From 28fd9353b95464401d8d65fbc5f628edfce57366 Mon Sep 17 00:00:00 2001 From: rdmorin Date: Tue, 3 Dec 2024 19:30:12 -0800 Subject: [PATCH 01/12] Update Readme.md --- resources/curated/Readme.md | 283 ++++++++++++++++-------------------- 1 file changed, 128 insertions(+), 155 deletions(-) diff --git a/resources/curated/Readme.md b/resources/curated/Readme.md index 314382de..ff2ba2da 100644 --- a/resources/curated/Readme.md +++ b/resources/curated/Readme.md @@ -13,161 +13,134 @@ This file contains four additional columns, which respectively report the mutati -| Gene | curated | aSHM | earliest_support | -|-----------|---------|-------|------------------| -| ACTB | TRUE | TRUE | 22343534 | -| ARID1A | TRUE | FALSE | 23292937 | -| ATM | TRUE | FALSE | 28985567 | -| B2M | TRUE | FALSE | 21796119 | -| BCL10 | TRUE | FALSE | | -| BCL11A | TRUE | TRUE | | -| BCL2 | TRUE | TRUE | | -| BCL6 | TRUE | TRUE | 21796119 | -| BCL7A | TRUE | TRUE | | -| BCOR | TRUE | FALSE | | -| BCR | TRUE | FALSE | | -| BIRC6 | TRUE | FALSE | 28985567 | -| BRAF | TRUE | FALSE | 22343534 | -| BTG1 | TRUE | TRUE | 21796119 | -| BTG2 | TRUE | TRUE | 21796119 | -| BTK | TRUE | FALSE | | -| CARD11 | TRUE | FALSE | 21796119 | -| CASP8 | TRUE | FALSE | 28985567 | -| CCND3 | TRUE | FALSE | 21796119 | -| CD274 | TRUE | FALSE | 21796119 | -| CD36 | TRUE | FALSE | | -| CD58 | TRUE | FALSE | 21796119 | -| CD70 | TRUE | FALSE | 21796119 | -| CD79B | TRUE | FALSE | 21796119 | -| CD83 | TRUE | TRUE | 29641966 | -| CDKN2A | TRUE | FALSE | | -| CIITA | TRUE | TRUE | 21796119 | -| CREBBP | TRUE | FALSE | | -| CXCR4 | TRUE | TRUE | 23131835 | -| DAZAP1 | TRUE | FALSE | | -| DDX3X | TRUE | FALSE | 29641966 | -| DTX1 | TRUE | TRUE | 29641966 | -| DUSP2 | TRUE | TRUE | 28985567 | -| EBF1 | TRUE | TRUE | 23174882 | -| EP300 | TRUE | FALSE | | -| ETS1 | TRUE | TRUE | 21796119 | -| ETV6 | TRUE | TRUE | | -| EZH2 | TRUE | FALSE | 20081860 | -| FAS | TRUE | FALSE | | -| FBXO11 | TRUE | FALSE | | -| FBXW7 | TRUE | FALSE | | -| FOXC1 | TRUE | FALSE | | -| FOXO1 | TRUE | FALSE | 21796119 | -| GNA13 | TRUE | FALSE | 21796119 | -| GNAI2 | TRUE | FALSE | | -| GRHPR | TRUE | TRUE | | -| HIST1H1B | TRUE | TRUE | | -| HIST1H1C | TRUE | TRUE | 21796119 | -| HIST1H1D | TRUE | TRUE | | -| HIST1H1E | TRUE | TRUE | | -| HIST1H2AC | TRUE | TRUE | | -| HIST1H2AM | TRUE | TRUE | | -| HIST1H2BC | TRUE | TRUE | 28985567 | -| HIST1H2BK | TRUE | TRUE | | -| HIST1H3B | TRUE | TRUE | | -| HIST2H2BE | TRUE | TRUE | | -| HLA-A | TRUE | FALSE | | -| HLA-B | TRUE | FALSE | | -| HLA-C | TRUE | FALSE | | -| HLA-DMA | TRUE | FALSE | | -| HLA-DMB | TRUE | FALSE | | -| HNRNPD | TRUE | FALSE | | -| HNRNPH1 | TRUE | FALSE | | -| HNRNPU | TRUE | FALSE | | -| HVCN1 | TRUE | FALSE | | -| ID3 | TRUE | FALSE | 22885699 | -| IL16 | TRUE | FALSE | | -| IL4R | TRUE | TRUE | 33684939 | -| IRF4 | TRUE | TRUE | 21796119 | -| IRF8 | TRUE | TRUE | 21796119 | -| ITPKB | TRUE | TRUE | 29641966 | -| KLF2 | TRUE | TRUE | 29641966 | -| KLHL14 | TRUE | FALSE | 23292937 | -| KLHL6 | TRUE | TRUE | 21796119 | -| KMT2C | TRUE | FALSE | 23292937 | -| KMT2D | TRUE | FALSE | 21796119 | -| KRAS | TRUE | FALSE | 22343534 | -| LCOR | TRUE | FALSE | | -| LTB | TRUE | TRUE | | -| LYN | TRUE | FALSE | | -| MCL1 | TRUE | FALSE | 28985567 | -| MEF2B | TRUE | TRUE | 21796119 | -| MEF2C | TRUE | TRUE | | -| MGA | TRUE | FALSE | 23292937 | -| MPEG1 | TRUE | FALSE | | -| MS4A1 | TRUE | TRUE | | -| MTOR | TRUE | FALSE | 23292937 | -| MYC | TRUE | TRUE | | -| MYD88 | TRUE | FALSE | 21179087 | -| MYOM2 | TRUE | FALSE | | -| NCOR2 | TRUE | FALSE | | -| NFKB1 | TRUE | FALSE | | -| NFKBIA | TRUE | FALSE | | -| NFKBIE | TRUE | FALSE | | -| NFKBIZ | TRUE | TRUE | | -| NLRC5 | TRUE | FALSE | | -| NOL9 | TRUE | FALSE | | -| NOTCH1 | TRUE | FALSE | 22343534 | -| NOTCH2 | TRUE | FALSE | | -| OSBPL10 | TRUE | TRUE | | -| P2RY8 | TRUE | FALSE | 22343534 | -| PCBP1 | TRUE | FALSE | | -| PIM1 | TRUE | TRUE | 11460166 | -| PIM2 | TRUE | TRUE | | -| POU2AF1 | TRUE | TRUE | | -| POU2F2 | TRUE | FALSE | | -| PPP1R9B | TRUE | FALSE | | -| PRDM1 | TRUE | FALSE | | -| PRKDC | TRUE | FALSE | | -| PTEN | TRUE | FALSE | | -| PTPRD | TRUE | FALSE | | -| RB1 | TRUE | FALSE | | -| RFX7 | TRUE | FALSE | | -| RFXAP | TRUE | FALSE | | -| RHOA | TRUE | FALSE | 11460166 | -| RRAGC | TRUE | FALSE | 26691987 | -| S1PR2 | TRUE | TRUE | | -| SETD1B | TRUE | FALSE | | -| SETD2 | TRUE | FALSE | | -| SF3B1 | TRUE | FALSE | | -| SGK1 | TRUE | TRUE | 21796119 | -| SIN3A | TRUE | FALSE | | -| SMARCA4 | TRUE | FALSE | 23292937 | -| SOCS1 | TRUE | TRUE | | -| SPEN | TRUE | FALSE | | -| STAT3 | TRUE | FALSE | | -| STAT6 | TRUE | FALSE | | -| TBL1XR1 | TRUE | FALSE | | -| TCL1A | TRUE | TRUE | | -| TET2 | TRUE | FALSE | | -| TMEM30A | TRUE | FALSE | 21796119 | -| TMSB4X | TRUE | TRUE | | -| TNFAIP3 | TRUE | FALSE | | -| TNFRSF14 | TRUE | FALSE | 20884631 | -| TOX | TRUE | FALSE | | -| TP53 | TRUE | FALSE | | -| TRAF3 | TRUE | FALSE | | -| TRIP12 | TRUE | FALSE | | -| TRRAP | TRUE | FALSE | | -| UBE2A | TRUE | FALSE | | -| UNC5C | TRUE | FALSE | | -| UNC5D | TRUE | FALSE | | -| USP7 | TRUE | FALSE | | -| VPS13B | TRUE | FALSE | | -| WEE1 | TRUE | FALSE | | -| XBP1 | TRUE | FALSE | | -| XPO1 | TRUE | FALSE | 26608593 | -| ZC3H12A | TRUE | FALSE | | -| ZFP36L1 | TRUE | TRUE | | -| ZNF292 | TRUE | FALSE | 23292937 | -| CXCR5 | TRUE | FALSE | 29641966 | -| TAP1 | TRUE | FALSE | 29641966 | - +|Gene|Tier|aSHM|QC|Mean|variant|quality|citekey|PMID|MutationEffect|Mutation-PMID|MutationEffect-citekey|LymphGen| +|:-:|:-:|:-:|:-:|:-:|:-:|:-:|:-:|:-:|:-:|:-:|:-:| +|ACTB|1|TRUE|NA|lohrDiscoveryPrioritizationSomatic2012|22343534|TRUE| +|ACTG1|1|TRUE|NA|fanComprehensiveCharacterizationDriver2020|32565964|FALSE| +|ARID1A|1|FALSE|NA|zhangGeneticHeterogeneityDiffuse2013|23292937|LOF|38458187|barisicARID1AOrchestratesSWI2024|TRUE| +|ATM|1|FALSE|NA|reddyGeneticFunctionalDrivers2017|28985567|LOF|11756177|camachoATMGeneInactivation2002|FALSE| +|B2M|1|FALSE|NA|morinFrequentMutationHistonemodifying2011|21796119|LOF|22137796|challa-malladiCombinedGeneticInactivation2011|FALSE| +|BCL10|1|FALSE|NA|morinFrequentMutationHistonemodifying2011|21796119|GOF|35658124|xiaBCL10MutationsDefine2022|TRUE| +|BCL2|1|TRUE|NA|tanakaFrequentIncidenceSomatic1992|1339299|TRUE| +|BCL6|1|TRUE|NA|morinFrequentMutationHistonemodifying2011|21796119|LOF|12504096|masclePointMutationsBCL62003|TRUE| +|BCL7A|1|TRUE|NA|morinFrequentMutationHistonemodifying2011|21796119|LOF|32576963|balinas-gaviraFrequentMutationsAminoterminal2020|FALSE| +|BIRC6|1|FALSE|NA|reddyGeneticFunctionalDrivers2017|28985567|FALSE| +|BRAF|1|FALSE|NA|tiacciBRAFMutationsHairycell2011|22343534|LOF|15035987|wanMechanismActivationRAFERK2004|FALSE| +|BTG1|1|TRUE|NA|morinFrequentMutationHistonemodifying2011|21796119|LOF|33021411|almasmoumFrequentLossBTG12021|TRUE| +|BTG2|1|TRUE|NA|morinFrequentMutationHistonemodifying2011|21796119|TRUE| +|BTK|1|FALSE|NA|albuquerqueEnhancingKnowledgeDiscovery2017|28327945|LOF|33419778|huFollicularLymphomaassociatedBTK2021|FALSE| +|CARD11|1|FALSE|NA|lenzOncogenicCARD11Mutations2008|18323416|GOF|18323416|lenzOncogenicCARD11Mutations2008|FALSE| +|CCND3|1|FALSE|NA|morinFrequentMutationHistonemodifying2011|21796119|GOF|22885699|schmitzBurkittLymphomaPathogenesis2012|FALSE| +|CD58|1|FALSE|NA|morinFrequentMutationHistonemodifying2011|21796119|LOF|22137796|challa-malladiCombinedGeneticInactivation2011|TRUE| +|CD70|1|FALSE|NA|morinFrequentMutationHistonemodifying2011|21796119|LOF|36471481|nieDualRoleCD702022|TRUE| +|CD79B|1|FALSE|NA|davisChronicActiveBcellreceptor2010|20054396|GOF|20054396|davisChronicActiveBcellreceptor2010|TRUE| +|CD83|1|TRUE|NA|morinMutationalStructuralAnalysis2013|23699601|TRUE| +|CDKN2A|1|FALSE|NA|morinMutationalStructuralAnalysis2013|23699601|LOF|19260062|kannengiesserFunctionalStructuralGenetic2009|TRUE| +|CIITA|1|TRUE|NA|morinFrequentMutationHistonemodifying2011|21796119|LOF|26549456|mottokGenomicAlterationsCIITA2015|TRUE| +|CREBBP|1|FALSE|NA|pasqualucciInactivatingMutationsAcetyltransferase2011|21390126|LOF|21390126|pasqualucciInactivatingMutationsAcetyltransferase2011|TRUE| +|CXCR4|1|TRUE|NA|khodabakhshiRecurrentTargetsAberrant2012|23131835|LOF|36089616|zmajkovicovaGenotypephenotypeCorrelationsWHIM2022|FALSE| +|DDX3X|1|FALSE|NA|reddyGeneticFunctionalDrivers2017|28985567|LOF|34437837|gongSequentialInverseDysregulation2021|TRUE| +|DTX1|1|TRUE|NA|zhangGeneticHeterogeneityDiffuse2013|23292937|TRUE| +|DUSP2|1|TRUE|NA|lohrDiscoveryPrioritizationSomatic2012|22343534|TRUE| +|EBF1|1|TRUE|NA|bohleRoleEarlyBcell2013|23174882|LOF|28692033|ramirez-komoSpontaneousLossLineage2017|FALSE| +|EEF1A1|1|FALSE|NA|chapuyMolecularSubtypesDiffuse2018|29713087|FALSE| +|EP300|1|FALSE|NA|pasqualucciInactivatingMutationsAcetyltransferase2011|21390126|LOF|21390126|pasqualucciInactivatingMutationsAcetyltransferase2011|TRUE| +|ETS1|1|TRUE|NA|morinFrequentMutationHistonemodifying2011|21796119|TRUE| +|ETV6|1|TRUE|NA|lohrDiscoveryPrioritizationSomatic2012|22343534|LOF|24997145|wangETV6MutationCohort2014|TRUE| +|EZH2|1|FALSE|NA|NA|morinSomaticMutationsAltering2010|20081860|GOF|21078963|sneeringerCoordinatedActivitiesWildtype2010|TRUE| +|FAS|1|FALSE|NA|schollMutationsRegionFAS2007|17487740|LOF|20935634|wangFasFADDDeathDomain2010|FALSE| +|FBXO11|1|FALSE|NA|arthurGenomewideDiscoverySomatic2018|30275490|LOF|22113614|duanFBXO11TargetsBCL62011|FALSE| +|FBXW7|1|FALSE|NA|zhangGeneticHeterogeneityDiffuse2013|23292937|LOF|32350066|saffieFBXW7TriggersDegradation2020|FALSE| +|FOXO1|1|FALSE|NA|morinFrequentMutationHistonemodifying2011|21796119|GOF|23460611|trinhAnalysisFOXO1Mutations|FALSE| +|GNA13|1|FALSE|NA|morinFrequentMutationHistonemodifying2011|21796119|LOF|25274307|muppidiLossSignalingGa132014|FALSE| +|GNAI2|1|FALSE|NA|morinMutationalStructuralAnalysis2013|23699601|GOF|25274307|muppidiLossSignalingGa132014|FALSE| +|GRB2|1|FALSE|NA|pasqualucciAnalysisCodingGenome2011|21804550|FALSE| +|GRHPR|1|TRUE|NA|schmitzGeneticsPathogenesisDiffuse2018|29641966|TRUE| +|HIST1H1B|1|TRUE|NA|chapuyMolecularSubtypesDiffuse2018|29713087|FALSE| +|HIST1H1C|1|TRUE|NA|morinFrequentMutationHistonemodifying2011|21796119|FALSE| +|HIST1H1D|1|TRUE|NA|morinMutationalStructuralAnalysis2013|23699601|FALSE| +|HIST1H1E|1|TRUE|NA|lohrDiscoveryPrioritizationSomatic2012|22343534|FALSE| +|HIST1H2AC|1|TRUE|NA|morinMutationalStructuralAnalysis2013|23699601|FALSE| +|HIST1H2AM|1|TRUE|NA|chapuyMolecularSubtypesDiffuse2018|29713087|FALSE| +|HIST1H2BC|1|TRUE|NA|lohrDiscoveryPrioritizationSomatic2012|22343534|FALSE| +|HIST1H2BK|1|TRUE|NA|zhangGeneticHeterogeneityDiffuse2013|23292937|FALSE| +|HIST1H3B|1|TRUE|NA|lohrDiscoveryPrioritizationSomatic2012|22343534|FALSE| +|HIST2H2BE|1|TRUE|NA|chapuyMolecularSubtypesDiffuse2018|29713087|FALSE| +|HLA-A|1|FALSE|NA|lohrDiscoveryPrioritizationSomatic2012|22343534|LOF|34050029|fangazioGeneticMechanismsHLAI2021|TRUE| +|HLA-B|1|FALSE|NA|lohrDiscoveryPrioritizationSomatic2012|22343534|LOF|34050029|fangazioGeneticMechanismsHLAI2021|TRUE| +|HLA-C|1|FALSE|NA|chapuyMolecularSubtypesDiffuse2018|29713087|LOF|34050029|fangazioGeneticMechanismsHLAI2021|FALSE| +|HLA-DMB|1|FALSE|NA|hubschmannMutationalMechanismsShaping2021|33953289|FALSE| +|HNRNPU|1|FALSE|NA|reddyGeneticFunctionalDrivers2017|28985567|FALSE| +|HVCN1|1|FALSE|NA|chapuyMolecularSubtypesDiffuse2018|29713087|FALSE| +|IKZF3|1|FALSE|NA|morinFrequentMutationHistonemodifying2011|21796119|GOF|33689703|lazarianHotspotMutationTranscription2021|FALSE| +|IL4R|1|TRUE|NA|dunsCharacterizationDLBCLPMBL2021|33684939|GOF|29467182|viganoSomaticIL4RMutations2018|FALSE| +|IRF4|1|TRUE|NA|morinFrequentMutationHistonemodifying2011|21796119|TRUE| +|IRF8|1|TRUE|NA|morinFrequentMutationHistonemodifying2011|21796119|LOF|38996030|qiuIRF8mutantCellLymphoma2024|TRUE| +|ITPKB|1|TRUE|NA|schmitzGeneticsPathogenesisDiffuse2018|29641966|LOF|29650799|tiacciPervasiveMutationsJAKSTAT2018|TRUE| +|JUNB|1|FALSE|PASS|3|lohrDiscoveryPrioritizationSomatic2012|22343534|TRUE| +|KLF2|1|TRUE|NA|pasqualucciAnalysisCodingGenome2011|21804550|TRUE| +|KLHL14|1|FALSE|NA|zhangGeneticHeterogeneityDiffuse2013|23292937|LOF|32127472|choiRegulationCellReceptordependent2020|TRUE| +|KLHL6|1|TRUE|NA|morinFrequentMutationHistonemodifying2011|21796119|LOF|29695787|choiLossKLHL6Promotes2018|FALSE| +|KMT2C|1|FALSE|NA|zhangGeneticHeterogeneityDiffuse2013|23292937|FALSE| +|KMT2D|1|FALSE|NA|morinFrequentMutationHistonemodifying2011|21796119|LOF|26366712|zhangDisruptionKMT2DPerturbs2015|TRUE| +|KRAS|1|FALSE|NA|lohrDiscoveryPrioritizationSomatic2012|22343534|GOF|9219684|scheffzekRasRasGAPComplexStructural1997|FALSE| +|LRRN3|1|FALSE|NA|zhangGeneticHeterogeneityDiffuse2013|23292937|FALSE| +|LTB|1|TRUE|NA|chapuyMolecularSubtypesDiffuse2018|29713087|FALSE| +|MEF2B|1|TRUE|NA|morinFrequentMutationHistonemodifying2011|21796119|NEO|23974956;|26245647|ponMEF2BMutationsNonHodgkin2015|TRUE| +|MEF2C|1|TRUE|NA|hubschmannMutationalMechanismsShaping2021|33953289|FALSE| +|MGA|1|FALSE|NA|reddyGeneticFunctionalDrivers2017|28985567|LOF|23039309|depaoliMGASuppressorMYC2013|FALSE| +|MIR142|1|TRUE|NA|kwanhianMicroRNA142Mutated202012|23342264|LOF|29724719|trissalMIR142LossofFunctionMutations2018|FALSE| +|MPEG1|1|FALSE|NA|morinMutationalStructuralAnalysis2013|23699601|TRUE| +|MS4A1|1|TRUE|NA|rushtonGeneticEvolutionaryPatterns2020|32589730|LOF|32589730|rushtonGeneticEvolutionaryPatterns2020|FALSE| +|MTOR|1|FALSE|NA|zhangGeneticHeterogeneityDiffuse2013|23292937|GOF|24631838|grabinerDiverseArrayCancerassociated2014|FALSE| +|MYC|1|TRUE|NA|pasqualucciHypermutationMultipleProtooncogenes2001|11460166|GOF|38565249|freieGermlinePointMutation2024|FALSE| +|MYD88|1|FALSE|NA|ngoOncogenicallyActiveMYD882011|21179087|GOF|21179087|ngoOncogenicallyActiveMYD882011|TRUE| +|NFKBIA|1|FALSE|NA|thomasMutationalAnalysisIkappaBalpha2004|15198731|LOF|10637284|jungnickelClonalDeleteriousMutations2000|TRUE| +|NFKBIE|1|FALSE|NA|morinGeneticLandscapesRelapsed2016|26647218|LOF|25987724|mansouriFunctionalLossIkBe2015|FALSE| +|NFKBIZ|1|TRUE|NA|morinGeneticLandscapesRelapsed2016|26647218|GOF|302754900|arthurGenomewideDiscoverySomatic2018|FALSE| +|NOL9|1|FALSE|NA|schmitzGeneticsPathogenesisDiffuse2018|29641966|TRUE| +|NOTCH1|1|FALSE|NA|pasqualucciAnalysisCodingGenome2011|21804550|GOF|29045844|ryanCellRegulomeLinks2017|TRUE| +|NOTCH2|1|FALSE|NA|zhangGeneticHeterogeneityDiffuse2013|23292937|GOF|19445024|leeGainoffunctionMutationsCopy2009|TRUE| +|OSBPL10|1|TRUE|NA|zhangGeneticHeterogeneityDiffuse2013|23292937|TRUE| +|P2RY8|1|FALSE|NA|lohrDiscoveryPrioritizationSomatic2012|22343534|LOF|25274307|muppidiLossSignalingGa132014|FALSE| +|PIM1|1|TRUE|NA|pasqualucciHypermutationMultipleProtooncogenes2001|11460166|GOF|27904766|kuoRolePIM1Ibrutinibresistant2016|TRUE| +|PIM2|1|TRUE|NA|reddyGeneticFunctionalDrivers2017|28985567|TRUE| +|POU2AF1|1|TRUE|NA|chapuyMolecularSubtypesDiffuse2018|29713087|LOF|30802265|gonzalez-rinconUnravelingTransformationFollicular2019|FALSE| +|POU2F2|1|FALSE|NA|lohrDiscoveryPrioritizationSomatic2012|22343534|LOF|26993806|hodsonRegulationNormalBcell2016|FALSE| +|PRDM1|1|FALSE|NA|pasqualucciInactivationPRDM1BLIMP12006|NA|LOF|16492805|pasqualucciInactivationPRDM1BLIMP12006|TRUE| +|PTEN|1|FALSE|NA|reddyGeneticFunctionalDrivers2017|28985567|LOF|23840064|pfeiferPTENLossDefines2013|FALSE| +|PTPN6|1|FALSE|PASS|3|reddyGeneticFunctionalDrivers2017|28985567|LOF|26565811|demosthenousLossFunctionMutations2015|FALSE| +|RB1|1|FALSE|NA|morinMutationalStructuralAnalysis2013|23699601|LOF|17332242|pinyolInactivationRB1Mantlecell2007|FALSE| +|RFX7|1|FALSE|NA|NA|arthurGenomewideDiscoverySomatic2018|30275490|LOF|30926791|weberPiggyBacTransposonTools2019|FALSE| +|RHOA|1|FALSE|NA|zhangGeneticHeterogeneityDiffuse2013|23292937|LOF|26616858|ohayreInactivatingMutationsGNA132016|FALSE| +|RRAGC|1|FALSE|NA|okosunRecurrentMTORC1activatingRRAGC2016|26691987|GOF|26691987|okosunRecurrentMTORC1activatingRRAGC2016|FALSE| +|S1PR2|1|TRUE|NA|morinFrequentMutationHistonemodifying2011|21796119|LOF|25274307|muppidiLossSignalingGa132014|TRUE| +|SETD1B|1|FALSE|NA|albuquerqueEnhancingKnowledgeDiscovery2017|28327945|LOF|TBD|TRUE| +|SF3B1|1|FALSE|NA|reddyGeneticFunctionalDrivers