffix: ' genes)'
24
----
25
-sankey-beta
26
-This study, New Tier 1, 6
27
-New Tier 1, PMBL Tier 1, 6
28
-This study, New Tier 2, 8
29
-New Tier 2, PMBL Tier 2, 8
30
-All other PMBL studies, PMBL Tier 1, 70
31
-All other PMBL studies, PMBL Tier 2, 74
32
-```
33
-
34
-## Novel genes reported in this study
35
-
36
-### Tier 1
37
-|New gene|PMBL tier|DLBCL tier|
38
-|:-|:-:|:-:|
39
-|[CD83](../CD83)|1 |1 |
40
-|[CREBBP](../CREBBP)|1 |1 |
41
-|[DUSP2](../DUSP2)|1 |1 |
42
-|[FOXO1](../FOXO1)|2 |1 |
43
-|[IL4R](../IL4R)|1 |1 |
44
-|[MYC](../MYC)|2 |1 |
45
-|[PIM1](../PIM1)|1 |1 |
46
-|[SGK1](../SGK1)|1 |1 |
47
-
48
-### Tier 2
49
-|New gene|PMBL tier|DLBCL tier|
50
-|:-|:-:|:-:|
51
-|[BIRC3](../BIRC3)|2 |2 |
52
-|[HRNR](../HRNR)|2 | |
53
-|[LPHN3](../LPHN3)|2 | |
54
-|[MCL1](../MCL1)|2 |2 |
55
-|[RFTN1](../RFTN1)|2 |2 |
56
-|[WDR87](../WDR87)|2 | |
57
-
58
-
59
-# Details
60
-
papers/fanComprehensiveCharacterizationDriver2020.md
... ...
@@ -0,0 +1,122 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @fanComprehensiveCharacterizationDriver2020
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|1|0|73|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 1
26
+New Tier 1, DLBCL Tier 1, 1
27
+This study, New Tier 2, 0
28
+New Tier 2, DLBCL Tier 2, 0
29
+This study, New Tier 3, 73
30
+New Tier 3, DLBCL Tier 3, 73
31
+All other DLBCL studies, DLBCL Tier 1, 124
32
+All other DLBCL studies, DLBCL Tier 2, 210
33
+All other DLBCL studies, DLBCL Tier 3, 314
34
+```
35
+
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|DLBCL tier|
40
+|:-|:-:|
41
+|[ACTG1](../ACTG1)|1 |
42
+
43
+### Tier 3
44
+|New gene|DLBCL tier|
45
+|:-|:-:|
46
+|[ABCB1](../ABCB1)|3 |
47
+|[AGA](../AGA)|3 |
48
+|[APMAP](../APMAP)|3 |
49
+|[ATP6V0A1](../ATP6V0A1)|3 |
50
+|[BRCA1](../BRCA1)|3 |
51
+|[CBX3](../CBX3)|3 |
52
+|[CDH1](../CDH1)|3 |
53
+|[CDKN1A](../CDKN1A)|3 |
54
+|[CGN](../CGN)|3 |
55
+|[CHEK2](../CHEK2)|3 |
56
+|[CSNK1A1](../CSNK1A1)|3 |
57
+|[CSNK2A1](../CSNK2A1)|3 |
58
+|[CYYR1](../CYYR1)|3 |
59
+|[DGCR8](../DGCR8)|3 |
60
+|[DHX33](../DHX33)|3 |
61
+|[DOCK5](../DOCK5)|3 |
62
+|[ECT2L](../ECT2L)|3 |
63
+|[EGFR](../EGFR)|3 |
64
+|[FAIM](../FAIM)|3 |
65
+|[FAM161A](../FAM161A)|3 |
66
+|[FLNA](../FLNA)|3 |
67
+|[FLT1](../FLT1)|3 |
68
+|[FN1](../FN1)|3 |
69
+|[FZD1](../FZD1)|3 |
70
+|[GATA2](../GATA2)|3 |
71
+|[GATA3](../GATA3)|3 |
72
+|[HFE](../HFE)|3 |
73
+|[HLA-DRB1](../HLA-DRB1)|3 |
74
+|[IL6ST](../IL6ST)|3 |
75
+|[ITGB4](../ITGB4)|3 |
76
+|[ITPR1](../ITPR1)|3 |
77
+|[KITLG](../KITLG)|3 |
78
+|[KLRC4](../KLRC4)|3 |
79
+|[LEPR](../LEPR)|3 |
80
+|[MAP2K3](../MAP2K3)|3 |
81
+|[MCM8](../MCM8)|3 |
82
+|[MLH1](../MLH1)|3 |
83
+|[MMEL1](../MMEL1)|3 |
84
+|[MSN](../MSN)|3 |
85
+|[NOTCH3](../NOTCH3)|3 |
86
+|[NUP153](../NUP153)|3 |
87
+|[PABPC1](../PABPC1)|3 |
88
+|[PDGFRB](../PDGFRB)|3 |
89
+|[PFN1](../PFN1)|3 |
90
+|[PGR](../PGR)|3 |
91
+|[PLCB4](../PLCB4)|3 |
92
+|[PLCG2](../PLCG2)|3 |
93
+|[POLD3](../POLD3)|3 |
94
+|[POLQ](../POLQ)|3 |
95
+|[PPP2R2B](../PPP2R2B)|3 |
96
+|[PTCH1](../PTCH1)|3 |
97
+|[RAF1](../RAF1)|3 |
98
+|[RAPGEF3](../RAPGEF3)|3 |
99
+|[RECQL4](../RECQL4)|3 |
100
+|[RET](../RET)|3 |
101
+|[RHPN2](../RHPN2)|3 |
102
+|[RIF1](../RIF1)|3 |
103
+|[RIMS4](../RIMS4)|3 |
104
+|[RPTOR](../RPTOR)|3 |
105
+|[SLC16A8](../SLC16A8)|3 |
106
+|[SMO](../SMO)|3 |
107
+|[SOS2](../SOS2)|3 |
108
+|[TECRL](../TECRL)|3 |
109
+|[TLN1](../TLN1)|3 |
110
+|[TLR4](../TLR4)|3 |
111
+|[TNPO1](../TNPO1)|3 |
112
+|[TPR](../TPR)|3 |
113
+|[TYRO3](../TYRO3)|3 |
114
+|[UBXN11](../UBXN11)|3 |
115
+|[UBXN2B](../UBXN2B)|3 |
116
+|[VANGL1](../VANGL1)|3 |
117
+|[ZMYM4](../ZMYM4)|3 |
118
+|[ZNF814](../ZNF814)|3 |
119
+
120
+
121
+# Details
122
+
papers/fanComprehensiveCharacterizationDriver2020b.md
... ...
@@ -1,114 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @fanComprehensiveCharacterizationDriver2020b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
-|:-:|:-:|:-:|:-:|
11
-|DLBCL|0|0|72|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 0
26
-New Tier 1, DLBCL Tier 1, 0
27
-This study, New Tier 2, 0
28
-New Tier 2, DLBCL Tier 2, 0
29
-This study, New Tier 3, 72
30
-New Tier 3, DLBCL Tier 3, 72
31
-All other DLBCL studies, DLBCL Tier 1, 127
32
-All other DLBCL studies, DLBCL Tier 2, 172
33
-All other DLBCL studies, DLBCL Tier 3, 309
34
-```
35
-
36
-### Tier 3
37
-|New gene|DLBCL tier|
38
-|:-|:-:|
39
-|[ABCB1](../ABCB1)|3 |
40
-|[AGA](../AGA)|3 |
41
-|[APMAP](../APMAP)|3 |
42
-|[ATP6V0A1](../ATP6V0A1)|3 |
43
-|[BRCA1](../BRCA1)|3 |
44
-|[CBX3](../CBX3)|3 |
45
-|[CDKN1A](../CDKN1A)|3 |
46
-|[CGN](../CGN)|3 |
47
-|[CHEK2](../CHEK2)|3 |
48
-|[CSNK1A1](../CSNK1A1)|3 |
49
-|[CSNK2A1](../CSNK2A1)|3 |
50
-|[CYYR1](../CYYR1)|3 |
51
-|[DGCR8](../DGCR8)|3 |
52
-|[DHX33](../DHX33)|3 |
53
-|[DOCK5](../DOCK5)|3 |
54
-|[ECT2L](../ECT2L)|3 |
55
-|[EGFR](../EGFR)|3 |
56
-|[FAIM](../FAIM)|3 |
57
-|[FAM161A](../FAM161A)|3 |
58
-|[FLNA](../FLNA)|3 |
59
-|[FLT1](../FLT1)|3 |
60
-|[FN1](../FN1)|3 |
61
-|[FZD1](../FZD1)|3 |
62
-|[GATA2](../GATA2)|3 |
63
-|[GATA3](../GATA3)|3 |
64
-|[HFE](../HFE)|3 |
65
-|[HLA-DRB1](../HLA-DRB1)|3 |
66
-|[IL6ST](../IL6ST)|3 |
67
-|[ITGB4](../ITGB4)|3 |
68
-|[ITPR1](../ITPR1)|3 |
69
-|[KITLG](../KITLG)|3 |
70
-|[KLRC4](../KLRC4)|3 |
71
-|[LEPR](../LEPR)|3 |
72
-|[MAP2K3](../MAP2K3)|3 |
73
-|[MCM8](../MCM8)|3 |
74
-|[MLH1](../MLH1)|3 |
75
-|[MMEL1](../MMEL1)|3 |
76
-|[MSN](../MSN)|3 |
77
-|[NOTCH3](../NOTCH3)|3 |
78
-|[NUP153](../NUP153)|3 |
79
-|[PABPC1](../PABPC1)|3 |
80
-|[PDGFRB](../PDGFRB)|3 |
81
-|[PFN1](../PFN1)|3 |
82
-|[PGR](../PGR)|3 |
83
-|[PLCB4](../PLCB4)|3 |
84
-|[PLCG2](../PLCG2)|3 |
85
-|[POLD3](../POLD3)|3 |
86
-|[POLQ](../POLQ)|3 |
87
-|[PPP2R2B](../PPP2R2B)|3 |
88
-|[PTCH1](../PTCH1)|3 |
89
-|[RAF1](../RAF1)|3 |
90
-|[RAPGEF3](../RAPGEF3)|3 |
91
-|[RECQL4](../RECQL4)|3 |
92
-|[RET](../RET)|3 |
93
-|[RHPN2](../RHPN2)|3 |
94
-|[RIF1](../RIF1)|3 |
95
-|[RIMS4](../RIMS4)|3 |
96
-|[RPTOR](../RPTOR)|3 |
97
-|[SLC16A8](../SLC16A8)|3 |
98
-|[SMO](../SMO)|3 |
99
-|[SOS2](../SOS2)|3 |
100
-|[TECRL](../TECRL)|3 |
101
-|[TLN1](../TLN1)|3 |
102
-|[TLR4](../TLR4)|3 |
103
-|[TNPO1](../TNPO1)|3 |
104
-|[TPR](../TPR)|3 |
105
-|[TYRO3](../TYRO3)|3 |
106
-|[UBXN11](../UBXN11)|3 |
107
-|[UBXN2B](../UBXN2B)|3 |
108
-|[VANGL1](../VANGL1)|3 |
109
-|[ZMYM4](../ZMYM4)|3 |
110
-|[ZNF814](../ZNF814)|3 |
111
-
112
-
113
-# Details
114
-
papers/ganapathiGeneticLandscapeDural2016.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @ganapathiGeneticLandscapeDural2016
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|MZL|1|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|MZL|1|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, MZL Tier 1, 1
27 27
This study, New Tier 2, 0
28 28
New Tier 2, MZL Tier 2, 0
29
+This study, New Tier 3, 0
30
+New Tier 3, MZL Tier 3, 0
29 31
All other MZL studies, MZL Tier 1, 41
30 32
All other MZL studies, MZL Tier 2, 74
33
+All other MZL studies, MZL Tier 3, 0
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/gomezUltraDeepSequencingReveals2023.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @gomezUltraDeepSequencingReveals2023
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|2|5|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|PMBL|2|9|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -24,10 +24,13 @@ config:
24 24
sankey-beta
25 25
This study, New Tier 1, 2
26 26
New Tier 1, PMBL Tier 1, 2
27
-This study, New Tier 2, 5
28
-New Tier 2, PMBL Tier 2, 5
29
-All other PMBL studies, PMBL Tier 1, 74
30
-All other PMBL studies, PMBL Tier 2, 77
27
+This study, New Tier 2, 9
28
+New Tier 2, PMBL Tier 2, 9
29
+This study, New Tier 3, 0
30
+New Tier 3, PMBL Tier 3, 0
31
+All other PMBL studies, PMBL Tier 1, 44
32
+All other PMBL studies, PMBL Tier 2, 103
33
+All other PMBL studies, PMBL Tier 3, 0
31 34
```
32 35
33 36
## Novel genes reported in this study
... ...
@@ -46,6 +49,10 @@ All other PMBL studies, PMBL Tier 2, 77
46 49
|[HLA-C](../HLA-C)|2 |
47 50
|[LIMD2](../LIMD2)|2 |
48 51
|[OR13C2](../OR13C2)|2 |
52
+|[PCDH7](../PCDH7)|2 |
53
+|[RDH12](../RDH12)|2 |
54
+|[SCN9A](../SCN9A)|2 |
55
+|[STRAP](../STRAP)|2 |
49 56
50 57
51 58
# Details
papers/grandeGenomewideDiscoverySomatic2019.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @grandeGenomewideDiscoverySomatic2019
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|BL|9|4|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|BL|11|2|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -22,12 +22,15 @@ config:
22 22
suffix: ' genes)'
23 23
---
24 24
sankey-beta
25
-This study, New Tier 1, 9
26
-New Tier 1, BL Tier 1, 9
27
-This study, New Tier 2, 4
28
-New Tier 2, BL Tier 2, 4
29
-All other BL studies, BL Tier 1, 20
30
-All other BL studies, BL Tier 2, 153
25
+This study, New Tier 1, 11
26
+New Tier 1, BL Tier 1, 11
27
+This study, New Tier 2, 2
28
+New Tier 2, BL Tier 2, 2
29
+This study, New Tier 3, 0
30
+New Tier 3, BL Tier 3, 0
31
+All other BL studies, BL Tier 1, 21
32
+All other BL studies, BL Tier 2, 70
33
+All other BL studies, BL Tier 3, 70
31 34
```
32 35
33 36
## Novel genes reported in this study
... ...
@@ -35,9 +38,11 @@ All other BL studies, BL Tier 2, 153
35 38
### Tier 1
36 39
|New gene|BL tier|
37 40
|:-|:-:|
41
+|[BACH2](../BACH2)|1 |
38 42
|[BCL7A](../BCL7A)|1 |
39 43
|[CHD8](../CHD8)|1 |
40 44
|[GNAI2](../GNAI2)|1 |
45
+|[HIST1H1E](../HIST1H1E)|1 |
41 46
|[KMT2D](../KMT2D)|1 |
42 47
|[RFX7](../RFX7)|1 |
43 48
|[SIN3A](../SIN3A)|1 |
... ...
@@ -48,9 +53,7 @@ All other BL studies, BL Tier 2, 153
48 53
### Tier 2
49 54
|New gene|BL tier|
50 55
|:-|:-:|
51
-|[BACH2](../BACH2)|2 |
52 56
|[CDKN2A](../CDKN2A)|2 |
53
-|[HIST1H1E](../HIST1H1E)|2 |
54 57
|[MIR142](../MIR142)|2 |
55 58
56 59
papers/gunawardanaRecurrentSomaticMutations2014.md
... ...
@@ -0,0 +1,45 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @gunawardanaRecurrentSomaticMutations2014
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|PMBL|1|0|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 1
26
+New Tier 1, PMBL Tier 1, 1
27
+This study, New Tier 2, 0
28
+New Tier 2, PMBL Tier 2, 0
29
+This study, New Tier 3, 0
30
+New Tier 3, PMBL Tier 3, 0
31
+All other PMBL studies, PMBL Tier 1, 45
32
+All other PMBL studies, PMBL Tier 2, 112
33
+All other PMBL studies, PMBL Tier 3, 0
34
+```
35
+
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|PMBL tier|
40
+|:-|:-:|
41
+|[PTPN1](../PTPN1)|1 |
42
+
43
+
44
+# Details
45
+
papers/gunawardanaRecurrentSomaticMutations2014c.md
... ...
@@ -1,42 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @gunawardanaRecurrentSomaticMutations2014c
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|1|0|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 1
26
-New Tier 1, PMBL Tier 1, 1
27
-This study, New Tier 2, 0
28
-New Tier 2, PMBL Tier 2, 0
29
-All other PMBL studies, PMBL Tier 1, 75
30
-All other PMBL studies, PMBL Tier 2, 82
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|PMBL tier|
37
-|:-|:-:|
38
-|[PTPN1](../PTPN1)|1 |
39
-
40
-
41
-# Details
42
-
papers/hubschmannMutationalMechanismsShaping2021.md
... ...
@@ -0,0 +1,92 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @hubschmannMutationalMechanismsShaping2021
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|FL|2|16|0|
12
+|DLBCL|4|20|3|
13
+```mermaid
14
+---
15
+config:
16
+ sankey:
17
+ showValues: true
18
+ linkColor: target
19
+ width: 600
20
+ height: 300
21
+ nodeAlignment: right
22
+ prefix: '('
23
+ suffix: ' genes)'
24
+---
25
+sankey-beta
26
+This study, New Tier 1, 4
27
+New Tier 1, DLBCL Tier 1, 4
28
+This study, New Tier 2, 20
29
+New Tier 2, DLBCL Tier 2, 20
30
+This study, New Tier 3, 3
31
+New Tier 3, DLBCL Tier 3, 3
32
+All other DLBCL studies, DLBCL Tier 1, 121
33
+All other DLBCL studies, DLBCL Tier 2, 190
34
+All other DLBCL studies, DLBCL Tier 3, 384
35
+```
36
+
37
+## Novel genes reported in this study
38
+
39
+### Tier 1
40
+|New gene|FL tier|DLBCL tier| Average variant quality | QC outcome |
41
+|:-|:-:|:-:|:-:|:-:|
42
+|[ACTG1](../ACTG1)|2 |1 || |
43
+|[EEF1A1](../EEF1A1)|1 |1 || |
44
+|[HLA-DMB](../HLA-DMB)| |1 || |
45
+|[MEF2C](../MEF2C)|2 |1 || |
46
+|[VMA21](../VMA21)|1 | || |
47
+
48
+### Tier 2
49
+|New gene|FL tier|DLBCL tier| Average variant quality | QC outcome |
50
+|:-|:-:|:-:|:-:|:-:|
51
+|[ADAMTS1](../ADAMTS1)| |2 |&starf; &starf; &starf; &star; &star; |PASS |
52
+|[ANKRD12](../ANKRD12)| |2 |&starf; &starf; &starf; &star; &star; |PASS |
53
+|[ATP6V1A](../ATP6V1A)|2 | || |
54
+|[CADPS2](../CADPS2)| |2 |&starf; &starf; &starf; &starf; &star; |PASS |
55
+|[CDC42BPB](../CDC42BPB)|2 | || |
56
+|[CNOT2](../CNOT2)| |2 |&starf; &starf; &starf; &starf; &star; |PASS |
57
+|[CPNE8](../CPNE8)|2 | || |
58
+|[DHX15](../DHX15)|2 | || |
59
+|[DHX16](../DHX16)| |2 |&starf; &starf; &starf; &starf; &star; |PASS |
60
+|[DNM2](../DNM2)| |2 |&starf; &starf; &starf; &star; &star; |PASS |
61
+|[FZR1](../FZR1)|2 | || |
62
+|[IKBKE](../IKBKE)| |2 |&starf; &starf; &starf; &starf; &star; |PASS |
63
+|[IRF1](../IRF1)| |2 |&starf; &starf; &starf; &star; &star; |PASS |
64
+|[JUP](../JUP)|2 | || |
65
+|[LAPTM5](../LAPTM5)|2 |2 |&starf; &starf; &starf; &starf; &star; |PASS |
66
+|[LRP12](../LRP12)| |2 |&starf; &starf; &starf; &star; &star; |PASS |
67
+|[MGEA5](../MGEA5)|2 | || |
68
+|[MYCBP2](../MYCBP2)|2 | || |
69
+|[PDS5B](../PDS5B)|2 |2 |&starf; &starf; &starf; &starf; &star; |PASS |
70
+|[PNPO](../PNPO)| |2 |&starf; &starf; &starf; &star; &star; |PASS |
71
+|[PPP4C](../PPP4C)|2 | || |
72
+|[PRKDC](../PRKDC)|2 |2 || |
73
+|[RAC2](../RAC2)| |2 |&starf; &starf; &starf; &star; &star; |PASS |
74
+|[RBM6](../RBM6)|2 | || |
75
+|[SIAH2](../SIAH2)| |2 |&starf; &starf; &starf; &star; &star; |PASS |
76
+|[SLC34A2](../SLC34A2)| |2 |&starf; &starf; &starf; &star; &star; |PASS |
77
+|[TPP1](../TPP1)|2 | || |
78
+|[TRAF6](../TRAF6)| |2 |&starf; &starf; &starf; &star; &star; |PASS |
79
+|[UNC5B](../UNC5B)| |2 |&starf; &starf; &starf; &star; &star; |PASS |
80
+|[WNK1](../WNK1)| |2 |&starf; &starf; &starf; &star; &star; |PASS |
81
+|[ZNF217](../ZNF217)| |2 |&starf; &starf; &starf; &star; &star; |PASS |
82
+
83
+### Tier 3
84
+|New gene|FL tier|DLBCL tier| Average variant quality | QC outcome |
85
+|:-|:-:|:-:|:-:|:-:|
86
+|[GAK](../GAK)| |3 |&starf; &starf; &star; &star; &star; |FAIL |
87
+|[HLA-DQA1](../HLA-DQA1)| |3 |&starf; &starf; &star; &star; &star; |FAIL |
88
+|[NR2F2](../NR2F2)| |3 |&starf; &starf; &star; &star; &star; |FAIL |
89
+
90
+
91
+# Details
92
+
papers/hubschmannMutationalMechanismsShaping2021b.md
... ...
