cf60739894f61b4a6e3cd05ab3521081d1ee715a
BL_genes.md
| ... | ... | @@ -3,6 +3,8 @@ title: 'BL genes' |
| 3 | 3 | bibliography: 'morinlab.bib' |
| 4 | 4 | csl: 'NLM.csl' |
| 5 | 5 | link-citations: true |
| 6 | +nocite: | |
|
| 7 | + @loveGeneticLandscapeMutations2012 |
|
| 6 | 8 | --- |
| 7 | 9 | |
| 8 | 10 | ## Origins of BL genes |
| ... | ... | @@ -11,198 +13,14 @@ link-citations: true |
| 11 | 13 | |
| 12 | 14 | ## Tier 1 BL genes |
| 13 | 15 | |
| 14 | -### *32 total* |
|
| 15 | - |
|
| 16 | -|Gene|Summary| First BL study | Other entities | QC result | |
|
| 17 | -|:-:|:--:|:-:|:-|:-| |
|
| 18 | -|[ARID1A](ARID1A)|Tier 1 GE[@loveGeneticLandscapeMutations2012], FE[@barisicARID1AOrchestratesSWI2024]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@krysiakRecurrentSomaticMutations2017; @rossiCodingGenomeSplenic2012; @wienandGenomicAnalysesFlowsorted2019; @zhangGeneticHeterogeneityDiffuse2013]|| |
|
| 19 | -|[BACH2](BACH2)|Tier 1 GE[@grandeGenomewideDiscoverySomatic2019]|[Grande et al](papers/grandeGenomewideDiscoverySomatic2019)||| |
|
| 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]|| |
|
| 22 | -|[BMP7](BMP7)|Tier 1 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||| |
|
| 23 | -|[CCND3](CCND3)|Tier 1 GE[@richterRecurrentMutationID32012], FE[@schmitzBurkittLymphomaPathogenesis2012]|[Richter et al](papers/richterRecurrentMutationID32012)|[@deschGenotypingCirculatingTumor2020; @jalladesExomeSequencingIdentifies2017; @morinFrequentMutationHistonemodifying2011]|| |
|
| 24 | -|[CHD8](CHD8)|Tier 1 GE[@grandeGenomewideDiscoverySomatic2019]|[Grande et al](papers/grandeGenomewideDiscoverySomatic2019)||| |
|
| 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; @nadeuGenomicEpigenomicInsights2020; @reddyGeneticFunctionalDrivers2017]|| |
|
| 44 | -|[TCF3](TCF3)|Tier 1 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)||| |
|
| 45 | -|[TCL1A](TCL1A)|Tier 1 GE[@grandeGenomewideDiscoverySomatic2019], aSHM|[Grande et al](papers/grandeGenomewideDiscoverySomatic2019)|[@reddyGeneticFunctionalDrivers2017]|| |
|
| 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]|| |
|
| 16 | +[[include:BL_Tier1.md]] |
|
| 50 | 17 | |
| 51 | 18 | ## Tier 2 BL genes |
| 52 | 19 | |
| 53 | -### *72 total* |
|
| 54 | - |
|
| 55 | -|Gene|Summary| First BL study | Other entities | QC result | |
|
| 56 | -|:-:|:--:|:-:|:-|:-| |
|
| 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]|| |
|
| 63 | -|[C16orf48](C16orf48)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)||| |
|
| 64 | -|[CARD4](CARD4)|Tier 2 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||PASS| |
|
| 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]|| |
|
| 70 | -|[CDKN2C](CDKN2C)|Tier 2 GE[@thomasGeneticSubgroupsInform2023]|[Thomas et al](papers/thomasGeneticSubgroupsInform2023)||| |
|
| 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| |
|
| 74 | -|[DHCR7](DHCR7)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)||| |
|
| 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)||| |
|
| 78 | -|[EHD1](EHD1)|Tier 2 GE[@thomasGeneticSubgroupsInform2023]|[Thomas et al](papers/thomasGeneticSubgroupsInform2023)||| |
|
| 79 | -|[EIF4A1](EIF4A1)|Tier 2 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||| |
|
| 80 | -|[ELP2](ELP2)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)||| |
|
| 81 | -|[EPPK1](EPPK1)|Tier 2 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||| |
|
| 82 | -|[ERAP1](ERAP1)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)||| |
|
| 83 | -|[EXOSC6](EXOSC6)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)||| |
|
| 84 | -|[EZH2](EZH2)|Tier 2 GE[@loveGeneticLandscapeMutations2012], FE[@sneeringerCoordinatedActivitiesWildtype2010]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@morinSomaticMutationsAltering2010; @mottokIntegrativeGenomicAnalysis2019]|PASS| |
|
| 85 | -|[FLYWCH1](FLYWCH1)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)||| |
|
| 86 | -|[GGTLA4](GGTLA4)|Tier 2 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||PASS| |
|
| 87 | -|[GTSE1](GTSE1)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)||| |
|
