diff --git a/resources/curated/dlbcl_genes.tsv b/resources/curated/dlbcl_genes.tsv index e3d0e160..2d4a3cf8 100644 --- a/resources/curated/dlbcl_genes.tsv +++ b/resources/curated/dlbcl_genes.tsv @@ -1,43 +1,43 @@ Gene Tier aSHM QC Mean variant quality citekey LymphGen PMID MutationEffect Mutation-PMID ACTB 1 TRUE NA lohrDiscoveryPrioritizationSomatic2012a TRUE 22343534 ACTG1 1 TRUE NA fanComprehensiveCharacterizationDriver2020b FALSE 33953289 -ARID1A 1 FALSE NA zhangGeneticHeterogeneityDiffuse2013 TRUE 23292937 -ATM 1 FALSE NA reddyGeneticFunctionalDrivers2017 FALSE 28985567 -B2M 1 FALSE NA morinFrequentMutationHistonemodifying2011 FALSE 21796119 -BCL10 1 FALSE NA morinFrequentMutationHistonemodifying2011 TRUE 21796119 +ARID1A 1 FALSE NA zhangGeneticHeterogeneityDiffuse2013 TRUE 23292937 LOF 38458187 +ATM 1 FALSE NA reddyGeneticFunctionalDrivers2017 FALSE 28985567 LOF 11756177 +B2M 1 FALSE NA morinFrequentMutationHistonemodifying2011 FALSE 21796119 LOF 22137796 +BCL10 1 FALSE NA morinFrequentMutationHistonemodifying2011 TRUE 21796119 GOF 35658124 BCL2 1 TRUE NA tanakaFrequentIncidenceSomatic1992 TRUE 1339299 -BCL6 1 TRUE NA morinFrequentMutationHistonemodifying2011 TRUE 21796119 -BCL7A 1 TRUE NA morinFrequentMutationHistonemodifying2011 FALSE 21796119 +BCL6 1 TRUE NA morinFrequentMutationHistonemodifying2011 TRUE 21796119 LOF 12504096 +BCL7A 1 TRUE NA morinFrequentMutationHistonemodifying2011 FALSE 21796119 LOF 32576963 BIRC6 1 FALSE NA reddyGeneticFunctionalDrivers2017 FALSE 28985567 -BRAF 1 FALSE NA tiacciBRAFMutationsHairycell2011a FALSE 22343534 -BTG1 1 TRUE NA morinFrequentMutationHistonemodifying2011 TRUE 21796119 +BRAF 1 FALSE NA tiacciBRAFMutationsHairycell2011a FALSE 22343534 LOF 15035987 +BTG1 1 TRUE NA morinFrequentMutationHistonemodifying2011 TRUE 21796119 LOF 33021411 BTG2 1 TRUE NA morinFrequentMutationHistonemodifying2011 TRUE 21796119 -BTK 1 FALSE NA albuquerqueEnhancingKnowledgeDiscovery2017a FALSE 28327945 -CARD11 1 FALSE NA lenzOncogenicCARD11Mutations2008 FALSE 18323416 -CCND3 1 FALSE NA morinFrequentMutationHistonemodifying2011 FALSE 21796119 -CD58 1 FALSE NA morinFrequentMutationHistonemodifying2011 TRUE 21796119 -CD70 1 FALSE NA morinFrequentMutationHistonemodifying2011 TRUE 21796119 -CD79B 1 FALSE NA morinFrequentMutationHistonemodifying2011 TRUE 21796119 +BTK 1 FALSE NA albuquerqueEnhancingKnowledgeDiscovery2017a FALSE 28327945 LOF 33419778 +CARD11 1 FALSE NA lenzOncogenicCARD11Mutations2008 FALSE 18323416 GOF 18323416 +CCND3 1 FALSE NA morinFrequentMutationHistonemodifying2011 FALSE 21796119 GOF 22885699 +CD58 1 FALSE NA morinFrequentMutationHistonemodifying2011 