2017|28985567|NEO|23160465|cazzolaBiologicClinicalSignificance2013|FALSE| +|SGK1|1|TRUE|NA|morinFrequentMutationHistonemodifying2011|21796119|GOF|33988691|gaoSGK1MutationsDLBCL2021|TRUE| +|SIN3A|1|FALSE|NA|chapuyMolecularSubtypesDiffuse2018|29713087|FALSE| +|SMARCA4|1|FALSE|NA|reddyGeneticFunctionalDrivers2017|28985567|LOF|33144586|fernandoFunctionalCharacterizationSMARCA42020|FALSE| +|SOCS1|1|TRUE|NA|morinFrequentMutationHistonemodifying2011|21796119|LOF|15572583|melznerBiallelicMutationSOCS12005|TRUE| +|SPEN|1|FALSE|NA|albuquerqueEnhancingKnowledgeDiscovery2017|28327945|TRUE| +|STAT3|1|FALSE|NA|morinFrequentMutationHistonemodifying2011|21796119|GOF|23861822|huNovelMissenseM206K2013|TRUE| +|STAT6|1|FALSE|NA|yildizActivatingSTAT6Mutations2015|25428220|GOF|35851155|mentzPARP14NovelTarget2022|TRUE| +|TAF1|1|FALSE|NA|morinMutationalStructuralAnalysis2013|23699601|FALSE| +|TBL1XR1|1|FALSE|NA|lohrDiscoveryPrioritizationSomatic2012|22343534|LOF|32619424|venturuttiTBL1XR1MutationsDrive2020|TRUE| +|TET2|1|FALSE|NA|albuquerqueEnhancingKnowledgeDiscovery2017|28327945|LOF|23831920|asmarGenomewideProfilingIdentifies2013|TRUE| +|TMEM30A|1|FALSE|NA|morinFrequentMutationHistonemodifying2011|21796119|LOF|32094924|ennishiTMEM30ALossoffunctionMutations2020|TRUE| +|TMSB4X|1|TRUE|NA|reddyGeneticFunctionalDrivers2017|28985567|FALSE| +|TNFAIP3|1|FALSE|NA|compagnoMutationsMultipleGenes2009|19412164|LOF|19412164|compagnoMutationsMultipleGenes2009|TRUE| +|TNFRSF14|1|FALSE|NA|morinFrequentMutationHistonemodifying2011|21796119|LOF|TBD|TRUE| +|TOX|1|FALSE|NA|reddyGeneticFunctionalDrivers2017|28985567|TRUE| +|TP53|1|FALSE|NA|morinFrequentMutationHistonemodifying2011|21796119|LOF|12826609|katoUnderstandingFunctionstructureFunctionmutation2003|TRUE| +|UBE2A|1|FALSE|NA|lohrDiscoveryPrioritizationSomatic2012|22343534|TRUE| +|WEE1|1|FALSE|NA|schmitzGeneticsPathogenesisDiffuse2018|29641966|TRUE| +|XPO1|1|FALSE|NA|mareschalWholeExomeSequencing2016|26608593|NEO|33007990|miloudiXPO1E571KMutationModifies2020|FALSE| +|ZC3H12A|1|FALSE|NA|chapuyMolecularSubtypesDiffuse2018|29713087|LOF|19747262|skalniakRegulatoryFeedbackLoop2009|FALSE| +|ZFP36L1|1|TRUE|NA|morinFrequentMutationHistonemodifying2011|21796119|TRUE| +|ZNF292|1|FALSE|NA|reddyGeneticFunctionalDrivers2017|28985567|FALSE| +|ZNF608|1|FALSE|NA|NA|morinMutationalStructuralAnalysis2013|23699601|FALSE| +|LCOR|1|FALSE|NA|novakWholeexomeAnalysisReveals2015|26314988|FALSE| ### Burkitt lymphoma The master curated list for BL including DLBCL genes that have been scrutinized within BL is can be found in `bl_genes.tsv` (or [here](bl_genes.tsv)). The earliest_support_BL column indicates the PubMed ID of the first study to nominate this gene as mutated in BL (or NA when not applicable). The frequency_BL_Thomas and frequency_BL_Panea columns report the percentage of patient samples with at least one non-silent mutation in this gene in the two studies. In the case of Panea et al, these numbers are based on the reanalysis of the exome data from this study by the Morin lab (as detailed in Dreval et al). The original frequencies based on the mutation calls from Panea et al are in the frequency_BL_Panea_original column. From b781e61642c40f1a1f0f8d2e2aa9e9554510b0ff Mon Sep 17 00:00:00 2001 From: rdmorin Date: Tue, 3 Dec 2024 19:30:43 -0800 Subject: [PATCH 02/12] Update Readme.md --- resources/curated/Readme.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/resources/curated/Readme.md b/resources/curated/Readme.md index ff2ba2da..72d40682 100644 --- a/resources/curated/Readme.md +++ b/resources/curated/Readme.md @@ -13,7 +13,7 @@ This file contains four additional columns, which respectively report the mutati -|Gene|Tier|aSHM|QC|Mean|variant|quality|citekey|PMID|MutationEffect|Mutation-PMID|MutationEffect-citekey|LymphGen| +|Gene|Tier|aSHM|QC|Mean variant quality|citekey|PMID|MutationEffect|Mutation-PMID|MutationEffect-citekey|LymphGen| |:-:|:-:|:-:|:-:|:-:|:-:|:-:|:-:|:-:|:-:|:-:|:-:| |ACTB|1|TRUE|NA|lohrDiscoveryPrioritizationSomatic2012|22343534|TRUE| |ACTG1|1|TRUE|NA|fanComprehensiveCharacterizationDriver2020|32565964|FALSE| From 5ee426d9deba99bc06559068767910b75ddfb85e Mon Sep 17 00:00:00 2001 From: rdmorin Date: Tue, 3 Dec 2024 19:31:09 -0800 Subject: [PATCH 03/12] Update Readme.md --- resources/curated/Readme.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/resources/curated/Readme.md b/resources/curated/Readme.md index 72d40682..5d7e545a 100644 --- a/resources/curated/Readme.md +++ b/resources/curated/Readme.md @@ -14,7 +14,7 @@ This file contains four additional columns, which respectively report the mutati |Gene|Tier|aSHM|QC|Mean variant quality|citekey|PMID|MutationEffect|Mutation-PMID|MutationEffect-citekey|LymphGen| -|:-:|:-:|:-:|:-:|:-:|:-:|:-:|:-:|:-:|:-:|:-:|:-:| +|:-:|:-:|:-:|:-:|:-:|:-:|:-:|:-:|:-:|:-:|:-:| |ACTB|1|TRUE|NA|lohrDiscoveryPrioritizationSomatic2012|22343534|TRUE| |ACTG1|1|TRUE|NA|fanComprehensiveCharacterizationDriver2020|32565964|FALSE| |ARID1A|1|FALSE|NA|zhangGeneticHeterogeneityDiffuse2013|23292937|LOF|38458187|barisicARID1AOrchestratesSWI2024|TRUE| From d65454f41916f10325bcbb39a7726ae1d1aa6446 Mon Sep 17 00:00:00 2001 From: rdmorin Date: Tue, 3 Dec 2024 19:33:32 -0800 Subject: [PATCH 04/12] Update Readme.md --- resources/curated/Readme.md | 256 ++++++++++++++++++------------------ 1 file changed, 129 insertions(+), 127 deletions(-) diff --git a/resources/curated/Readme.md b/resources/curated/Readme.md index 5d7e545a..bd7ccd48 100644 --- a/resources/curated/Readme.md +++ b/resources/curated/Readme.md @@ -14,133 +14,135 @@ This file contains four additional columns, which respectively report the mutati |Gene|Tier|aSHM|QC|Mean variant quality|citekey|PMID|MutationEffect|Mutation-PMID|MutationEffect-citekey|LymphGen| -|:-:|:-:|:-:|:-:|:-:|:-:|:-:|:-:|:-:|:-:|:-:| -|ACTB|1|TRUE|NA|lohrDiscoveryPrioritizationSomatic2012|22343534|TRUE| -|ACTG1|1|TRUE|NA|fanComprehensiveCharacterizationDriver2020|32565964|FALSE| -|ARID1A|1|FALSE|NA|zhangGeneticHeterogeneityDiffuse2013|23292937|LOF|38458187|barisicARID1AOrchestratesSWI2024|TRUE| -|ATM|1|FALSE|NA|reddyGeneticFunctionalDrivers2017|28985567|LOF|11756177|camachoATMGeneInactivation2002|FALSE| -|B2M|1|FALSE|NA|morinFrequentMutationHistonemodifying2011|21796119|LOF|22137796|challa-malladiCombinedGeneticInactivation2011|FALSE| -|BCL10|1|FALSE|NA|morinFrequentMutationHistonemodifying2011|21796119|GOF|35658124|xiaBCL10MutationsDefine2022|TRUE| -|BCL2|1|TRUE|NA|tanakaFrequentIncidenceSomatic1992|1339299|TRUE| -|BCL6|1|TRUE|NA|morinFrequentMutationHistonemodifying2011|21796119|LOF|12504096|masclePointMutationsBCL62003|TRUE| -|BCL7A|1|TRUE|NA|morinFrequentMutationHistonemodifying2011|21796119|LOF|32576963|balinas-gaviraFrequentMutationsAminoterminal2020|FALSE| -|BIRC6|1|FALSE|NA|reddyGeneticFunctionalDrivers2017|28985567|FALSE| -|BRAF|1|FALSE|NA|tiacciBRAFMutationsHairycell2011|22343534|LOF|15035987|wanMechanismActivationRAFERK2004|FALSE| -|BTG1|1|TRUE|NA|morinFrequentMutationHistonemodifying2011|21796119|LOF|33021411|almasmoumFrequentLossBTG12021|TRUE| -|BTG2|1|TRUE|NA|morinFrequentMutationHistonemodifying2011|21796119|TRUE| -|BTK|1|FALSE|NA|albuquerqueEnhancingKnowledgeDiscovery2017|28327945|LOF|33419778|huFollicularLymphomaassociatedBTK2021|FALSE| -|CARD11|1|FALSE|NA|lenzOncogenicCARD11Mutations2008|18323416|GOF|18323416|lenzOncogenicCARD11Mutations2008|FALSE| -|CCND3|1|FALSE|NA|morinFrequentMutationHistonemodifying2011|21796119|GOF|22885699|schmitzBurkittLymphomaPathogenesis2012|FALSE| -|CD58|1|FALSE|NA|morinFrequentMutationHistonemodifying2011|21796119|LOF|22137796|challa-malladiCombinedGeneticInactivation2011|TRUE| -|CD70|1|FALSE|NA|morinFrequentMutationHistonemodifying2011|21796119|LOF|36471481|nieDualRoleCD702022|TRUE| -|CD79B|1|FALSE|NA|davisChronicActiveBcellreceptor2010|20054396|GOF|20054396|davisChronicActiveBcellreceptor2010|TRUE| -|CD83|1|TRUE|NA|morinMutationalStructuralAnalysis2013|23699601|TRUE| -|CDKN2A|1|FALSE|NA|morinMutationalStructuralAnalysis2013|23699601|LOF|19260062|kannengiesserFunctionalStructuralGenetic2