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--- a +++ b/resources/curated/Readme.md @@ -0,0 +1,335 @@ +# Curated lymphoma gene lists + +# What these files are and what they are not + +These lists are meant to be comprehensive lists of genes that are (reportedly) enriched for non-silent or other driver mutations in one or more B-cell lymphomas. As a result, contain many genes that are likely not relevant to these malignancies and some genes may be missing if they are only affected by aberrant somatic hypermutation (aSHM) but not demonstrated to be _bona fide_ drivers. Comprehensive lists of regions affected by aSHM are provided separately but are not considered gene lists per-se because they are not all within genes. The completeness of these lists is a blessing and a curse. Be sure to filter the lists based on how stringent you would like to be. Most people will be interested in just the core lists. + +## 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. +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._ + + + +|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||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||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||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)). + +### Follicular lymphoma + +The master curated list for FL including DLBCL genes that have been scrutinized within BL is can be found in `fl_genes.tsv` (or [here](fl_genes.tsv)). + +### aSHM regions + +We provide two (somewhat redundant) files that each represent the coordinates of genomic regions we have identified as being targets of aberrant somatic hypermutation (aSHM) from our analysis of DLBCL genomes. Use the bed file if you need that format, otherwise refer to the txt file for more complete details about the regions. _Contributors willing to help fill in regions you think need to be added to this list are encouraged to submit a GitHub issue and we'll review the data we have to determine if this is warranted._ + +The following three files are semi-redundant representations of the same information. This is the coordinates for regions of the genome commonly affected by aSHM in DLBCL. [This version](somatic_hypermutation_locations_with_DLBCL_frequencies.tsv) includes additional columns tracking the number and percentage of DLBCL genomes with mutations in each region based on our meta-analysis. + +`somatic_hypermutation_locations_GRCh37.txt` + +`somatic_hypermutation_locations_with_DLBCL_frequencies.tsv` + +`somatic_hypermutation_locations_GRCh37.bed` + +## How to contribute + +These lists may be incomplete and may contain errors. If you believe a gene is missing, is mis-attributed, etc please let us know. _Contributors willing to help fill in missing data (genes, citations, hot spots) are encouraged to submit a GitHub issue._ + +## How to cite + +If you use the information in these lists please cite the following papers: + +### DLBCL gene list + +Minimum Information for Reporting a Genomics Experiment. Dreval K, Boutros PC, Morin RD. +Blood. 2022 Oct 11:blood.2022016095. doi: 10.1182/blood.2022016095. PMID: 36219881 + +### BL gene list + +GENETIC SUBGROUPS INFORM ON PATHOBIOLOGY IN ADULT AND PEDIATRIC BURKITT LYMPHOMA. Thomas N, Dreval K et al. Blood. 2022 Oct 6:blood.2022016534. doi: 10.1182/blood.2022016534. PMID: 36201743 + +### SHM regions + +Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma. Arthur et al. Nat Commun. 2018 Oct 1;9(1):4001. doi: 10.1038/s41467-018-06354-3. + +Super-enhancer hypermutation alters oncogene expression in B cell lymphoma. Bal E et al. Nature. 2022 Jul;607(7920):808-815. doi: 10.1038/s41586-022-04906-8. Epub 2022 Jul 6.