@@ -1,82 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @hubschmannMutationalMechanismsShaping2021b
7
-## Summary of novel genes
8
-
9
-|Entity| Total| Tier 1| Tier 2| Tier 2 Pass| Tier 2 Fail| Fail rate |
10
-|:-:|:-:|:-:|:-:|:-:|:-:|:-:|
11
-|DLBCL or FL|38|4|34|31|3| 9% |
12
-
13
-
14
-```mermaid
15
----
16
-config:
17
- sankey:
18
- showValues: true
19
- linkColor: target
20
- width: 600
21
- height: 300
22
- nodeAlignment: right
23
- prefix: '('
24
- suffix: ' genes)'
25
----
26
-sankey-beta
27
-New to this study, FL or DLBCL Tier 1, 4
28
-New to this study, FL or DLBCL Tier 2, 34
29
-FL or DLBCL Tier 2, Pass QC, 31
30
-FL or DLBCL Tier 2, Fail QC, 3
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|FL tier|DLBCL tier|
37
-|:-|:-:|:-:|
38
-|[ACTG1](../ACTG1)|2 |1 |
39
-|[EEF1A1](../EEF1A1)|1 |1 |
40
-|[FBXO11](../FBXO11)| |1 |
41
-|[VMA21](../VMA21)|1 | |
42
-
43
-### Tier 2
44
-|New gene|FL tier|DLBCL tier|Average variant quality|QC outcome|
45
-|:-|:-:|:-:|:-:|:-:|
46
-|[ADAMTS1](../ADAMTS1)| |2 |&starf; &starf; &starf; &star; &star; | **Pass** |
47
-|[ANKRD12](../ANKRD12)| |2 |&starf; &starf; &starf; &star; &star; | **Pass** |
48
-|[ATP6V1A](../ATP6V1A)|2 | |&starf; &starf; &starf; &starf; &star; | **Pass** |
49
-|[CADPS2](../CADPS2)| |2 |&starf; &starf; &starf; &starf; &star; | **Pass** |
50
-|[CDC42BPB](../CDC42BPB)|2 | |&starf; &starf; &starf; &star; &star;|**Pass**|
51
-|[CNOT2](../CNOT2)| |2 |&starf; &starf; &starf; &starf; &star;|**Pass**|
52
-|[CPNE8](../CPNE8)|2 | |&starf; &starf; &starf; &starf; &star;|**Pass**|
53
-|[DHX15](../DHX15)|2 | |&starf; &starf; &starf; &starf; &star;|**Pass**|
54
-|[DHX16](../DHX16)| |2 |&starf; &starf; &starf; &starf; &star;|**Pass**|
55
-|[DNM2](../DNM2)| |2 |&starf; &starf; &starf; &star; &star;|**Pass**|
56
-|[FZR1](../FZR1)|2 | |&starf; &starf; &starf; &star; &star;|**Pass**|
57
-|[IKBKE](../IKBKE)| |2 |&starf; &starf; &starf; &starf; &star;|**Pass**|
58
-|[IRF1](../IRF1)| |2 |&starf; &starf; &starf; &star; &star;|**Pass**|
59
-|[JUP](../JUP)|2 | |&starf; &starf; &starf; &starf; &star;|**Pass**|
60
-|[LAPTM5](../LAPTM5)|2 |2 |&starf; &starf; &starf; &starf; &star;|**Pass**|
61
-|[LRP12](../LRP12)| |2 |&starf; &starf; &starf; &star; &star;|**Pass**|
62
-|[MGEA5](../MGEA5)|2 | |&starf; &starf; &starf; &star; &star;|**Pass**|
63
-|[MYCBP2](../MYCBP2)|2 | |&starf; &starf; &starf; &starf; &star;|**Pass**|
64
-|[PDS5B](../PDS5B)|2 |2 |&starf; &starf; &starf; &star; &star;|**Pass**|
65
-|[PNPO](../PNPO)| |2 |&starf; &starf; &starf; &star; &star;|**Pass**|
66
-|[PPP4C](../PPP4C)|2 | |&starf; &starf; &starf; &starf; &star;|**Pass**|
67
-|[PRKDC](../PRKDC)|2 |2 |&starf; &starf; &starf; &star; &star;|**Pass**|
68
-|[RAC2](../RAC2)| |2 |&starf; &starf; &starf; &star; &star;|**Pass**|
69
-|[RBM6](../RBM6)|2 | |&starf; &starf; &starf; &star; &star;|**Pass**|
70
-|[SIAH2](../SIAH2)| |2 |&starf; &starf; &starf; &star; &star;|**Pass**|
71
-|[SLC34A2](../SLC34A2)| |2 |&starf; &starf; &starf; &star; &star;|**Pass**|
72
-|[TPP1](../TPP1)|2 | |&starf; &starf; &starf; &star; &star;|**Pass**|
73
-|[TRAF6](../TRAF6)| |2 |&starf; &starf; &starf; &star; &star;|**Pass**|
74
-|[UNC5B](../UNC5B)| |2 |&starf; &starf; &starf; &star; &star;|**Pass**|
75
-|[WNK1](../WNK1)| |2 |&starf; &starf; &starf; &star; &star;|**Pass**|
76
-|[ZNF217](../ZNF217)| |2 |&starf; &starf; &starf; &star; &star;|**Pass**|
77
-|[HLA-DQA1](../HLA-DQA1)| |2 |&starf; &starf;&star; &star; &star;|**Fail**|
78
-|[GAK](../GAK)| |2 |&starf; &starf; &star; &star; &star;|**Fail**|
79
-|[NR2F2](../NR2F2)| |2 |&starf; &starf; &star; &star; &star;|**Fail**|
80
-
81
-# Details
82
-
papers/jalladesExomeSequencingIdentifies2017.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @jalladesExomeSequencingIdentifies2017
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|MZL|2|26|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|MZL|2|26|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 2
26 26
New Tier 1, MZL Tier 1, 2
27 27
This study, New Tier 2, 26
28 28
New Tier 2, MZL Tier 2, 26
29
+This study, New Tier 3, 0
30
+New Tier 3, MZL Tier 3, 0
29 31
All other MZL studies, MZL Tier 1, 40
30 32
All other MZL studies, MZL Tier 2, 48
33
+All other MZL studies, MZL Tier 3, 0
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/jardinRecurrentMutationsExportin2016.md
... ...
@@ -0,0 +1,45 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @jardinRecurrentMutationsExportin2016
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|PMBL|1|0|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 1
26
+New Tier 1, PMBL Tier 1, 1
27
+This study, New Tier 2, 0
28
+New Tier 2, PMBL Tier 2, 0
29
+This study, New Tier 3, 0
30
+New Tier 3, PMBL Tier 3, 0
31
+All other PMBL studies, PMBL Tier 1, 45
32
+All other PMBL studies, PMBL Tier 2, 112
33
+All other PMBL studies, PMBL Tier 3, 0
34
+```
35
+
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|PMBL tier|
40
+|:-|:-:|
41
+|[XPO1](../XPO1)|1 |
42
+
43
+
44
+# Details
45
+
papers/jardinRecurrentMutationsExportin2016a.md
... ...
@@ -1,42 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @jardinRecurrentMutationsExportin2016a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|1|0|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 1
26
-New Tier 1, PMBL Tier 1, 1
27
-This study, New Tier 2, 0
28
-New Tier 2, PMBL Tier 2, 0
29
-All other PMBL studies, PMBL Tier 1, 75
30
-All other PMBL studies, PMBL Tier 2, 82
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|PMBL tier|
37
-|:-|:-:|
38
-|[XPO1](../XPO1)|1 |
39
-
40
-
41
-# Details
42
-
papers/johnstonCmycHypermutationBurkitt1992.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @johnstonCmycHypermutationBurkitt1992
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|BL|1|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|BL|1|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, BL Tier 1, 1
27 27
This study, New Tier 2, 0
28 28
New Tier 2, BL Tier 2, 0
29
-All other BL studies, BL Tier 1, 28
30
-All other BL studies, BL Tier 2, 157
29
+This study, New Tier 3, 0
30
+New Tier 3, BL Tier 3, 0
31
+All other BL studies, BL Tier 1, 31
32
+All other BL studies, BL Tier 2, 72
33
+All other BL studies, BL Tier 3, 70
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/khodabakhshiRecurrentTargetsAberrant2012.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @khodabakhshiRecurrentTargetsAberrant2012
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|1|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|1|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, DLBCL Tier 1, 1
27 27
This study, New Tier 2, 0
28 28
New Tier 2, DLBCL Tier 2, 0
29
-All other DLBCL studies, DLBCL Tier 1, 127
30
-All other DLBCL studies, DLBCL Tier 2, 198
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
31
+All other DLBCL studies, DLBCL Tier 1, 124
32
+All other DLBCL studies, DLBCL Tier 2, 210
33
+All other DLBCL studies, DLBCL Tier 3, 387
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/krysiakRecurrentSomaticMutations2017.md
... ...
@@ -0,0 +1,70 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @krysiakRecurrentSomaticMutations2017
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|FL|15|7|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 15
26
+New Tier 1, FL Tier 1, 15
27
+This study, New Tier 2, 7
28
+New Tier 2, FL Tier 2, 7
29
+This study, New Tier 3, 0
30
+New Tier 3, FL Tier 3, 0
31
+All other FL studies, FL Tier 1, 39
32
+All other FL studies, FL Tier 2, 52
33
+All other FL studies, FL Tier 3, 0
34
+```
35
+
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|FL tier|
40
+|:-|:-:|
41
+|[ARID1A](../ARID1A)|1 |
42
+|[BCL7A](../BCL7A)|1 |
43
+|[BTK](../BTK)|1 |
44
+|[HIST1H1B](../HIST1H1B)|1 |
45
+|[HIST1H1D](../HIST1H1D)|1 |
46
+|[HIST1H1E](../HIST1H1E)|1 |
47
+|[HIST1H2AC](../HIST1H2AC)|1 |
48
+|[HIST1H2AG](../HIST1H2AG)|1 |
49
+|[HIST1H2AM](../HIST1H2AM)|1 |
50
+|[HIST1H2BC](../HIST1H2BC)|1 |
51
+|[HIST1H2BG](../HIST1H2BG)|1 |
52
+|[HVCN1](../HVCN1)|1 |
53
+|[POU2AF1](../POU2AF1)|1 |
54
+|[POU2F2](../POU2F2)|1 |
55
+|[SMARCA4](../SMARCA4)|1 |
56
+
57
+### Tier 2
58
+|New gene|FL tier|
59
+|:-|:-:|
60
+|[CXCR4](../CXCR4)|2 |
61
+|[EGR1](../EGR1)|2 |
62
+|[HIST1H2BD](../HIST1H2BD)|2 |
63
+|[HIST1H2BM](../HIST1H2BM)|2 |
64
+|[HIST1H3G](../HIST1H3G)|2 |
65
+|[HIST1H3I](../HIST1H3I)|2 |
66
+|[ZNF608](../ZNF608)|2 |
67
+
68
+
69
+# Details
70
+
papers/krysiakRecurrentSomaticMutations2017b.md
... ...
@@ -1,67 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @krysiakRecurrentSomaticMutations2017b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|FL|17|5|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 17
26
-New Tier 1, FL Tier 1, 17
27
-This study, New Tier 2, 5
28
-New Tier 2, FL Tier 2, 5
29
-All other FL studies, FL Tier 1, 49
30
-All other FL studies, FL Tier 2, 45
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|FL tier|
37
-|:-|:-:|
38
-|[ARID1A](../ARID1A)|1 |
39
-|[BCL7A](../BCL7A)|1 |
40
-|[BTK](../BTK)|1 |
41
-|[HIST1H1B](../HIST1H1B)|1 |
42
-|[HIST1H1D](../HIST1H1D)|1 |
43
-|[HIST1H1E](../HIST1H1E)|1 |
44
-|[HIST1H2AC](../HIST1H2AC)|1 |
45
-|[HIST1H2AG](../HIST1H2AG)|1 |
46
-|[HIST1H2AM](../HIST1H2AM)|1 |
47
-|[HIST1H2BC](../HIST1H2BC)|1 |
48
-|[HIST1H2BD](../HIST1H2BD)|1 |
49
-|[HIST1H2BG](../HIST1H2BG)|1 |
50
-|[HIST1H3G](../HIST1H3G)|1 |
51
-|[HVCN1](../HVCN1)|1 |
52
-|[POU2AF1](../POU2AF1)|1 |
53
-|[POU2F2](../POU2F2)|1 |
54
-|[SMARCA4](../SMARCA4)|1 |
55
-
56
-### Tier 2
57
-|New gene|FL tier|
58
-|:-|:-:|
59
-|[CXCR4](../CXCR4)|2 |
60
-|[EGR1](../EGR1)|2 |
61
-|[HIST1H2BM](../HIST1H2BM)|2 |
62
-|[HIST1H3I](../HIST1H3I)|2 |
63
-|[ZNF608](../ZNF608)|2 |
64
-
65
-
66
-# Details
67
-
papers/kwanhianMicroRNA142Mutated202012.md
... ...
@@ -0,0 +1,45 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @kwanhianMicroRNA142Mutated202012
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|1|0|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 1
26
+New Tier 1, DLBCL Tier 1, 1
27
+This study, New Tier 2, 0
28
+New Tier 2, DLBCL Tier 2, 0
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
31
+All other DLBCL studies, DLBCL Tier 1, 124
32
+All other DLBCL studies, DLBCL Tier 2, 210
33
+All other DLBCL studies, DLBCL Tier 3, 387
34
+```
35
+
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|DLBCL tier|
40
+|:-|:-:|
41
+|[MIR142](../MIR142)|1 |
42
+
43
+
44
+# Details
45
+
papers/kwanhianMicroRNA142Mutated202012b.md
... ...
@@ -1,40 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @kwanhianMicroRNA142Mutated202012b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|0|1|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 0
26
-New Tier 1, DLBCL Tier 1, 0
27
-This study, New Tier 2, 1
28
-New Tier 2, DLBCL Tier 2, 1
29
-All other DLBCL studies, DLBCL Tier 1, 128
30
-All other DLBCL studies, DLBCL Tier 2, 197
31
-```
32
-
33
-### Tier 2
34
-|New gene|DLBCL tier|
35
-|:-|:-:|
36
-|[MIR142](../MIR142)|2 |
37
-
38
-
39
-# Details
40
-
papers/lenzOncogenicCARD11Mutations2008.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @lenzOncogenicCARD11Mutations2008
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|1|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|1|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, DLBCL Tier 1, 1
27 27
This study, New Tier 2, 0
28 28
New Tier 2, DLBCL Tier 2, 0
29
-All other DLBCL studies, DLBCL Tier 1, 127
30
-All other DLBCL studies, DLBCL Tier 2, 198
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
31
+All other DLBCL studies, DLBCL Tier 1, 124
32
+All other DLBCL studies, DLBCL Tier 2, 210
33
+All other DLBCL studies, DLBCL Tier 3, 387
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/lohrDiscoveryPrioritizationSomatic2012.md
... ...
@@ -0,0 +1,89 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @lohrDiscoveryPrioritizationSomatic2012
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|14|27|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 14
26
+New Tier 1, DLBCL Tier 1, 14
27
+This study, New Tier 2, 27
28
+New Tier 2, DLBCL Tier 2, 27
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
31
+All other DLBCL studies, DLBCL Tier 1, 111
32
+All other DLBCL studies, DLBCL Tier 2, 183
33
+All other DLBCL studies, DLBCL Tier 3, 387
34
+```
35
+
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|DLBCL tier| Average variant quality | QC outcome |
40
+|:-|:-:|:-:|:-:|
41
+|[ACTB](../ACTB)|1 || |
42
+|[DUSP2](../DUSP2)|1 || |
43
+|[ETV6](../ETV6)|1 || |
44
+|[HIST1H1E](../HIST1H1E)|1 || |
45
+|[HIST1H2BC](../HIST1H2BC)|1 || |
46
+|[HIST1H3B](../HIST1H3B)|1 || |
47
+|[HLA-A](../HLA-A)|1 || |
48
+|[HLA-B](../HLA-B)|1 || |
49
+|[JUNB](../JUNB)|1 |&starf; &starf; &starf; &star; &star; |PASS |
50
+|[KRAS](../KRAS)|1 || |
51
+|[P2RY8](../P2RY8)|1 || |
52
+|[POU2F2](../POU2F2)|1 || |
53
+|[TBL1XR1](../TBL1XR1)|1 || |
54
+|[UBE2A](../UBE2A)|1 || |
55
+
56
+### Tier 2
57
+|New gene|DLBCL tier| Average variant quality | QC outcome |
58
+|:-|:-:|:-:|:-:|
59
+|[BCR](../BCR)|2 || |
60
+|[CPS1](../CPS1)|2 || |
61
+|[GABRA1](../GABRA1)|2 || |
62
+|[H1FOO](../H1FOO)|2 || |
63
+|[HIST1H2AL](../HIST1H2AL)|2 || |
64
+|[HIST1H2BO](../HIST1H2BO)|2 || |
65
+|[HIST1H3A](../HIST1H3A)|2 || |
66
+|[KRTAP5-5](../KRTAP5-5)|2 || |
67
+|[OR6K3](../OR6K3)|2 || |
68
+|[PASD1](../PASD1)|2 || |
69
+|[PCDHB6](../PCDHB6)|2 || |
70
+|[PCLO](../PCLO)|2 || |
71
+|[PDGFC](../PDGFC)|2 || |
72
+|[PTPN21](../PTPN21)|2 || |
73
+|[RBP3](../RBP3)|2 || |
74
+|[S1PR1](../S1PR1)|2 || |
75
+|[SLC38A8](../SLC38A8)|2 || |
76
+|[SLITRK6](../SLITRK6)|2 || |
77
+|[SRPX](../SRPX)|2 || |
78
+|[SYN2](../SYN2)|2 || |
79
+|[TBP](../TBP)|2 || |
80
+|[TMSL3](../TMSL3)|2 || |
81
+|[TNF](../TNF)|2 || |
82
+|[UNC5C](../UNC5C)|2 || |
83
+|[UNC5D](../UNC5D)|2 || |
84
+|[VAX1](../VAX1)|2 || |
85
+|[ZNF385B](../ZNF385B)|2 || |
86
+
87
+
88
+# Details
89
+
papers/lohrDiscoveryPrioritizationSomatic2012a.md
... ...
@@ -1,49 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @lohrDiscoveryPrioritizationSomatic2012a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|3|1|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 3
26
-New Tier 1, DLBCL Tier 1, 3
27
-This study, New Tier 2, 1
28
-New Tier 2, DLBCL Tier 2, 1
29
-All other DLBCL studies, DLBCL Tier 1, 125
30
-All other DLBCL studies, DLBCL Tier 2, 197
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|DLBCL tier|
37
-|:-|:-:|
38
-|[ACTB](../ACTB)|1 |
39
-|[KRAS](../KRAS)|1 |
40
-|[P2RY8](../P2RY8)|1 |
41
-
42
-### Tier 2
43
-|New gene|DLBCL tier|
44
-|:-|:-:|
45
-|[PCLO](../PCLO)|2 |
46
-
47
-
48
-# Details
49
-
papers/louissaintPediatrictypeNodalFollicular2016.md
... ...
