FL_genes.md
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@@ -11,15 +11,18 @@ link-citations: true
11 11
12 12
## Tier 1 FL genes
13 13
14
-### *49 total*
14
+### *57 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]||
18 19
|[ARID1A](ARID1A)|Tier 1 GE[@krysiakRecurrentSomaticMutations2017b], FE[@barisicARID1AOrchestratesSWI2024], aSHM|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017b)|[@loveGeneticLandscapeMutations2012; @rossiCodingGenomeSplenic2012c; @wienandGenomicAnalysesFlowsorted2019b; @zhangGeneticHeterogeneityDiffuse2013]||
19 20
|[ATP6AP1](ATP6AP1)|Tier 1 GE[@okosunRecurrentMTORC1activatingRRAGC2016a]|[Okosun et al](papers/okosunRecurrentMTORC1activatingRRAGC2016a)|||
20 21
|[ATP6V1B2](ATP6V1B2)|Tier 1 GE[@okosunRecurrentMTORC1activatingRRAGC2016a]|[Okosun et al](papers/okosunRecurrentMTORC1activatingRRAGC2016a)|||
21 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 et al](papers/russler-germainMutationsAssociatedProgression2023b)|[@morinFrequentMutationHistonemodifying2011; @spinaGeneticsNodalMarginal2016b]||
22 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]||
23 26
|[BCL7A](BCL7A)|Tier 1 GE[@krysiakRecurrentSomaticMutations2017b], FE[@balinas-gaviraFrequentMutationsAminoterminal2020b], aSHM|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017b)|[@grandeGenomewideDiscoverySomatic2019; @morinFrequentMutationHistonemodifying2011; @reichelFlowSortingExome2015a]||
24 27
|[BTK](BTK)|Tier 1 GE[@krysiakRecurrentSomaticMutations2017b], aSHM|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017b)|[@albuquerqueEnhancingKnowledgeDiscovery2017a]||
25 28
|[CARD11](CARD11)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@lenzOncogenicCARD11Mutations2008], CE[@zhaoExpressionPrognosticValue2016], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@lenzOncogenicCARD11Mutations2008; @wuGeneticHeterogeneityPrimary2016; @yanBCRTLRSignaling2012a]||
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@@ -27,11 +30,14 @@ link-citations: true
27 30
|[CD83](CD83)|Tier 1 GE[@russler-germainMutationsAssociatedProgression2023b], aSHM|[Russler et al](papers/russler-germainMutationsAssociatedProgression2023b)|[@dunsCharacterizationDLBCLPMBL2021b; @morinMutationalStructuralAnalysis2013; @paneaWholeGenomeLandscape2019]||
28 31
|[CREBBP](CREBBP)|Tier 1 GE[@pasqualucciInactivatingMutationsAcetyltransferase2011a], FE[@pasqualucciInactivatingMutationsAcetyltransferase2011a], aSHM|[Pasqualucci et al](papers/pasqualucciInactivatingMutationsAcetyltransferase2011a)|[@dunsCharacterizationDLBCLPMBL2021b; @loveGeneticLandscapeMutations2012; @parryWholeExomeSequencing2013]||
29 32
|[CTSS](CTSS)|Tier 1 GE[@barariaCathepsinAlterationsInduce2020c]|[Bararia et al](papers/barariaCathepsinAlterationsInduce2020c)|||
33
+|[EBF1](EBF1)|Tier 1 GE, aSHM||[@bohleRoleEarlyBcell2013; @reichelFlowSortingExome2015a; @thomasGeneticSubgroupsInform2023]||
30 34
|[EEF1A1](EEF1A1)|Tier 1 GE[@hubschmannMutationalMechanismsShaping2021b], CE[@gongExpressionClinicalValue2021], aSHM|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)|[@reichelFlowSortingExome2015a]||
31 35
|[EP300](EP300)|Tier 1 GE[@pasqualucciInactivatingMutationsAcetyltransferase2011a], FE[@pasqualucciInactivatingMutationsAcetyltransferase2011a], aSHM|[Pasqualucci et al](papers/pasqualucciInactivatingMutationsAcetyltransferase2011a)|[@rossiCodingGenomeSplenic2012c]||
32 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]||
33 38
