From c1a5a7831c3610591fbd432fcbc0c25197dfce47 Mon Sep 17 00:00:00 2001 From: Krysta Coyle Date: Tue, 3 Sep 2024 10:50:09 -0700 Subject: [PATCH 1/3] removed non-functional studies --- resources/curated/bl_genes.tsv | 6 +++--- resources/curated/dlbcl_genes.tsv | 8 ++++---- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/resources/curated/bl_genes.tsv b/resources/curated/bl_genes.tsv index c075f89f..590acd90 100644 --- a/resources/curated/bl_genes.tsv +++ b/resources/curated/bl_genes.tsv @@ -11,10 +11,10 @@ DDX3X 1 schmitzBurkittLymphomaPathogenesis2012 22885699 LOF 34437837 FBXO11 1 richterRecurrentMutationID32012a 23143595 LOF 22113614 FOXO1 1 schmitzBurkittLymphomaPathogenesis2012 22885699 GOF 23460611 GNA13 1 loveGeneticLandscapeMutations2012 23143597 LOF 26616858 -GNAI2 1 grandeGenomewideDiscoverySomatic2019 30617194 GOF 23699601 +GNAI2 1 grandeGenomewideDiscoverySomatic2019 30617194 HIST1H1E 1 TRUE grandeGenomewideDiscoverySomatic2019 31558468 -HNRNPU 1 TRUE paneaWholeGenomeLandscape2019 31558468 LOF 36201743 -ID3 1 richterRecurrentMutationID32012a 23143595 LOF 23143595 +HNRNPU 1 TRUE paneaWholeGenomeLandscape2019 31558468 +ID3 1 richterRecurrentMutationID32012a 23143595 KMT2D 1 grandeGenomewideDiscoverySomatic2019 30617194 LOF 26366712 MYC 1 TRUE johnstonCmycHypermutationBurkitt1992 1297477 GOF 38565249 P2RY8 1 muppidiLossSignalingGa132014b 25274307 LOF 25274307 diff --git a/resources/curated/dlbcl_genes.tsv b/resources/curated/dlbcl_genes.tsv index feed2f80..26b0c2e9 100644 --- a/resources/curated/dlbcl_genes.tsv +++ b/resources/curated/dlbcl_genes.tsv @@ -24,7 +24,7 @@ CIITA 1 TRUE NA morinFrequentMutationHistonemodifying2011 21796119 LOF 26549456 CREBBP 1 FALSE NA pasqualucciInactivatingMutationsAcetyltransferase2011a 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 LOF 28183850 merirantaDeltex1MutationsPredict2017 TRUE +DTX1 1 TRUE NA zhangGeneticHeterogeneityDiffuse2013 23292937 TRUE DUSP2 1 TRUE NA lohrDiscoveryPrioritizationSomatic2012a 22343534 TRUE EBF1 1 TRUE NA bohleRoleEarlyBcell2013 23174882 LOF 28692033 ramirez-komoSpontaneousLossLineage2017 FALSE EEF1A1 1 FALSE NA chapuyMolecularSubtypesDiffuse2018b 29713087 FALSE @@ -53,7 +53,7 @@ HIST2H2BE 1 TRUE NA chapuyMolecularSubtypesDiffuse2018b 29713087 FALSE HLA-A 1 FALSE NA lohrDiscoveryPrioritizationSomatic2012a 22343534 LOF 34050029 fangazioGeneticMechanismsHLAI2021 TRUE HLA-B 1 FALSE NA lohrDiscoveryPrioritizationSomatic2012a 22343534 LOF 34050029 fangazioGeneticMechanismsHLAI2021 TRUE HLA-C 1 FALSE NA chapuyMolecularSubtypesDiffuse2018b 29713087 LOF 34050029 fangazioGeneticMechanismsHLAI2021 FALSE -HLA-DMB 1 FALSE NA hubschmannMutationalMechanismsShaping2021b 33953289 LOF 7528727 shamanAnalysisHLADMBMutants1995 FALSE +HLA-DMB 1 FALSE NA hubschmannMutationalMechanismsShaping2021b 33953289 FALSE HNRNPU 1 FALSE NA reddyGeneticFunctionalDrivers2017 28985567 FALSE HVCN1 1 FALSE NA chapuyMolecularSubtypesDiffuse2018b 29713087 FALSE IKZF3 1 FALSE NA morinFrequentMutationHistonemodifying2011 21796119 GOF 33689703 lazarianHotspotMutationTranscription2021 FALSE @@ -81,7 +81,7 @@ MYC 1 TRUE NA pasqualucciHypermutationMultipleProtooncogenes2001a 11460166 GOF MYD88 1 FALSE NA ngoOncogenicallyActiveMYD882011a 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 30275490 arthurGenomewideDiscoverySomatic2018 FALSE +NFKBIZ 1 TRUE NA morinGeneticLandscapesRelapsed2016 26647218 GOF 302754900 arthurGenomewideDiscoverySomatic2018 FALSE NOL9 1 FALSE NA schmitzGeneticsPathogenesisDiffuse2018a 