TRUE 21796119 LOF 22137796 +CD70 1 FALSE NA morinFrequentMutationHistonemodifying2011 TRUE 21796119 LOF 36471481 +CD79B 1 FALSE NA morinFrequentMutationHistonemodifying2011 TRUE 21796119 GOF 29669863 CD83 1 TRUE NA morinMutationalStructuralAnalysis2013 TRUE 23699601 -CDKN2A 1 FALSE NA morinMutationalStructuralAnalysis2013 TRUE 23699601 -CIITA 1 TRUE NA morinFrequentMutationHistonemodifying2011 TRUE 21796119 -CREBBP 1 FALSE NA pasqualucciInactivatingMutationsAcetyltransferase2011a TRUE 21390126 -CXCR4 1 TRUE NA khodabakhshiRecurrentTargetsAberrant2012 FALSE 23131835 -DDX3X 1 FALSE NA reddyGeneticFunctionalDrivers2017 TRUE -DTX1 1 TRUE NA zhangGeneticHeterogeneityDiffuse2013 TRUE 23292937 +CDKN2A 1 FALSE NA morinMutationalStructuralAnalysis2013 TRUE 23699601 LOF 19260062 +CIITA 1 TRUE NA morinFrequentMutationHistonemodifying2011 TRUE 21796119 LOF 26549456 +CREBBP 1 FALSE NA pasqualucciInactivatingMutationsAcetyltransferase2011a TRUE 21390126 LOF 33431788 +CXCR4 1 TRUE NA khodabakhshiRecurrentTargetsAberrant2012 FALSE 23131835 LOF 36089616 +DDX3X 1 FALSE NA reddyGeneticFunctionalDrivers2017 TRUE LOF 34437837 +DTX1 1 TRUE NA zhangGeneticHeterogeneityDiffuse2013 TRUE 23292937 LOF 28183850 DUSP2 1 TRUE NA lohrDiscoveryPrioritizationSomatic2012a TRUE 22343534 -EBF1 1 TRUE NA bohleRoleEarlyBcell2013 FALSE 23174882 +EBF1 1 TRUE NA bohleRoleEarlyBcell2013 FALSE 23174882 LOF 28692033 EEF1A1 1 FALSE NA chapuyMolecularSubtypesDiffuse2018b FALSE 33953289 -EP300 1 FALSE NA pasqualucciInactivatingMutationsAcetyltransferase2011a TRUE 21390126 +EP300 1 FALSE NA pasqualucciInactivatingMutationsAcetyltransferase2011a TRUE 21390126 LOF 10700188 ETS1 1 TRUE NA morinFrequentMutationHistonemodifying2011 TRUE 21796119 -ETV6 1 TRUE NA lohrDiscoveryPrioritizationSomatic2012a TRUE 22343534 -EZH2 1 FALSE NA NA morinSomaticMutationsAltering2010a TRUE 20081860 GOF -FAS 1 FALSE NA schollMutationsRegionFAS2007 FALSE 17487740 -FBXO11 1 FALSE NA arthurGenomewideDiscoverySomatic2018 FALSE 33953289 -FBXW7 1 FALSE NA zhangGeneticHeterogeneityDiffuse2013 FALSE 23292937 -FOXO1 1 FALSE NA morinFrequentMutationHistonemodifying2011 FALSE 21796119 -GNA13 1 FALSE NA morinFrequentMutationHistonemodifying2011 FALSE 21796119 -GNAI2 1 FALSE NA morinMutationalStructuralAnalysis2013 FALSE 23699601 +ETV6 1 TRUE NA lohrDiscoveryPrioritizationSomatic2012a TRUE 22343534 LOF 24997145 +EZH2 1 FALSE NA NA morinSomaticMutationsAltering2010a TRUE 20081860 GOF 21078963 +FAS 1 FALSE NA schollMutationsRegionFAS2007 FALSE 17487740 LOF 20935634 +FBXO11 1 FALSE NA arthurGenomewideDiscoverySomatic2018 FALSE 33953289 