009|TRUE| -|CIITA|1|TRUE|NA|morinFrequentMutationHistonemodifying2011|21796119|LOF|26549456|mottokGenomicAlterationsCIITA2015|TRUE| -|CREBBP|1|FALSE|NA|pasqualucciInactivatingMutationsAcetyltransferase2011|21390126|LOF|21390126|pasqualucciInactivatingMutationsAcetyltransferase2011|TRUE| -|CXCR4|1|TRUE|NA|khodabakhshiRecurrentTargetsAberrant2012|23131835|LOF|36089616|zmajkovicovaGenotypephenotypeCorrelationsWHIM2022|FALSE| -|DDX3X|1|FALSE|NA|reddyGeneticFunctionalDrivers2017|28985567|LOF|34437837|gongSequentialInverseDysregulation2021|TRUE| -|DTX1|1|TRUE|NA|zhangGeneticHeterogeneityDiffuse2013|23292937|TRUE| -|DUSP2|1|TRUE|NA|lohrDiscoveryPrioritizationSomatic2012|22343534|TRUE| -|EBF1|1|TRUE|NA|bohleRoleEarlyBcell2013|23174882|LOF|28692033|ramirez-komoSpontaneousLossLineage2017|FALSE| -|EEF1A1|1|FALSE|NA|chapuyMolecularSubtypesDiffuse2018|29713087|FALSE| -|EP300|1|FALSE|NA|pasqualucciInactivatingMutationsAcetyltransferase2011|21390126|LOF|21390126|pasqualucciInactivatingMutationsAcetyltransferase2011|TRUE| -|ETS1|1|TRUE|NA|morinFrequentMutationHistonemodifying2011|21796119|TRUE| -|ETV6|1|TRUE|NA|lohrDiscoveryPrioritizationSomatic2012|22343534|LOF|24997145|wangETV6MutationCohort2014|TRUE| -|EZH2|1|FALSE|NA|NA|morinSomaticMutationsAltering2010|20081860|GOF|21078963|sneeringerCoordinatedActivitiesWildtype2010|TRUE| -|FAS|1|FALSE|NA|schollMutationsRegionFAS2007|17487740|LOF|20935634|wangFasFADDDeathDomain2010|FALSE| -|FBXO11|1|FALSE|NA|arthurGenomewideDiscoverySomatic2018|30275490|LOF|22113614|duanFBXO11TargetsBCL62011|FALSE| -|FBXW7|1|FALSE|NA|zhangGeneticHeterogeneityDiffuse2013|23292937|LOF|32350066|saffieFBXW7TriggersDegradation2020|FALSE| -|FOXO1|1|FALSE|NA|morinFrequentMutationHistonemodifying2011|21796119|GOF|23460611|trinhAnalysisFOXO1Mutations|FALSE| -|GNA13|1|FALSE|NA|morinFrequentMutationHistonemodifying2011|21796119|LOF|25274307|muppidiLossSignalingGa132014|FALSE| -|GNAI2|1|FALSE|NA|morinMutationalStructuralAnalysis2013|23699601|GOF|25274307|muppidiLossSignalingGa132014|FALSE| -|GRB2|1|FALSE|NA|pasqualucciAnalysisCodingGenome2011|21804550|FALSE| -|GRHPR|1|TRUE|NA|schmitzGeneticsPathogenesisDiffuse2018|29641966|TRUE| -|HIST1H1B|1|TRUE|NA|chapuyMolecularSubtypesDiffuse2018|29713087|FALSE| -|HIST1H1C|1|TRUE|NA|morinFrequentMutationHistonemodifying2011|21796119|FALSE| -|HIST1H1D|1|TRUE|NA|morinMutationalStructuralAnalysis2013|23699601|FALSE| -|HIST1H1E|1|TRUE|NA|lohrDiscoveryPrioritizationSomatic2012|22343534|FALSE| -|HIST1H2AC|1|TRUE|NA|morinMutationalStructuralAnalysis2013|23699601|FALSE| -|HIST1H2AM|1|TRUE|NA|chapuyMolecularSubtypesDiffuse2018|29713087|FALSE| -|HIST1H2BC|1|TRUE|NA|lohrDiscoveryPrioritizationSomatic2012|22343534|FALSE| -|HIST1H2BK|1|TRUE|NA|zhangGeneticHeterogeneityDiffuse2013|23292937|FALSE| -|HIST1H3B|1|TRUE|NA|lohrDiscoveryPrioritizationSomatic2012|22343534|FALSE| -|HIST2H2BE|1|TRUE|NA|chapuyMolecularSubtypesDiffuse2018|29713087|FALSE| -|HLA-A|1|FALSE|NA|lohrDiscoveryPrioritizationSomatic2012|22343534|LOF|34050029|fangazioGeneticMechanismsHLAI2021|TRUE| -|HLA-B|1|FALSE|NA|lohrDiscoveryPrioritizationSomatic2012|22343534|LOF|34050029|fangazioGeneticMechanismsHLAI2021|TRUE| -|HLA-C|1|FALSE|NA|chapuyMolecularSubtypesDiffuse2018|29713087|LOF|34050029|fangazioGeneticMechanismsHLAI2021|FALSE| -|HLA-DMB|1|FALSE|NA|hubschmannMutationalMechanismsShaping2021|33953289|FALSE| -|HNRNPU|1|FALSE|NA|reddyGeneticFunctionalDrivers2017|28985567|FALSE| -|HVCN1|1|FALSE|NA|chapuyMolecularSubtypesDiffuse2018|29713087|FALSE| -|IKZF3|1|FALSE|NA|morinFrequentMutationHistonemodifying2011|21796119|GOF|33689703|lazarianHotspotMutationTranscription2021|FALSE| -|IL4R|1|TRUE|NA|dunsCharacterizationDLBCLPMBL2021|33684939|GOF|29467182|viganoSomaticIL4RMutations2018|FALSE| -|IRF4|1|TRUE|NA|morinFrequentMutationHistonemodifying2011|21796119|TRUE| -|IRF8|1|TRUE|NA|morinFrequentMutationHistonemodifying2011|21796119|LOF|38996030|qiuIRF8mutantCellLymphoma2024|TRUE| -|ITPKB|1|TRUE|NA|schmitzGeneticsPathogenesisDiffuse2018|29641966|LOF|29650799|tiacciPervasiveMutationsJAKSTAT2018|TRUE| -|JUNB|1|FALSE|PASS|3|lohrDiscoveryPrioritizationSomatic2012|22343534|TRUE| -|KLF2|1|TRUE|NA|pasqualucciAnalysisCodingGenome2011|21804550|TRUE| -|KLHL14|1|FALSE|NA|zhangGeneticHeterogeneityDiffuse2013|23292937|LOF|32127472|choiRegulationCellReceptordependent2020|TRUE| -|KLHL6|1|TRUE|NA|morinFrequentMutationHistonemodifying2011|21796119|LOF|29695787|choiLossKLHL6Promotes2018|FALSE| -|KMT2C|1|FALSE|NA|zhangGeneticHeterogeneityDiffuse2013|23292937|FALSE| -|KMT2D|1|FALSE|NA|morinFrequentMutationHistonemodifying2011|21796119|LOF|26366712|zhangDisruptionKMT2DPerturbs2015|TRUE| -|KRAS|1|FALSE|NA|lohrDiscoveryPrioritizationSomatic2012|22343534|GOF|9219684|scheffzekRasRasGAPComplexStructural1997|FALSE| -|LRRN3|1|FALSE|NA|zhangGeneticHeterogeneityDiffuse2013|23292937|FALSE| -|LTB|1|TRUE|NA|chapuyMolecularSubtypesDiffuse2018|29713087|FALSE| -|MEF2B|1|TRUE|NA|morinFrequentMutationHistonemodifying2011|21796119|NEO|23974956;|26245647|ponMEF2BMutationsNonHodgkin2015|TRUE| -|MEF2C|1|TRUE|NA|hubschmannMutationalMechanismsShaping2021|33953289|FALSE| -|MGA|1|FALSE|NA|reddyGeneticFunctionalDrivers2017|28985567|LOF|23039309|depaoliMGASuppressorMYC2013|FALSE| -|MIR142|1|TRUE|NA|kwanhianMicroRNA142Mutated202012|23342264|LOF|29724719|trissalMIR142LossofFunctionMutations2018|FALSE| -|MPEG1|1|FALSE|NA|morinMutationalStructuralAnalysis2013|23699601|TRUE| -|MS4A1|1|TRUE|NA|rushtonGeneticEvolutionaryPatterns2020|32589730|LOF|32589730|rushtonGeneticEvolutionaryPatterns2020|FALSE| -|MTOR|1|FALSE|NA|zhangGeneticHeterogeneityDiffuse2013|23292937|GOF|24631838|grabinerDiverseArrayCancerassociated2014|FALSE| -|MYC|1|TRUE|NA|pasqualucciHypermutationMultipleProtooncogenes2001|11460166|GOF|38565249|freieGermlinePointMutation2024|FALSE| -|MYD88|1|FALSE|NA|ngoOncogenicallyActiveMYD882011|21179087|GOF|21179087|ngoOncogenicallyActiveMYD882011|TRUE| -|NFKBIA|1|FALSE|NA|thomasMutationalAnalysisIkappaBalpha2004|15198731|LOF|10637284|jungnickelClonalDeleteriousMutations2000|TRUE| -|NFKBIE|1|FALSE|NA|morinGeneticLandscapesRelapsed2016|26647218|LOF|25987724|mansouriFunctionalLossIkBe2015|FALSE| -|NFKBIZ|1|TRUE|NA|morinGeneticLandscapesRelapsed2016|26647218|GOF|302754900|arthurGenomewideDiscoverySomatic2018|FALSE| -|NOL9|1|FALSE|NA|schmitzGeneticsPathogenesisDiffuse2018|29641966|TRUE| -|NOTCH1|1|FALSE|NA|pasqualucciAnalysisCodingGenome2011|21804550|GOF|29045844|ryanCellRegulomeLinks2017|TRUE| -|NOTCH2|1|FALSE|NA|zhangGeneticHeterogeneityDiffuse2013|23292937|GOF|19445024|leeGainoffunctionMutationsCopy2009|TRUE| -|OSBPL10|1|TRUE|NA|zhangGeneticHeterogeneityDiffuse2013|23292937|TRUE| -|P2RY8|1|FALSE|NA|lohrDiscoveryPrioritizationSomatic2012|22343534|LOF|25274307|muppidiLossSignalingGa132014|FALSE| -|PIM1|1|TRUE|NA|pasqualucciHypermutationMultipleProtooncogenes2001|11460166|GOF|27904766|kuoRolePIM1Ibrutinibresistant2016|TRUE| -|PIM2|1|TRUE|NA|reddyGeneticFunctionalDrivers2017|28985567|TRUE| -|POU2AF1|1|TRUE|NA|chapuyMolecularSubtypesDiffuse2018|29713087|LOF|30802265|gonzalez-rinconUnravelingTransformationFollicular2019|FALSE| -|POU2F2|1|FALSE|NA|lohrDiscoveryPrioritizationSomatic2012|22343534|LOF|26993806|hodsonRegulationNormalBcell2016|FALSE| -|PRDM1|1|FALSE|NA|pasqualucciInactivationPRDM1BLIMP12006|NA|LOF|16492805|pasqualucciInactivationPRDM1BLIMP12006|TRUE| -|PTEN|1|FALSE|NA|reddyGeneticFunctionalDrivers2017|28985567|LOF|23840064|pfeiferPTENLossDefines2013|FALSE| -|PTPN6|1|FALSE|PASS|3|reddyGeneticFunctionalDrivers2017|28985567|LOF|26565811|demosthenousLossFunctionMutations2015|FALSE| -|RB1|1|FALSE|NA|morinMutationalStructuralAnalysis2013|23699601|LOF|17332242|pinyolInactivationRB1Mantlecell2007|FALSE| -|RFX7|1|FALSE|NA|NA|arthurGenomewideDiscoverySomatic2018|30275490|LOF|30926791|weberPiggyBacTransposonTools2019|FALSE| -|RHOA|1|FALSE|NA|zhangGeneticHeterogeneityDiffuse2013|23292937|LOF|26616858|ohayreInactivatingMutationsGNA132016|FALSE| -|RRAGC|1|FALSE|NA|okosunRecurrentMTORC1activatingRRAGC2016|26691987|GOF|26691987|okosunRecurrentMTORC1activatingRRAGC2016|FALSE| -|S1PR2|1|TRUE|NA|morinFrequentMutationHistonemodifying2011|21796119|LOF|25274307|muppidiLossSignalingGa132014|TRUE| -|SETD1B|1|FALSE|NA|albuquerqueEnhancingKnowledgeDiscovery2017|28327945|LOF|TBD|TRUE| -|SF3B1|1|FALSE|NA|reddyGeneticFunctionalDrivers2017|28985567|NEO|23160465|cazzolaBiologicClinicalSignificance2013|FALSE| -|SGK1|1|TRUE|NA|morinFrequentMutationHistonemodifying2011|21796119|GOF|33988691|gaoSGK1MutationsDLBCL2021|TRUE| -|SIN3A|1|FALSE|NA|chapuyMolecularSubtypesDiffuse2018|29713087|FALSE| -|SMARCA4|1|FALSE|NA|reddyGeneticFunctionalDrivers2017|28985567|LOF|33144586|fernandoFunctionalCharacterizationSMARCA42020|FALSE| -|SOCS1|1|TRUE|NA|morinFrequentMutationHistonemodifying2011|21796119|LOF|15572583|melznerBiallelicMutationSOCS12005|TRUE| -|SPEN|1|FALSE|NA|albuquerqueEnhancingKnowledgeDiscovery2017|28327945|TRUE| -|STAT3|1|FALSE|NA|morinFrequentMutationHistonemodifying2011|21796119|GOF|23861822|huNovelMissenseM206K2013|TRUE| -|STAT6|1|FALSE|NA|yildizActivatingSTAT6Mutations2015|25428220|GOF|35851155|mentzPARP14NovelTarget2022|TRUE| -|TAF1|1|FALSE|NA|morinMutationalStructuralAnalysis2013|23699601|FALSE| -|TBL1XR1|1|FALSE|NA|lohrDiscoveryPrioritizationSomatic2012|22343534|LOF|32619424|venturuttiTBL1XR1MutationsDrive2020|TRUE| -|TET2|1|FALSE|NA|albuquerqueEnhancingKnowledgeDiscovery2017|28327945|LOF|23831920|asmarGenomewideProfilingIdentifies2013|TRUE| -|TMEM30A|1|FALSE|NA|morinFrequentMutationHistonemodifying2011|21796119|LOF|32094924|ennishiTMEM30ALossoffunctionMutations2020|TRUE| -|TMSB4X|1|TRUE|NA|reddyGeneticFunctionalDrivers2017|28985567|FALSE| -|TNFAIP3|1|FALSE|NA|compagnoMutationsMultipleGenes2009|19412164|LOF|19412164|compagnoMutationsMultipleGenes2009|TRUE| -|TNFRSF14|1|FALSE|NA|morinFrequentMutationHistonemodifying2011|21796119|LOF|TBD|TRUE| -|TOX|1|FALSE|NA|reddyGeneticFunctionalDrivers2017|28985567|TRUE| -|TP53|1|FALSE|NA|morinFrequentMutationHistonemodifying2011|21796119|LOF|12826609|katoUnderstandingFunctionstructureFunctionmutation2003|TRUE| -|UBE2A|1|FALSE|NA|lohrDiscoveryPrioritizationSomatic2012|22343534|TRUE| -|WEE1|1|FALSE|NA|schmitzGeneticsPathogenesisDiffuse2018|29641966|TRUE| -|XPO1|1|FALSE|NA|mareschalWholeExomeSequencing2016|26608593|NEO|33007990|miloudiXPO1E571KMutationModifies2020|FALSE| -|ZC3H12A|1|FALSE|NA|chapuyMolecularSubtypesDiffuse2018|29713087|LOF|19747262|skalniakRegulatoryFeedbackLoop2009|FALSE| -|ZFP36L1|1|TRUE|NA|morinFrequentMutationHistonemodifying2011|21796119|TRUE| -|ZNF292|1|FALSE|NA|reddyGeneticFunctionalDrivers2017|28985567|FALSE| -|ZNF608|1|FALSE|NA|NA|morinMutationalStructuralAnalysis2013|23699601|FALSE| -|LCOR|1|FALSE|NA|novakWholeexomeAnalysisReveals2015|26314988|FALSE| +|:-:|:-:|:-:|:-:|:-:|:-:|:-:|:-:|:-:| +|ACTB|1|TRUE|NA||lohrDiscoveryPrioritizationSomatic2012|22343534||||TRUE +|ACTG1|1|TRUE|NA||fanComprehensiveCharacterizationDriver2020|32565964||||FALSE +|ARID1A|1|FALSE|NA||zhangGeneticHeterogeneityDiffuse2013|23292937|LOF|38458187|barisicARID1AOrchestratesSWI2024|TRUE +|ATM|1|FALSE|NA||reddyGeneticFunctionalDrivers2017|28985567|LOF|11756177|camachoATMGeneInactivation2002|FALSE +|B2M|1|FALSE|NA||morinFrequentMutationHistonemodifying2011|21796119|LOF|22137796|challa-malladiCombinedGeneticInactivation2011|FALSE +|BCL10|1|FALSE|NA||morinFrequentMutationHistonemodifying2011|21796119|GOF|35658124|xiaBCL10MutationsDefine2022|TRUE +|BCL2|1|TRUE|NA||tanakaFrequentIncidenceSomatic1992|1339299||||TRUE +|BCL6|1|TRUE|NA||morinFrequentMutationHistonemodifying2011|21796119|LOF|12504096|masclePointMutationsBCL62003|TRUE +|BCL7A|1|TRUE|NA||morinFrequentMutationHistonemodifying2011|21796119|LOF|32576963|balinas-gaviraFrequentMutationsAminoterminal2020|FALSE +|BIRC6|1|FALSE|NA||reddyGeneticFunctionalDrivers2017|28985567||||FALSE +|BRAF|1|FALSE|NA||tiacciBRAFMutationsHairycell2011|22343534|LOF|15035987|wanMechanismActivationRAFERK2004|FALSE +|BTG1|1|TRUE|NA||morinFrequentMutationHistonemodifying2011|21796119|LOF|33021411|almasmoumFrequentLossBTG12021|TRUE +|BTG2|1|TRUE|NA||morinFrequentMutationHistonemodifying2011|21796119||||TRUE +|BTK|1|FALSE|NA||albuquerqueEnhancingKnowledgeDiscovery2017|28327945|LOF|33419778|huFollicularLymphomaassociatedBTK2021|FALSE +|CARD11|1|FALSE|NA||lenzOncogenicCARD11Mutations2008|18323416|GOF|18323416|lenzOncogenicCARD11Mutations2008|FALSE +|CCND3|1|FALSE|NA||morinFrequentMutationHistonemodifying2011|21796119|GOF|22885699|schmitzBurkittLymphomaPathogenesis2012|FALSE +|CD58|1|FALSE|NA||morinFrequentMutationHistonemodifying2011|21796119|LOF|22137796|challa-malladiCombinedGeneticInactivation2011|TRUE +|CD70|1|FALSE|NA||morinFrequentMutationHistonemodifying2011|21796119|LOF|36471481|nieDualRoleCD702022|TRUE +|CD79B|1|FALSE|NA||davisChronicActiveBcellreceptor2010|20054396|GOF|20054396|davisChronicActiveBcellreceptor2010|TRUE +|CD83|1|TRUE|NA||morinMutationalStructuralAnalysis2013|23699601||||TRUE +|CDKN2A|1|FALSE|NA||morinMutationalStructuralAnalysis2013|23699601|LOF|19260062|kannengiesserFunctionalStructuralGenetic2009|TRUE +|CIITA|1|TRUE|NA||morinFrequentMutationHistonemodifying2011|21796119|LOF|26549456|mottokGenomicAlterationsCIITA2015|TRUE +|CREBBP|1|FALSE|NA||pasqualucciInactivatingMutationsAcetyltransferase2011|21390126|LOF|21390126|pasqualucciInactivatingMutationsAcetyltransferase2011|TRUE +|CXCR4|1|TRUE|NA||khodabakhshiRecurrentTargetsAberrant2012|23131835|LOF|36089616|zmajkovicovaGenotypephenotypeCorrelationsWHIM2022|FALSE +|DDX3X|1|FALSE|NA||reddyGeneticFunctionalDrivers2017|28985567|LOF|34437837|gongSequentialInverseDysregulation2021|TRUE +|DTX1|1|TRUE|NA||zhangGeneticHeterogeneityDiffuse2013|23292937||||TRUE +|DUSP2|1|TRUE|NA||lohrDiscoveryPrioritizationSomatic2012|22343534||||TRUE +|EBF1|1|TRUE|NA||bohleRoleEarlyBcell2013|23174882|LOF|28692033|ramirez-komoSpontaneousLossLineage2017|FALSE +|EEF1A1|1|FALSE|NA||chapuyMolecularSubtypesDiffuse2018|29713087||||FALSE +|EP300|1|FALSE|NA||pasqualucciInactivatingMutationsAcetyltransferase2011|21390126|LOF|21390126|pasqualucciInactivatingMutationsAcetyltransferase2011|TRUE +|ETS1|1|TRUE|NA||morinFrequentMutationHistonemodifying2011|21796119||||TRUE +|ETV6|1|TRUE|NA||lohrDiscoveryPrioritizationSomatic2012|22343534|LOF|24997145|wangETV6MutationCohort2014|TRUE +|EZH2|1|FALSE|NA|NA|morinSomaticMutationsAltering2010|20081860|GOF|21078963|sneeringerCoordinatedActivitiesWildtype2010|TRUE +|FAS|1|FALSE|NA||schollMutationsRegionFAS2007|17487740|LOF|20935634|wangFasFADDDeathDomain2010|FALSE +|FBXO11|1|FALSE|NA||arthurGenomewideDiscoverySomatic2018|30275490|LOF|22113614|duanFBXO11TargetsBCL62011|FALSE +|FBXW7|1|FALSE|NA||zhangGeneticHeterogeneityDiffuse2013|23292937|LOF|32350066|saffieFBXW7TriggersDegradation2020|FALSE +|FOXO1|1|FALSE|NA||morinFrequentMutationHistonemodifying2011|21796119|GOF|23460611|trinhAnalysisFOXO1Mutations|FALSE +|GNA13|1|FALSE|NA||morinFrequentMutationHistonemodifying2011|21796119|LOF|25274307|muppidiLossSignalingGa132014|FALSE +|GNAI2|1|FALSE|NA||morinMutationalStructuralAnalysis2013|23699601|GOF|25274307|muppidiLossSignalingGa132014|FALSE +|GRB2|1|FALSE|NA||pasqualucciAnalysisCodingGenome2011|21804550||||FALSE +|GRHPR|1|TRUE|NA||schmitzGeneticsPathogenesisDiffuse2018|29641966||||TRUE +|HIST1H1B|1|TRUE|NA||chapuyMolecularSubtypesDiffuse2018|29713087||||FALSE +|HIST1H1C|1|TRUE|NA||morinFrequentMutationHistonemodifying2011|21796119||||FALSE +|HIST1H1D|1|TRUE|NA||morinMutationalStructuralAnalysis2013|23699601||||FALSE +|HIST1H1E|1|TRUE|NA||lohrDiscoveryPrioritizationSomatic2012|22343534||||FALSE +|HIST1H2AC|1|TRUE|NA||morinMutationalStructuralAnalysis2013|23699601||||FALSE +|HIST1H2AM|1|TRUE|NA||chapuyMolecularSubtypesDiffuse2018|29713087||||FALSE +|HIST1H2BC|1|TRUE|NA||lohrDiscoveryPrioritizationSomatic2012|22343534||||FALSE +|HIST1H2BK|1|TRUE|NA||zhangGeneticHeterogeneityDiffuse2013|23292937||||FALSE +|HIST1H3B|1|TRUE|NA||lohrDiscoveryPrioritizationSomatic2012|22343534||||FALSE +|HIST2H2BE|1|TRUE|NA||chapuyMolecularSubtypesDiffuse2018|29713087||||FALSE +|HLA-A|1|FALSE|NA||lohrDiscoveryPrioritizationSomatic2012|22343534|LOF|34050029|fangazioGeneticMechanismsHLAI2021|TRUE +|HLA-B|1|FALSE|NA||lohrDiscoveryPrioritizationSomatic2012|22343534|LOF|34050029|fangazioGeneticMechanismsHLAI2021|TRUE +|HLA-C|1|FALSE|NA||chapuyMolecularSubtypesDiffuse2018|29713087|LOF|34050029|fangazioGeneticMechanismsHLAI2021|FALSE +|HLA-DMB|1|FALSE|NA||hubschmannMutationalMechanismsShaping2021|33953289||||FALSE +|HNRNPU|1|FALSE|NA||reddyGeneticFunctionalDrivers2017|28985567||||FALSE +|HVCN1|1|FALSE|NA||chapuyMolecularSubtypesDiffuse2018|29713087||||FALSE +|IKZF3|1|FALSE|NA||morinFrequentMutationHistonemodifying2011|21796119|GOF|33689703|lazarianHotspotMutationTranscription2021|FALSE +|IL4R|1|TRUE|NA||dunsCharacterizationDLBCLPMBL2021|33684939|GOF|29467182|viganoSomaticIL4RMutations2018|FALSE +|IRF4|1|TRUE|NA||morinFrequentMutationHistonemodifying2011|21796119||||TRUE +|IRF8|1|TRUE|NA||morinFrequentMutationHistonemodifying2011|21796119|LOF|38996030|qiuIRF8mutantCellLymphoma2024|TRUE +|ITPKB|1|TRUE|NA||schmitzGeneticsPathogenesisDiffuse2018|29641966|LOF|29650799|tiacciPervasiveMutationsJAKSTAT2018|TRUE +|JUNB|1|FALSE|PASS|3|lohrDiscoveryPrioritizationSomatic2012|22343534||||TRUE +|KLF2|1|TRUE|NA||pasqualucciAnalysisCodingGenome2011|21804550||||TRUE +|KLHL14|1|FALSE|NA||zhangGeneticHeterogeneityDiffuse2013|23292937|LOF|32127472|choiRegulationCellReceptordependent2020|TRUE +|KLHL6|1|TRUE|NA||morinFrequentMutationHistonemodifying2011|21796119|LOF|29695787|choiLossKLHL6Promotes2018|FALSE +|KMT2C|1|FALSE|NA||zhangGeneticHeterogeneityDiffuse2013|23292937||||FALSE +|KMT2D|1|FALSE|NA||morinFrequentMutationHistonemodifying2011|21796119|LOF|26366712|zhangDisruptionKMT2DPerturbs2015|TRUE +|KRAS|1|FALSE|NA||lohrDiscoveryPrioritizationSomatic2012|22343534|GOF|9219684|scheffzekRasRasGAPComplexStructural1997|FALSE +|LRRN3|1|FALSE|NA||zhangGeneticHeterogeneityDiffuse2013|23292937||||FALSE +|LTB|1|TRUE|NA||chapuyMolecularSubtypesDiffuse2018|29713087||||FALSE +|MEF2B|1|TRUE|NA||morinFrequentMutationHistonemodifying2011|21796119|NEO|23974956; 26245647|ponMEF2BMutationsNonHodgkin2015|TRUE +|MEF2C|1|TRUE|NA||hubschmannMutationalMechanismsShaping2021|33953289||||FALSE +|MGA|1|FALSE|NA||reddyGeneticFunctionalDrivers2017|28985567|LOF|23039309|depaoliMGASuppressorMYC2013|FALSE +|MIR142|1|TRUE|NA||kwanhianMicroRNA142Mutated202012|23342264|LOF|29724719|trissalMIR142LossofFunctionMutations2018|FALSE +|MPEG1|1|FALSE|NA||morinMutationalStructuralAnalysis2013|23699601||||TRUE +|MS4A1|1|TRUE|NA||rushtonGeneticEvolutionaryPatterns2020|32589730|LOF|32589730|rushtonGeneticEvolutionaryPatterns2020|FALSE +|MTOR|1|FALSE|NA||zhangGeneticHeterogeneityDiffuse2013|23292937|GOF|24631838|grabinerDiverseArrayCancerassociated2014|FALSE +|MYC|1|TRUE|NA||pasqualucciHypermutationMultipleProtooncogenes2001|11460166|GOF|38565249|freieGermlinePointMutation2024|FALSE +|MYD88|1|FALSE|NA||ngoOncogenicallyActiveMYD882011|21179087|GOF|21179087|ngoOncogenicallyActiveMYD882011|TRUE +|NFKBIA|1|FALSE|NA||thomasMutationalAnalysisIkappaBalpha2004|15198731|LOF|10637284|jungnickelClonalDeleteriousMutations2000|TRUE +|NFKBIE|1|FALSE|NA||morinGeneticLandscapesRelapsed2016|26647218|LOF|25987724|mansouriFunctionalLossIkBe2015|FALSE +|NFKBIZ|1|TRUE|NA||morinGeneticLandscapesRelapsed2016|26647218|GOF|302754900|arthurGenomewideDiscoverySomatic2018|FALSE +|NOL9|1|FALSE|NA||schmitzGeneticsPathogenesisDiffuse2018|29641966||||TRUE +|NOTCH1|1|FALSE|NA||pasqualucciAnalysisCodingGenome2011|21804550|GOF|29045844|ryanCellRegulomeLinks2017|TRUE +|NOTCH2|1|FALSE|NA||zhangGeneticHeterogeneityDiffuse2013|23292937|GOF|19445024|leeGainoffunctionMutationsCopy2009|TRUE +|OSBPL10|1|TRUE|NA||zhangGeneticHeterogeneityDiffuse2013|23292937||||TRUE +|P2RY8|1|FALSE|NA||lohrDiscoveryPrioritizationSomatic2012|22343534|LOF|25274307|muppidiLossSignalingGa132014|FALSE +|PIM1|1|TRUE|NA||pasqualucciHypermutationMultipleProtooncogenes2001|11460166|GOF|27904766|kuoRolePIM1Ibrutinibresistant2016|TRUE +|PIM2|1|TRUE|NA||reddyGeneticFunctionalDrivers2017|28985567||||TRUE +|POU2AF1|1|TRUE|NA||chapuyMolecularSubtypesDiffuse2018|29713087|LOF|30802265|gonzalez-rinconUnravelingTransformationFollicular2019|FALSE +|POU2F2|1|FALSE|NA||lohrDiscoveryPrioritizationSomatic2012|22343534|LOF|26993806|hodsonRegulationNormalBcell2016|FALSE +|PRDM1|1|FALSE|NA||pasqualucciInactivationPRDM1BLIMP12006|NA|LOF|16492805|pasqualucciInactivationPRDM1BLIMP12006|TRUE +|PTEN|1|FALSE|NA||reddyGeneticFunctionalDrivers2017|28985567|LOF|23840064|pfeiferPTENLossDefines2013|FALSE +|PTPN6|1|FALSE|PASS|3|reddyGeneticFunctionalDrivers2017|28985567|LOF|26565811|demosthenousLossFunctionMutations2015|FALSE +|RB1|1|FALSE|NA||morinMutationalStructuralAnalysis2013|23699601|LOF|17332242|pinyolInactivationRB1Mantlecell2007|FALSE +|RFX7|1|FALSE|NA|NA|arthurGenomewideDiscoverySomatic2018|30275490|LOF|30926791|weberPiggyBacTransposonTools2019|FALSE +|RHOA|1|FALSE|NA||zhangGeneticHeterogeneityDiffuse2013|23292937|LOF|26616858|ohayreInactivatingMutationsGNA132016|FALSE +|RRAGC|1|FALSE|NA||okosunRecurrentMTORC1activatingRRAGC2016|26691987|GOF|26691987|okosunRecurrentMTORC1activatingRRAGC2016|FALSE +|S1PR2|1|TRUE|NA||morinFrequentMutationHistonemodifying2011|21796119|LOF|25274307|muppidiLossSignalingGa132014|TRUE +|SETD1B|1|FALSE|NA||albuquerqueEnhancingKnowledgeDiscovery2017|28327945|LOF|TBD||TRUE +|SF3B1|1|FALSE|NA||reddyGeneticFunctionalDrivers2017|28985567|NEO|23160465|cazzolaBiologicClinicalSignificance2013|FALSE +|SGK1|1|TRUE|NA||morinFrequentMutationHistonemodifying2011|21796119|GOF|33988691|gaoSGK1MutationsDLBCL2021|TRUE +|SIN3A|1|FALSE|NA||chapuyMolecularSubtypesDiffuse2018|29713087||||FALSE +|SMARCA4|1|FALSE|NA||reddyGeneticFunctionalDrivers2017|28985567|LOF|33144586|fernandoFunctionalCharacterizationSMARCA42020|FALSE +|SOCS1|1|TRUE|NA||morinFrequentMutationHistonemodifying2011|21796119|LOF|15572583|melznerBiallelicMutationSOCS12005|TRUE +|SPEN|1|FALSE|NA||albuquerqueEnhancingKnowledgeDiscovery2017|28327945||||TRUE +|STAT3|1|FALSE|NA||morinFrequentMutationHistonemodifying2011|21796119|GOF|23861822|huNovelMissenseM206K2013|TRUE +|STAT6|1|FALSE|NA||yildizActivatingSTAT6Mutations2015|25428220|GOF|35851155|mentzPARP14NovelTarget2022|TRUE +|TAF1|1|FALSE|NA||morinMutationalStructuralAnalysis2013|23699601||||FALSE +|TBL1XR1|1|FALSE|NA||lohrDiscoveryPrioritizationSomatic2012|22343534|LOF|32619424|venturuttiTBL1XR1MutationsDrive2020|TRUE +|TET2|1|FALSE|NA||albuquerqueEnhancingKnowledgeDiscovery2017|28327945|LOF|23831920|asmarGenomewideProfilingIdentifies2013|TRUE +|TMEM30A|1|FALSE|NA||morinFrequentMutationHistonemodifying2011|21796119|LOF|32094924|ennishiTMEM30ALossoffunctionMutations2020|TRUE +|TMSB4X|1|TRUE|NA||reddyGeneticFunctionalDrivers2017|28985567||||FALSE +|TNFAIP3|1|FALSE|NA||compagnoMutationsMultipleGenes2009|19412164|LOF|19412164|compagnoMutationsMultipleGenes2009|TRUE +|TNFRSF14|1|FALSE|NA||morinFrequentMutationHistonemodifying2011|21796119|LOF|TBD||TRUE +|TOX|1|FALSE|NA||reddyGeneticFunctionalDrivers2017|28985567||||TRUE +|TP53|1|FALSE|NA||morinFrequentMutationHistonemodifying2011|21796119|LOF|12826609|katoUnderstandingFunctionstructureFunctionmutation2003|TRUE +|UBE2A|1|FALSE|NA||lohrDiscoveryPrioritizationSomatic2012|22343534||||TRUE +|WEE1|1|FALSE|NA||schmitzGeneticsPathogenesisDiffuse2018|29641966||||TRUE +|XPO1|1|FALSE|NA||mareschalWholeExomeSequencing2016|26608593|NEO|33007990|miloudiXPO1E571KMutationModifies2020|FALSE +|ZC3H12A|1|FALSE|NA||chapuyMolecularSubtypesDiffuse2018|29713087|LOF|19747262|skalniakRegulatoryFeedbackLoop2009|FALSE +|ZFP36L1|1|TRUE|NA||morinFrequentMutationHistonemodifying2011|21796119||||TRUE +|ZNF292|1|FALSE|NA||reddyGeneticFunctionalDrivers2017|28985567||||FALSE +|ZNF608|1|FALSE|NA|NA|morinMutationalStructuralAnalysis2013|23699601||||FALSE +|LCOR|1|FALSE|NA||novakWholeexomeAnalysisReveals2015|26314988||||FALSE + + ### Burkitt lymphoma The master curated list for BL including DLBCL genes that have been scrutinized within BL is can be found in `bl_genes.tsv` (or [here](bl_genes.tsv)). The earliest_support_BL column indicates the PubMed ID of the first study to nominate this gene as mutated in BL (or NA when not applicable). The frequency_BL_Thomas and frequency_BL_Panea columns report the percentage of patient samples with at least one non-silent mutation in this gene in the two studies. In the case of Panea et al, these numbers are based on the reanalysis of the exome data from this study by the Morin lab (as detailed in Dreval et al). The original frequencies based on the mutation calls from Panea et al are in the frequency_BL_Panea_original column. From c868f0e0321f6849aada48a72e1819761e3c66bd Mon Sep 17 00:00:00 2001 From: rdmorin Date: Tue, 3 Dec 2024 19:33:52 -0800 Subject: [PATCH 05/12] Update Readme.md --- resources/curated/Readme.