29641966 TRUE NOTCH1 1 FALSE NA pasqualucciAnalysisCodingGenome2011 21804550 GOF 29045844 ryanCellRegulomeLinks2017 TRUE NOTCH2 1 FALSE NA zhangGeneticHeterogeneityDiffuse2013 23292937 GOF 19445024 leeGainoffunctionMutationsCopy2009 TRUE @@ -106,7 +106,7 @@ SIN3A 1 FALSE NA chapuyMolecularSubtypesDiffuse2018b 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 albuquerqueEnhancingKnowledgeDiscovery2017a 28327945 TRUE -STAT3 1 FALSE NA morinFrequentMutationHistonemodifying2011 21796119 GOF 31861597 zhuSTAT3ActivationOncogenesis2019 TRUE +STAT3 1 FALSE NA morinFrequentMutationHistonemodifying2011 21796119 GOF 23861822 huNovelMissenseM206K2013a TRUE STAT6 1 FALSE NA yildizActivatingSTAT6Mutations2015c 25428220 GOF 35851155 mentzPARP14NovelTarget2022 TRUE TAF1 1 FALSE NA morinMutationalStructuralAnalysis2013 23699601 FALSE TBL1XR1 1 FALSE NA lohrDiscoveryPrioritizationSomatic2012a 22343534 LOF 32619424 venturuttiTBL1XR1MutationsDrive2020 TRUE From c95ece73ff35ae3c325767aa241d6a83b417927c Mon Sep 17 00:00:00 2001 From: Krysta Coyle Date: Tue, 3 Sep 2024 12:08:22 -0700 Subject: [PATCH 2/3] remove non-functional refs from mutation columns --- resources/curated/fl_genes.tsv | 152 ++++++++++++++++----------------- 1 file changed, 76 insertions(+), 76 deletions(-) diff --git a/resources/curated/fl_genes.tsv b/resources/curated/fl_genes.tsv index 602b73e0..a99c27be 100644 --- a/resources/curated/fl_genes.tsv +++ b/resources/curated/fl_genes.tsv @@ -1,29 +1,31 @@ -Gene Tier aSHM QC Mean Variant Quality citekey PMID MutationEffect Mutation-PMID -ACTB 1 TRUE drevalGeneticSubdivisionsFollicular2023 37084389 -ARID1A 1 krysiakRecurrentSomaticMutations2017b 28064239 LOF 38458187 -ATP6AP1 1 okosunRecurrentMTORC1activatingRRAGC2016a 26691987 -ATP6V1B2 1 okosunRecurrentMTORC1activatingRRAGC2016a 26691987 LOF 28064239 +EZH2 1 morinSomaticMutationsAltering2010a 20081860 GOF 21078963 +CREBBP 1 pasqualucciInactivatingMutationsAcetyltransferase2011a 21390126 LOF 21390126 +EP300 1 pasqualucciInactivatingMutationsAcetyltransferase2011a 21390126 LOF 21390126 B2M 1 morinFrequentMutationHistonemodifying2011 21796119 LOF 22137796 -BCL10 1 russler-germainMutationsAssociatedProgression2023b 37493986 GOF 35658124 BCL2 1 TRUE morinFrequentMutationHistonemodifying2011 21796119 -BCL6 1 TRUE drevalGeneticSubdivisionsFollicular2023 37084389 LOF 12504096 -BCL7A 1 TRUE krysiakRecurrentSomaticMutations2017b 28064239 LOF 32576963 -BTK 1 krysiakRecurrentSomaticMutations2017b 28064239 LOF 33419778 CARD11 1 morinFrequentMutationHistonemodifying2011 21796119 GOF 18323416 CCND3 1 morinFrequentMutationHistonemodifying2011 21796119 GOF 22885699 -CD83 1 TRUE russler-germainMutationsAssociatedProgression2023b 37493986 -CREBBP 1 pasqualucciInactivatingMutationsAcetyltransferase2011a 21390126 LOF 21390126 -CTSS 1 barariaCathepsinAlterationsInduce2020c 32330423 GOF 32330455 -EBF1 1 TRUE drevalGeneticSubdivisionsFollicular2023 37084389 LOF 28692033 -EEF1A1 1 hubschmannMutationalMechanismsShaping2021b 33953289 -EP300 1 pasqualucciInactivatingMutationsAcetyltransferase2011a 21390126 LOF 21390126 -EZH2 1 morinSomaticMutationsAltering2010a 20081860 GOF 21078963 FAS 1 morinFrequentMutationHistonemodifying2011 21796119 LOF 20935634 FOXO1 1 morinFrequentMutationHistonemodifying2011 21796119 GOF 23460611 GNA13 1 morinFrequentMutationHistonemodifying2011 21796119 LOF 26616858 -GNAI2 1 drevalGeneticSubdivisionsFollicular2023 37084389 GOF 23699601 -HIST1H1B 1 TRUE krysiakRecurrentSomaticMutations2017b 