@@ -0,0 +1,45 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @louissaintPediatrictypeNodalFollicular2016
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|FL|1|0|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 1
26
+New Tier 1, FL Tier 1, 1
27
+This study, New Tier 2, 0
28
+New Tier 2, FL Tier 2, 0
29
+This study, New Tier 3, 0
30
+New Tier 3, FL Tier 3, 0
31
+All other FL studies, FL Tier 1, 53
32
+All other FL studies, FL Tier 2, 59
33
+All other FL studies, FL Tier 3, 0
34
+```
35
+
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|FL tier|
40
+|:-|:-:|
41
+|[MAP2K1](../MAP2K1)|1 |
42
+
43
+
44
+# Details
45
+
papers/louissaintPediatrictypeNodalFollicular2016a.md
... ...
@@ -1,42 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @louissaintPediatrictypeNodalFollicular2016a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|FL|1|0|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 1
26
-New Tier 1, FL Tier 1, 1
27
-This study, New Tier 2, 0
28
-New Tier 2, FL Tier 2, 0
29
-All other FL studies, FL Tier 1, 65
30
-All other FL studies, FL Tier 2, 50
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|FL tier|
37
-|:-|:-:|
38
-|[MAP2K1](../MAP2K1)|1 |
39
-
40
-
41
-# Details
42
-
papers/loveGeneticLandscapeMutations2012.md
... ...
@@ -40,10 +40,9 @@ significance in BL.
40 40
41 41
## Summary of novel genes
42 42
43
-|Entity| Total| Tier 1| Tier 2| Tier 2 Pass| Tier 2 Fail| Fail rate |
44
-|:-:|:-:|:-:|:-:|:-:|:-:|:-:|
45
-|BL|60|3|57|9|48| 84% |
46
-
43
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
44
+|:-:|:-:|:-:|:-:|
45
+|BL|5|7|48|
47 46
```mermaid
48 47
---
49 48
config:
... ...
@@ -57,85 +56,91 @@ config:
57 56
suffix: ' genes)'
58 57
---
59 58
sankey-beta
60
-New to this study, BL Tier 1, 3
61
-New to this study, BL Tier 2, 56
62
-BL Tier 2, Pass QC, 9
63
-BL Tier 2, Fail QC, 47
59
+This study, New Tier 1, 5
60
+New Tier 1, BL Tier 1, 5
61
+This study, New Tier 2, 7
62
+New Tier 2, BL Tier 2, 7
63
+This study, New Tier 3, 48
64
+New Tier 3, BL Tier 3, 48
65
+All other BL studies, BL Tier 1, 27
66
+All other BL studies, BL Tier 2, 65
67
+All other BL studies, BL Tier 3, 22
64 68
```
65 69
66 70
## Novel genes reported in this study
67 71
68 72
### Tier 1
69
-|New gene|BL tier|
70
-|:-|:-:|
71
-|[ARID1A](../ARID1A)|1 |
72
-|[GNA13](../GNA13)|1 |
73
-|[PTEN](../PTEN)|1 |
73
+|New gene|BL tier| Average variant quality | QC outcome |
74
+|:-|:-:|:-:|:-:|
75
+|[ARID1A](../ARID1A)|1 || |
76
+|[BCL6](../BCL6)|1 |&starf; &starf; &starf; &starf; &star; |PASS |
77
+|[CREBBP](../CREBBP)|1 |&starf; &starf; &starf; &starf; &star; |PASS |
78
+|[GNA13](../GNA13)|1 || |
79
+|[PTEN](../PTEN)|1 || |
74 80
75 81
### Tier 2
76
-|Novel gene|DLBCL tier|Average variant quality|QC outcome|
82
+|New gene|BL tier| Average variant quality | QC outcome |
77 83
|:-|:-:|:-:|:-:|
78
-|[BCL6](../BCL6)|2 |&starf; &starf; &starf; &starf; &star;|**Pass**|
79
-|[CARD4](../CARD4)|2 |&starf; &starf; &starf; &starf; &star;|**Pass**|
80
-|[CDC73](../CDC73)|2 |&starf; &starf; &starf; &star; &star;|**Pass**|
81
-|[CREBBP](../CREBBP)|2 |&starf; &starf; &starf; &starf; &star;|**Pass**|
82
-|[EZH2](../EZH2)|2 |&starf; &starf; &starf; &starf; &starf;|**Pass**|
83
-|[GGTLA4](../GGTLA4)|2 |&starf; &starf; &starf; &starf; &star;|**Pass**|
84
-|[P2RY2](../P2RY2)|2 |&starf; &starf; &starf; &starf; &star;|**Pass**|
85
-|[NBEAL1](../NBEAL1)|2 |&starf; &starf; &starf; &starf; &star;|**Pass**|
86
-|[RANBP6](../RANBP6)|2 |&starf; &starf; &starf; &starf; &starf;|**Pass**|
87
-|[ACAD9](../ACAD9)|2 |&starf; &star; &star; &star; &star;|**Fail**|
88
-|[ACE](../ACE)|2 |&starf; &star; &star; &star; &star;|**Fail**|
89
-|[ATP2C2](../ATP2C2)|2 |&starf; &starf; &star; &star; &star;|**Fail**|
90
-|[BRAF](../BRAF)|2 |&starf; &star; &star; &star; &star;|**Fail**|
91
-|[BRD4](../BRD4)|2 |&starf; &star; &star; &star; &star;|**Fail**|
92
-|[BTG2](../BTG2)|2 |&starf; &star; &star; &star; &star;|**Fail**|
93
-|[C6orf27](../C6orf27)|2 |*Germline*|**Fail**|
94
-|[CAD](../CAD)|2 |&starf; &star; &star; &star; &star;|**Fail**|
95
-|[CCT6B](../CCT6B)|2 |*Germline*|**Fail**|
96
-|[CDH17](../CDH17)|2 |&starf; &star; &star; &star; &star;|**Fail**|
97
-|[COL4A2](../COL4A2)|2 |&starf; &star; &star; &star; &star;|**Fail**|
98
-|[CYB5D1](../CYB5D1)|2 |&starf; &starf; &star; &star; &star;|**Fail**|
99
-|[CYP4F22](../CYP4F22)|2 |&starf; &star; &star; &star; &star;|**Fail**|
100
-|[DLGAP1](../DLGAP1)|2 |&starf; &star; &star; &star; &star;|**Fail**|
101
-|[DTX1](../DTX1)|2|&starf; &star; &star; &star; &star;|**Fail**|
102
-|[EIF2C4](../EIF2C4)|2 |&starf; &star; &star; &star; &star;|**Fail**|
103
-|[EML2](../EML2)|2 |&starf; &star; &star; &star; &star;|**Fail**|
104
-|[ENTPD3](../ENTPD3)|2 |&starf; &starf; &star; &star; &star;|**Fail**|
105
-|[EPHB2](../EPHB2)|2 |&starf; &starf; &star; &star; &star;|**Fail**|
106
-|[FAM129B](../FAM129B)|2 |&starf; &starf; &star; &star; &star;|**Fail**|
107
-|[FGFR3](../FGFR3)|2 |&starf; &star; &star; &star; &star;|**Fail**|
108
-|[FTCD](../FTCD)|2 |*Germline*|**Fail**|
109
-|[GRIK5](../GRIK5)|2 |&starf; &star; &star; &star; &star;|**Fail**|
110
-|[ICK](../ICK)|2 |&starf; &star; &star; &star; &star;|**Fail**|
111
-|[ITPR3](../ITPR3)|2 |&starf; &star; &star; &star; &star;|**Fail**|
112
-|[KIFC3](../KIFC3)|2 |&starf; &star; &star; &star; &star;|**Fail**|
113
-|[MAP3K6](../MAP3K6)|2 |&starf; &star; &star; &star; &star;|**Fail**|
114
-|[MYH10](../MYH10)|2 |&starf; &star; &star; &star; &star;|**Fail**|
115
-|[NOTCH1](../NOTCH1)|2 |&starf; &star; &star; &star; &star;|**Fail**|
116
-|[NRXN2](../NRXN2)|2 |&starf; &star; &star; &star; &star;|**Fail**|
117
-|[PC](../PC)|2 |&starf; &star; &star; &star; &star;|**Fail**|
118
-|[POLRMT](../POLRMT)|2 |&starf; &star; &star; &star; &star;|**Fail**|
119
-|[POR](../POR)|2 |&starf; &star; &star; &star; &star;|**Fail**|
120
-|[PRSS22](../PRSS22)|2 |&starf; &star; &star; &star; &star;|**Fail**|
121
-|[PTPRN](../PTPRN)|2 |&starf; &star; &star; &star; &star;|**Fail**|
122
-|[RBP3](../RBP3)|2 |&starf; &star; &star; &star; &star;|**Fail**|
123
-|[RET](../RET)|2 |&starf; &star; &star; &star; &star;|**Fail**|
124
-|[SALL3](../SALL3)|2 |&starf; &starf; &star; &star; &star;|**Fail**|
125
-|[SAPS2](../SAPS2)|2 |&starf; &star; &star; &star; &star;|**Fail**|
126
-|[SBF1](../SBF1)|2 |&starf; &starf; &star; &star; &star;|**Fail**|
127
-|[SF3B1](../SF3B1)|2 |&starf; &starf; &starf; &starf; &star;|**Fail**|
128
-|[SHANK1](../SHANK1)|2 |&starf; &star; &star; &star; &star;|**Fail**|
129
-|[SLC29A2](../SLC29A2)|2 |&starf; &star; &star; &star; &star;|**Fail**|
130
-|[SYNGAP1](../SYNGAP1)|2 |&starf; &star; &star; &star; &star;|**Fail**|
131
-|[TBC1D9B](../TBC1D9B)|2 |&starf; &star; &star; &star; &star;|**Fail**|
132
-|[TIGD6](../TIGD6)|2 |&starf; &star; &star; &star; &star;|**Fail**|
133
-|[TPST2](../TPST2)|2 |&star; &star; &star; &star; &star;|**Fail**|
134
-|[ZNF229](../ZNF229)|2 |*Germline*|**Fail**|
135
-
136
-## See Also
137
-
138
-The primary data supporting each of the mutations reported in this study can be viewed in [IGV reports](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Love/)
84
+|[CARD4](../CARD4)|2 |&starf; &starf; &starf; &starf; &star; |PASS |
85
+|[CDC73](../CDC73)|2 |&starf; &starf; &starf; &star; &star; |PASS |
86
+|[EZH2](../EZH2)|2 |&starf; &starf; &starf; &starf; &starf; |PASS |
87
+|[GGTLA4](../GGTLA4)|2 |&starf; &starf; &starf; &starf; &star; |PASS |
88
+|[NBEAL1](../NBEAL1)|2 |&starf; &starf; &starf; &starf; &star; |PASS |
89
+|[P2RY2](../P2RY2)|2 |&starf; &starf; &starf; &starf; &star; |PASS |
90
+|[RANBP6](../RANBP6)|2 |&starf; &starf; &starf; &starf; &starf; |PASS |
91
+
92
+### Tier 3
93
+|New gene|BL tier| Average variant quality | QC outcome |
94
+|:-|:-:|:-:|:-:|
95
+|[ACAD9](../ACAD9)|3 |&starf; &star; &star; &star; &star; |FAIL |
96
+|[ACE](../ACE)|3 |&starf; &star; &star; &star; &star; |FAIL |
97
+|[ATP2C2](../ATP2C2)|3 |&starf; &starf; &star; &star; &star; |FAIL |
98
+|[BRAF](../BRAF)|3 |&starf; &star; &star; &star; &star; |FAIL |
99
+|[BRD4](../BRD4)|3 |&starf; &star; &star; &star; &star; |FAIL |
100
+|[BTG2](../BTG2)|3 |&starf; &star; &star; &star; &star; |FAIL |
101
+|[C6orf27](../C6orf27)|3 |*Germline*|FAIL |
102
+|[CAD](../CAD)|3 |&starf; &star; &star; &star; &star; |FAIL |
103
+|[CCT6B](../CCT6B)|3 |*Germline*|FAIL |
104
+|[CDH17](../CDH17)|3 |&starf; &star; &star; &star; &star; |FAIL |
105
+|[COL4A2](../COL4A2)|3 |&starf; &star; &star; &star; &star; |FAIL |
106
+|[CYB5D1](../CYB5D1)|3 |&starf; &starf; &star; &star; &star; |FAIL |
107
+|[CYP4F22](../CYP4F22)|3 |&starf; &star; &star; &star; &star; |FAIL |
108
+|[DLGAP1](../DLGAP1)|3 |&starf; &star; &star; &star; &star; |FAIL |
109
+|[DTX1](../DTX1)|3 |&starf; &star; &star; &star; &star; |FAIL |
110
+|[EIF2C4](../EIF2C4)|3 |&starf; &star; &star; &star; &star; |FAIL |
111
+|[EML2](../EML2)|3 |&starf; &star; &star; &star; &star; |FAIL |
112
+|[ENTPD3](../ENTPD3)|3 |&starf; &starf; &star; &star; &star; |FAIL |
113
+|[EPHB2](../EPHB2)|3 |&starf; &starf; &star; &star; &star; |FAIL |
114
+|[FAM129B](../FAM129B)|3 |&starf; &starf; &star; &star; &star; |FAIL |
115
+|[FGFR3](../FGFR3)|3 |&starf; &star; &star; &star; &star; |FAIL |
116
+|[FTCD](../FTCD)|3 |*Germline*|FAIL |
117
+|[GRIK5](../GRIK5)|3 |&starf; &star; &star; &star; &star; |FAIL |
118
+|[ICK](../ICK)|3 |&starf; &star; &star; &star; &star; |FAIL |
119
+|[ITPR3](../ITPR3)|3 |&starf; &star; &star; &star; &star; |FAIL |
120
+|[KIFC3](../KIFC3)|3 |&starf; &star; &star; &star; &star; |FAIL |
121
+|[MAP3K6](../MAP3K6)|3 |&starf; &star; &star; &star; &star; |FAIL |
122
+|[MYH10](../MYH10)|3 |&starf; &star; &star; &star; &star; |FAIL |
123
+|[NOTCH1](../NOTCH1)|3 |&starf; &star; &star; &star; &star; |FAIL |
124
+|[NRXN2](../NRXN2)|3 |&starf; &star; &star; &star; &star; |FAIL |
125
+|[PC](../PC)|3 |&starf; &star; &star; &star; &star; |FAIL |
126
+|[POLRMT](../POLRMT)|3 |&starf; &star; &star; &star; &star; |FAIL |
127
+|[POR](../POR)|3 |&starf; &star; &star; &star; &star; |FAIL |
128
+|[PRSS22](../PRSS22)|3 |&starf; &star; &star; &star; &star; |FAIL |
129
+|[PTPRN](../PTPRN)|3 |&starf; &star; &star; &star; &star; |FAIL |
130
+|[RBP3](../RBP3)|3 |&starf; &star; &star; &star; &star; |FAIL |
131
+|[RET](../RET)|3 |&starf; &star; &star; &star; &star; |FAIL |
132
+|[SALL3](../SALL3)|3 |&starf; &starf; &star; &star; &star; |FAIL |
133
+|[SAPS2](../SAPS2)|3 |&starf; &star; &star; &star; &star; |FAIL |
134
+|[SBF1](../SBF1)|3 |&starf; &starf; &star; &star; &star; |FAIL |
135
+|[SF3B1](../SF3B1)|3 |&starf; &starf; &starf; &starf; &star; |FAIL |
136
+|[SHANK1](../SHANK1)|3 |&starf; &star; &star; &star; &star; |FAIL |
137
+|[SLC29A2](../SLC29A2)|3 |&starf; &star; &star; &star; &star; |FAIL |
138
+|[SYNGAP1](../SYNGAP1)|3 |&starf; &star; &star; &star; &star; |FAIL |
139
+|[TBC1D9B](../TBC1D9B)|3 |&starf; &star; &star; &star; &star; |FAIL |
140
+|[TIGD6](../TIGD6)|3 |&starf; &star; &star; &star; &star; |FAIL |
141
+|[TPST2](../TPST2)|3 |&star; &star; &star; &star; &star; |FAIL |
142
+|[ZNF229](../ZNF229)|3 |*Germline*|FAIL |
143
+
139 144
140 145
# Details
141 146
papers/mansouriFrequentNFKBIEDeletions2016.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @mansouriFrequentNFKBIEDeletions2016
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|1|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|PMBL|1|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, PMBL Tier 1, 1
27 27
This study, New Tier 2, 0
28 28
New Tier 2, PMBL Tier 2, 0
29
-All other PMBL studies, PMBL Tier 1, 75
30
-All other PMBL studies, PMBL Tier 2, 82
29
+This study, New Tier 3, 0
30
+New Tier 3, PMBL Tier 3, 0
31
+All other PMBL studies, PMBL Tier 1, 45
32
+All other PMBL studies, PMBL Tier 2, 112
33
+All other PMBL studies, PMBL Tier 3, 0
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/mareschalWholeExomeSequencing2016.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @mareschalWholeExomeSequencing2016
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|2|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|1|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -22,12 +22,15 @@ config:
22 22
suffix: ' genes)'
23 23
---
24 24
sankey-beta
25
-This study, New Tier 1, 2
26
-New Tier 1, DLBCL Tier 1, 2
25
+This study, New Tier 1, 1
26
+New Tier 1, DLBCL Tier 1, 1
27 27
This study, New Tier 2, 0
28 28
New Tier 2, DLBCL Tier 2, 0
29
-All other DLBCL studies, DLBCL Tier 1, 126
30
-All other DLBCL studies, DLBCL Tier 2, 198
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
31
+All other DLBCL studies, DLBCL Tier 1, 124
32
+All other DLBCL studies, DLBCL Tier 2, 210
33
+All other DLBCL studies, DLBCL Tier 3, 387
31 34
```
32 35
33 36
## Novel genes reported in this study
... ...
@@ -35,7 +38,6 @@ All other DLBCL studies, DLBCL Tier 2, 198
35 38
### Tier 1
36 39
|New gene|DLBCL tier|
37 40
|:-|:-:|
38
-|[TBL1XR1](../TBL1XR1)|1 |
39 41
|[XPO1](../XPO1)|1 |
40 42
41 43
papers/morinFrequentMutationHistonemodifying2011.md
... ...
@@ -8,8 +8,8 @@ bibliography: 'morinlab.bib'
8 8
9 9
|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10 10
|:-:|:-:|:-:|:-:|
11
-|DLBCL|29|4|0|
12
-|FL|21|4|0|
11
+|FL|20|5|0|
12
+|DLBCL|31|3|0|
13 13
```mermaid
14 14
---
15 15
config:
... ...