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/resources/curated/Readme.md b/resources/curated/Readme.md index bd7ccd48..3ecb5d34 100644 --- a/resources/curated/Readme.md +++ b/resources/curated/Readme.md @@ -14,7 +14,7 @@ This file contains four additional columns, which respectively report the mutati |Gene|Tier|aSHM|QC|Mean variant quality|citekey|PMID|MutationEffect|Mutation-PMID|MutationEffect-citekey|LymphGen| -|:-:|:-:|:-:|:-:|:-:|:-:|:-:|:-:|:-:| +|:-:|:-:|:-:|:-:|:-:|:-:|:-:|:-:|:-:|:-:|:-:| |ACTB|1|TRUE|NA||lohrDiscoveryPrioritizationSomatic2012|22343534||||TRUE |ACTG1|1|TRUE|NA||fanComprehensiveCharacterizationDriver2020|32565964||||FALSE |ARID1A|1|FALSE|NA||zhangGeneticHeterogeneityDiffuse2013|23292937|LOF|38458187|barisicARID1AOrchestratesSWI2024|TRUE From 0b29cb2c9143b29b602a3889b02fed311ac9dc33 Mon Sep 17 00:00:00 2001 From: rdmorin Date: Tue, 3 Dec 2024 19:34:31 -0800 Subject: [PATCH 06/12] Update Readme.md --- resources/curated/Readme.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/resources/curated/Readme.md b/resources/curated/Readme.md index 3ecb5d34..c343851c 100644 --- a/resources/curated/Readme.md +++ b/resources/curated/Readme.md @@ -47,7 +47,7 @@ This file contains four additional columns, which respectively report the mutati |EP300|1|FALSE|NA||pasqualucciInactivatingMutationsAcetyltransferase2011|21390126|LOF|21390126|pasqualucciInactivatingMutationsAcetyltransferase2011|TRUE |ETS1|1|TRUE|NA||morinFrequentMutationHistonemodifying2011|21796119||||TRUE |ETV6|1|TRUE|NA||lohrDiscoveryPrioritizationSomatic2012|22343534|LOF|24997145|wangETV6MutationCohort2014|TRUE -|EZH2|1|FALSE|NA|NA|morinSomaticMutationsAltering2010|20081860|GOF|21078963|sneeringerCoordinatedActivitiesWildtype2010|TRUE +|EZH2|1|FALSE|NA||morinSomaticMutationsAltering2010|20081860|GOF|21078963|sneeringerCoordinatedActivitiesWildtype2010|TRUE |FAS|1|FALSE|NA||schollMutationsRegionFAS2007|17487740|LOF|20935634|wangFasFADDDeathDomain2010|FALSE |FBXO11|1|FALSE|NA||arthurGenomewideDiscoverySomatic2018|30275490|LOF|22113614|duanFBXO11TargetsBCL62011|FALSE |FBXW7|1|FALSE|NA||zhangGeneticHeterogeneityDiffuse2013|23292937|LOF|32350066|saffieFBXW7TriggersDegradation2020|FALSE From 1235d70c8ab0d5e83e338d7297927414574f62c4 Mon Sep 17 00:00:00 2001 From: rdmorin Date: Tue, 3 Dec 2024 19:34:55 -0800 Subject: [PATCH 07/12] Update Readme.md --- resources/curated/Readme.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/resources/curated/Readme.md b/resources/curated/Readme.md index c343851c..18d3c029 100644 --- a/resources/curated/Readme.md +++ b/resources/curated/Readme.md @@ -111,7 +111,7 @@ This file contains four additional columns, which respectively report the mutati |PTEN|1|FALSE|NA||reddyGeneticFunctionalDrivers2017|28985567|LOF|23840064|pfeiferPTENLossDefines2013|FALSE |PTPN6|1|FALSE|PASS|3|reddyGeneticFunctionalDrivers2017|28985567|LOF|26565811|demosthenousLossFunctionMutations2015|FALSE |RB1|1|FALSE|NA||morinMutationalStructuralAnalysis2013|23699601|LOF|17332242|pinyolInactivationRB1Mantlecell2007|FALSE -|RFX7|1|FALSE|NA|NA|arthurGenomewideDiscoverySomatic2018|30275490|LOF|30926791|weberPiggyBacTransposonTools2019|FALSE +|RFX7|1|FALSE|NA||arthurGenomewideDiscoverySomatic2018|30275490|LOF|30926791|weberPiggyBacTransposonTools2019|FALSE |RHOA|1|FALSE|NA||zhangGeneticHeterogeneityDiffuse2013|23292937|LOF|26616858|ohayreInactivatingMutationsGNA132016|FALSE |RRAGC|1|FALSE|NA||okosunRecurrentMTORC1activatingRRAGC2016|26691987|GOF|26691987|okosunRecurrentMTORC1activatingRRAGC2016|FALSE |S1PR2|1|TRUE|NA||morinFrequentMutationHistonemodifying2011|21796119|LOF|25274307|muppidiLossSignalingGa132014|TRUE @@ -139,7 +139,7 @@ This file contains four additional columns, which respectively report the mutati |ZC3H12A|1|FALSE|NA||chapuyMolecularSubtypesDiffuse2018|29713087|LOF|19747262|skalniakRegulatoryFeedbackLoop2009|FALSE |ZFP36L1|1|TRUE|NA||morinFrequentMutationHistonemodifying2011|21796119||||TRUE |ZNF292|1|FALSE|NA||reddyGeneticFunctionalDrivers2017|28985567||||FALSE -|ZNF608|1|FALSE|NA|NA|morinMutationalStructuralAnalysis2013|23699601||||FALSE +|ZNF608|1|FALSE|NA||morinMutationalStructuralAnalysis2013|23699601||||FALSE |LCOR|1|FALSE|NA||novakWholeexomeAnalysisReveals2015|26314988||||FALSE From 0f97f64ffee461686cfa4f8298b198b82a7561db Mon Sep 17 00:00:00 2001 From: rdmorin Date: Tue, 3 Dec 2024 19:37:04 -0800 Subject: [PATCH 08/12] Update Readme.md --- resources/curated/Readme.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/resources/curated/Readme.md b/resources/curated/Readme.md index 18d3c029..d8cd1d3c 100644 --- a/resources/curated/Readme.md +++ b/resources/curated/Readme.md @@ -8,8 +8,8 @@ These lists are meant to be comprehensive lists of genes that are (reportedly) e ### DLBCL -The master curated gene list for DLBCL including all genes nominated by any exome/genome-wide study can be found in this directory in `dlbcl_genes.tsv` or [here](dlbcl_genes.tsv). Most of the columns in this file are self-explanatory. The earliest_support column is meant to refer to the PubMed ID of the first study that nominated that gene as a significantly mutated gene in DLBCL. The columns Chapuy, Reddy and LymphGen indicate TRUE/FALSE for whether each gene was nominated/reported by that study. The next column (curated) is TRUE only for genes that have made it to the curated core list of DLBCL genes. -This file contains four additional columns, which respectively report the mutation frequency in the cohorts from Chapuy et al, Schmitz et al, Reddy et al If a gene has been identified from additional information, this is from our compendium of genomes in the GAMBL project. The Lacy column indicates whether the gene was sequenced by Lacy et al. The core gene list at the time this document was prepared is shown below along with a few key columns from the file. _This may not match the actual file, depending on whether this document is kept up to date. Please refer to the the file rather than this list._ The separate file `dlbcl_genes_with_mutation_frequencies.tsv` ([here](dlbcl_genes_with_mutation_frequencies.tsv)) is intended to include all genes nominated to be recurrently/significantly mutated in DLBCL. It contains columns indicating, where possible, which study nominated the gene. +The master curated gene list for DLBCL including all genes nominated by any exome/genome-wide study can be found in this directory in `dlbcl_genes.tsv` or [here](dlbcl_genes.tsv). Most of the columns in this file are self-explanatory. The citekey and PMID columns respectively refer to the BibTex citekey and PubMed ID of the first study that nominated that gene as a significantly mutated gene in DLBCL. +The core gene list at the time this document was prepared is shown below. _This may not match the actual file, depending on whether this document is kept up to date. Please refer to [this file](dlbcl_genes.tsv) rather than the table you see below._ From 065c589016a6309b57843a69bf81902e96431d64 Mon Sep 17 00:00:00 2001 From: rdmorin Date: Tue, 3 Dec 2024 19:40:43 -0800 Subject: [PATCH 09/12] Update Readme.md --- resources/curated/Readme.