| 88 | -|[HIST1H3D](HIST1H3D)|Tier 2 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||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| |
|
| 95 | -|[KANK2](KANK2)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)||| |
|
| 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]|| |
|
| 101 | -|[MYO18A](MYO18A)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)||| |
|
| 102 | -|[NBEAL1](NBEAL1)|Tier 2 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||PASS| |
|
| 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)||| |
|
| 105 | -|[P2RY2](P2RY2)|Tier 2 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||PASS| |
|
| 106 | -|[PDCD11](PDCD11)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)||| |
|
| 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 | -|[RANBP6](RANBP6)|Tier 2 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||PASS| |
|
| 112 | -|[REV3L](REV3L)|Tier 2 GE[@burkhardtClinicalRelevanceMolecular2022]|[Burkhardt et al](papers/burkhardtClinicalRelevanceMolecular2022)||| |
|
| 113 | -|[RNF144B](RNF144B)|Tier 2 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||PASS| |
|
| 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 | -|[TOP2A](TOP2A)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)||| |
|
| 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 | -|[WDR90](WDR90)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)||| |
|
| 122 | -|[WHAMM](WHAMM)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)||| |
|
| 123 | -|[WNK2](WNK2)|Tier 2 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||PASS| |
|
| 124 | -|[YY1AP1](YY1AP1)|Tier 2 GE[@schmitzBurkittLymphomaPathogenesis2012]|[Schmitz et al](papers/schmitzBurkittLymphomaPathogenesis2012)||| |
|
| 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)||| |
|
| 20 | +[[include:BL_Tier2.md]] |
|
| 129 | 21 | |
| 130 | 22 | ## Tier 3 BL genes |
| 131 | 23 | |
| 132 | -### *70 total* |
|
| 133 | - |
|
| 134 | -|Gene|Summary| First BL study | Other entities | QC result | |
|
| 135 | -|:-:|:--:|:-:|:-|:-| |
|
| 136 | -|[ACAD9](ACAD9)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL| |
|
| 137 | -|[ACE](ACE)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@zhangGeneticHeterogeneityDiffuse2013]|FAIL| |
|
| 138 | -|[ALPK2](ALPK2)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||FAIL| |
|
| 139 | -|[ATP2C2](ATP2C2)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||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 | -|[C6orf27](C6orf27)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL| |
|
| 144 | -|[CAD](CAD)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@zhangGeneticHeterogeneityDiffuse2013]|FAIL| |
|
| 145 | -|[CCT6B](CCT6B)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL| |
|
| 146 | -|[CD79B](CD79B)|Tier 3 GE[@paneaWholeGenomeLandscape2019], FE[@davisChronicActiveBcellreceptor2010]|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@davisChronicActiveBcellreceptor2010; @drevalGeneticSubdivisionsFollicular2023]|FAIL| |
|
| 147 | -|[CDH17](CDH17)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL| |
|
| 148 | -|[COL4A2](COL4A2)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL| |
|
| 149 | -|[CTCF](CTCF)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||FAIL| |
|
| 150 | -|[CYB5D1](CYB5D1)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL| |
|
| 151 | -|[CYP4F22](CYP4F22)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL| |
|
| 152 | -|[DLGAP1](DLGAP1)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@zhangGeneticHeterogeneityDiffuse2013]|FAIL| |
|
| 153 | -|[DNMT1](DNMT1)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||FAIL| |
|
| 154 | -|[DTX1](DTX1)|Tier 3 GE[@loveGeneticLandscapeMutations2012], aSHM|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@gomezUltraDeepSequencingReveals2023; @rossiCodingGenomeSplenic2012; @zhangGeneticHeterogeneityDiffuse2013]|FAIL| |
|
| 155 | -|[EIF2C4](EIF2C4)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL| |
|
| 156 | -|[EML2](EML2)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL| |
|
| 157 | -|[ENTPD3](ENTPD3)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL| |
|
| 158 | -|[EPHB2](EPHB2)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL| |