@@ -23,59 +23,60 @@ config:
23 23
suffix: ' genes)'
24 24
---
25 25
sankey-beta
26
-This study, New Tier 1, 29
27
-New Tier 1, DLBCL Tier 1, 29
28
-This study, New Tier 2, 4
29
-New Tier 2, DLBCL Tier 2, 4
26
+This study, New Tier 1, 31
27
+New Tier 1, DLBCL Tier 1, 31
28
+This study, New Tier 2, 3
29
+New Tier 2, DLBCL Tier 2, 3
30 30
This study, New Tier 3, 0
31 31
New Tier 3, DLBCL Tier 3, 0
32
-All other DLBCL studies, DLBCL Tier 1, 100
33
-All other DLBCL studies, DLBCL Tier 2, 174
34
-All other DLBCL studies, DLBCL Tier 3, 385
32
+All other DLBCL studies, DLBCL Tier 1, 94
33
+All other DLBCL studies, DLBCL Tier 2, 207
34
+All other DLBCL studies, DLBCL Tier 3, 387
35 35
```
36 36
37 37
## Novel genes reported in this study
38 38
39 39
### Tier 1
40
-|New gene|DLBCL tier|FL tier|
40
+|New gene|FL tier|DLBCL tier|
41 41
|:-|:-:|:-:|
42 42
|[B2M](../B2M)|1 |1 |
43
-|[BCL10](../BCL10)|1 |2 |
43
+|[BCL10](../BCL10)|1 |1 |
44 44
|[BCL2](../BCL2)|1 |1 |
45 45
|[BCL6](../BCL6)|1 |1 |
46 46
|[BCL7A](../BCL7A)|1 |1 |
47
-|[BTG1](../BTG1)|1 |1 |
48
-|[BTG2](../BTG2)|1 |1 |
47
+|[BTG1](../BTG1)|2 |1 |
48
+|[BTG2](../BTG2)|2 |1 |
49 49
|[CARD11](../CARD11)|1 |1 |
50 50
|[CCND3](../CCND3)|1 |1 |
51
-|[CD58](../CD58)|1 | |
52
-|[CD70](../CD70)|1 |2 |
53
-|[CD79B](../CD79B)|1 |2 |
54
-|[ETS1](../ETS1)|1 | |
51
+|[CD58](../CD58)| |1 |
52
+|[CD70](../CD70)|2 |1 |
53
+|[CIITA](../CIITA)| |1 |
54
+|[ETS1](../ETS1)| |1 |
55
+|[FAS](../FAS)|1 |1 |
55 56
|[FOXO1](../FOXO1)|1 |1 |
56 57
|[GNA13](../GNA13)|1 |1 |
57 58
|[HIST1H1C](../HIST1H1C)|1 |1 |
58
-|[IKZF3](../IKZF3)|1 | |
59
+|[IKZF3](../IKZF3)| |1 |
59 60
|[IRF4](../IRF4)|1 |1 |
60 61
|[IRF8](../IRF8)|1 |1 |
61 62
|[KLHL6](../KLHL6)|1 |1 |
62 63
|[KMT2D](../KMT2D)|1 |1 |
63 64
|[MEF2B](../MEF2B)|1 |1 |
64
-|[S1PR2](../S1PR2)|1 |1 |
65
+|[S1PR2](../S1PR2)|2 |1 |
65 66
|[SGK1](../SGK1)|1 |1 |
66 67
|[SOCS1](../SOCS1)|1 |1 |
67
-|[TMEM30A](../TMEM30A)|1 |2 |
68
+|[STAT3](../STAT3)| |1 |
69
+|[TMEM30A](../TMEM30A)|2 |1 |
68 70
|[TNFRSF14](../TNFRSF14)|1 |1 |
69 71
|[TP53](../TP53)|1 |1 |
70
-|[ZFP36L1](../ZFP36L1)|1 | |
72
+|[ZFP36L1](../ZFP36L1)| |1 |
71 73
72 74
### Tier 2
73
-|New gene|DLBCL tier|FL tier|
75
+|New gene|FL tier|DLBCL tier|
74 76
|:-|:-:|:-:|
75
-|[CD274](../CD274)|2 | |
76
-|[CIITA](../CIITA)|2 | |
77
-|[FAT2](../FAT2)|2 | |
78
-|[RAPGEF1](../RAPGEF1)|2 | |
77
+|[CD274](../CD274)| |2 |
78
+|[FAT2](../FAT2)| |2 |
79
+|[RAPGEF1](../RAPGEF1)| |2 |
79 80
80 81
81 82
# Details
papers/morinGeneticLandscapesRelapsed2016.md
... ...
@@ -28,9 +28,9 @@ This study, New Tier 2, 0
28 28
New Tier 2, DLBCL Tier 2, 0
29 29
This study, New Tier 3, 0
30 30
New Tier 3, DLBCL Tier 3, 0
31
-All other DLBCL studies, DLBCL Tier 1, 127
32
-All other DLBCL studies, DLBCL Tier 2, 178
33
-All other DLBCL studies, DLBCL Tier 3, 385
31
+All other DLBCL studies, DLBCL Tier 1, 123
32
+All other DLBCL studies, DLBCL Tier 2, 210
33
+All other DLBCL studies, DLBCL Tier 3, 387
34 34
```
35 35
36 36
## Novel genes reported in this study
papers/morinMutationalStructuralAnalysis2013.md
... ...
@@ -8,7 +8,7 @@ bibliography: 'morinlab.bib'
8 8
9 9
|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10 10
|:-:|:-:|:-:|:-:|
11
-|DLBCL|9|21|7|
11
+|DLBCL|9|23|7|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -24,13 +24,13 @@ config:
24 24
sankey-beta
25 25
This study, New Tier 1, 9
26 26
New Tier 1, DLBCL Tier 1, 9
27
-This study, New Tier 2, 21
28
-New Tier 2, DLBCL Tier 2, 21
27
+This study, New Tier 2, 23
28
+New Tier 2, DLBCL Tier 2, 23
29 29
This study, New Tier 3, 7
30 30
New Tier 3, DLBCL Tier 3, 7
31
-All other DLBCL studies, DLBCL Tier 1, 120
32
-All other DLBCL studies, DLBCL Tier 2, 157
33
-All other DLBCL studies, DLBCL Tier 3, 378
31
+All other DLBCL studies, DLBCL Tier 1, 116
32
+All other DLBCL studies, DLBCL Tier 2, 187
33
+All other DLBCL studies, DLBCL Tier 3, 380
34 34
```
35 35
36 36
## Novel genes reported in this study
... ...
@@ -52,9 +52,11 @@ All other DLBCL studies, DLBCL Tier 3, 378
52 52
|New gene|DLBCL tier| Average variant quality | QC outcome |
53 53
|:-|:-:|:-:|:-:|
54 54
|[ABI3BP](../ABI3BP)|2 |&starf; &starf; &starf; &star; &star; |PASS |
55
+|[ARAP2](../ARAP2)|2 || |
55 56
|[CDH9](../CDH9)|2 |&starf; &starf; &starf; &star; &star; |PASS |
56 57
|[CNTNAP5](../CNTNAP5)|2 |&starf; &starf; &starf; &starf; &star; |PASS |
57 58
|[DNAH5](../DNAH5)|2 |&starf; &starf; &starf; &starf; &star; |PASS |
59
+|[DSEL](../DSEL)|2 || |
58 60
|[DSG4](../DSG4)|2 |&starf; &starf; &starf; &star; &star; |PASS |
59 61
|[FAT4](../FAT4)|2 |&starf; &starf; &starf; &star; &star; |PASS |
60 62
|[HDAC7](../HDAC7)|2 |&starf; &starf; &starf; &star; &star; |PASS |
... ...
@@ -62,7 +64,7 @@ All other DLBCL studies, DLBCL Tier 3, 378
62 64
|[IFNGR1](../IFNGR1)|2 |&starf; &starf; &starf; &starf; &star; |PASS |
63 65
|[MPDZ](../MPDZ)|2 |&starf; &starf; &starf; &starf; &star; |PASS |
64 66
|[NLRP5](../NLRP5)|2 |&starf; &starf; &starf; &star; &star; |PASS |
65
-|[ODZ3](../ODZ3)|2 |&starf; &starf; &starf; &star; &star; |PASS |
67
+|[ODZ2](../ODZ2)|2 |&starf; &starf; &starf; &star; &star; |PASS |
66 68
|[P2RX5](../P2RX5)|2 |&starf; &starf; &starf; &star; &star; |PASS |
67 69
|[PASK](../PASK)|2 |&starf; &starf; &starf; &starf; &star; |PASS |
68 70
|[PCDHB11](../PCDHB11)|2 |&starf; &starf; &starf; &star; &star; |PASS |
papers/morinSomaticMutationsAltering2010.md
... ...
@@ -0,0 +1,46 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @morinSomaticMutationsAltering2010
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|1|0|0|
12
+|FL|1|0|0|
13
+```mermaid
14
+---
15
+config:
16
+ sankey:
17
+ showValues: true
18
+ linkColor: target
19
+ width: 600
20
+ height: 300
21
+ nodeAlignment: right
22
+ prefix: '('
23
+ suffix: ' genes)'
24
+---
25
+sankey-beta
26
+This study, New Tier 1, 1
27
+New Tier 1, DLBCL Tier 1, 1
28
+This study, New Tier 2, 0
29
+New Tier 2, DLBCL Tier 2, 0
30
+This study, New Tier 3, 0
31
+New Tier 3, DLBCL Tier 3, 0
32
+All other DLBCL studies, DLBCL Tier 1, 124
33
+All other DLBCL studies, DLBCL Tier 2, 210
34
+All other DLBCL studies, DLBCL Tier 3, 387
35
+```
36
+
37
+## Novel genes reported in this study
38
+
39
+### Tier 1
40
+|New gene|DLBCL tier|FL tier|
41
+|:-|:-:|:-:|
42
+|[EZH2](../EZH2)|1 |1 |
43
+
44
+
45
+# Details
46
+
papers/morinSomaticMutationsAltering2010a.md
... ...
@@ -1,46 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @morinSomaticMutationsAltering2010a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
-|:-:|:-:|:-:|:-:|
11
-|DLBCL|1|0|0|
12
-|FL|1|0|0|
13
-```mermaid
14
----
15
-config:
16
- sankey:
17
- showValues: true
18
- linkColor: target
19
- width: 600
20
- height: 300
21
- nodeAlignment: right
22
- prefix: '('
23
- suffix: ' genes)'
24
----
25
-sankey-beta
26
-This study, New Tier 1, 1
27
-New Tier 1, FL Tier 1, 1
28
-This study, New Tier 2, 0
29
-New Tier 2, FL Tier 2, 0
30
-This study, New Tier 3, 0
31
-New Tier 3, FL Tier 3, 0
32
-All other FL studies, FL Tier 1, 65
33
-All other FL studies, FL Tier 2, 49
34
-All other FL studies, FL Tier 3, 0
35
-```
36
-
37
-## Novel genes reported in this study
38
-
39
-### Tier 1
40
-|New gene|DLBCL tier|FL tier|
41
-|:-|:-:|:-:|
42
-|[EZH2](../EZH2)|1 |1 |
43
-
44
-
45
-# Details
46
-
papers/mottokGenomicAlterationsCIITA2015.md
... ...
@@ -0,0 +1,45 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @mottokGenomicAlterationsCIITA2015
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|PMBL|1|0|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 1
26
+New Tier 1, PMBL Tier 1, 1
27
+This study, New Tier 2, 0
28
+New Tier 2, PMBL Tier 2, 0
29
+This study, New Tier 3, 0
30
+New Tier 3, PMBL Tier 3, 0
31
+All other PMBL studies, PMBL Tier 1, 45
32
+All other PMBL studies, PMBL Tier 2, 112
33
+All other PMBL studies, PMBL Tier 3, 0
34
+```
35
+
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|PMBL tier|
40
+|:-|:-:|
41
+|[CIITA](../CIITA)|1 |
42
+
43
+
44
+# Details
45
+
papers/mottokGenomicAlterationsCIITA2015b.md
... ...
@@ -1,42 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @mottokGenomicAlterationsCIITA2015b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|1|0|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 1
26
-New Tier 1, PMBL Tier 1, 1
27
-This study, New Tier 2, 0
28
-New Tier 2, PMBL Tier 2, 0
29
-All other PMBL studies, PMBL Tier 1, 75
30
-All other PMBL studies, PMBL Tier 2, 82
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|PMBL tier|
37
-|:-|:-:|
38
-|[CIITA](../CIITA)|1 |
39
-
40
-
41
-# Details
42
-
papers/mottokIntegrativeGenomicAnalysis2019.md
... ...
@@ -0,0 +1,69 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @mottokIntegrativeGenomicAnalysis2019
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|PMBL|6|15|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 6
26
+New Tier 1, PMBL Tier 1, 6
27
+This study, New Tier 2, 15
28
+New Tier 2, PMBL Tier 2, 15
29
+This study, New Tier 3, 0
30
+New Tier 3, PMBL Tier 3, 0
31
+All other PMBL studies, PMBL Tier 1, 40
32
+All other PMBL studies, PMBL Tier 2, 97
33
+All other PMBL studies, PMBL Tier 3, 0
34
+```
35
+
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|PMBL tier|
40
+|:-|:-:|
41
+|[CISH](../CISH)|1 |
42
+|[DDX3X](../DDX3X)|1 |
43
+|[EZH2](../EZH2)|1 |
44
+|[IRF8](../IRF8)|1 |
45
+|[JAK1](../JAK1)|1 |
46
+|[MS4A1](../MS4A1)|1 |
47
+
48
+### Tier 2
49
+|New gene|PMBL tier|
50
+|:-|:-:|
51
+|[CXCR5](../CXCR5)|2 |
52
+|[EPHA7](../EPHA7)|2 |
53
+|[GCSAM](../GCSAM)|2 |
54
+|[HIST1H2BC](../HIST1H2BC)|2 |
55
+|[HIST1H4E](../HIST1H4E)|2 |
56
+|[HIST1H4J](../HIST1H4J)|2 |
57
+|[IL13RA1](../IL13RA1)|2 |
58
+|[IL1RAPL2](../IL1RAPL2)|2 |
59
+|[IRF2BP2](../IRF2BP2)|2 |
60
+|[IRF4](../IRF4)|2 |
61
+|[JUNB](../JUNB)|2 |
62
+|[MAGEC2](../MAGEC2)|2 |
63
+|[NFKB2](../NFKB2)|2 |
64
+|[RGS1](../RGS1)|2 |
65
+|[VMP1](../VMP1)|2 |
66
+
67
+
68
+# Details
69
+
papers/mottokIntegrativeGenomicAnalysis2019b.md
... ...
@@ -1,66 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @mottokIntegrativeGenomicAnalysis2019b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|6|15|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 6
26
-New Tier 1, PMBL Tier 1, 6
27
-This study, New Tier 2, 15
28
-New Tier 2, PMBL Tier 2, 15
29
-All other PMBL studies, PMBL Tier 1, 70
30
-All other PMBL studies, PMBL Tier 2, 67
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|PMBL tier|
37
-|:-|:-:|
38
-|[CISH](../CISH)|1 |
39
-|[DDX3X](../DDX3X)|1 |
40
-|[EZH2](../EZH2)|1 |
41
-|[IRF8](../IRF8)|1 |
42
-|[JAK1](../JAK1)|1 |
43
-|[MS4A1](../MS4A1)|1 |
44
-
45
-### Tier 2
46
-|New gene|PMBL tier|
47
-|:-|:-:|
48
-|[CXCR5](../CXCR5)|2 |
49
-|[EPHA7](../EPHA7)|2 |
50
-|[GCSAM](../GCSAM)|2 |
51
-|[HIST1H2BC](../HIST1H2BC)|2 |
52
-|[HIST1H4E](../HIST1H4E)|2 |
53
-|[HIST1H4J](../HIST1H4J)|2 |
54
-|[IL13RA1](../IL13RA1)|2 |
55
-|[IL1RAPL2](../IL1RAPL2)|2 |
56
-|[IRF2BP2](../IRF2BP2)|2 |
57
-|[IRF4](../IRF4)|2 |
58
-|[JUNB](../JUNB)|2 |
59
-|[MAGEC2](../MAGEC2)|2 |
60
-|[NFKB2](../NFKB2)|2 |
61
-|[RGS1](../RGS1)|2 |
62
-|[VMP1](../VMP1)|2 |
63
-
64
-
65
-# Details
66
-
papers/muppidiLossSignalingGa132014.md
... ...
@@ -0,0 +1,51 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @muppidiLossSignalingGa132014
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|BL|1|2|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 1
26
+New Tier 1, BL Tier 1, 1
27
+This study, New Tier 2, 2
28
+New Tier 2, BL Tier 2, 2
29
+This study, New Tier 3, 0
30
+New Tier 3, BL Tier 3, 0
31
+All other BL studies, BL Tier 1, 31
32
+All other BL studies, BL Tier 2, 70
33
+All other BL studies, BL Tier 3, 70
34
+```
35
+
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|BL tier|
40
+|:-|:-:|
41
+|[P2RY8](../P2RY8)|1 |
42
+
43
+### Tier 2
44
+|New gene|BL tier|
45
+|:-|:-:|
46
+|[ARHGEF1](../ARHGEF1)|2 |
47
+|[S1PR2](../S1PR2)|2 |
48
+
49
+
50
+# Details
51
+
papers/muppidiLossSignalingGa132014b.md
... ...
@@ -1,48 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @muppidiLossSignalingGa132014b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|BL|1|2|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 1
26
-New Tier 1, BL Tier 1, 1
27
-This study, New Tier 2, 2
28
-New Tier 2, BL Tier 2, 2
29
-All other BL studies, BL Tier 1, 28
30
-All other BL studies, BL Tier 2, 155
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|BL tier|
37
-|:-|:-:|
38
-|[P2RY8](../P2RY8)|1 |
39
-
40
-### Tier 2
41
-|New gene|BL tier|
42
-|:-|:-:|
43
-|[ARHGEF1](../ARHGEF1)|2 |
44
-|[S1PR2](../S1PR2)|2 |
45
-
46
-
47
-# Details
48
-
papers/nadeuGenomicEpigenomicInsights2020.md
... ...
@@ -0,0 +1,50 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @nadeuGenomicEpigenomicInsights2020b
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|MCL|3|2|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 3
26
+New Tier 1, MCL Tier 1, 3
27
+This study, New Tier 2, 2
28
+New Tier 2, MCL Tier 2, 2
29
+All other MCL studies, MCL Tier 1, 20
30
+All other MCL studies, MCL Tier 2, 44
31
+```
32
+
33
+## Novel genes reported in this study
34
+
35
+### Tier 1
36
+|New gene|MCL tier|
37
+|:-|:-:|
38
+|[SMARCA4](../SMARCA4)|1 |
39
+|[SYNE1](../SYNE1)|1 |
40
+|[TERT](../TERT)|1 |
41
+
42
+### Tier 2
43
+|New gene|MCL tier|
44
+|:-|:-:|
45
+|[BCOR](../BCOR)|2 |
46
+|[SMARCB1](../SMARCB1)|2 |
47
+
48
+
49
+# Details
50
+
papers/nadeuGenomicEpigenomicInsights2020b.md
... ...
@@ -1,50 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @nadeuGenomicEpigenomicInsights2020b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|MCL|3|2|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 3
26
-New Tier 1, MCL Tier 1, 3
27
-This study, New Tier 2, 2
28
-New Tier 2, MCL Tier 2, 2
29
-All other MCL studies, MCL Tier 1, 20
30
-All other MCL studies, MCL Tier 2, 44
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|MCL tier|
37
-|:-|:-:|
38
-|[SMARCA4](../SMARCA4)|1 |
39
-|[SYNE1](../SYNE1)|1 |
40
-|[TERT](../TERT)|1 |
41
-
42
-### Tier 2
43
-|New gene|MCL tier|
44
-|:-|:-:|
45
-|[BCOR](../BCOR)|2 |
46
-|[SMARCB1](../SMARCB1)|2 |
47
-
48
-
49
-# Details
50
-
papers/ngoOncogenicallyActiveMYD882011.md
... ...
@@ -0,0 +1,45 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @ngoOncogenicallyActiveMYD882011
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|1|0|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 1
26
+New Tier 1, DLBCL Tier 1, 1
27
+This study, New Tier 2, 0
28
+New Tier 2, DLBCL Tier 2, 0
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
31
+All other DLBCL studies, DLBCL Tier 1, 124
32
+All other DLBCL studies, DLBCL Tier 2, 210
33
+All other DLBCL studies, DLBCL Tier 3, 387
34
+```
35
+
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|DLBCL tier|
40
+|:-|:-:|
41
+|[MYD88](../MYD88)|1 |
42
+
43
+
44
+# Details
45
+
papers/ngoOncogenicallyActiveMYD882011a.md
... ...
@@ -1,42 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @ngoOncogenicallyActiveMYD882011a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|1|0|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 1
26
-New Tier 1, DLBCL Tier 1, 1
27
-This study, New Tier 2, 0
28
-New Tier 2, DLBCL Tier 2, 0
29
-All other DLBCL studies, DLBCL Tier 1, 127
30
-All other DLBCL studies, DLBCL Tier 2, 198
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|DLBCL tier|
37
-|:-|:-:|
38
-|[MYD88](../MYD88)|1 |
39
-
40
-
41
-# Details
42
-
papers/okosunRecurrentMTORC1activatingRRAGC2016.md
... ...
@@ -0,0 +1,48 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @okosunRecurrentMTORC1activatingRRAGC2016
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|FL|3|0|0|
12
+|DLBCL|1|0|0|
13
+```mermaid
14
+---
15
+config:
16
+ sankey:
17
+ showValues: true
18
+ linkColor: target
19
+ width: 600
20
+ height: 300
21
+ nodeAlignment: right
22
+ prefix: '('
23
+ suffix: ' genes)'
24
+---
25
+sankey-beta
26
+This study, New Tier 1, 3
27
+New Tier 1, FL Tier 1, 3
28
+This study, New Tier 2, 0
29
+New Tier 2, FL Tier 2, 0
30
+This study, New Tier 3, 0
31
+New Tier 3, FL Tier 3, 0
32
+All other FL studies, FL Tier 1, 51
33
+All other FL studies, FL Tier 2, 59
34
+All other FL studies, FL Tier 3, 0
35
+```
36
+
37
+## Novel genes reported in this study
38
+
39
+### Tier 1
40
+|New gene|FL tier|DLBCL tier|
41
+|:-|:-:|:-:|
42
+|[ATP6AP1](../ATP6AP1)|1 | |
43
+|[ATP6V1B2](../ATP6V1B2)|1 | |
44
+|[RRAGC](../RRAGC)|1 |1 |
45
+
46
+
47
+# Details
48
+
papers/okosunRecurrentMTORC1activatingRRAGC2016a.md
... ...