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/resources/curated/Readme.md b/resources/curated/Readme.md index d8cd1d3c..13db169d 100644 --- a/resources/curated/Readme.md +++ b/resources/curated/Readme.md @@ -8,7 +8,9 @@ These lists are meant to be comprehensive lists of genes that are (reportedly) e ### DLBCL -The master curated gene list for DLBCL including all genes nominated by any exome/genome-wide study can be found in this directory in `dlbcl_genes.tsv` or [here](dlbcl_genes.tsv). Most of the columns in this file are self-explanatory. The citekey and PMID columns respectively refer to the BibTex citekey and PubMed ID of the first study that nominated that gene as a significantly mutated gene in DLBCL. +The master curated gene list for DLBCL including all genes nominated by any exome/genome-wide study can be found in this directory in `dlbcl_genes.tsv` or [here](dlbcl_genes.tsv). Most of the columns in this file are self-explanatory. The second column (Tier) refers to our confidence in the gene. Each gene is assigned to one of three based on the extent of data supporting its role in that entity, with Tier 1 and Tier 2 respectively representing the high- and moderate-confidence genes. Genes of particularly low confidence can also be assigned to a third tier, though not all lists contain Tier 3 genes. +![image](https://github.com/user-attachments/assets/1c82000d-73c1-41a1-8259-912e575a93c8) + The citekey and PMID columns respectively refer to the BibTex citekey and PubMed ID of the first study that nominated that gene as a significantly mutated gene in DLBCL. The core gene list at the time this document was prepared is shown below. _This may not match the actual file, depending on whether this document is kept up to date. Please refer to [this file](dlbcl_genes.tsv) rather than the table you see below._ From 41c7122500c810e32c135ab8ebb5a4f6f036a691 Mon Sep 17 00:00:00 2001 From: rdmorin Date: Tue, 3 Dec 2024 19:41:02 -0800 Subject: [PATCH 10/12] Update Readme.md --- resources/curated/Readme.md | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/resources/curated/Readme.md b/resources/curated/Readme.md index 13db169d..f520ce18 100644 --- a/resources/curated/Readme.md +++ b/resources/curated/Readme.md @@ -8,9 +8,7 @@ These lists are meant to be comprehensive lists of genes that are (reportedly) e ### DLBCL -The master curated gene list for DLBCL including all genes nominated by any exome/genome-wide study can be found in this directory in `dlbcl_genes.tsv` or [here](dlbcl_genes.tsv). Most of the columns in this file are self-explanatory. The second column (Tier) refers to our confidence in the gene. Each gene is assigned to one of three based on the extent of data supporting its role in that entity, with Tier 1 and Tier 2 respectively representing the high- and moderate-confidence genes. Genes of particularly low confidence can also be assigned to a third tier, though not all lists contain Tier 3 genes. -![image](https://github.com/user-attachments/assets/1c82000d-73c1-41a1-8259-912e575a93c8) - The citekey and PMID columns respectively refer to the BibTex citekey and PubMed ID of the first study that nominated that gene as a significantly mutated gene in DLBCL. +The master curated gene list for DLBCL including all genes nominated by any exome/genome-wide study can be found in this directory in `dlbcl_genes.tsv` or [here](dlbcl_genes.tsv). Most of the columns in this file are self-explanatory. The second column (Tier) refers to our confidence in the gene. Each gene is assigned to one of three based on the extent of data supporting its role in that entity, with Tier 1 and Tier 2 respectively representing the high- and moderate-confidence genes. Genes of particularly low confidence can also be assigned to a third tier, though not all lists contain Tier 3 genes. The citekey and PMID columns respectively refer to the BibTex citekey and PubMed ID of the first study that nominated that gene as a significantly mutated gene in DLBCL. The core gene list at the time this document was prepared is shown below. _This may not match the actual file, depending on whether this document is kept up to date. Please refer to [this file](dlbcl_genes.tsv) rather than the table you see below._ From 6404f92403824a89229f7060407639849164b63c Mon Sep 17 00:00:00 2001 From: rdmorin Date: Tue, 3 Dec 2024 22:13:59 -0800 Subject: [PATCH 11/12] Update Readme.md --- resources/curated/Readme.md | 149 ++++++++++++++++++++++++++++++++++++ 1 file changed, 149 insertions(+) diff --git a/resources/curated/Readme.md b/resources/curated/Readme.md index f520ce18..420b682b 100644 --- a/resources/curated/Readme.md +++ b/resources/curated/Readme.md @@ -6,6 +6,155 @@ These lists are meant to be comprehensive lists of genes that are (reportedly) e ## The lists +### DLBCL, FL and BL combined list + +|Gene|DLBCL Tier|FL Tier|BL Tier| +|:-:|:-:|:-:| +|ARID1A|1|1|1| +|BCL6|1|1|1| +|BCL7A|1|1|1| +|CCND3|1|1|1| +|CREBBP|1|1|1| +|EZH2|1|1|1| +|FOXO1|1|1|1| +|GNA13|1|1|1| +|GNAI2|1|1|1| +|HIST1H1E|1|1|1| +|IGLL5|1|1|1| +|KMT2D|1|1|1| +|MYC|1|1|1| +|SMARCA4|1|1|1| +|TP53|1|1|1| +|B2M|1|1|2| +|BCL2|1|1|2| +|CARD11|1|1|2| +|CD83|1|1|2| +|EBF1|1|1|2| +|HIST1H1B|1|1|2| +|IRF8|1|1|2| +|PIM1|1|1|2| +|TBL1XR1|1|1|2| +|TNFRSF14|1|1|2| +|HIST1H1C|1|1|3| +|HIST1H2AM|1|1|3| +|ACTB|1|1|| +|BCL10|1|1|| +|BTK|1|1|| +|EEF1A1|1|1|| +|EP300|1|1|| +|FAS|1|1|| +|HIST1H1D|1|1|| +|HIST1H2AC|1|1|| +|HIST1H2BC|1|1|| +|HVCN1|1|1|| +|KLHL6|1|1|| +|MEF2B|1|1|| +|POU2AF1|1|1|| +|POU2F2|1|1|| +|RRAGC|1|1|| +|SGK1|1|1|| +|SOCS1|1|1|| +|STAT6|1|1|| +|TMSB4X|1|1|| +|TNFAIP3|1|1|| +|DDX3X|1|2|1| +|P2RY8|1|2|1| +|RHOA|1|2|1| +|BTG1|1|2|2| +|CXCR4|1|2|2| +|S1PR2|1|2|2| +|BTG2|1|2|3| +|CD79B|1|2|3| +|ACTG1|1|2|| +|CD70|1|2|| +|DUSP2|1|2|| +|IRF4|1|2|| +|ITPKB|1|2|| +|KLF2|1|2|| +|LTB|1|2|| +|MEF2C|1|2|| +|MYD88|1|2|| +|NFKBIA|1|2|| +|TMEM30A|1|2|| +|ZNF608|1|2|| +|FBXO11|1||1| +|HNRNPU|1||1| +|PTEN|1||1| +|RFX7|1||1| +|SIN3A|1||1| +|CDKN2A|1||2| +|IKZF3|1||2| +|KMT2C|1||2| +|PRDM1|1||2| +|TET2|1||2| +|ZFP36L1|1||2| +|BRAF|1||3| +|DTX1|1||3| +|ETS1|1||3| +|HIST1H2BK|1||3| +|MTOR|1||3| +|NOTCH1|1||3| +|SF3B1|1||3| +|ATM|1||| +|BIRC6|1||| +|CD58|1||| +|CIITA|1||| +|ETV6|1||| +|FBXW7|1||| +|GRB2|1||| +|GRHPR|1||| +|HIST1H3B|1||| +|HIST2H2BE|1||| +|HLA-A|1||| +|HLA-B|1||| +|HLA-C|1||| +|HLA-DMB|1||| +|IL4R|1||| +|JUNB|1||| +|KLHL14|1||| +|KRAS|1||| +|LCOR|1||| +|LRRN3|1||| +|MGA|1||| +|MPEG1|1||| +|MS4A1|1||| +|NFKBIE|1||| +|NFKBIZ|1||| +|NOL9|1||| +|NOTCH2|1||| +|OSBPL10|1||| +|PIM2|1||| +|PTPN6|1||| +|RB1|1||| +|SETD1B|1||| +|SPEN|1||| +|STAT3|1||| +|TAF1|1||| +|TOX|1||| +|UBE2A|1||| +|WEE1|1||| +|XPO1|1||| +|ZC3H12A|1||| +|ZNF292|1||| +|HIST1H2AG|2|1|3| +|MAP2K1|2|1|| +|ID3|2||1| +|TCL1A|2||1| +|USP7|2||1| +|WNK1|2||1| +|PHF6|3||1| +|ATP6AP1||1|| +|ATP6V1B2||1|| +|CTSS||1|| +|HIST1H2BG||1|| +|VMA21||1|| +|BACH2|||1| +|BMP7|||1| +|CHD8|||1| +|PCBP1|||1| +|TCF3|||1| +|TFAP4|||1| + ### DLBCL The master curated gene list for DLBCL including all genes nominated by any exome/genome-wide study can be found in this directory in `dlbcl_genes.tsv` or [here](dlbcl_genes.tsv). Most of the columns in this file are self-explanatory. The second column (Tier) refers to our confidence in the gene. Each gene is assigned to one of three based on the extent of data supporting its role in that entity, with Tier 1 and Tier 2 respectively representing the high- and moderate-confidence genes. Genes of particularly low confidence can also be assigned to a third tier, though not all lists contain Tier 3 genes. The citekey and PMID columns respectively refer to the BibTex citekey and PubMed ID of the first study that nominated that gene as a significantly mutated gene in DLBCL. From 1f81f7dbf408023dd2aa671542b77a8272cd4e7f Mon Sep 17 00:00:00 2001 From: rdmorin Date: Tue, 3 Dec 2024 22:14:16 -0800 Subject: [PATCH 12/12] Update Readme.md --- resources/curated/Readme.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/resources/curated/Readme.md b/resources/curated/Readme.md index 420b682b..a77c30ad 100644 --- a/resources/curated/Readme.md +++ b/resources/curated/Readme.md @@ -9,7 +9,7 @@ These lists are meant to be comprehensive lists of genes that are (reportedly) e ### DLBCL, FL and BL combined list |Gene|DLBCL Tier|FL Tier|BL Tier| -|:-:|:-:|:-:| +|:-:|:-:|:-:|:-:| |ARID1A|1|1|1| |BCL6|1|1|1| |BCL7A|1|1|1|