28064239 HIST1H1C 1 TRUE morinFrequentMutationHistonemodifying2011 21796119 +IRF8 1 TRUE morinFrequentMutationHistonemodifying2011 21796119 LOF 38996030 +KLHL6 1 TRUE morinFrequentMutationHistonemodifying2011 21796119 LOF 29695787 +KMT2D 1 morinFrequentMutationHistonemodifying2011 21796119 LOF 26366712 +MEF2B 1 TRUE morinFrequentMutationHistonemodifying2011 21796119 NEO 23974956; 26245647 +SGK1 1 TRUE morinFrequentMutationHistonemodifying2011 21796119 GOF 33988691 +TNFRSF14 1 cheungAcquiredTNFRSF14Mutations2010a 21796119 +TP53 1 morinFrequentMutationHistonemodifying2011 21796119 LOF 12826609 +BTG2 2 TRUE drevalGeneticSubdivisionsFollicular2023 21796119 +TMEM30A 2 morinFrequentMutationHistonemodifying2011 21796119 +STAT6 1 yildizActivatingSTAT6Mutations2015c 25428220 GOF 35851155 +ATP6AP1 1 okosunRecurrentMTORC1activatingRRAGC2016a 26691987 +ATP6V1B2 1 okosunRecurrentMTORC1activatingRRAGC2016a 26691987 LOF 28064239 +MAP2K1 1 louissaintPediatrictypeNodalFollicular2016a 27325104 GOF 28533310 +ARID1A 1 krysiakRecurrentSomaticMutations2017b 28064239 LOF 38458187 +BCL7A 1 TRUE krysiakRecurrentSomaticMutations2017b 28064239 LOF 32576963 +BTK 1 krysiakRecurrentSomaticMutations2017b 28064239 LOF 33419778 +HIST1H1B 1 TRUE krysiakRecurrentSomaticMutations2017b 28064239 HIST1H1D 1 TRUE krysiakRecurrentSomaticMutations2017b 28064239 HIST1H1E 1 TRUE krysiakRecurrentSomaticMutations2017b 28064239 HIST1H2AC 1 TRUE krysiakRecurrentSomaticMutations2017b 28064239 @@ -32,83 +34,81 @@ HIST1H2AM 1 TRUE krysiakRecurrentSomaticMutations2017b 28064239 HIST1H2BC 1 TRUE krysiakRecurrentSomaticMutations2017b 28064239 HIST1H2BG 1 TRUE krysiakRecurrentSomaticMutations2017b 28064239 HVCN1 1 krysiakRecurrentSomaticMutations2017b 28064239 -IRF4 1 TRUE drevalGeneticSubdivisionsFollicular2023 37084389 -IRF8 1 TRUE morinFrequentMutationHistonemodifying2011 21796119 LOF 38996030 -KLHL6 1 TRUE morinFrequentMutationHistonemodifying2011 21796119 LOF 29695787 -KMT2D 1 morinFrequentMutationHistonemodifying2011 21796119 LOF 26366712 -MAP2K1 1 louissaintPediatrictypeNodalFollicular2016a 27325104 GOF 28533310 -MEF2B 1 TRUE morinFrequentMutationHistonemodifying2011 21796119 NEO 23974956; 26245647 -MYC 1 TRUE NA NA GOF 38565249 -PIM1 1 TRUE drevalGeneticSubdivisionsFollicular2023 NA GOF 27904766 -POU2AF1 1 krysiakRecurrentSomaticMutations2017b 28064239 LOF 30802265 +POU2AF1 1 krysiakRecurrentSomaticMutations2017b 28064239 POU2F2 1 krysiakRecurrentSomaticMutations2017b 28064239 LOF 26993806 -RRAGC 1 okosunRecurrentMTORC1activatingRRAGC2016a NA GOF 26691987 -SGK1 1 TRUE morinFrequentMutationHistonemodifying2011 21796119 GOF 33988691 SMARCA4 1 krysiakRecurrentSomaticMutations2017b 28064239 LOF 33144586 -SOCS1 1 TRUE drevalGeneticSubdivisionsFollicular2023 NA LOF 15572583 -STAT6 1 yildizActivatingSTAT6Mutations2015c 25428220 GOF 35851155 -TBL1XR1 1 drevalGeneticSubdivisionsFollicular2023 37084389 LOF 32619424 -TMSB4X 1 TRUE drevalGeneticSubdivisionsFollicular2023 37084389 -TNFAIP3 1 drevalGeneticSubdivisionsFollicular2023 37084389 LOF 19412164 -TNFRSF14 1 cheungAcquiredTNFRSF14Mutations2010a 21796119 LOF 21796119 -TP53 1 morinFrequentMutationHistonemodifying2011 21796119 LOF 12826609 +CXCR4 2 TRUE krysiakRecurrentSomaticMutations2017b 28064239 +EGR1 2 krysiakRecurrentSomaticMutations2017b 28064239 +HIST1H2BD 2 TRUE krysiakRecurrentSomaticMutations2017b 28064239 +HIST1H2BM 2 TRUE krysiakRecurrentSomaticMutations2017b 28064239 +HIST1H3G 2 TRUE krysiakRecurrentSomaticMutations2017b 28064239 +HIST1H3I 2 TRUE krysiakRecurrentSomaticMutations2017b 28064239 +ZNF608 2 krysiakRecurrentSomaticMutations2017b 28064239 +CTSS 1 barariaCathepsinAlterationsInduce2020c 32330423 GOF 32330455 +EEF1A1 1 hubschmannMutationalMechanismsShaping2021b 33953289 VMA21 1 hubschmannMutationalMechanismsShaping2021b 33953289 LOF 35287545 -ABL2 2 russler-germainMutationsAssociatedProgression2023b 37563306 ACTG1 2 TRUE hubschmannMutationalMechanismsShaping2021b 33953289 ATP6V1A 2 PASS 4 hubschmannMutationalMechanismsShaping2021b 33953289 -BIRC6 2 NA NA -BTG1 2 TRUE drevalGeneticSubdivisionsFollicular2023 NA -BTG2 2 TRUE drevalGeneticSubdivisionsFollicular2023 21796119 -CD70 2 russler-germainMutationsAssociatedProgression2023b 37493986 -CD79B 2 drevalGeneticSubdivisionsFollicular2023 NA CDC42BPB 2 PASS 3 hubschmannMutationalMechanismsShaping2021b 33953289 -CILP 2 russler-germainMutationsAssociatedProgression2023b 37493986 CPNE8 2 PASS 4 hubschmannMutationalMechanismsShaping2021b 33953289 -CXCR4 2 TRUE krysiakRecurrentSomaticMutations2017b 28064239 -CYP2A6 2 russler-germainMutationsAssociatedProgression2023b 37493986 -DDX3X 2 NA 37084389 DHX15 2 PASS 4 hubschmannMutationalMechanismsShaping2021b 33953289 -DTX1 2 TRUE NA NA -DUSP2 2 TRUE drevalGeneticSubdivisionsFollicular2023 NA -EGR1 2 krysiakRecurrentSomaticMutations2017b 28064239 FZR1 2 PASS 3 hubschmannMutationalMechanismsShaping2021b 33953289 -GBP7 2 russler-germainMutationsAssociatedProgression2023b 37563306 -GRM6 2 russler-germainMutationsAssociatedProgression2023b 37493986 -HIST1H2BD 2 TRUE krysiakRecurrentSomaticMutations2017b 28064239 -HIST1H2BM 2 TRUE krysiakRecurrentSomaticMutations2017b 28064239 -HIST1H3B 2 TRUE NA NA -HIST1H3G 2 TRUE krysiakRecurrentSomaticMutations2017b 28064239 -HIST1H3I 2 TRUE krysiakRecurrentSomaticMutations2017b 28064239 -HLA-B 2 NA NA -IGLL5 2 TRUE russler-germainMutationsAssociatedProgression2023b 37493986 -ITPKB 2 TRUE drevalGeneticSubdivisionsFollicular2023 NA JUP 2 PASS 4 hubschmannMutationalMechanismsShaping2021b 33953289 -KIR3DL1 2 russler-germainMutationsAssociatedProgression2023b 37563306 -KLF2 2 TRUE drevalGeneticSubdivisionsFollicular2023 NA LAPTM5 2 PASS 4 hubschmannMutationalMechanismsShaping2021b 33953289 -LTB 2 TRUE drevalGeneticSubdivisionsFollicular2023 NA -MAGEC1 2 russler-germainMutationsAssociatedProgression2023b 37563306 -MAP7D1 2 russler-germainMutationsAssociatedProgression2023b 37563306 -MEF2C 2 TRUE NA NA MGEA5 2 PASS 3 hubschmannMutationalMechanismsShaping2021b 33953289 -MKI67 2 russler-germainMutationsAssociatedProgression2023b 37493986 MYCBP2 2 PASS 4 hubschmannMutationalMechanismsShaping2021b 33953289 -MYD88 2 drevalGeneticSubdivisionsFollicular2023 NA -NFKBIA 2 russler-germainMutationsAssociatedProgression2023b 37493986 -OR8H2 2 russler-germainMutationsAssociatedProgression2023b 37493986 -P2RY8 2 drevalGeneticSubdivisionsFollicular2023 NA PDS5B 2 PASS 3 hubschmannMutationalMechanismsShaping2021b 33953289 PPP4C 2 PASS 4 hubschmannMutationalMechanismsShaping2021b 33953289 PRKDC 2 hubschmannMutationalMechanismsShaping2021b 33953289 -PTPRD 2 drevalGeneticSubdivisionsFollicular2023 NA -PZP 2 russler-germainMutationsAssociatedProgression2023b 37493986 RBM6 2 hubschmannMutationalMechanismsShaping2021b 33953289 -S1PR2 2 TRUE drevalGeneticSubdivisionsFollicular2023 NA +TPP1 2 hubschmannMutationalMechanismsShaping2021b 33953289 +ACTB 1 TRUE drevalGeneticSubdivisionsFollicular2023 37084389 +BCL6 1 TRUE drevalGeneticSubdivisionsFollicular2023 37084389 LOF 12504096 +EBF1 1 TRUE drevalGeneticSubdivisionsFollicular2023 37084389 LOF 28692033 +GNAI2 1 drevalGeneticSubdivisionsFollicular2023 37084389 +IRF4 1 TRUE drevalGeneticSubdivisionsFollicular2023 37084389 +TBL1XR1 1 drevalGeneticSubdivisionsFollicular2023 37084389 LOF 32619424 +TMSB4X 1 TRUE drevalGeneticSubdivisionsFollicular2023 37084389 +TNFAIP3 1 drevalGeneticSubdivisionsFollicular2023 37084389 LOF 19412164 +DDX3X 2 NA 37084389 +BCL10 1 russler-germainMutationsAssociatedProgression2023b 37493986 GOF 35658124 +CD83 1 TRUE russler-germainMutationsAssociatedProgression2023b 37493986 +CD70 2 russler-germainMutationsAssociatedProgression2023b 37493986 +CILP 2 russler-germainMutationsAssociatedProgression2023b 37493986 +CYP2A6 2 russler-germainMutationsAssociatedProgression2023b 37493986 +GRM6 2 russler-germainMutationsAssociatedProgression2023b 37493986 +IGLL5 2 TRUE russler-germainMutationsAssociatedProgression2023b 37493986 +MKI67 2 russler-germainMutationsAssociatedProgression2023b 37493986 +NFKBIA 2 russler-germainMutationsAssociatedProgression2023b 37493986 +OR8H2 2 russler-germainMutationsAssociatedProgression2023b 37493986 +PZP 2 russler-germainMutationsAssociatedProgression2023b 37493986 SHROOM3 2 russler-germainMutationsAssociatedProgression2023b 37493986 SRRM2 2 russler-germainMutationsAssociatedProgression2023b 37493986 STAB2 2 russler-germainMutationsAssociatedProgression2023b 37493986 -TMEM30A 2 morinFrequentMutationHistonemodifying2011 21796119 -TPP1 2 hubschmannMutationalMechanismsShaping2021b 33953289 XIRP2 2 russler-germainMutationsAssociatedProgression2023b 37493986 +ABL2 2 russler-germainMutationsAssociatedProgression2023b 37563306 +GBP7 2 russler-germainMutationsAssociatedProgression2023b 37563306 +KIR3DL1 2 russler-germainMutationsAssociatedProgression2023b 37563306 +MAGEC1 2 russler-germainMutationsAssociatedProgression2023b 37563306 +MAP7D1 2 russler-germainMutationsAssociatedProgression2023b 37563306 +MYC 1 TRUE NA NA GOF 38565249 +PIM1 1 TRUE drevalGeneticSubdivisionsFollicular2023 NA GOF 27904766 +RRAGC 1 okosunRecurrentMTORC1activatingRRAGC2016a NA GOF 26691987 +SOCS1 1 TRUE drevalGeneticSubdivisionsFollicular2023 NA LOF 15572583 +BIRC6 2 NA NA +BTG1 2 TRUE drevalGeneticSubdivisionsFollicular2023 NA +CD79B 2 drevalGeneticSubdivisionsFollicular2023 NA +DTX1 2 TRUE NA NA +DUSP2 2 TRUE drevalGeneticSubdivisionsFollicular2023 NA +HIST1H3B 2 TRUE NA NA +HLA-B 2 NA NA +ITPKB 2 TRUE drevalGeneticSubdivisionsFollicular2023 NA +KLF2 2 TRUE drevalGeneticSubdivisionsFollicular2023 NA +LTB 2 TRUE drevalGeneticSubdivisionsFollicular2023 NA +MEF2C 2 TRUE NA NA +MYD88 2 drevalGeneticSubdivisionsFollicular2023 NA +P2RY8 2 drevalGeneticSubdivisionsFollicular2023 NA +PTPRD 2 drevalGeneticSubdivisionsFollicular2023 NA +S1PR2 2 TRUE drevalGeneticSubdivisionsFollicular2023 NA ZC3H12A 2 NA NA -ZNF608 2 krysiakRecurrentSomaticMutations2017b 28064239 \ No newline at end of file +Gene Tier aSHM QC Mean Variant Quality citekey PMID MutationEffect Mutation-PMID \ No newline at end of file From 2abfa359157ece8d85a3e23bb3cd44de7b7ddd56 Mon Sep 17 00:00:00 2001 From: Krysta Coyle Date: Tue, 3 Sep 2024 15:29:14 -0700 Subject: [PATCH 3/3] resorted to original format --- resources/curated/fl_genes.tsv | 150 ++++++++++++++++----------------- 1 file changed, 75 insertions(+), 75 deletions(-) diff --git a/resources/curated/fl_genes.tsv b/resources/curated/fl_genes.tsv index a99c27be..16f7e632 100644 --- a/resources/curated/fl_genes.tsv +++ b/resources/curated/fl_genes.tsv @@ -1,31 +1,29 @@ -EZH2 1 morinSomaticMutationsAltering2010a 20081860 GOF 21078963 -CREBBP 1 pasqualucciInactivatingMutationsAcetyltransferase2011a 21390126 LOF 21390126 -EP300 1 pasqualucciInactivatingMutationsAcetyltransferase2011a 21390126 LOF 21390126 +Gene Tier aSHM QC Mean Variant Quality citekey PMID MutationEffect Mutation-PMID +ACTB 1 TRUE drevalGeneticSubdivisionsFollicular2023 37084389 +ARID1A 1 krysiakRecurrentSomaticMutations2017b 28064239 LOF 38458187 +ATP6AP1 1 okosunRecurrentMTORC1activatingRRAGC2016a 26691987 +ATP6V1B2 1 okosunRecurrentMTORC1activatingRRAGC2016a 26691987 LOF 28064239 B2M 1 morinFrequentMutationHistonemodifying2011 21796119 LOF 22137796 +BCL10 1 russler-germainMutationsAssociatedProgression2023b 37493986 GOF 35658124 BCL2 1 TRUE morinFrequentMutationHistonemodifying2011 21796119 +BCL6 1 TRUE drevalGeneticSubdivisionsFollicular2023 37084389 LOF 12504096 +BCL7A 1 TRUE krysiakRecurrentSomaticMutations2017b 28064239 LOF 32576963 +BTK 1 krysiakRecurrentSomaticMutations2017b 28064239 LOF 33419778 CARD11 1 morinFrequentMutationHistonemodifying2011 21796119 GOF 18323416 CCND3 1 morinFrequentMutationHistonemodifying2011 21796119 GOF 22885699 +CD83 1 TRUE russler-germainMutationsAssociatedProgression2023b 37493986 +CREBBP 1 pasqualucciInactivatingMutationsAcetyltransferase2011a 21390126 LOF 21390126 +CTSS 1 barariaCathepsinAlterationsInduce2020c 32330423 GOF 32330455 +EBF1 1 TRUE drevalGeneticSubdivisionsFollicular2023 37084389 LOF 28692033 +EEF1A1 1 hubschmannMutationalMechanismsShaping2021b 33953289 +EP300 1 pasqualucciInactivatingMutationsAcetyltransferase2011a 21390126 LOF 21390126 +EZH2 1 morinSomaticMutationsAltering2010a 20081860 GOF 21078963 FAS 1 morinFrequentMutationHistonemodifying2011 21796119 LOF 20935634 FOXO1 1 morinFrequentMutationHistonemodifying2011 21796119 GOF 23460611 GNA13 1 morinFrequentMutationHistonemodifying2011 21796119 LOF 26616858 -HIST1H1C 1 TRUE morinFrequentMutationHistonemodifying2011 21796119 -IRF8 1 TRUE morinFrequentMutationHistonemodifying2011 21796119 LOF 38996030 -KLHL6 1 TRUE morinFrequentMutationHistonemodifying2011 21796119 LOF 29695787 -KMT2D 1 morinFrequentMutationHistonemodifying2011 21796119 LOF 26366712 -MEF2B 1 TRUE morinFrequentMutationHistonemodifying2011 21796119 NEO 23974956; 26245647 -SGK1 1 TRUE morinFrequentMutationHistonemodifying2011 21796119 GOF 33988691 -TNFRSF14 1 cheungAcquiredTNFRSF14Mutations2010a 21796119 -TP53 1 morinFrequentMutationHistonemodifying2011 21796119 LOF 12826609 -BTG2 2 TRUE drevalGeneticSubdivisionsFollicular2023 21796119 -TMEM30A 2 morinFrequentMutationHistonemodifying2011 21796119 -STAT6 1 yildizActivatingSTAT6Mutations2015c 25428220 GOF 35851155 -ATP6AP1 1 okosunRecurrentMTORC1activatingRRAGC2016a 26691987 -ATP6V1B2 1 okosunRecurrentMTORC1activatingRRAGC2016a 26691987 LOF 28064239 -MAP2K1 1 louissaintPediatrictypeNodalFollicular2016a 27325104 GOF 28533310 -ARID1A 1 krysiakRecurrentSomaticMutations2017b 28064239 LOF 38458187 -BCL7A 1 TRUE krysiakRecurrentSomaticMutations2017b 28064239 LOF 32576963 -BTK 1 krysiakRecurrentSomaticMutations2017b 28064239 LOF 33419778 +GNAI2 1 drevalGeneticSubdivisionsFollicular2023 37084389 HIST1H1B 1 TRUE krysiakRecurrentSomaticMutations2017b 28064239 +HIST1H1C 1 TRUE morinFrequentMutationHistonemodifying2011 21796119 HIST1H1D 1 TRUE krysiakRecurrentSomaticMutations2017b 28064239 HIST1H1E 1 TRUE krysiakRecurrentSomaticMutations2017b 28064239 HIST1H2AC 1 TRUE krysiakRecurrentSomaticMutations2017b 