@@ -1,45 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @okosunRecurrentMTORC1activatingRRAGC2016a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|1|0|
12
-|FL|3|0|
13
-```mermaid
14
----
15
-config:
16
- sankey:
17
- showValues: true
18
- linkColor: target
19
- width: 600
20
- height: 300
21
- nodeAlignment: right
22
- prefix: '('
23
- suffix: ' genes)'
24
----
25
-sankey-beta
26
-This study, New Tier 1, 3
27
-New Tier 1, FL Tier 1, 3
28
-This study, New Tier 2, 0
29
-New Tier 2, FL Tier 2, 0
30
-All other FL studies, FL Tier 1, 63
31
-All other FL studies, FL Tier 2, 50
32
-```
33
-
34
-## Novel genes reported in this study
35
-
36
-### Tier 1
37
-|New gene|DLBCL tier|FL tier|
38
-|:-|:-:|:-:|
39
-|[ATP6AP1](../ATP6AP1)| |1 |
40
-|[ATP6V1B2](../ATP6V1B2)| |1 |
41
-|[RRAGC](../RRAGC)|1 |1 |
42
-
43
-
44
-# Details
45
-
papers/oricchioGeneticEpigeneticInactivation2017.md
... ...
@@ -0,0 +1,40 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @oricchioGeneticEpigeneticInactivation2017b
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|FL|0|1|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 0
26
+New Tier 1, FL Tier 1, 0
27
+This study, New Tier 2, 1
28
+New Tier 2, FL Tier 2, 1
29
+All other FL studies, FL Tier 1, 66
30
+All other FL studies, FL Tier 2, 49
31
+```
32
+
33
+### Tier 2
34
+|New gene|FL tier|
35
+|:-|:-:|
36
+|[SESN1](../SESN1)|2 |
37
+
38
+
39
+# Details
40
+
papers/oricchioGeneticEpigeneticInactivation2017b.md
... ...
@@ -1,40 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @oricchioGeneticEpigeneticInactivation2017b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|FL|0|1|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 0
26
-New Tier 1, FL Tier 1, 0
27
-This study, New Tier 2, 1
28
-New Tier 2, FL Tier 2, 1
29
-All other FL studies, FL Tier 1, 66
30
-All other FL studies, FL Tier 2, 49
31
-```
32
-
33
-### Tier 2
34
-|New gene|FL tier|
35
-|:-|:-:|
36
-|[SESN1](../SESN1)|2 |
37
-
38
-
39
-# Details
40
-
papers/ottoGeneticLesionsTRAF32012.md
... ...
@@ -0,0 +1,46 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @ottoGeneticLesionsTRAF32012
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|PMBL|2|0|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 2
26
+New Tier 1, PMBL Tier 1, 2
27
+This study, New Tier 2, 0
28
+New Tier 2, PMBL Tier 2, 0
29
+This study, New Tier 3, 0
30
+New Tier 3, PMBL Tier 3, 0
31
+All other PMBL studies, PMBL Tier 1, 44
32
+All other PMBL studies, PMBL Tier 2, 112
33
+All other PMBL studies, PMBL Tier 3, 0
34
+```
35
+
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|PMBL tier|
40
+|:-|:-:|
41
+|[MAP3K14](../MAP3K14)|1 |
42
+|[TRAF3](../TRAF3)|1 |
43
+
44
+
45
+# Details
46
+
papers/ottoGeneticLesionsTRAF32012a.md
... ...
@@ -1,43 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @ottoGeneticLesionsTRAF32012a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|2|0|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 2
26
-New Tier 1, PMBL Tier 1, 2
27
-This study, New Tier 2, 0
28
-New Tier 2, PMBL Tier 2, 0
29
-All other PMBL studies, PMBL Tier 1, 74
30
-All other PMBL studies, PMBL Tier 2, 82
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|PMBL tier|
37
-|:-|:-:|
38
-|[MAP3K14](../MAP3K14)|1 |
39
-|[TRAF3](../TRAF3)|1 |
40
-
41
-
42
-# Details
43
-
papers/paneaWholeGenomeLandscape2019.md
... ...
@@ -8,7 +8,7 @@ bibliography: 'morinlab.bib'
8 8
9 9
|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10 10
|:-:|:-:|:-:|:-:|
11
-|BL|4|13|22|
11
+|BL|2|15|22|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -22,14 +22,14 @@ config:
22 22
suffix: ' genes)'
23 23
---
24 24
sankey-beta
25
-This study, New Tier 1, 4
26
-New Tier 1, BL Tier 1, 4
27
-This study, New Tier 2, 13
28
-New Tier 2, BL Tier 2, 13
25
+This study, New Tier 1, 2
26
+New Tier 1, BL Tier 1, 2
27
+This study, New Tier 2, 15
28
+New Tier 2, BL Tier 2, 15
29 29
This study, New Tier 3, 22
30 30
New Tier 3, BL Tier 3, 22
31
-All other BL studies, BL Tier 1, 25
32
-All other BL studies, BL Tier 2, 62
31
+All other BL studies, BL Tier 1, 30
32
+All other BL studies, BL Tier 2, 57
33 33
All other BL studies, BL Tier 3, 48
34 34
```
35 35
... ...
@@ -39,8 +39,6 @@ All other BL studies, BL Tier 3, 48
39 39
|New gene|BL tier| Average variant quality | QC outcome |
40 40
|:-|:-:|:-:|:-:|
41 41
|[BMP7](../BMP7)|1 || |
42
-|[EIF4A1](../EIF4A1)|1 || |
43
-|[EPPK1](../EPPK1)|1 || |
44 42
|[HNRNPU](../HNRNPU)|1 || |
45 43
46 44
### Tier 2
... ...
@@ -48,6 +46,8 @@ All other BL studies, BL Tier 3, 48
48 46
|:-|:-:|:-:|:-:|
49 47
|[CD83](../CD83)|2 |&starf; &starf; &starf; &star; &star; |PASS |
50 48
|[CXCR4](../CXCR4)|2 |&starf; &starf; &starf; &starf; &star; |PASS |
49
+|[EIF4A1](../EIF4A1)|2 || |
50
+|[EPPK1](../EPPK1)|2 || |
51 51
|[HIST1H3D](../HIST1H3D)|2 |&starf; &starf; &starf; &star; &star; |PASS |
52 52
|[HIST1H3I](../HIST1H3I)|2 |&starf; &starf; &starf; &starf; &star; |PASS |
53 53
|[HIST1H4J](../HIST1H4J)|2 |&starf; &starf; &starf; &star; &star; |PASS |
papers/pararajalingamCodingNoncodingDrivers2020.md
... ...
@@ -6,10 +6,10 @@ bibliography: 'morinlab.bib'
6 6
# @pararajalingamCodingNoncodingDrivers2020
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|2|3|
12
-|MCL|6|1|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|2|4|0|
12
+|MCL|6|1|0|
13 13
```mermaid
14 14
---
15 15
config:
... ...
@@ -27,8 +27,11 @@ This study, New Tier 1, 6
27 27
New Tier 1, MCL Tier 1, 6
28 28
This study, New Tier 2, 1
29 29
New Tier 2, MCL Tier 2, 1
30
+This study, New Tier 3, 0
31
+New Tier 3, MCL Tier 3, 0
30 32
All other MCL studies, MCL Tier 1, 17
31 33
All other MCL studies, MCL Tier 2, 45
34
+All other MCL studies, MCL Tier 3, 0
32 35
```
33 36
34 37
## Novel genes reported in this study
... ...
@@ -41,7 +44,7 @@ All other MCL studies, MCL Tier 2, 45
41 44
|[EWSR1](../EWSR1)| |1 |
42 45
|[HNRNPH1](../HNRNPH1)|2 |1 |
43 46
|[NFKBIE](../NFKBIE)|1 |1 |
44
-|[S1PR1](../S1PR1)| |1 |
47
+|[S1PR1](../S1PR1)|2 |1 |
45 48
|[UBR5](../UBR5)|2 |1 |
46 49
47 50
papers/parryWholeExomeSequencing2013.md
... ...
@@ -6,10 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @parryWholeExomeSequencing2013
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|MZL|0|8|
12
-|DLBCL|3|1|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|MZL|0|7|0|
13 12
```mermaid
14 13
---
15 14
config:
... ...
@@ -25,29 +24,25 @@ config:
25 24
sankey-beta
26 25
This study, New Tier 1, 0
27 26
New Tier 1, MZL Tier 1, 0
28
-This study, New Tier 2, 8
29
-New Tier 2, MZL Tier 2, 8
27
+This study, New Tier 2, 7
28
+New Tier 2, MZL Tier 2, 7
29
+This study, New Tier 3, 0
30
+New Tier 3, MZL Tier 3, 0
30 31
All other MZL studies, MZL Tier 1, 42
31
-All other MZL studies, MZL Tier 2, 66
32
+All other MZL studies, MZL Tier 2, 67
33
+All other MZL studies, MZL Tier 3, 0
32 34
```
33 35
34
-## Novel genes reported in this study
35
-
36
-### Tier 1
37
-|New gene|MZL tier|DLBCL tier|
38
-|:-|:-:|:-:|
39
-|[CREBBP](../CREBBP)|2 |1 |
40
-|[FBXO11](../FBXO11)|2 |1 |
41
-|[TRRAP](../TRRAP)|2 |1 |
42
-
43 36
### Tier 2
44
-|New gene|MZL tier|DLBCL tier|
45
-|:-|:-:|:-:|
46
-|[AMOTL1](../AMOTL1)|2 | |
47
-|[CBFA2T3](../CBFA2T3)|2 | |
48
-|[FAT4](../FAT4)|2 |2 |
49
-|[PLA2G4D](../PLA2G4D)|2 | |
50
-|[USH2A](../USH2A)|2 | |
37
+|New gene|MZL tier|
38
+|:-|:-:|
39
+|[AMOTL1](../AMOTL1)|2 |
40
+|[CBFA2T3](../CBFA2T3)|2 |
41
+|[CREBBP](../CREBBP)|2 |
42
+|[FAT4](../FAT4)|2 |
43
+|[FBXO11](../FBXO11)|2 |
44
+|[PLA2G4D](../PLA2G4D)|2 |
45
+|[USH2A](../USH2A)|2 |
51 46
52 47
53 48
# Details
papers/pasqualucciAnalysisCodingGenome2011.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @pasqualucciAnalysisCodingGenome2011
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|3|4|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|3|35|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -24,10 +24,13 @@ config:
24 24
sankey-beta
25 25
This study, New Tier 1, 3
26 26
New Tier 1, DLBCL Tier 1, 3
27
-This study, New Tier 2, 4
28
-New Tier 2, DLBCL Tier 2, 4
29
-All other DLBCL studies, DLBCL Tier 1, 125
30
-All other DLBCL studies, DLBCL Tier 2, 194
27
+This study, New Tier 2, 35
28
+New Tier 2, DLBCL Tier 2, 35
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
31
+All other DLBCL studies, DLBCL Tier 1, 122
32
+All other DLBCL studies, DLBCL Tier 2, 175
33
+All other DLBCL studies, DLBCL Tier 3, 387
31 34
```
32 35
33 36
## Novel genes reported in this study
... ...
@@ -42,10 +45,41 @@ All other DLBCL studies, DLBCL Tier 2, 194
42 45
### Tier 2
43 46
|New gene|DLBCL tier|
44 47
|:-|:-:|
48
+|[ADAMTSL3](../ADAMTSL3)|2 |
49
+|[AKAP8](../AKAP8)|2 |
50
+|[ANKLE2](../ANKLE2)|2 |
51
+|[BCL2L10](../BCL2L10)|2 |
52
+|[BRSK1](../BRSK1)|2 |
53
+|[C12orf35](../C12orf35)|2 |
54
+|[CAMTA1](../CAMTA1)|2 |
45 55
|[CD36](../CD36)|2 |
56
+|[CYTSB](../CYTSB)|2 |
57
+|[DCHS1](../DCHS1)|2 |
58
+|[DPYD](../DPYD)|2 |
59
+|[DSC3](../DSC3)|2 |
60
+|[DUSP27](../DUSP27)|2 |
61
+|[DUSP9](../DUSP9)|2 |
62
+|[FBXO31](../FBXO31)|2 |
63
+|[HMGB1](../HMGB1)|2 |
46 64
|[HNF1B](../HNF1B)|2 |
65
+|[KDM2B](../KDM2B)|2 |
66
+|[MAGEC3](../MAGEC3)|2 |
67
+|[MED12L](../MED12L)|2 |
68
+|[MTMR8](../MTMR8)|2 |
69
+|[MYO1G](../MYO1G)|2 |
47 70
|[MYOM2](../MYOM2)|2 |
71
+|[OFD1](../OFD1)|2 |
72
+|[PMS1](../PMS1)|2 |
73
+|[PPP2R5A](../PPP2R5A)|2 |
74
+|[RASGEF1A](../RASGEF1A)|2 |
75
+|[RGAG1](../RGAG1)|2 |
76
+|[SERPINA1](../SERPINA1)|2 |
77
+|[SMARCA1](../SMARCA1)|2 |
78
+|[TLL2](../TLL2)|2 |
48 79
|[TRAF3](../TRAF3)|2 |
80
+|[TSC22D1](../TSC22D1)|2 |
81
+|[ZNF521](../ZNF521)|2 |
82
+|[ZWILCH](../ZWILCH)|2 |
49 83
50 84
51 85
# Details
papers/pasqualucciHypermutationMultipleProtooncogenes2001.md
... ...
@@ -0,0 +1,52 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @pasqualucciHypermutationMultipleProtooncogenes2001
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|2|2|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 2
26
+New Tier 1, DLBCL Tier 1, 2
27
+This study, New Tier 2, 2
28
+New Tier 2, DLBCL Tier 2, 2
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
31
+All other DLBCL studies, DLBCL Tier 1, 123
32
+All other DLBCL studies, DLBCL Tier 2, 208
33
+All other DLBCL studies, DLBCL Tier 3, 387
34
+```
35
+
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|DLBCL tier|
40
+|:-|:-:|
41
+|[MYC](../MYC)|1 |
42
+|[PIM1](../PIM1)|1 |
43
+
44
+### Tier 2
45
+|New gene|DLBCL tier|
46
+|:-|:-:|
47
+|[PAX5](../PAX5)|2 |
48
+|[RHOH](../RHOH)|2 |
49
+
50
+
51
+# Details
52
+
papers/pasqualucciHypermutationMultipleProtooncogenes2001a.md
... ...
@@ -1,49 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @pasqualucciHypermutationMultipleProtooncogenes2001a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|2|2|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 2
26
-New Tier 1, DLBCL Tier 1, 2
27
-This study, New Tier 2, 2
28
-New Tier 2, DLBCL Tier 2, 2
29
-All other DLBCL studies, DLBCL Tier 1, 126
30
-All other DLBCL studies, DLBCL Tier 2, 196
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|DLBCL tier|
37
-|:-|:-:|
38
-|[MYC](../MYC)|1 |
39
-|[PIM1](../PIM1)|1 |
40
-
41
-### Tier 2
42
-|New gene|DLBCL tier|
43
-|:-|:-:|
44
-|[PAX5](../PAX5)|2 |
45
-|[RHOH](../RHOH)|2 |
46
-
47
-
48
-# Details
49
-
papers/pasqualucciInactivatingMutationsAcetyltransferase2011.md
... ...
@@ -0,0 +1,47 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @pasqualucciInactivatingMutationsAcetyltransferase2011
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|2|0|0|
12
+|FL|2|0|0|
13
+```mermaid
14
+---
15
+config:
16
+ sankey:
17
+ showValues: true
18
+ linkColor: target
19
+ width: 600
20
+ height: 300
21
+ nodeAlignment: right
22
+ prefix: '('
23
+ suffix: ' genes)'
24
+---
25
+sankey-beta
26
+This study, New Tier 1, 2
27
+New Tier 1, DLBCL Tier 1, 2
28
+This study, New Tier 2, 0
29
+New Tier 2, DLBCL Tier 2, 0
30
+This study, New Tier 3, 0
31
+New Tier 3, DLBCL Tier 3, 0
32
+All other DLBCL studies, DLBCL Tier 1, 123
33
+All other DLBCL studies, DLBCL Tier 2, 210
34
+All other DLBCL studies, DLBCL Tier 3, 387
35
+```
36
+
37
+## Novel genes reported in this study
38
+
39
+### Tier 1
40
+|New gene|DLBCL tier|FL tier|
41
+|:-|:-:|:-:|
42
+|[CREBBP](../CREBBP)|1 |1 |
43
+|[EP300](../EP300)|1 |1 |
44
+
45
+
46
+# Details
47
+
papers/pasqualucciInactivatingMutationsAcetyltransferase2011a.md
... ...
@@ -1,44 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @pasqualucciInactivatingMutationsAcetyltransferase2011a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|2|0|
12
-|FL|2|0|
13
-```mermaid
14
----
15
-config:
16
- sankey:
17
- showValues: true
18
- linkColor: target
19
- width: 600
20
- height: 300
21
- nodeAlignment: right
22
- prefix: '('
23
- suffix: ' genes)'
24
----
25
-sankey-beta
26
-This study, New Tier 1, 2
27
-New Tier 1, FL Tier 1, 2
28
-This study, New Tier 2, 0
29
-New Tier 2, FL Tier 2, 0
30
-All other FL studies, FL Tier 1, 64
31
-All other FL studies, FL Tier 2, 50
32
-```
33
-
34
-## Novel genes reported in this study
35
-
36
-### Tier 1
37
-|New gene|DLBCL tier|FL tier|
38
-|:-|:-:|:-:|
39
-|[CREBBP](../CREBBP)|1 |1 |
40
-|[EP300](../EP300)|1 |1 |
41
-
42
-
43
-# Details
44
-
papers/pasqualucciInactivationPRDM1BLIMP12006.md
... ...
@@ -0,0 +1,45 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @pasqualucciInactivationPRDM1BLIMP12006
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|1|0|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 1
26
+New Tier 1, DLBCL Tier 1, 1
27
+This study, New Tier 2, 0
28
+New Tier 2, DLBCL Tier 2, 0
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
31
+All other DLBCL studies, DLBCL Tier 1, 124
32
+All other DLBCL studies, DLBCL Tier 2, 210
33
+All other DLBCL studies, DLBCL Tier 3, 387
34
+```
35
+
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|DLBCL tier|
40
+|:-|:-:|
41
+|[PRDM1](../PRDM1)|1 |
42
+
43
+
44
+# Details
45
+
papers/pasqualucciInactivationPRDM1BLIMP12006a.md
... ...
@@ -1,42 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @pasqualucciInactivationPRDM1BLIMP12006a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|1|0|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 1
26
-New Tier 1, DLBCL Tier 1, 1
27
-This study, New Tier 2, 0
28
-New Tier 2, DLBCL Tier 2, 0
29
-All other DLBCL studies, DLBCL Tier 1, 127
30
-All other DLBCL studies, DLBCL Tier 2, 198
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|DLBCL tier|
37
-|:-|:-:|
38
-|[PRDM1](../PRDM1)|1 |
39
-
40
-
41
-# Details
42
-
papers/reddyGeneticFunctionalDrivers2017.md
... ...
@@ -8,7 +8,7 @@ bibliography: 'morinlab.bib'
8 8
9 9
|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10 10
|:-:|:-:|:-:|:-:|
11
-|DLBCL|10|24|26|
11
+|DLBCL|13|28|26|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -22,15 +22,15 @@ config:
22 22
suffix: ' genes)'
23 23
---
24 24
sankey-beta
25
-This study, New Tier 1, 10
26
-New Tier 1, DLBCL Tier 1, 10
27
-This study, New Tier 2, 24
28
-New Tier 2, DLBCL Tier 2, 24
25
+This study, New Tier 1, 13
26
+New Tier 1, DLBCL Tier 1, 13
27
+This study, New Tier 2, 28
28
+New Tier 2, DLBCL Tier 2, 28
29 29
This study, New Tier 3, 26
30 30
New Tier 3, DLBCL Tier 3, 26
31
-All other DLBCL studies, DLBCL Tier 1, 119
32
-All other DLBCL studies, DLBCL Tier 2, 154
33
-All other DLBCL studies, DLBCL Tier 3, 359
31
+All other DLBCL studies, DLBCL Tier 1, 112
32
+All other DLBCL studies, DLBCL Tier 2, 182
33
+All other DLBCL studies, DLBCL Tier 3, 361
34 34
```
35 35
36 36
## Novel genes reported in this study
... ...