LOF 22113614 +FBXW7 1 FALSE NA zhangGeneticHeterogeneityDiffuse2013 FALSE 23292937 LOF 32350066 +FOXO1 1 FALSE NA morinFrequentMutationHistonemodifying2011 FALSE 21796119 GOF 23460611 +GNA13 1 FALSE NA morinFrequentMutationHistonemodifying2011 FALSE 21796119 LOF 26616858 +GNAI2 1 FALSE NA morinMutationalStructuralAnalysis2013 FALSE 23699601 GOF 23699601 GRB2 1 FALSE NA pasqualucciAnalysisCodingGenome2011 FALSE 21804550 GRHPR 1 TRUE NA schmitzGeneticsPathogenesisDiffuse2018a TRUE 30275490 HIST1H1B 1 TRUE NA chapuyMolecularSubtypesDiffuse2018b FALSE 29713087 @@ -50,77 +50,77 @@ HIST1H2BC 1 TRUE NA lohrDiscoveryPrioritizationSomatic2012a FALSE 22343534 HIST1H2BK 1 TRUE NA zhangGeneticHeterogeneityDiffuse2013 FALSE 23292937 HIST1H3B 1 TRUE NA lohrDiscoveryPrioritizationSomatic2012a FALSE 22343534 HIST2H2BE 1 TRUE NA chapuyMolecularSubtypesDiffuse2018b FALSE 29641966 -HLA-A 1 FALSE NA lohrDiscoveryPrioritizationSomatic2012a TRUE 22343534 -HLA-B 1 FALSE NA lohrDiscoveryPrioritizationSomatic2012a TRUE 22343534 -HLA-C 1 FALSE NA chapuyMolecularSubtypesDiffuse2018b FALSE 29713087 -HLA-DMB 1 FALSE NA hubschmannMutationalMechanismsShaping2021b FALSE 33953289 -HNRNPU 1 FALSE NA reddyGeneticFunctionalDrivers2017 FALSE 28985567 +HLA-A 1 FALSE NA lohrDiscoveryPrioritizationSomatic2012a TRUE 22343534 LOF 34050029 +HLA-B 1 FALSE NA lohrDiscoveryPrioritizationSomatic2012a TRUE 22343534 LOF 34050029 +HLA-C 1 FALSE NA chapuyMolecularSubtypesDiffuse2018b FALSE 29713087 LOF 34050029 +HLA-DMB 1 FALSE NA hubschmannMutationalMechanismsShaping2021b FALSE 33953289 LOF 7528727 +HNRNPU 1 FALSE NA reddyGeneticFunctionalDrivers2017 FALSE 28985567 LOF 36201743 HVCN1 1 FALSE NA chapuyMolecularSubtypesDiffuse2018b FALSE 29713087 -IKZF3 1 FALSE NA morinFrequentMutationHistonemodifying2011 FALSE 21796119 -IL4R 1 TRUE NA dunsCharacterizationDLBCLPMBL2021b FALSE 33684939 +IKZF3 1 FALSE NA morinFrequentMutationHistonemodifying2011 FALSE 21796119 GOF 33689703 +IL4R 1 TRUE NA dunsCharacterizationDLBCLPMBL2021b FALSE 33684939 GOF 29467182 IRF4 1 TRUE NA morinFrequentMutationHistonemodifying2011 TRUE 21796119 -IRF8 1 TRUE NA morinFrequentMutationHistonemodifying2011 TRUE 21796119 -ITPKB 1 TRUE NA schmitzGeneticsPathogenesisDiffuse2018a TRUE 29641966 +IRF8 1 TRUE NA morinFrequentMutationHistonemodifying2011 TRUE 21796119 LOF 38996030 +ITPKB 1 TRUE NA schmitzGeneticsPathogenesisDiffuse2018a TRUE 29641966 LOF 29650799 JUNB 1 FALSE PASS 3 lohrDiscoveryPrioritizationSomatic2012a TRUE 28985567 KLF2 1 TRUE NA pasqualucciAnalysisCodingGenome2011 TRUE 21804550 -KLHL14 1 FALSE NA zhangGeneticHeterogeneityDiffuse2013 