|[FOXO1](FOXO1)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@trinhAnalysisFOXO1Mutations], CE[@trinhAnalysisFOXO1Mutations], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@dunsCharacterizationDLBCLPMBL2021b; @schmitzBurkittLymphomaPathogenesis2012]||
34 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]||
35 41
|[HIST1H1B](HIST1H1B)|Tier 1 GE[@krysiakRecurrentSomaticMutations2017b], aSHM|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017b)|[@chapuyMolecularSubtypesDiffuse2018b; @sarkozyMutationalLandscapeGray2021a]||
36 42
|[HIST1H1C](HIST1H1C)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@paneaWholeGenomeLandscape2019]||
37 43
|[HIST1H1D](HIST1H1D)|Tier 1 GE[@krysiakRecurrentSomaticMutations2017b], aSHM|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017b)|[@jalladesExomeSequencingIdentifies2017; @morinMutationalStructuralAnalysis2013]||
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@@ -51,12 +57,14 @@ link-citations: true
51 57
|[KMT2D](KMT2D)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@liLossCREBBPKMT2D2024], CE[@rushtonGeneticEvolutionaryPatterns2020], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@beaLandscapeSomaticMutations2013; @deschGenotypingCirculatingTumor2020; @grandeGenomewideDiscoverySomatic2019; @rossiCodingGenomeSplenic2012c]||
52 58
|[MAP2K1](MAP2K1)|Tier 1 GE[@louissaintPediatrictypeNodalFollicular2016a], aSHM|[Louissaint et al](papers/louissaintPediatrictypeNodalFollicular2016a)|[@shinBRAFV600EMAP2K12015]||
53 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]||
54 61
|[PIM1](PIM1)|Tier 1 GE[@drevalGeneticSubdivisionsFollicular2023], CE[@guoSGK1MutationStatus2022b], aSHM|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@burkhardtClinicalRelevanceMolecular2022b; @dunsCharacterizationDLBCLPMBL2021b; @pasqualucciHypermutationMultipleProtooncogenes2001a]||
55 62
|[POU2AF1](POU2AF1)|Tier 1 GE[@krysiakRecurrentSomaticMutations2017b], aSHM|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017b)|[@chapuyMolecularSubtypesDiffuse2018b]||
56 63
|[POU2F2](POU2F2)|Tier 1 GE[@krysiakRecurrentSomaticMutations2017b], FE[@hodsonRegulationNormalBcell2016a], aSHM|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017b)|[@lohrDiscoveryPrioritizationSomatic2012a]||
57 64
|[RRAGC](RRAGC)|Tier 1 GE[@okosunRecurrentMTORC1activatingRRAGC2016a], FE[@ortega-molinaOncogenicRagGTPase2019b], aSHM|[Okosun et al](papers/okosunRecurrentMTORC1activatingRRAGC2016a)|||
58 65
|[SGK1](SGK1)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@hartmannHighlyRecurrentMutations2016b], CE[@guoSGK1MutationStatus2022b], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@dunsCharacterizationDLBCLPMBL2021b]||
59 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]||
60 68
|[STAT6](STAT6)|Tier 1 GE[@yildizActivatingSTAT6Mutations2015c], FE[@yildizActivatingSTAT6Mutations2015c], aSHM|[Yildiz et al](papers/yildizActivatingSTAT6Mutations2015c)|[@ritzRecurrentMutationsSTAT62009a]||
61 69
|[TBL1XR1](TBL1XR1)|Tier 1 GE, FE[@venturuttiTBL1XR1MutationsDrive2020b], aSHM||[@lohrDiscoveryPrioritizationSomatic2012a; @rossiCodingGenomeSplenic2012c]||
62 70
|[TMSB4X](TMSB4X)|Tier 1 GE, aSHM||[@zhangGeneticHeterogeneityDiffuse2013]||
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@@ -67,16 +75,13 @@ link-citations: true
67 75
68 76
## Tier 2 FL genes
69 77
70
-### *64 total*
78
+### *56 total*
71 79
72 80
|Gene|Summary| First FL study | Other entities | QC result |
73 81
|:-:|:--:|:-:|:-|:-|
74 82