|
| 159 | -|[ETS1](ETS1)|Tier 3 GE[@paneaWholeGenomeLandscape2019], aSHM|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@morinFrequentMutationHistonemodifying2011]|FAIL| |
|
| 160 | -|[FAM129B](FAM129B)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL| |
|
| 161 | -|[FGFR3](FGFR3)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL| |
|
| 162 | -|[FTCD](FTCD)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL| |
|
| 163 | -|[FZD3](FZD3)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||FAIL| |
|
| 164 | -|[GRIK5](GRIK5)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL| |
|
| 165 | -|[HIST1H1C](HIST1H1C)|Tier 3 GE[@paneaWholeGenomeLandscape2019], aSHM|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@morinFrequentMutationHistonemodifying2011]|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 | -|[HIST1H3H](HIST1H3H)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||FAIL| |
|
| 170 | -|[HIST1H3J](HIST1H3J)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||FAIL| |
|
| 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)|[@tiacciPervasiveMutationsJAKSTAT2018]|FAIL| |
|
| 173 | -|[KCNK10](KCNK10)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||FAIL| |
|
| 174 | -|[KIFC3](KIFC3)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL| |
|
| 175 | -|[MAP3K6](MAP3K6)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL| |
|
| 176 | -|[MME](MME)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||FAIL| |
|
| 177 | -|[MTOR](MTOR)|Tier 3 GE[@paneaWholeGenomeLandscape2019], FE[@grabinerDiverseArrayCancerassociated2014]|[Panea et al](papers/paneaWholeGenomeLandscape2019)|[@zhangGeneticHeterogeneityDiffuse2013]|FAIL| |
|
| 178 | -|[MYH10](MYH10)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||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 | -|[PABPC4L](PABPC4L)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||FAIL| |
|
| 182 | -|[PC](PC)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL| |
|
| 183 | -|[PCDHA11](PCDHA11)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||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 | -|[POLRMT](POLRMT)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL| |
|
| 187 | -|[POR](POR)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL| |
|
| 188 | -|[PRSS22](PRSS22)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL| |
|
| 189 | -|[PTPRN](PTPRN)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL| |
|
| 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)|[@lohrDiscoveryPrioritizationSomatic2012]|FAIL| |
|
| 192 | -|[RET](RET)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@fanComprehensiveCharacterizationDriver2020]|FAIL| |
|
| 193 | -|[SALL3](SALL3)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@zhangGenomicLandscapeMantle2014]|FAIL| |
|
| 194 | -|[SAPS2](SAPS2)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL| |
|
| 195 | -|[SBF1](SBF1)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL| |
|
| 196 | -|[SF3B1](SF3B1)|Tier 3 GE[@loveGeneticLandscapeMutations2012], FE[@cazzolaBiologicClinicalSignificance2013]|[Love et al](papers/loveGeneticLandscapeMutations2012)|[@reddyGeneticFunctionalDrivers2017]|FAIL| |
|
| 197 | -|[SHANK1](SHANK1)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL| |
|
| 198 | -|[SLC29A2](SLC29A2)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL| |
|
| 199 | -|[SNTB2](SNTB2)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||FAIL| |
|
| 200 | -|[SYNGAP1](SYNGAP1)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL| |
|
| 201 | -|[TBC1D9B](TBC1D9B)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL| |
|
| 202 | -|[TIGD6](TIGD6)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL| |
|
| 203 | -|[TPST2](TPST2)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL| |
|
| 204 | -|[WDR7](WDR7)|Tier 3 GE[@paneaWholeGenomeLandscape2019]|[Panea et al](papers/paneaWholeGenomeLandscape2019)||FAIL| |
|
| 205 | -|[ZNF229](ZNF229)|Tier 3 GE[@loveGeneticLandscapeMutations2012]|[Love et al](papers/loveGeneticLandscapeMutations2012)||FAIL| |
|
| 206 | - |
|
| 24 | +[[include:BL_Tier3.md]] |
|
| 207 | 25 | |
| 208 | 26 | # References |