28064239 @@ -34,81 +32,83 @@ HIST1H2AM 1 TRUE krysiakRecurrentSomaticMutations2017b 28064239 HIST1H2BC 1 TRUE krysiakRecurrentSomaticMutations2017b 28064239 HIST1H2BG 1 TRUE krysiakRecurrentSomaticMutations2017b 28064239 HVCN1 1 krysiakRecurrentSomaticMutations2017b 28064239 +IRF4 1 TRUE drevalGeneticSubdivisionsFollicular2023 37084389 +IRF8 1 TRUE morinFrequentMutationHistonemodifying2011 21796119 LOF 38996030 +KLHL6 1 TRUE morinFrequentMutationHistonemodifying2011 21796119 LOF 29695787 +KMT2D 1 morinFrequentMutationHistonemodifying2011 21796119 LOF 26366712 +MAP2K1 1 louissaintPediatrictypeNodalFollicular2016a 27325104 GOF 28533310 +MEF2B 1 TRUE morinFrequentMutationHistonemodifying2011 21796119 NEO 23974956; 26245647 +MYC 1 TRUE NA NA GOF 38565249 +PIM1 1 TRUE drevalGeneticSubdivisionsFollicular2023 NA GOF 27904766 POU2AF1 1 krysiakRecurrentSomaticMutations2017b 28064239 POU2F2 1 krysiakRecurrentSomaticMutations2017b 28064239 LOF 26993806 +RRAGC 1 okosunRecurrentMTORC1activatingRRAGC2016a NA GOF 26691987 +SGK1 1 TRUE morinFrequentMutationHistonemodifying2011 21796119 GOF 33988691 SMARCA4 1 krysiakRecurrentSomaticMutations2017b 28064239 LOF 33144586 -CXCR4 2 TRUE krysiakRecurrentSomaticMutations2017b 28064239 -EGR1 2 krysiakRecurrentSomaticMutations2017b 28064239 -HIST1H2BD 2 TRUE krysiakRecurrentSomaticMutations2017b 28064239 -HIST1H2BM 2 TRUE krysiakRecurrentSomaticMutations2017b 28064239 -HIST1H3G 2 TRUE krysiakRecurrentSomaticMutations2017b 28064239 -HIST1H3I 2 TRUE krysiakRecurrentSomaticMutations2017b 28064239 -ZNF608 2 krysiakRecurrentSomaticMutations2017b 28064239 -CTSS 1 barariaCathepsinAlterationsInduce2020c 32330423 GOF 32330455 -EEF1A1 1 hubschmannMutationalMechanismsShaping2021b 33953289 -VMA21 1 hubschmannMutationalMechanismsShaping2021b 33953289 LOF 35287545 -ACTG1 2 TRUE hubschmannMutationalMechanismsShaping2021b 33953289 -ATP6V1A 2 PASS 4 hubschmannMutationalMechanismsShaping2021b 33953289 -CDC42BPB 2 PASS 3 hubschmannMutationalMechanismsShaping2021b 33953289 -CPNE8 2 PASS 4 hubschmannMutationalMechanismsShaping2021b 33953289 -DHX15 2 PASS 4 hubschmannMutationalMechanismsShaping2021b 33953289 -FZR1 2 PASS 3 hubschmannMutationalMechanismsShaping2021b 33953289 -JUP 2 PASS 4 hubschmannMutationalMechanismsShaping2021b 33953289 -LAPTM5 2 PASS 4 hubschmannMutationalMechanismsShaping2021b 33953289 -MGEA5 2 PASS 3 hubschmannMutationalMechanismsShaping2021b 33953289 -MYCBP2 2 PASS 4 hubschmannMutationalMechanismsShaping2021b 33953289 -PDS5B 2 PASS 3 hubschmannMutationalMechanismsShaping2021b 33953289 -PPP4C 2 PASS 4 hubschmannMutationalMechanismsShaping2021b 33953289 -PRKDC 2 hubschmannMutationalMechanismsShaping2021b 33953289 -RBM6 2 hubschmannMutationalMechanismsShaping2021b 33953289 -TPP1 2 hubschmannMutationalMechanismsShaping2021b 33953289 -ACTB 1 TRUE drevalGeneticSubdivisionsFollicular2023 37084389 -BCL6 1 TRUE drevalGeneticSubdivisionsFollicular2023 37084389 LOF 12504096 -EBF1 1 TRUE drevalGeneticSubdivisionsFollicular2023 37084389 LOF 28692033 -GNAI2 1 drevalGeneticSubdivisionsFollicular2023 37084389 -IRF4 1 TRUE drevalGeneticSubdivisionsFollicular2023 37084389 +SOCS1 1 TRUE drevalGeneticSubdivisionsFollicular2023 NA LOF 15572583 +STAT6 1 yildizActivatingSTAT6Mutations2015c 25428220 GOF 35851155 TBL1XR1 1 drevalGeneticSubdivisionsFollicular2023 37084389 LOF 32619424 TMSB4X 1 TRUE drevalGeneticSubdivisionsFollicular2023 37084389 TNFAIP3 1 drevalGeneticSubdivisionsFollicular2023 37084389 LOF 19412164 -DDX3X 2 NA 37084389 -BCL10 