TRUE 23292937 -KLHL6 1 TRUE NA morinFrequentMutationHistonemodifying2011 FALSE 21796119 +KLHL14 1 FALSE NA zhangGeneticHeterogeneityDiffuse2013 TRUE 23292937 LOF 32127472 +KLHL6 1 TRUE NA morinFrequentMutationHistonemodifying2011 FALSE 21796119 LOF 29695787 KMT2C 1 FALSE NA zhangGeneticHeterogeneityDiffuse2013 FALSE 23292937 -KMT2D 1 FALSE NA morinFrequentMutationHistonemodifying2011 TRUE 21796119 -KRAS 1 FALSE NA lohrDiscoveryPrioritizationSomatic2012a FALSE 22343534 +KMT2D 1 FALSE NA morinFrequentMutationHistonemodifying2011 TRUE 21796119 LOF 26366712 +KRAS 1 FALSE NA lohrDiscoveryPrioritizationSomatic2012a FALSE 22343534 GOF 9219684 LRRN3 1 FALSE NA zhangGeneticHeterogeneityDiffuse2013 FALSE 23292937 LTB 1 TRUE NA chapuyMolecularSubtypesDiffuse2018b FALSE 29713087 -MEF2B 1 TRUE NA morinFrequentMutationHistonemodifying2011 TRUE 21796119 +MEF2B 1 TRUE NA morinFrequentMutationHistonemodifying2011 TRUE 21796119 NEO 23974956; 26245647 MEF2C 1 TRUE NA hubschmannMutationalMechanismsShaping2021b FALSE 30275490 -MGA 1 FALSE NA reddyGeneticFunctionalDrivers2017 FALSE 23292937 -MIR142 1 TRUE NA kwanhianMicroRNA142Mutated202012b FALSE 23342264 +MGA 1 FALSE NA reddyGeneticFunctionalDrivers2017 FALSE 23292937 LOF 23039309 +MIR142 1 TRUE NA kwanhianMicroRNA142Mutated202012b FALSE 23342264 LOF 29724719 MPEG1 1 FALSE NA morinMutationalStructuralAnalysis2013 TRUE 23699601 -MS4A1 1 TRUE NA rushtonGeneticEvolutionaryPatterns2020 FALSE 32589730 -MTOR 1 FALSE NA zhangGeneticHeterogeneityDiffuse2013 FALSE 23292937 -MYC 1 TRUE NA pasqualucciHypermutationMultipleProtooncogenes2001a FALSE NA -MYD88 1 FALSE NA ngoOncogenicallyActiveMYD882011a TRUE 21179087 -NFKBIA 1 FALSE NA thomasMutationalAnalysisIkappaBalpha2004 TRUE 15198731 -NFKBIE 1 FALSE NA morinGeneticLandscapesRelapsed2016 FALSE 26647218 -NFKBIZ 1 TRUE NA morinGeneticLandscapesRelapsed2016 FALSE 26647218 +MS4A1 1 TRUE NA rushtonGeneticEvolutionaryPatterns2020 FALSE 32589730 LOF 32589730 +MTOR 1 FALSE NA zhangGeneticHeterogeneityDiffuse2013 FALSE 23292937 GOF 24631838 +MYC 1 TRUE NA pasqualucciHypermutationMultipleProtooncogenes2001a FALSE NA GOF 38565249 +MYD88 1 FALSE NA ngoOncogenicallyActiveMYD882011a TRUE 21179087 GOF 21179087 +NFKBIA 1 FALSE NA thomasMutationalAnalysisIkappaBalpha2004 TRUE 15198731 LOF 10637284 +NFKBIE 1 FALSE NA morinGeneticLandscapesRelapsed2016 FALSE 26647218 LOF 25987724 +NFKBIZ 1 TRUE NA morinGeneticLandscapesRelapsed2016 FALSE 26647218 GOF 30275490 NOL9 1 FALSE NA schmitzGeneticsPathogenesisDiffuse2018a TRUE 29641966 -NOTCH1 1 FALSE NA pasqualucciAnalysisCodingGenome2011 TRUE 21804550 -NOTCH2 1 FALSE NA