@@ -42,10 +42,13 @@ All other DLBCL studies, DLBCL Tier 3, 359
42 42
|[BIRC6](../BIRC6)|1 || |
43 43
|[DDX3X](../DDX3X)|1 || |
44 44
|[HNRNPU](../HNRNPU)|1 || |
45
-|[JUNB](../JUNB)|1 |&starf; &starf; &starf; &star; &star; |PASS |
46 45
|[MGA](../MGA)|1 || |
46
+|[PIM2](../PIM2)|1 || |
47 47
|[PTEN](../PTEN)|1 || |
48
+|[PTPN6](../PTPN6)|1 |&starf; &starf; &starf; &star; &star; |PASS |
48 49
|[SF3B1](../SF3B1)|1 || |
50
+|[SMARCA4](../SMARCA4)|1 || |
51
+|[TMSB4X](../TMSB4X)|1 || |
49 52
|[TOX](../TOX)|1 || |
50 53
|[ZNF292](../ZNF292)|1 || |
51 54
... ...
@@ -63,18 +66,22 @@ All other DLBCL studies, DLBCL Tier 3, 359
63 66
|[HNRNPD](../HNRNPD)|2 || |
64 67
|[IKBKB](../IKBKB)|2 |&starf; &starf; &starf; &star; &star; |PASS |
65 68
|[IL16](../IL16)|2 || |
69
+|[INO80](../INO80)|2 || |
70
+|[JAK1](../JAK1)|2 || |
71
+|[JAK3](../JAK3)|2 || |
66 72
|[KCMF1](../KCMF1)|2 |&starf; &starf; &starf; &star; &star; |PASS |
67 73
|[MAGT1](../MAGT1)|2 |&starf; &starf; &starf; &star; &star; |PASS |
68 74
|[MCL1](../MCL1)|2 |&starf; &starf; &starf; &star; &star; |PASS |
69 75
|[MECOM](../MECOM)|2 |&starf; &starf; &starf; &star; &star; |PASS |
70 76
|[MET](../MET)|2 |&starf; &starf; &starf; &star; &star; |PASS |
71 77
|[MSH6](../MSH6)|2 |&starf; &starf; &starf; &star; &star; |PASS |
72
-|[PTPN6](../PTPN6)|2 |&starf; &starf; &starf; &star; &star; |PASS |
73 78
|[SETD5](../SETD5)|2 |&starf; &starf; &starf; &star; &star; |PASS |
79
+|[STAT5B](../STAT5B)|2 || |
74 80
|[TCL1A](../TCL1A)|2 || |
75 81
|[TGFBR2](../TGFBR2)|2 |&starf; &starf; &starf; &star; &star; |PASS |
76 82
|[TIPARP](../TIPARP)|2 |&starf; &starf; &starf; &star; &star; |PASS |
77 83
|[YY1](../YY1)|2 |&starf; &starf; &starf; &star; &star; |PASS |
84
+|[ZEB2](../ZEB2)|2 || |
78 85
|[ZFX](../ZFX)|2 |&starf; &starf; &starf; &star; &star; |PASS |
79 86
80 87
### Tier 3
papers/reichelFlowSortingExome2015.md
... ...
@@ -0,0 +1,77 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @reichelFlowSortingExome2015
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|PMBL|11|18|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 11
26
+New Tier 1, PMBL Tier 1, 11
27
+This study, New Tier 2, 18
28
+New Tier 2, PMBL Tier 2, 18
29
+This study, New Tier 3, 0
30
+New Tier 3, PMBL Tier 3, 0
31
+All other PMBL studies, PMBL Tier 1, 35
32
+All other PMBL studies, PMBL Tier 2, 94
33
+All other PMBL studies, PMBL Tier 3, 0
34
+```
35
+
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|PMBL tier|
40
+|:-|:-:|
41
+|[B2M](../B2M)|1 |
42
+|[CSF2RB](../CSF2RB)|1 |
43
+|[EBF1](../EBF1)|1 |
44
+|[EEF1A1](../EEF1A1)|1 |
45
+|[GNA13](../GNA13)|1 |
46
+|[HIST1H1E](../HIST1H1E)|1 |
47
+|[ITPKB](../ITPKB)|1 |
48
+|[PIM2](../PIM2)|1 |
49
+|[UBE2A](../UBE2A)|1 |
50
+|[WEE1](../WEE1)|1 |
51
+|[ZFP36L1](../ZFP36L1)|1 |
52
+
53
+### Tier 2
54
+|New gene|PMBL tier|
55
+|:-|:-:|
56
+|[ARIH2](../ARIH2)|2 |
57
+|[BCL7A](../BCL7A)|2 |
58
+|[DMD](../DMD)|2 |
59
+|[EGR1](../EGR1)|2 |
60
+|[HECW2](../HECW2)|2 |
61
+|[HELLS](../HELLS)|2 |
62
+|[HIST1H3B](../HIST1H3B)|2 |
63
+|[HIST1H4C](../HIST1H4C)|2 |
64
+|[MPDZ](../MPDZ)|2 |
65
+|[NEK1](../NEK1)|2 |
66
+|[RANBP2](../RANBP2)|2 |
67
+|[SENP7](../SENP7)|2 |
68
+|[SETDB1](../SETDB1)|2 |
69
+|[SIAH2](../SIAH2)|2 |
70
+|[TBC1D15](../TBC1D15)|2 |
71
+|[TICRR](../TICRR)|2 |
72
+|[TRIP11](../TRIP11)|2 |
73
+|[ZNF217](../ZNF217)|2 |
74
+
75
+
76
+# Details
77
+
papers/reichelFlowSortingExome2015a.md
... ...
@@ -1,74 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @reichelFlowSortingExome2015a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|11|18|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 11
26
-New Tier 1, PMBL Tier 1, 11
27
-This study, New Tier 2, 18
28
-New Tier 2, PMBL Tier 2, 18
29
-All other PMBL studies, PMBL Tier 1, 65
30
-All other PMBL studies, PMBL Tier 2, 64
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|PMBL tier|
37
-|:-|:-:|
38
-|[B2M](../B2M)|1 |
39
-|[CSF2RB](../CSF2RB)|1 |
40
-|[EBF1](../EBF1)|1 |
41
-|[EEF1A1](../EEF1A1)|1 |
42
-|[GNA13](../GNA13)|1 |
43
-|[HIST1H1E](../HIST1H1E)|1 |
44
-|[ITPKB](../ITPKB)|1 |
45
-|[PIM2](../PIM2)|1 |
46
-|[UBE2A](../UBE2A)|1 |
47
-|[WEE1](../WEE1)|1 |
48
-|[ZFP36L1](../ZFP36L1)|1 |
49
-
50
-### Tier 2
51
-|New gene|PMBL tier|
52
-|:-|:-:|
53
-|[ARIH2](../ARIH2)|2 |
54
-|[BCL7A](../BCL7A)|2 |
55
-|[DMD](../DMD)|2 |
56
-|[EGR1](../EGR1)|2 |
57
-|[HECW2](../HECW2)|2 |
58
-|[HELLS](../HELLS)|2 |
59
-|[HIST1H3B](../HIST1H3B)|2 |
60
-|[HIST1H4C](../HIST1H4C)|2 |
61
-|[MPDZ](../MPDZ)|2 |
62
-|[NEK1](../NEK1)|2 |
63
-|[RANBP2](../RANBP2)|2 |
64
-|[SENP7](../SENP7)|2 |
65
-|[SETDB1](../SETDB1)|2 |
66
-|[SIAH2](../SIAH2)|2 |
67
-|[TBC1D15](../TBC1D15)|2 |
68
-|[TICRR](../TICRR)|2 |
69
-|[TRIP11](../TRIP11)|2 |
70
-|[ZNF217](../ZNF217)|2 |
71
-
72
-
73
-# Details
74
-
papers/richterRecurrentMutationID32012.md
... ...
@@ -0,0 +1,49 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @richterRecurrentMutationID32012
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|BL|5|0|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 5
26
+New Tier 1, BL Tier 1, 5
27
+This study, New Tier 2, 0
28
+New Tier 2, BL Tier 2, 0
29
+This study, New Tier 3, 0
30
+New Tier 3, BL Tier 3, 0
31
+All other BL studies, BL Tier 1, 27
32
+All other BL studies, BL Tier 2, 72
33
+All other BL studies, BL Tier 3, 70
34
+```
35
+
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|BL tier|
40
+|:-|:-:|
41
+|[CCND3](../CCND3)|1 |
42
+|[FBXO11](../FBXO11)|1 |
43
+|[ID3](../ID3)|1 |
44
+|[RHOA](../RHOA)|1 |
45
+|[SMARCA4](../SMARCA4)|1 |
46
+
47
+
48
+# Details
49
+
papers/richterRecurrentMutationID32012a.md
... ...
@@ -1,46 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @richterRecurrentMutationID32012a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|BL|5|0|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 5
26
-New Tier 1, BL Tier 1, 5
27
-This study, New Tier 2, 0
28
-New Tier 2, BL Tier 2, 0
29
-All other BL studies, BL Tier 1, 24
30
-All other BL studies, BL Tier 2, 157
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|BL tier|
37
-|:-|:-:|
38
-|[CCND3](../CCND3)|1 |
39
-|[FBXO11](../FBXO11)|1 |
40
-|[ID3](../ID3)|1 |
41
-|[RHOA](../RHOA)|1 |
42
-|[SMARCA4](../SMARCA4)|1 |
43
-
44
-
45
-# Details
46
-
papers/ritzRecurrentMutationsSTAT62009.md
... ...
@@ -0,0 +1,45 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @ritzRecurrentMutationsSTAT62009
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|PMBL|1|0|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 1
26
+New Tier 1, PMBL Tier 1, 1
27
+This study, New Tier 2, 0
28
+New Tier 2, PMBL Tier 2, 0
29
+This study, New Tier 3, 0
30
+New Tier 3, PMBL Tier 3, 0
31
+All other PMBL studies, PMBL Tier 1, 45
32
+All other PMBL studies, PMBL Tier 2, 112
33
+All other PMBL studies, PMBL Tier 3, 0
34
+```
35
+
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|PMBL tier|
40
+|:-|:-:|
41
+|[STAT6](../STAT6)|1 |
42
+
43
+
44
+# Details
45
+
papers/ritzRecurrentMutationsSTAT62009a.md
... ...
@@ -1,42 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @ritzRecurrentMutationsSTAT62009a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|1|0|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 1
26
-New Tier 1, PMBL Tier 1, 1
27
-This study, New Tier 2, 0
28
-New Tier 2, PMBL Tier 2, 0
29
-All other PMBL studies, PMBL Tier 1, 75
30
-All other PMBL studies, PMBL Tier 2, 82
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|PMBL tier|
37
-|:-|:-:|
38
-|[STAT6](../STAT6)|1 |
39
-
40
-
41
-# Details
42
-
papers/rossiAlterationBIRC3Multiple2011.md
... ...
@@ -0,0 +1,53 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @rossiAlterationBIRC3Multiple2011
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|MZL|4|1|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 4
26
+New Tier 1, MZL Tier 1, 4
27
+This study, New Tier 2, 1
28
+New Tier 2, MZL Tier 2, 1
29
+This study, New Tier 3, 0
30
+New Tier 3, MZL Tier 3, 0
31
+All other MZL studies, MZL Tier 1, 38
32
+All other MZL studies, MZL Tier 2, 73
33
+All other MZL studies, MZL Tier 3, 0
34
+```
35
+
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|MZL tier|
40
+|:-|:-:|
41
+|[BIRC3](../BIRC3)|1 |
42
+|[MAP3K14](../MAP3K14)|1 |
43
+|[TNFAIP3](../TNFAIP3)|1 |
44
+|[TRAF3](../TRAF3)|1 |
45
+
46
+### Tier 2
47
+|New gene|MZL tier|
48
+|:-|:-:|
49
+|[IKBKB](../IKBKB)|2 |
50
+
51
+
52
+# Details
53
+
papers/rossiAlterationBIRC3Multiple2011a.md
... ...
@@ -1,50 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @rossiAlterationBIRC3Multiple2011a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|MZL|4|1|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 4
26
-New Tier 1, MZL Tier 1, 4
27
-This study, New Tier 2, 1
28
-New Tier 2, MZL Tier 2, 1
29
-All other MZL studies, MZL Tier 1, 38
30
-All other MZL studies, MZL Tier 2, 73
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|MZL tier|
37
-|:-|:-:|
38
-|[BIRC3](../BIRC3)|1 |
39
-|[MAP3K14](../MAP3K14)|1 |
40
-|[TNFAIP3](../TNFAIP3)|1 |
41
-|[TRAF3](../TRAF3)|1 |
42
-
43
-### Tier 2
44
-|New gene|MZL tier|
45
-|:-|:-:|
46
-|[IKBKB](../IKBKB)|2 |
47
-
48
-
49
-# Details
50
-
papers/rossiCodingGenomeSplenic2012.md
... ...
@@ -0,0 +1,69 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @rossiCodingGenomeSplenic2012
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|MZL|10|11|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 10
26
+New Tier 1, MZL Tier 1, 10
27
+This study, New Tier 2, 11
28
+New Tier 2, MZL Tier 2, 11
29
+This study, New Tier 3, 0
30
+New Tier 3, MZL Tier 3, 0
31
+All other MZL studies, MZL Tier 1, 32
32
+All other MZL studies, MZL Tier 2, 63
33
+All other MZL studies, MZL Tier 3, 0
34
+```
35
+
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|MZL tier|
40
+|:-|:-:|
41
+|[ARID1A](../ARID1A)|1 |
42
+|[DTX1](../DTX1)|1 |
43
+|[EP300](../EP300)|1 |
44
+|[KMT2D](../KMT2D)|1 |
45
+|[NOTCH1](../NOTCH1)|1 |
46
+|[NOTCH2](../NOTCH2)|1 |
47
+|[SIN3A](../SIN3A)|1 |
48
+|[SPEN](../SPEN)|1 |
49
+|[TBL1XR1](../TBL1XR1)|1 |
50
+|[TP53](../TP53)|1 |
51
+
52
+### Tier 2
53
+|New gene|MZL tier|
54
+|:-|:-:|
55
+|[CD79A](../CD79A)|2 |
56
+|[EGR1](../EGR1)|2 |
57
+|[EGR2](../EGR2)|2 |
58
+|[GPS2](../GPS2)|2 |
59
+|[HIST1H2AG](../HIST1H2AG)|2 |
60
+|[HIST1H2BK](../HIST1H2BK)|2 |
61
+|[MCRS1](../MCRS1)|2 |
62
+|[MSL2](../MSL2)|2 |
63
+|[SWAP70](../SWAP70)|2 |
64
+|[TRRAP](../TRRAP)|2 |
65
+|[WAC](../WAC)|2 |
66
+
67
+
68
+# Details
69
+
papers/rossiCodingGenomeSplenic2012c.md
... ...
@@ -1,67 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @rossiCodingGenomeSplenic2012c
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|12|2|
12
-|MZL|10|11|
13
-```mermaid
14
----
15
-config:
16
- sankey:
17
- showValues: true
18
- linkColor: target
19
- width: 600
20
- height: 300
21
- nodeAlignment: right
22
- prefix: '('
23
- suffix: ' genes)'
24
----
25
-sankey-beta
26
-This study, New Tier 1, 10
27
-New Tier 1, MZL Tier 1, 10
28
-This study, New Tier 2, 11
29
-New Tier 2, MZL Tier 2, 11
30
-All other MZL studies, MZL Tier 1, 32
31
-All other MZL studies, MZL Tier 2, 63
32
-```
33
-
34
-## Novel genes reported in this study
35
-
36
-### Tier 1
37
-|New gene|DLBCL tier|MZL tier|
38
-|:-|:-:|:-:|
39
-|[ARID1A](../ARID1A)|1 |1 |
40
-|[DTX1](../DTX1)|1 |1 |
41
-|[EP300](../EP300)|1 |1 |
42
-|[HIST1H2BK](../HIST1H2BK)|1 |2 |
43
-|[KMT2D](../KMT2D)|1 |1 |
44
-|[NOTCH1](../NOTCH1)|1 |1 |
45
-|[NOTCH2](../NOTCH2)|1 |1 |
46
-|[SIN3A](../SIN3A)|1 |1 |
47
-|[SPEN](../SPEN)|1 |1 |
48
-|[TBL1XR1](../TBL1XR1)|1 |1 |
49
-|[TP53](../TP53)|1 |1 |
50
-|[TRRAP](../TRRAP)|1 |2 |
51
-
52
-### Tier 2
53
-|New gene|DLBCL tier|MZL tier|
54
-|:-|:-:|:-:|
55
-|[CD79A](../CD79A)| |2 |
56
-|[EGR1](../EGR1)| |2 |
57
-|[EGR2](../EGR2)| |2 |
58
-|[GPS2](../GPS2)| |2 |
59
-|[HIST1H2AG](../HIST1H2AG)|2 |2 |
60
-|[MCRS1](../MCRS1)| |2 |
61
-|[MSL2](../MSL2)| |2 |
62
-|[SWAP70](../SWAP70)| |2 |
63
-|[WAC](../WAC)|2 |2 |
64
-
65
-
66
-# Details
67
-
papers/rushtonGeneticEvolutionaryPatterns2020.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @rushtonGeneticEvolutionaryPatterns2020
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|1|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|1|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, DLBCL Tier 1, 1
27 27
This study, New Tier 2, 0
28 28
New Tier 2, DLBCL Tier 2, 0
29
-All other DLBCL studies, DLBCL Tier 1, 127
30
-All other DLBCL studies, DLBCL Tier 2, 198
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
31
+All other DLBCL studies, DLBCL Tier 1, 124
32
+All other DLBCL studies, DLBCL Tier 2, 210
33
+All other DLBCL studies, DLBCL Tier 3, 387
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/russler-germainMutationsAssociatedProgression2023.md
... ...
@@ -0,0 +1,68 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @russler-germainMutationsAssociatedProgression2023
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|FL|2|18|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 2
26
+New Tier 1, FL Tier 1, 2
27
+This study, New Tier 2, 18
28
+New Tier 2, FL Tier 2, 18
29
+This study, New Tier 3, 0
30
+New Tier 3, FL Tier 3, 0
31
+All other FL studies, FL Tier 1, 52
32
+All other FL studies, FL Tier 2, 41
33
+All other FL studies, FL Tier 3, 0
34
+```
35
+
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|FL tier|
40
+|:-|:-:|
41
+|[BCL10](../BCL10)|1 |
42
+|[CD83](../CD83)|1 |
43
+
44
+### Tier 2
45
+|New gene|FL tier|
46
+|:-|:-:|
47
+|[ABL2](../ABL2)|2 |
48
+|[CD70](../CD70)|2 |
49
+|[CILP](../CILP)|2 |
50
+|[CYP2A6](../CYP2A6)|2 |
51
+|[GBP7](../GBP7)|2 |
52
+|[GRM6](../GRM6)|2 |
53
+|[IGLL5](../IGLL5)|2 |
54
+|[KIR3DL1](../KIR3DL1)|2 |
55
+|[MAGEC1](../MAGEC1)|2 |
56
+|[MAP7D1](../MAP7D1)|2 |
57
+|[MKI67](../MKI67)|2 |
58
+|[NFKBIA](../NFKBIA)|2 |
59
+|[OR8H2](../OR8H2)|2 |
60
+|[PZP](../PZP)|2 |
61
+|[SHROOM3](../SHROOM3)|2 |
62
+|[SRRM2](../SRRM2)|2 |
63
+|[STAB2](../STAB2)|2 |
64
+|[XIRP2](../XIRP2)|2 |
65
+
66
+
67
+# Details
68
+
papers/russler-germainMutationsAssociatedProgression2023b.md
... ...
@@ -1,65 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @russler-germainMutationsAssociatedProgression2023b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|FL|1|19|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 1
26
-New Tier 1, FL Tier 1, 1
27
-This study, New Tier 2, 19
28
-New Tier 2, FL Tier 2, 19
29
-All other FL studies, FL Tier 1, 65
30
-All other FL studies, FL Tier 2, 31
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|FL tier|
37
-|:-|:-:|
38
-|[CD83](../CD83)|1 |
39
-
40
-### Tier 2
41
-|New gene|FL tier|
42
-|:-|:-:|
43
-|[ABL2](../ABL2)|2 |
44
-|[BCL10](../BCL10)|2 |
45
-|[CD70](../CD70)|2 |
46
-|[CILP](../CILP)|2 |
47
-|[CYP2A6](../CYP2A6)|2 |
48
-|[GBP7](../GBP7)|2 |
49
-|[GRM6](../GRM6)|2 |
50
-|[IGLL5](../IGLL5)|2 |
51
-|[KIR3DL1](../KIR3DL1)|2 |
52
-|[MAGEC1](../MAGEC1)|2 |
53
-|[MAP7D1](../MAP7D1)|2 |
54
-|[MKI67](../MKI67)|2 |
55
-|[NFKBIA](../NFKBIA)|2 |
56
-|[OR8H2](../OR8H2)|2 |
57
-|[PZP](../PZP)|2 |
58
-|[SHROOM3](../SHROOM3)|2 |
59
-|[SRRM2](../SRRM2)|2 |
60
-|[STAB2](../STAB2)|2 |
61
-|[XIRP2](../XIRP2)|2 |
62
-
63
-
64
-# Details
65
-
papers/sarkozyMutationalLandscapeGray2021.md
... ...