|[ABL2](ABL2)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023b]|[Russler et al](papers/russler-germainMutationsAssociatedProgression2023b)|||
75
-|[ACTB](ACTB)|Tier 2 GE[@drevalGeneticSubdivisionsFollicular2023], aSHM|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@lohrDiscoveryPrioritizationSomatic2012a; @wienandGenomicAnalysesFlowsorted2019b]||
76 83
|[ACTG1](ACTG1)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021b], aSHM|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)|[@deschGenotypingCirculatingTumor2020; @spinaGeneticsNodalMarginal2016b]||
77 84
|[ATP6V1A](ATP6V1A)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021b]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)|||
78
-|[BCL10](BCL10)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023b], FE[@xiaBCL10MutationsDefine2022], aSHM|[Russler et al](papers/russler-germainMutationsAssociatedProgression2023b)|[@morinFrequentMutationHistonemodifying2011; @spinaGeneticsNodalMarginal2016b]||
79
-|[BCL6](BCL6)|Tier 2 GE[@drevalGeneticSubdivisionsFollicular2023], FE[@balSuperenhancerHypermutationAlters2022], aSHM|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@loveGeneticLandscapeMutations2012; @morinFrequentMutationHistonemodifying2011]||
80 85
|[BIRC6](BIRC6)|Tier 2 GE, aSHM||[@reddyGeneticFunctionalDrivers2017; @sarkozyMutationalLandscapeGray2021a]||
81 86
|[BTG1](BTG1)|Tier 2 GE[@drevalGeneticSubdivisionsFollicular2023], FE[@mlynarczykBTG1MutationYields2023b], aSHM|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@burkhardtClinicalRelevanceMolecular2022b; @morinFrequentMutationHistonemodifying2011; @sarkozyMutationalLandscapeGray2021a]||
82 87
|[BTG2](BTG2)|Tier 2 GE[@drevalGeneticSubdivisionsFollicular2023], CE[@guoMutationBTG2Gene2022b], aSHM|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@loveGeneticLandscapeMutations2012; @morinFrequentMutationHistonemodifying2011]||
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@@ -91,12 +96,9 @@ link-citations: true
91 96
|[DHX15](DHX15)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021b]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)|||
92 97
|[DTX1](DTX1)|Tier 2 GE, FE[@demirandaExomeSequencingReveals2014], CE[@merirantaDeltex1MutationsPredict2017b], aSHM||[@gomezUltraDeepSequencingReveals2023; @loveGeneticLandscapeMutations2012; @rossiCodingGenomeSplenic2012c; @zhangGeneticHeterogeneityDiffuse2013]||
93 98
|[DUSP2](DUSP2)|Tier 2 GE[@drevalGeneticSubdivisionsFollicular2023], aSHM|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@dunsCharacterizationDLBCLPMBL2021b; @lohrDiscoveryPrioritizationSomatic2012a]||
94
-|[EBF1](EBF1)|Tier 2 GE, aSHM||[@bohleRoleEarlyBcell2013; @reichelFlowSortingExome2015a; @thomasGeneticSubgroupsInform2023]||
95 99
|[EGR1](EGR1)|Tier 2 GE[@krysiakRecurrentSomaticMutations2017b]|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017b)|[@reichelFlowSortingExome2015a; @rossiCodingGenomeSplenic2012c]||
96
-|[FAS](FAS)|Tier 2 GE, FE[@seebergerLossFasCD952001], aSHM||[@schollMutationsRegionFAS2007; @spinaGeneticsNodalMarginal2016b]||
97 100
|[FZR1](FZR1)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021b]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)|||
98 101
|[GBP7](GBP7)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023b]|[Russler et al](papers/russler-germainMutationsAssociatedProgression2023b)|||
99
-|[GNAI2](GNAI2)|Tier 2 GE, aSHM||[@grandeGenomewideDiscoverySomatic2019; @morinMutationalStructuralAnalysis2013]||