zhangGeneticHeterogeneityDiffuse2013 TRUE 23292937 +NOTCH1 1 FALSE NA pasqualucciAnalysisCodingGenome2011 TRUE 21804550 GOF 29045844 +NOTCH2 1 FALSE NA zhangGeneticHeterogeneityDiffuse2013 TRUE 23292937 GOF 19445024 OSBPL10 1 TRUE NA zhangGeneticHeterogeneityDiffuse2013 TRUE 23292937 -P2RY8 1 FALSE NA lohrDiscoveryPrioritizationSomatic2012a FALSE 22343534 -PIM1 1 TRUE NA pasqualucciHypermutationMultipleProtooncogenes2001a TRUE 11460166 +P2RY8 1 FALSE NA lohrDiscoveryPrioritizationSomatic2012a FALSE 22343534 LOF 25274307 +PIM1 1 TRUE NA pasqualucciHypermutationMultipleProtooncogenes2001a TRUE 11460166 GOF 27904766 PIM2 1 TRUE NA reddyGeneticFunctionalDrivers2017 TRUE 30275490 -POU2AF1 1 TRUE NA chapuyMolecularSubtypesDiffuse2018b FALSE 29713087 -POU2F2 1 FALSE NA lohrDiscoveryPrioritizationSomatic2012a FALSE 22343534 -PRDM1 1 FALSE NA pasqualucciInactivationPRDM1BLIMP12006a TRUE NA -PTEN 1 FALSE NA reddyGeneticFunctionalDrivers2017 FALSE -PTPN6 1 FALSE PASS 3 reddyGeneticFunctionalDrivers2017 FALSE 28985567 -RB1 1 FALSE NA morinMutationalStructuralAnalysis2013 FALSE 23699601 -RFX7 1 FALSE NA NA arthurGenomewideDiscoverySomatic2018 FALSE NA -RHOA 1 FALSE NA zhangGeneticHeterogeneityDiffuse2013 FALSE 23292937 -RRAGC 1 FALSE NA okosunRecurrentMTORC1activatingRRAGC2016a FALSE 26691987 -S1PR2 1 TRUE NA morinFrequentMutationHistonemodifying2011 TRUE 21796119 -SETD1B 1 FALSE NA albuquerqueEnhancingKnowledgeDiscovery2017a TRUE 28327945 -SF3B1 1 FALSE NA reddyGeneticFunctionalDrivers2017 FALSE -SGK1 1 TRUE NA morinFrequentMutationHistonemodifying2011 TRUE 21796119 +POU2AF1 1 TRUE NA chapuyMolecularSubtypesDiffuse2018b FALSE 29713087 LOF 30802265 +POU2F2 1 FALSE NA lohrDiscoveryPrioritizationSomatic2012a FALSE 22343534 LOF 26993806 +PRDM1 1 FALSE NA pasqualucciInactivationPRDM1BLIMP12006a TRUE NA LOF 16492805 +PTEN 1 FALSE NA reddyGeneticFunctionalDrivers2017 FALSE LOF 23840064 +PTPN6 1 FALSE PASS 3 reddyGeneticFunctionalDrivers2017 FALSE 28985567 LOF 26565811 +RB1 1 FALSE NA morinMutationalStructuralAnalysis2013 FALSE 23699601 LOF 17332242 +RFX7 1 FALSE NA NA arthurGenomewideDiscoverySomatic2018 FALSE NA LOF 30926791 +RHOA 1 FALSE NA zhangGeneticHeterogeneityDiffuse2013 FALSE 23292937 LOF 26616858 +RRAGC 1 FALSE NA okosunRecurrentMTORC1activatingRRAGC2016a FALSE 26691987 GOF 26691987 +S1PR2 1 TRUE NA morinFrequentMutationHistonemodifying2011 TRUE 21796119 LOF 25274307 +SETD1B 1 FALSE NA albuquerqueEnhancingKnowledgeDiscovery2017a TRUE 28327945 LOF 21796119 +SF3B1 1 FALSE NA reddyGeneticFunctionalDrivers2017 FALSE NEO 23160465 +SGK1 1 TRUE NA morinFrequentMutationHistonemodifying2011 