@@ -0,0 +1,59 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @sarkozyMutationalLandscapeGray2021
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|PMBL|5|6|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 5
26
+New Tier 1, PMBL Tier 1, 5
27
+This study, New Tier 2, 6
28
+New Tier 2, PMBL Tier 2, 6
29
+This study, New Tier 3, 0
30
+New Tier 3, PMBL Tier 3, 0
31
+All other PMBL studies, PMBL Tier 1, 41
32
+All other PMBL studies, PMBL Tier 2, 106
33
+All other PMBL studies, PMBL Tier 3, 0
34
+```
35
+
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|PMBL tier|
40
+|:-|:-:|
41
+|[BIRC6](../BIRC6)|1 |
42
+|[BTG1](../BTG1)|1 |
43
+|[HIST1H1B](../HIST1H1B)|1 |
44
+|[KMT2C](../KMT2C)|1 |
45
+|[SPEN](../SPEN)|1 |
46
+
47
+### Tier 2
48
+|New gene|PMBL tier|
49
+|:-|:-:|
50
+|[ABCA13](../ABCA13)|2 |
51
+|[BCL2](../BCL2)|2 |
52
+|[LRRN3](../LRRN3)|2 |
53
+|[MFHAS1](../MFHAS1)|2 |
54
+|[NCOR2](../NCOR2)|2 |
55
+|[RELN](../RELN)|2 |
56
+
57
+
58
+# Details
59
+
papers/sarkozyMutationalLandscapeGray2021a.md
... ...
@@ -1,56 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @sarkozyMutationalLandscapeGray2021a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|5|6|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 5
26
-New Tier 1, PMBL Tier 1, 5
27
-This study, New Tier 2, 6
28
-New Tier 2, PMBL Tier 2, 6
29
-All other PMBL studies, PMBL Tier 1, 71
30
-All other PMBL studies, PMBL Tier 2, 76
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|PMBL tier|
37
-|:-|:-:|
38
-|[BIRC6](../BIRC6)|1 |
39
-|[BTG1](../BTG1)|1 |
40
-|[HIST1H1B](../HIST1H1B)|1 |
41
-|[KMT2C](../KMT2C)|1 |
42
-|[SPEN](../SPEN)|1 |
43
-
44
-### Tier 2
45
-|New gene|PMBL tier|
46
-|:-|:-:|
47
-|[ABCA13](../ABCA13)|2 |
48
-|[BCL2](../BCL2)|2 |
49
-|[LRRN3](../LRRN3)|2 |
50
-|[MFHAS1](../MFHAS1)|2 |
51
-|[NCOR2](../NCOR2)|2 |
52
-|[RELN](../RELN)|2 |
53
-
54
-
55
-# Details
56
-
papers/schmitzBurkittLymphomaPathogenesis2012.md
... ...
@@ -6,10 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @schmitzBurkittLymphomaPathogenesis2012
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|2|3|
12
-|BL|4|16|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|BL|4|15|0|
13 12
```mermaid
14 13
---
15 14
config:
... ...
@@ -25,41 +24,43 @@ config:
25 24
sankey-beta
26 25
This study, New Tier 1, 4
27 26
New Tier 1, BL Tier 1, 4
28
-This study, New Tier 2, 16
29
-New Tier 2, BL Tier 2, 16
30
-All other BL studies, BL Tier 1, 25
31
-All other BL studies, BL Tier 2, 141
27
+This study, New Tier 2, 15
28
+New Tier 2, BL Tier 2, 15
29
+This study, New Tier 3, 0
30
+New Tier 3, BL Tier 3, 0
31
+All other BL studies, BL Tier 1, 28
32
+All other BL studies, BL Tier 2, 57
33
+All other BL studies, BL Tier 3, 70
32 34
```
33 35
34 36
## Novel genes reported in this study
35 37
36 38
### Tier 1
37
-|New gene|DLBCL tier|BL tier|
38
-|:-|:-:|:-:|
39
-|[DDX3X](../DDX3X)|1 |1 |
40
-|[FOXO1](../FOXO1)|1 |1 |
41
-|[ID3](../ID3)|2 |1 |
42
-|[TCF3](../TCF3)| |1 |
39
+|New gene|BL tier|
40
+|:-|:-:|
41
+|[DDX3X](../DDX3X)|1 |
42
+|[FOXO1](../FOXO1)|1 |
43
+|[PCBP1](../PCBP1)|1 |
44
+|[TCF3](../TCF3)|1 |
43 45
44 46
### Tier 2
45
-|New gene|DLBCL tier|BL tier|
46
-|:-|:-:|:-:|
47
-|[C16orf48](../C16orf48)| |2 |
48
-|[DHCR7](../DHCR7)| |2 |
49
-|[ELP2](../ELP2)| |2 |
50
-|[EXOSC6](../EXOSC6)| |2 |
51
-|[FLYWCH1](../FLYWCH1)| |2 |
52
-|[GTSE1](../GTSE1)| |2 |
53
-|[KANK2](../KANK2)| |2 |
54
-|[MKI67](../MKI67)| |2 |
55
-|[MYO18A](../MYO18A)| |2 |
56
-|[NCOR2](../NCOR2)|2 |2 |
57
-|[PCBP1](../PCBP1)|2 |2 |
58
-|[PDCD11](../PDCD11)| |2 |
59
-|[TOP2A](../TOP2A)| |2 |
60
-|[WDR90](../WDR90)| |2 |
61
-|[WHAMM](../WHAMM)| |2 |
62
-|[YY1AP1](../YY1AP1)| |2 |
47
+|New gene|BL tier|
48
+|:-|:-:|
49
+|[C16orf48](../C16orf48)|2 |
50
+|[DHCR7](../DHCR7)|2 |
51
+|[ELP2](../ELP2)|2 |
52
+|[EXOSC6](../EXOSC6)|2 |
53
+|[FLYWCH1](../FLYWCH1)|2 |
54
+|[GTSE1](../GTSE1)|2 |
55
+|[KANK2](../KANK2)|2 |
56
+|[MKI67](../MKI67)|2 |
57
+|[MYO18A](../MYO18A)|2 |
58
+|[NCOR2](../NCOR2)|2 |
59
+|[PDCD11](../PDCD11)|2 |
60
+|[TOP2A](../TOP2A)|2 |
61
+|[WDR90](../WDR90)|2 |
62
+|[WHAMM](../WHAMM)|2 |
63
+|[YY1AP1](../YY1AP1)|2 |
63 64
64 65
65 66
# Details
papers/schmitzGeneticsPathogenesisDiffuse2018.md
... ...
@@ -0,0 +1,66 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @schmitzGeneticsPathogenesisDiffuse2018
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|4|14|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 4
26
+New Tier 1, DLBCL Tier 1, 4
27
+This study, New Tier 2, 14
28
+New Tier 2, DLBCL Tier 2, 14
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
31
+All other DLBCL studies, DLBCL Tier 1, 121
32
+All other DLBCL studies, DLBCL Tier 2, 196
33
+All other DLBCL studies, DLBCL Tier 3, 387
34
+```
35
+
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|DLBCL tier|
40
+|:-|:-:|
41
+|[GRHPR](../GRHPR)|1 |
42
+|[ITPKB](../ITPKB)|1 |
43
+|[NOL9](../NOL9)|1 |
44
+|[WEE1](../WEE1)|1 |
45
+
46
+### Tier 2
47
+|New gene|DLBCL tier|
48
+|:-|:-:|
49
+|[CXCR5](../CXCR5)|2 |
50
+|[EIF2AK3](../EIF2AK3)|2 |
51
+|[FOXC1](../FOXC1)|2 |
52
+|[GPC5](../GPC5)|2 |
53
+|[GSG2](../GSG2)|2 |
54
+|[ID3](../ID3)|2 |
55
+|[KLHL21](../KLHL21)|2 |
56
+|[LAMA5](../LAMA5)|2 |
57
+|[MYBPC2](../MYBPC2)|2 |
58
+|[PAPOLG](../PAPOLG)|2 |
59
+|[PRKDC](../PRKDC)|2 |
60
+|[SEL1L3](../SEL1L3)|2 |
61
+|[TAP1](../TAP1)|2 |
62
+|[UBE2J1](../UBE2J1)|2 |
63
+
64
+
65
+# Details
66
+
papers/schmitzGeneticsPathogenesisDiffuse2018a.md
... ...
@@ -1,61 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @schmitzGeneticsPathogenesisDiffuse2018a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|7|9|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 7
26
-New Tier 1, DLBCL Tier 1, 7
27
-This study, New Tier 2, 9
28
-New Tier 2, DLBCL Tier 2, 9
29
-All other DLBCL studies, DLBCL Tier 1, 121
30
-All other DLBCL studies, DLBCL Tier 2, 189
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|DLBCL tier|
37
-|:-|:-:|
38
-|[CXCR5](../CXCR5)|1 |
39
-|[DDX3X](../DDX3X)|1 |
40
-|[DTX1](../DTX1)|1 |
41
-|[HIST2H2BE](../HIST2H2BE)|1 |
42
-|[ITPKB](../ITPKB)|1 |
43
-|[NOL9](../NOL9)|1 |
44
-|[WEE1](../WEE1)|1 |
45
-
46
-### Tier 2
47
-|New gene|DLBCL tier|
48
-|:-|:-:|
49
-|[FOXC1](../FOXC1)|2 |
50
-|[GPC5](../GPC5)|2 |
51
-|[GSG2](../GSG2)|2 |
52
-|[KLHL21](../KLHL21)|2 |
53
-|[LAMA5](../LAMA5)|2 |
54
-|[MYBPC2](../MYBPC2)|2 |
55
-|[PAPOLG](../PAPOLG)|2 |
56
-|[PRKDC](../PRKDC)|2 |
57
-|[TAP1](../TAP1)|2 |
58
-
59
-
60
-# Details
61
-
papers/schmitzTNFAIP3A20Tumor2009.md
... ...
@@ -0,0 +1,45 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @schmitzTNFAIP3A20Tumor2009
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|PMBL|1|0|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 1
26
+New Tier 1, PMBL Tier 1, 1
27
+This study, New Tier 2, 0
28
+New Tier 2, PMBL Tier 2, 0
29
+This study, New Tier 3, 0
30
+New Tier 3, PMBL Tier 3, 0
31
+All other PMBL studies, PMBL Tier 1, 45
32
+All other PMBL studies, PMBL Tier 2, 112
33
+All other PMBL studies, PMBL Tier 3, 0
34
+```
35
+
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|PMBL tier|
40
+|:-|:-:|
41
+|[TNFAIP3](../TNFAIP3)|1 |
42
+
43
+
44
+# Details
45
+
papers/schmitzTNFAIP3A20Tumor2009a.md
... ...
@@ -1,42 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @schmitzTNFAIP3A20Tumor2009a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|1|0|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 1
26
-New Tier 1, PMBL Tier 1, 1
27
-This study, New Tier 2, 0
28
-New Tier 2, PMBL Tier 2, 0
29
-All other PMBL studies, PMBL Tier 1, 75
30
-All other PMBL studies, PMBL Tier 2, 82
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|PMBL tier|
37
-|:-|:-:|
38
-|[TNFAIP3](../TNFAIP3)|1 |
39
-
40
-
41
-# Details
42
-
papers/schneiderAlterationsCD58Gene2015.md
... ...
@@ -0,0 +1,45 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @schneiderAlterationsCD58Gene2015
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|PMBL|1|0|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 1
26
+New Tier 1, PMBL Tier 1, 1
27
+This study, New Tier 2, 0
28
+New Tier 2, PMBL Tier 2, 0
29
+This study, New Tier 3, 0
30
+New Tier 3, PMBL Tier 3, 0
31
+All other PMBL studies, PMBL Tier 1, 45
32
+All other PMBL studies, PMBL Tier 2, 112
33
+All other PMBL studies, PMBL Tier 3, 0
34
+```
35
+
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|PMBL tier|
40
+|:-|:-:|
41
+|[CD58](../CD58)|1 |
42
+
43
+
44
+# Details
45
+
papers/schneiderAlterationsCD58Gene2015a.md
... ...
@@ -1,42 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @schneiderAlterationsCD58Gene2015a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|1|0|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 1
26
-New Tier 1, PMBL Tier 1, 1
27
-This study, New Tier 2, 0
28
-New Tier 2, PMBL Tier 2, 0
29
-All other PMBL studies, PMBL Tier 1, 75
30
-All other PMBL studies, PMBL Tier 2, 82
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|PMBL tier|
37
-|:-|:-:|
38
-|[CD58](../CD58)|1 |
39
-
40
-
41
-# Details
42
-
papers/schollMutationsRegionFAS2007.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @schollMutationsRegionFAS2007
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|1|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|1|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, DLBCL Tier 1, 1
27 27
This study, New Tier 2, 0
28 28
New Tier 2, DLBCL Tier 2, 0
29
-All other DLBCL studies, DLBCL Tier 1, 127
30
-All other DLBCL studies, DLBCL Tier 2, 198
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
31
+All other DLBCL studies, DLBCL Tier 1, 124
32
+All other DLBCL studies, DLBCL Tier 2, 210
33
+All other DLBCL studies, DLBCL Tier 3, 387
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/shinBRAFV600EMAP2K12015.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @shinBRAFV600EMAP2K12015
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|0|1|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|0|1|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 0
26 26
New Tier 1, DLBCL Tier 1, 0
27 27
This study, New Tier 2, 1
28 28
New Tier 2, DLBCL Tier 2, 1
29
-All other DLBCL studies, DLBCL Tier 1, 128
30
-All other DLBCL studies, DLBCL Tier 2, 197
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
31
+All other DLBCL studies, DLBCL Tier 1, 125
32
+All other DLBCL studies, DLBCL Tier 2, 209
33
+All other DLBCL studies, DLBCL Tier 3, 387
31 34
```
32 35
33 36
### Tier 2
papers/spinaGeneticsNodalMarginal2016.md
... ...
@@ -0,0 +1,79 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @spinaGeneticsNodalMarginal2016
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|MZL|8|23|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 8
26
+New Tier 1, MZL Tier 1, 8
27
+This study, New Tier 2, 23
28
+New Tier 2, MZL Tier 2, 23
29
+This study, New Tier 3, 0
30
+New Tier 3, MZL Tier 3, 0
31
+All other MZL studies, MZL Tier 1, 34
32
+All other MZL studies, MZL Tier 2, 51
33
+All other MZL studies, MZL Tier 3, 0
34
+```
35
+
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|MZL tier|
40
+|:-|:-:|
41
+|[BCL10](../BCL10)|1 |
42
+|[FAS](../FAS)|1 |
43
+|[FAT1](../FAT1)|1 |
44
+|[ID3](../ID3)|1 |
45
+|[NCOR2](../NCOR2)|1 |
46
+|[NOL9](../NOL9)|1 |
47
+|[PTPRD](../PTPRD)|1 |
48
+|[TNFRSF14](../TNFRSF14)|1 |
49
+
50
+### Tier 2
51
+|New gene|MZL tier|
52
+|:-|:-:|
53
+|[ABCA13](../ABCA13)|2 |
54
+|[ACTG1](../ACTG1)|2 |
55
+|[ADD2](../ADD2)|2 |
56
+|[AMN](../AMN)|2 |
57
+|[AOC2](../AOC2)|2 |
58
+|[C6orf103](../C6orf103)|2 |
59
+|[CDC42BPB](../CDC42BPB)|2 |
60
+|[CDKN2A](../CDKN2A)|2 |
61
+|[CLGN](../CLGN)|2 |
62
+|[CNBP](../CNBP)|2 |
63
+|[CNKSR2](../CNKSR2)|2 |
64
+|[GPR98](../GPR98)|2 |
65
+|[LRP1B](../LRP1B)|2 |
66
+|[PACRG](../PACRG)|2 |
67
+|[PARK2](../PARK2)|2 |
68
+|[PLXNB3](../PLXNB3)|2 |
69
+|[RCOR1](../RCOR1)|2 |
70
+|[RPL1L](../RPL1L)|2 |
71
+|[SAMD5](../SAMD5)|2 |
72
+|[SCG3](../SCG3)|2 |
73
+|[STXBP5](../STXBP5)|2 |
74
+|[TAF1](../TAF1)|2 |
75
+|[TCTN2](../TCTN2)|2 |
76
+
77
+
78
+# Details
79
+
papers/spinaGeneticsNodalMarginal2016b.md
... ...
@@ -1,76 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @spinaGeneticsNodalMarginal2016b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|MZL|8|23|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 8
26
-New Tier 1, MZL Tier 1, 8
27
-This study, New Tier 2, 23
28
-New Tier 2, MZL Tier 2, 23
29
-All other MZL studies, MZL Tier 1, 34
30
-All other MZL studies, MZL Tier 2, 51
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|MZL tier|
37
-|:-|:-:|
38
-|[BCL10](../BCL10)|1 |
39
-|[FAS](../FAS)|1 |
40
-|[FAT1](../FAT1)|1 |
41
-|[ID3](../ID3)|1 |
42
-|[NCOR2](../NCOR2)|1 |
43
-|[NOL9](../NOL9)|1 |
44
-|[PTPRD](../PTPRD)|1 |
45
-|[TNFRSF14](../TNFRSF14)|1 |
46
-
47
-### Tier 2
48
-|New gene|MZL tier|
49
-|:-|:-:|
50
-|[ABCA13](../ABCA13)|2 |
51
-|[ACTG1](../ACTG1)|2 |
52
-|[ADD2](../ADD2)|2 |
53
-|[AMN](../AMN)|2 |
54
-|[AOC2](../AOC2)|2 |
55
-|[C6orf103](../C6orf103)|2 |
56
-|[CDC42BPB](../CDC42BPB)|2 |
57
-|[CDKN2A](../CDKN2A)|2 |
58
-|[CLGN](../CLGN)|2 |
59
-|[CNKSR2](../CNKSR2)|2 |
60
-|[GPR98](../GPR98)|2 |
61
-|[LRP1B](../LRP1B)|2 |
62
-|[PACRG](../PACRG)|2 |
63
-|[PARK2](../PARK2)|2 |
64
-|[PLXNB3](../PLXNB3)|2 |
65
-|[RCOR1](../RCOR1)|2 |
66
-|[RPL1L](../RPL1L)|2 |
67
-|[SAMD5](../SAMD5)|2 |
68
-|[SCG3](../SCG3)|2 |
69
-|[STXBP5](../STXBP5)|2 |
70
-|[TAF1](../TAF1)|2 |
71
-|[TCTN2](../TCTN2)|2 |
72
-|[ZNF9](../ZNF9)|2 |
73
-
74
-
75
-# Details
76
-
papers/tanakaFrequentIncidenceSomatic1992.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @tanakaFrequentIncidenceSomatic1992
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|1|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|1|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, DLBCL Tier 1, 1
27 27
This study, New Tier 2, 0
28 28
New Tier 2, DLBCL Tier 2, 0
29
-All other DLBCL studies, DLBCL Tier 1, 127
30
-All other DLBCL studies, DLBCL Tier 2, 198
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
31
+All other DLBCL studies, DLBCL Tier 1, 124
32
+All other DLBCL studies, DLBCL Tier 2, 210
33
+All other DLBCL studies, DLBCL Tier 3, 387
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/thomasGeneticSubgroupsInform2023.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @thomasGeneticSubgroupsInform2023
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|BL|2|3|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|BL|2|4|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -24,10 +24,13 @@ config:
24 24
sankey-beta
25 25
This study, New Tier 1, 2
26 26
New Tier 1, BL Tier 1, 2
27
-This study, New Tier 2, 3
28
-New Tier 2, BL Tier 2, 3
29
-All other BL studies, BL Tier 1, 27
30
-All other BL studies, BL Tier 2, 154
27
+This study, New Tier 2, 4
28
+New Tier 2, BL Tier 2, 4
29
+This study, New Tier 3, 0
30
+New Tier 3, BL Tier 3, 0
31
+All other BL studies, BL Tier 1, 30
32
+All other BL studies, BL Tier 2, 68
33
+All other BL studies, BL Tier 3, 70
31 34
```
32 35
33 36
## Novel genes reported in this study
... ...