100 102
|[GRM6](GRM6)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023b]|[Russler et al](papers/russler-germainMutationsAssociatedProgression2023b)|||
101 103
|[HIST1H2BM](HIST1H2BM)|Tier 2 GE[@krysiakRecurrentSomaticMutations2017b]|[Krysiak et al](papers/krysiakRecurrentSomaticMutations2017b)|||
102 104
|[HIST1H3B](HIST1H3B)|Tier 2 GE, aSHM||[@lohrDiscoveryPrioritizationSomatic2012a; @reichelFlowSortingExome2015a]||
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@@ -113,7 +115,6 @@ link-citations: true
113 115
|[MEF2C](MEF2C)|Tier 2 GE, FE[@jingjingNovelMEF2CMutation2020], aSHM||[@arthurGenomewideDiscoverySomatic2018]||
114 116
|[MGEA5](MGEA5)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021b]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)|||
115 117
|[MKI67](MKI67)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023b]|[Russler et al](papers/russler-germainMutationsAssociatedProgression2023b)|[@schmitzBurkittLymphomaPathogenesis2012]||
116
-|[MYC](MYC)|Tier 2 GE, FE[@giallongoIdentificationCmycOncogene1983], CE[@christieCMYCTranslocation142008], aSHM||[@dunsCharacterizationDLBCLPMBL2021b; @jalladesExomeSequencingIdentifies2017; @johnstonCmycHypermutationBurkitt1992; @pasqualucciHypermutationMultipleProtooncogenes2001a]||
117 118
|[MYCBP2](MYCBP2)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021b]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)|||
118 119
|[MYD88](MYD88)|Tier 2 GE[@drevalGeneticSubdivisionsFollicular2023], FE[@ngoOncogenicallyActiveMYD882011a], CE[@guoSGK1MutationStatus2022b], aSHM|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@ngoOncogenicallyActiveMYD882011a; @yanBCRTLRSignaling2012a]||
119 120
|[NFKBIA](NFKBIA)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023b], aSHM|[Russler et al](papers/russler-germainMutationsAssociatedProgression2023b)|[@thomasMutationalAnalysisIkappaBalpha2004; @wienandGenomicAnalysesFlowsorted2019b]||
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@@ -127,7 +128,6 @@ link-citations: true
127 128
|[RBM6](RBM6)|Tier 2 GE[@hubschmannMutationalMechanismsShaping2021b]|[Hubschmann et al](papers/hubschmannMutationalMechanismsShaping2021b)|||
128 129
|[S1PR2](S1PR2)|Tier 2 GE[@drevalGeneticSubdivisionsFollicular2023], FE[@floriHematopoieticOncoproteinFOXP12016], aSHM|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@morinFrequentMutationHistonemodifying2011; @muppidiLossSignalingGa132014b]||
129 130
|[SHROOM3](SHROOM3)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023b]|[Russler et al](papers/russler-germainMutationsAssociatedProgression2023b)|||
130
-|[SOCS1](SOCS1)|Tier 2 GE[@drevalGeneticSubdivisionsFollicular2023], FE[@melznerBiallelicMutationSOCS12005a], aSHM|[Dreval et al](papers/drevalGeneticSubdivisionsFollicular2023)|[@morinFrequentMutationHistonemodifying2011; @wenigerMutationsTumorSuppressor2006a]||
131 131
|[SRRM2](SRRM2)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023b], aSHM|[Russler et al](papers/russler-germainMutationsAssociatedProgression2023b)|[@morinMutationalStructuralAnalysis2013]||
132 132
|[STAB2](STAB2)|Tier 2 GE[@russler-germainMutationsAssociatedProgression2023b]|[Russler et al](papers/russler-germainMutationsAssociatedProgression2023b)|||
133 133
|[TMEM30A](TMEM30A)|Tier 2 GE[@morinFrequentMutationHistonemodifying2011], FE[@ennishiTMEM30ALossoffunctionMutations2020b], CE[@ennishiTMEM30ALossoffunctionMutations2020b], aSHM|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|||