TRUE 21796119 GOF 33988691 SIN3A 1 FALSE NA chapuyMolecularSubtypesDiffuse2018b FALSE 29713087 -SMARCA4 1 FALSE NA reddyGeneticFunctionalDrivers2017 FALSE 22343534 -SOCS1 1 TRUE NA morinFrequentMutationHistonemodifying2011 TRUE 21796119 +SMARCA4 1 FALSE NA reddyGeneticFunctionalDrivers2017 FALSE 22343534 LOF 33144586 +SOCS1 1 TRUE NA morinFrequentMutationHistonemodifying2011 TRUE 21796119 LOF 15572583 SPEN 1 FALSE NA albuquerqueEnhancingKnowledgeDiscovery2017a TRUE 28327945 -STAT3 1 FALSE NA morinFrequentMutationHistonemodifying2011 TRUE 22343534 -STAT6 1 FALSE NA yildizActivatingSTAT6Mutations2015c TRUE 25428220 +STAT3 1 FALSE NA morinFrequentMutationHistonemodifying2011 TRUE 22343534 GOF 31861597 +STAT6 1 FALSE NA yildizActivatingSTAT6Mutations2015c TRUE 25428220 GOF 35851155 TAF1 1 FALSE NA morinMutationalStructuralAnalysis2013 FALSE 23699601 -TBL1XR1 1 FALSE NA lohrDiscoveryPrioritizationSomatic2012a TRUE 22343534 -TET2 1 FALSE NA albuquerqueEnhancingKnowledgeDiscovery2017a TRUE 28327945 -TMEM30A 1 FALSE NA morinFrequentMutationHistonemodifying2011 TRUE 21796119 +TBL1XR1 1 FALSE NA lohrDiscoveryPrioritizationSomatic2012a TRUE 22343534 LOF 32619424 +TET2 1 FALSE NA albuquerqueEnhancingKnowledgeDiscovery2017a TRUE 28327945 LOF 23831920 +TMEM30A 1 FALSE NA morinFrequentMutationHistonemodifying2011 TRUE 21796119 LOF 32094924 TMSB4X 1 TRUE NA reddyGeneticFunctionalDrivers2017 FALSE 23292937 -TNFAIP3 1 FALSE NA compagnoMutationsMultipleGenes2009a TRUE 19412164 -TNFRSF14 1 FALSE NA morinFrequentMutationHistonemodifying2011 TRUE 21796119 +TNFAIP3 1 FALSE NA compagnoMutationsMultipleGenes2009a TRUE 19412164 LOF 19412164 +TNFRSF14 1 FALSE NA morinFrequentMutationHistonemodifying2011 TRUE 21796119 LOF 21796119 TOX 1 FALSE NA reddyGeneticFunctionalDrivers2017 TRUE 28985567 -TP53 1 FALSE NA morinFrequentMutationHistonemodifying2011 TRUE 22343534 LOF +TP53 1 FALSE NA morinFrequentMutationHistonemodifying2011 TRUE 22343534 LOF 12826609 UBE2A 1 FALSE NA lohrDiscoveryPrioritizationSomatic2012a TRUE 22343534 WEE1 1 FALSE NA schmitzGeneticsPathogenesisDiffuse2018a TRUE 29641966 -XPO1 1 FALSE NA mareschalWholeExomeSequencing2016 FALSE 26608593 -ZC3H12A 1 FALSE NA chapuyMolecularSubtypesDiffuse2018b FALSE 29713087 +XPO1 1 FALSE NA mareschalWholeExomeSequencing2016 FALSE 26608593 NEO 33007990 +ZC3H12A 1 FALSE NA chapuyMolecularSubtypesDiffuse2018b FALSE 29713087 LOF 19747262 ZFP36L1 1 TRUE NA morinFrequentMutationHistonemodifying2011 TRUE 21796119 ZNF292 1 FALSE NA reddyGeneticFunctionalDrivers2017 FALSE 23292937 ZNF608 1 FALSE NA NA morinMutationalStructuralAnalysis2013 FALSE 23292937