@@ -44,6 +47,7 @@ All other BL studies, BL Tier 2, 154
44 47
|[CDKN2C](../CDKN2C)|2 |
45 48
|[EBF1](../EBF1)|2 |
46 49
|[EHD1](../EHD1)|2 |
50
+|[TET2](../TET2)|2 |
47 51
48 52
49 53
# Details
papers/thomasMutationalAnalysisIkappaBalpha2004.md
... ...
@@ -0,0 +1,45 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @thomasMutationalAnalysisIkappaBalpha2004
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|1|0|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 1
26
+New Tier 1, DLBCL Tier 1, 1
27
+This study, New Tier 2, 0
28
+New Tier 2, DLBCL Tier 2, 0
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
31
+All other DLBCL studies, DLBCL Tier 1, 124
32
+All other DLBCL studies, DLBCL Tier 2, 210
33
+All other DLBCL studies, DLBCL Tier 3, 387
34
+```
35
+
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|DLBCL tier|
40
+|:-|:-:|
41
+|[NFKBIA](../NFKBIA)|1 |
42
+
43
+
44
+# Details
45
+
papers/tiacciBRAFMutationsHairycell2011.md
... ...
@@ -0,0 +1,45 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @tiacciBRAFMutationsHairycell2011
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|1|0|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 1
26
+New Tier 1, DLBCL Tier 1, 1
27
+This study, New Tier 2, 0
28
+New Tier 2, DLBCL Tier 2, 0
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
31
+All other DLBCL studies, DLBCL Tier 1, 124
32
+All other DLBCL studies, DLBCL Tier 2, 210
33
+All other DLBCL studies, DLBCL Tier 3, 387
34
+```
35
+
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|DLBCL tier|
40
+|:-|:-:|
41
+|[BRAF](../BRAF)|1 |
42
+
43
+
44
+# Details
45
+
papers/tiacciBRAFMutationsHairycell2011a.md
... ...
@@ -1,42 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @tiacciBRAFMutationsHairycell2011a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|1|0|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 1
26
-New Tier 1, DLBCL Tier 1, 1
27
-This study, New Tier 2, 0
28
-New Tier 2, DLBCL Tier 2, 0
29
-All other DLBCL studies, DLBCL Tier 1, 127
30
-All other DLBCL studies, DLBCL Tier 2, 198
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|DLBCL tier|
37
-|:-|:-:|
38
-|[BRAF](../BRAF)|1 |
39
-
40
-
41
-# Details
42
-
papers/tiacciPervasiveMutationsJAKSTAT2018.md
... ...
@@ -0,0 +1,58 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @tiacciPervasiveMutationsJAKSTAT2018
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|PMBL|1|9|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 1
26
+New Tier 1, PMBL Tier 1, 1
27
+This study, New Tier 2, 9
28
+New Tier 2, PMBL Tier 2, 9
29
+This study, New Tier 3, 0
30
+New Tier 3, PMBL Tier 3, 0
31
+All other PMBL studies, PMBL Tier 1, 45
32
+All other PMBL studies, PMBL Tier 2, 103
33
+All other PMBL studies, PMBL Tier 3, 0
34
+```
35
+
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|PMBL tier|
40
+|:-|:-:|
41
+|[TP53](../TP53)|1 |
42
+
43
+### Tier 2
44
+|New gene|PMBL tier|
45
+|:-|:-:|
46
+|[AKAP6](../AKAP6)|2 |
47
+|[DGKB](../DGKB)|2 |
48
+|[ITPR3](../ITPR3)|2 |
49
+|[NUP214](../NUP214)|2 |
50
+|[PRUNE2](../PRUNE2)|2 |
51
+|[SETD5](../SETD5)|2 |
52
+|[STAT5B](../STAT5B)|2 |
53
+|[TNIP1](../TNIP1)|2 |
54
+|[ZCCHC11](../ZCCHC11)|2 |
55
+
56
+
57
+# Details
58
+
papers/tiacciPervasiveMutationsJAKSTAT2018b.md
... ...
@@ -1,55 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @tiacciPervasiveMutationsJAKSTAT2018b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|1|9|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 1
26
-New Tier 1, PMBL Tier 1, 1
27
-This study, New Tier 2, 9
28
-New Tier 2, PMBL Tier 2, 9
29
-All other PMBL studies, PMBL Tier 1, 75
30
-All other PMBL studies, PMBL Tier 2, 73
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|PMBL tier|
37
-|:-|:-:|
38
-|[TP53](../TP53)|1 |
39
-
40
-### Tier 2
41
-|New gene|PMBL tier|
42
-|:-|:-:|
43
-|[AKAP6](../AKAP6)|2 |
44
-|[DGKB](../DGKB)|2 |
45
-|[ITPR3](../ITPR3)|2 |
46
-|[NUP214](../NUP214)|2 |
47
-|[PRUNE2](../PRUNE2)|2 |
48
-|[SETD5](../SETD5)|2 |
49
-|[STAT5B](../STAT5B)|2 |
50
-|[TNIP1](../TNIP1)|2 |
51
-|[ZCCHC11](../ZCCHC11)|2 |
52
-
53
-
54
-# Details
55
-
papers/vandenbrandRecurrentMutationsGenes2017.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @vandenbrandRecurrentMutationsGenes2017
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|MZL|0|2|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|MZL|0|2|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 0
26 26
New Tier 1, MZL Tier 1, 0
27 27
This study, New Tier 2, 2
28 28
New Tier 2, MZL Tier 2, 2
29
+This study, New Tier 3, 0
30
+New Tier 3, MZL Tier 3, 0
29 31
All other MZL studies, MZL Tier 1, 42
30 32
All other MZL studies, MZL Tier 2, 72
33
+All other MZL studies, MZL Tier 3, 0
31 34
```
32 35
33 36
### Tier 2
papers/viganoSomaticIL4RMutations2018.md
... ...
@@ -0,0 +1,45 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @viganoSomaticIL4RMutations2018
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|PMBL|1|0|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 1
26
+New Tier 1, PMBL Tier 1, 1
27
+This study, New Tier 2, 0
28
+New Tier 2, PMBL Tier 2, 0
29
+This study, New Tier 3, 0
30
+New Tier 3, PMBL Tier 3, 0
31
+All other PMBL studies, PMBL Tier 1, 45
32
+All other PMBL studies, PMBL Tier 2, 112
33
+All other PMBL studies, PMBL Tier 3, 0
34
+```
35
+
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|PMBL tier|
40
+|:-|:-:|
41
+|[IL4R](../IL4R)|1 |
42
+
43
+
44
+# Details
45
+
papers/viganoSomaticIL4RMutations2018b.md
... ...
@@ -1,42 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @viganoSomaticIL4RMutations2018b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|1|0|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 1
26
-New Tier 1, PMBL Tier 1, 1
27
-This study, New Tier 2, 0
28
-New Tier 2, PMBL Tier 2, 0
29
-All other PMBL studies, PMBL Tier 1, 75
30
-All other PMBL studies, PMBL Tier 2, 82
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|PMBL tier|
37
-|:-|:-:|
38
-|[IL4R](../IL4R)|1 |
39
-
40
-
41
-# Details
42
-
papers/wenigerMutationsTumorSuppressor2006.md
... ...
@@ -0,0 +1,50 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @wenigerMutationsTumorSuppressor2006
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|PMBL|1|1|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 1
26
+New Tier 1, PMBL Tier 1, 1
27
+This study, New Tier 2, 1
28
+New Tier 2, PMBL Tier 2, 1
29
+This study, New Tier 3, 0
30
+New Tier 3, PMBL Tier 3, 0
31
+All other PMBL studies, PMBL Tier 1, 45
32
+All other PMBL studies, PMBL Tier 2, 111
33
+All other PMBL studies, PMBL Tier 3, 0
34
+```
35
+
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|PMBL tier|
40
+|:-|:-:|
41
+|[SOCS1](../SOCS1)|1 |
42
+
43
+### Tier 2
44
+|New gene|PMBL tier|
45
+|:-|:-:|
46
+|[GPR126](../GPR126)|2 |
47
+
48
+
49
+# Details
50
+
papers/wenigerMutationsTumorSuppressor2006a.md
... ...
@@ -1,47 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @wenigerMutationsTumorSuppressor2006a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|1|1|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 1
26
-New Tier 1, PMBL Tier 1, 1
27
-This study, New Tier 2, 1
28
-New Tier 2, PMBL Tier 2, 1
29
-All other PMBL studies, PMBL Tier 1, 75
30
-All other PMBL studies, PMBL Tier 2, 81
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|PMBL tier|
37
-|:-|:-:|
38
-|[SOCS1](../SOCS1)|1 |
39
-
40
-### Tier 2
41
-|New gene|PMBL tier|
42
-|:-|:-:|
43
-|[GPR126](../GPR126)|2 |
44
-
45
-
46
-# Details
47
-
papers/wienandGenomicAnalysesFlowsorted2019.md
... ...
@@ -0,0 +1,55 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @wienandGenomicAnalysesFlowsorted2019
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|PMBL|4|3|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 4
26
+New Tier 1, PMBL Tier 1, 4
27
+This study, New Tier 2, 3
28
+New Tier 2, PMBL Tier 2, 3
29
+This study, New Tier 3, 0
30
+New Tier 3, PMBL Tier 3, 0
31
+All other PMBL studies, PMBL Tier 1, 42
32
+All other PMBL studies, PMBL Tier 2, 109
33
+All other PMBL studies, PMBL Tier 3, 0
34
+```
35
+
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|PMBL tier|
40
+|:-|:-:|
41
+|[ACTB](../ACTB)|1 |
42
+|[ARID1A](../ARID1A)|1 |
43
+|[HLA-B](../HLA-B)|1 |
44
+|[NFKBIA](../NFKBIA)|1 |
45
+
46
+### Tier 2
47
+|New gene|PMBL tier|
48
+|:-|:-:|
49
+|[DNAH12](../DNAH12)|2 |
50
+|[IKBKB](../IKBKB)|2 |
51
+|[RBM38](../RBM38)|2 |
52
+
53
+
54
+# Details
55
+
papers/wienandGenomicAnalysesFlowsorted2019b.md
... ...
@@ -1,52 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @wienandGenomicAnalysesFlowsorted2019b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|4|3|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 4
26
-New Tier 1, PMBL Tier 1, 4
27
-This study, New Tier 2, 3
28
-New Tier 2, PMBL Tier 2, 3
29
-All other PMBL studies, PMBL Tier 1, 72
30
-All other PMBL studies, PMBL Tier 2, 79
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|PMBL tier|
37
-|:-|:-:|
38
-|[ACTB](../ACTB)|1 |
39
-|[ARID1A](../ARID1A)|1 |
40
-|[HLA-B](../HLA-B)|1 |
41
-|[NFKBIA](../NFKBIA)|1 |
42
-
43
-### Tier 2
44
-|New gene|PMBL tier|
45
-|:-|:-:|
46
-|[DNAH12](../DNAH12)|2 |
47
-|[IKBKB](../IKBKB)|2 |
48
-|[RBM38](../RBM38)|2 |
49
-
50
-
51
-# Details
52
-
papers/wildaInactivationARFMDM2p53Pathway2004.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @wildaInactivationARFMDM2p53Pathway2004
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|BL|1|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|BL|1|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, BL Tier 1, 1
27 27
This study, New Tier 2, 0
28 28
New Tier 2, BL Tier 2, 0
29
-All other BL studies, BL Tier 1, 28
30
-All other BL studies, BL Tier 2, 157
29
+This study, New Tier 3, 0
30
+New Tier 3, BL Tier 3, 0
31
+All other BL studies, BL Tier 1, 31
32
+All other BL studies, BL Tier 2, 72
33
+All other BL studies, BL Tier 3, 70
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/wuGeneticHeterogeneityPrimary2016.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @wuGeneticHeterogeneityPrimary2016
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|MCL|1|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|MCL|1|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, MCL Tier 1, 1
27 27
This study, New Tier 2, 0
28 28
New Tier 2, MCL Tier 2, 0
29
+This study, New Tier 3, 0
30
+New Tier 3, MCL Tier 3, 0
29 31
All other MCL studies, MCL Tier 1, 22
30 32
All other MCL studies, MCL Tier 2, 46
33
+All other MCL studies, MCL Tier 3, 0
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/yanBCRTLRSignaling2012.md
... ...
@@ -0,0 +1,46 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @yanBCRTLRSignaling2012
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|MZL|2|0|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 2
26
+New Tier 1, MZL Tier 1, 2
27
+This study, New Tier 2, 0
28
+New Tier 2, MZL Tier 2, 0
29
+This study, New Tier 3, 0
30
+New Tier 3, MZL Tier 3, 0
31
+All other MZL studies, MZL Tier 1, 40
32
+All other MZL studies, MZL Tier 2, 74
33
+All other MZL studies, MZL Tier 3, 0
34
+```
35
+
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|MZL tier|
40
+|:-|:-:|
41
+|[CARD11](../CARD11)|1 |
42
+|[MYD88](../MYD88)|1 |
43
+
44
+
45
+# Details
46
+
papers/yanBCRTLRSignaling2012a.md
... ...
@@ -1,43 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @yanBCRTLRSignaling2012a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|MZL|2|0|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 2
26
-New Tier 1, MZL Tier 1, 2
27
-This study, New Tier 2, 0
28
-New Tier 2, MZL Tier 2, 0
29
-All other MZL studies, MZL Tier 1, 40
30
-All other MZL studies, MZL Tier 2, 74
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|MZL tier|
37
-|:-|:-:|
38
-|[CARD11](../CARD11)|1 |
39
-|[MYD88](../MYD88)|1 |
40
-
41
-
42
-# Details
43
-
papers/yildizActivatingSTAT6Mutations2015.md
... ...
@@ -0,0 +1,46 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @yildizActivatingSTAT6Mutations2015
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|1|0|0|
12
+|FL|1|0|0|
13
+```mermaid
14
+---
15
+config:
16
+ sankey:
17
+ showValues: true
18
+ linkColor: target
19
+ width: 600
20
+ height: 300
21
+ nodeAlignment: right
22
+ prefix: '('
23
+ suffix: ' genes)'
24
+---
25
+sankey-beta
26
+This study, New Tier 1, 1
27
+New Tier 1, DLBCL Tier 1, 1
28
+This study, New Tier 2, 0
29
+New Tier 2, DLBCL Tier 2, 0
30
+This study, New Tier 3, 0
31
+New Tier 3, DLBCL Tier 3, 0
32
+All other DLBCL studies, DLBCL Tier 1, 124
33
+All other DLBCL studies, DLBCL Tier 2, 210
34
+All other DLBCL studies, DLBCL Tier 3, 387
35
+```
36
+
37
+## Novel genes reported in this study
38
+
39
+### Tier 1
40
+|New gene|DLBCL tier|FL tier|
41
+|:-|:-:|:-:|
42
+|[STAT6](../STAT6)|1 |1 |
43
+
44
+
45
+# Details
46
+
papers/yildizActivatingSTAT6Mutations2015c.md
... ...
@@ -1,43 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @yildizActivatingSTAT6Mutations2015c
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|1|0|
12
-|FL|1|0|
13
-```mermaid
14
----
15
-config:
16
- sankey:
17
- showValues: true
18
- linkColor: target
19
- width: 600
20
- height: 300
21
- nodeAlignment: right
22
- prefix: '('
23
- suffix: ' genes)'
24
----
25
-sankey-beta
26
-This study, New Tier 1, 1
27
-New Tier 1, DLBCL Tier 1, 1
28
-This study, New Tier 2, 0
29
-New Tier 2, DLBCL Tier 2, 0
30
-All other DLBCL studies, DLBCL Tier 1, 127
31
-All other DLBCL studies, DLBCL Tier 2, 198
32
-```
33
-
34
-## Novel genes reported in this study
35
-
36
-### Tier 1
37
-|New gene|DLBCL tier|FL tier|
38
-|:-|:-:|:-:|
39
-|[STAT6](../STAT6)|1 |1 |
40
-
41
-
42
-# Details
43
-
papers/zhangGeneticHeterogeneityDiffuse2013.md
... ...
@@ -8,7 +8,7 @@ bibliography: 'morinlab.bib'
8 8
9 9
|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10 10
|:-:|:-:|:-:|:-:|
11
-|DLBCL|12|14|271|
11
+|DLBCL|11|8|272|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -22,15 +22,15 @@ config:
22 22
suffix: ' genes)'
23 23
---
24 24
sankey-beta
25
-This study, New Tier 1, 12
26
-New Tier 1, DLBCL Tier 1, 12
27
-This study, New Tier 2, 14
28
-New Tier 2, DLBCL Tier 2, 14
29
-This study, New Tier 3, 271
30
-New Tier 3, DLBCL Tier 3, 271
31
-All other DLBCL studies, DLBCL Tier 1, 117
32
-All other DLBCL studies, DLBCL Tier 2, 164
33
-All other DLBCL studies, DLBCL Tier 3, 114
25
+This study, New Tier 1, 11
26
+New Tier 1, DLBCL Tier 1, 11
27
+This study, New Tier 2, 8
28
+New Tier 2, DLBCL Tier 2, 8
29
+This study, New Tier 3, 272
30
+New Tier 3, DLBCL Tier 3, 272
31
+All other DLBCL studies, DLBCL Tier 1, 114
32
+All other DLBCL studies, DLBCL Tier 2, 202
33
+All other DLBCL studies, DLBCL Tier 3, 115
34 34
```
35 35
36 36
## Novel genes reported in this study
... ...
@@ -49,7 +49,6 @@ All other DLBCL studies, DLBCL Tier 3, 114
49 49
|[NOTCH2](../NOTCH2)|1 |
50 50
|[OSBPL10](../OSBPL10)|1 |
51 51
|[RHOA](../RHOA)|1 |
52
-|[TRRAP](../TRRAP)|1 |
53 52
54 53
### Tier 2
55 54
|New gene|DLBCL tier|
... ...
@@ -57,17 +56,11 @@ All other DLBCL studies, DLBCL Tier 3, 114
57 56
|[ANKRD17](../ANKRD17)|2 |
58 57
|[BTBD3](../BTBD3)|2 |
59 58
|[DDX10](../DDX10)|2 |
60
-|[INO80](../INO80)|2 |
61
-|[JAK1](../JAK1)|2 |
62
-|[JAK3](../JAK3)|2 |
63 59
|[NF1](../NF1)|2 |
64 60
|[PIK3CD](../PIK3CD)|2 |
65 61
|[PIK3R1](../PIK3R1)|2 |
66 62
|[SETD2](../SETD2)|2 |
67 63
|[SMEK1](../SMEK1)|2 |
68
-|[STAT5B](../STAT5B)|2 |
69
-|[UBR5](../UBR5)|2 |
70
-|[ZEB2](../ZEB2)|2 |
71 64
72 65
### Tier 3
73 66
|New gene|DLBCL tier|
... ...
@@ -321,6 +314,7 @@ All other DLBCL studies, DLBCL Tier 3, 114
321 314
|[TPRKB](../TPRKB)|3 |
322 315
|[TRIM37](../TRIM37)|3 |
323 316
|[TRIP11](../TRIP11)|3 |
317
+|[TRRAP](../TRRAP)|3 |
324 318
|[TSC2](../TSC2)|3 |
325 319
|[TSHZ2](../TSHZ2)|3 |
326 320
|[UHRF1BP1L](../UHRF1BP1L)|3 |
papers/zhangGenomicLandscapeMantle2014.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @zhangGenomicLandscapeMantle2014
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|MCL|2|26|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|MCL|2|26|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 2
26 26
New Tier 1, MCL Tier 1, 2
27 27
This study, New Tier 2, 26
28 28
New Tier 2, MCL Tier 2, 26
29
+This study, New Tier 3, 0
30
+New Tier 3, MCL Tier 3, 0
29 31
All other MCL studies, MCL Tier 1, 21
30 32
All other MCL studies, MCL Tier 2, 20
33
+All other MCL studies, MCL Tier 3, 0
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/zhouSporadicEndemicBurkitt2019.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @zhouSporadicEndemicBurkitt2019
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|BL|0|1|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|BL|0|1|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 0
26 26
New Tier 1, BL Tier 1, 0
27 27
This study, New Tier 2, 1
28 28
New Tier 2, BL Tier 2, 1
29
-All other BL studies, BL Tier 1, 29
30
-All other BL studies, BL Tier 2, 156
29
+This study, New Tier 3, 0
30
+New Tier 3, BL Tier 3, 0
31
+All other BL studies, BL Tier 1, 32
32
+All other BL studies, BL Tier 2, 71
33
+All other BL studies, BL Tier 3, 70
31 34
```
32 35
33 36
### Tier 2