1 russler-germainMutationsAssociatedProgression2023b 37493986 GOF 35658124 -CD83 1 TRUE russler-germainMutationsAssociatedProgression2023b 37493986 -CD70 2 russler-germainMutationsAssociatedProgression2023b 37493986 -CILP 2 russler-germainMutationsAssociatedProgression2023b 37493986 -CYP2A6 2 russler-germainMutationsAssociatedProgression2023b 37493986 -GRM6 2 russler-germainMutationsAssociatedProgression2023b 37493986 -IGLL5 2 TRUE russler-germainMutationsAssociatedProgression2023b 37493986 -MKI67 2 russler-germainMutationsAssociatedProgression2023b 37493986 -NFKBIA 2 russler-germainMutationsAssociatedProgression2023b 37493986 -OR8H2 2 russler-germainMutationsAssociatedProgression2023b 37493986 -PZP 2 russler-germainMutationsAssociatedProgression2023b 37493986 -SHROOM3 2 russler-germainMutationsAssociatedProgression2023b 37493986 -SRRM2 2 russler-germainMutationsAssociatedProgression2023b 37493986 -STAB2 2 russler-germainMutationsAssociatedProgression2023b 37493986 -XIRP2 2 russler-germainMutationsAssociatedProgression2023b 37493986 +TNFRSF14 1 cheungAcquiredTNFRSF14Mutations2010a 21796119 +TP53 1 morinFrequentMutationHistonemodifying2011 21796119 LOF 12826609 +VMA21 1 hubschmannMutationalMechanismsShaping2021b 33953289 LOF 35287545 ABL2 2 russler-germainMutationsAssociatedProgression2023b 37563306 -GBP7 2 russler-germainMutationsAssociatedProgression2023b 37563306 -KIR3DL1 2 russler-germainMutationsAssociatedProgression2023b 37563306 -MAGEC1 2 russler-germainMutationsAssociatedProgression2023b 37563306 -MAP7D1 2 russler-germainMutationsAssociatedProgression2023b 37563306 -MYC 1 TRUE NA NA GOF 38565249 -PIM1 1 TRUE drevalGeneticSubdivisionsFollicular2023 NA GOF 27904766 -RRAGC 1 okosunRecurrentMTORC1activatingRRAGC2016a NA GOF 26691987 -SOCS1 1 TRUE drevalGeneticSubdivisionsFollicular2023 NA LOF 15572583 +ACTG1 2 TRUE hubschmannMutationalMechanismsShaping2021b 33953289 +ATP6V1A 2 PASS 4 hubschmannMutationalMechanismsShaping2021b 33953289 BIRC6 2 NA NA BTG1 2 TRUE drevalGeneticSubdivisionsFollicular2023 NA +BTG2 2 TRUE drevalGeneticSubdivisionsFollicular2023 21796119 +CD70 2 russler-germainMutationsAssociatedProgression2023b 37493986 CD79B 2 drevalGeneticSubdivisionsFollicular2023 NA +CDC42BPB 2 PASS 3 hubschmannMutationalMechanismsShaping2021b 33953289 +CILP 2 russler-germainMutationsAssociatedProgression2023b 37493986 +CPNE8 2 PASS 4 hubschmannMutationalMechanismsShaping2021b 33953289 +CXCR4 2 TRUE krysiakRecurrentSomaticMutations2017b 28064239 +CYP2A6 2 russler-germainMutationsAssociatedProgression2023b 37493986 +DDX3X 2 NA 37084389 +DHX15 2 PASS 4 hubschmannMutationalMechanismsShaping2021b 33953289 DTX1 2 TRUE NA NA DUSP2 2 TRUE drevalGeneticSubdivisionsFollicular2023 NA +EGR1 2 krysiakRecurrentSomaticMutations2017b 28064239 +FZR1 2 PASS 3 hubschmannMutationalMechanismsShaping2021b 33953289 +GBP7 2 russler-germainMutationsAssociatedProgression2023b 37563306 +GRM6 2 russler-germainMutationsAssociatedProgression2023b 37493986 +HIST1H2BD 2 TRUE krysiakRecurrentSomaticMutations2017b 28064239 +HIST1H2BM 2 TRUE krysiakRecurrentSomaticMutations2017b 28064239 HIST1H3B 2 TRUE NA NA +HIST1H3G 2 TRUE krysiakRecurrentSomaticMutations2017b 28064239 +HIST1H3I 2 TRUE krysiakRecurrentSomaticMutations2017b 28064239 HLA-B 2 NA NA +IGLL5 2 TRUE russler-germainMutationsAssociatedProgression2023b 37493986 ITPKB 2 TRUE drevalGeneticSubdivisionsFollicular2023 NA +JUP 2 PASS 4 hubschmannMutationalMechanismsShaping2021b 33953289 +KIR3DL1 2 russler-germainMutationsAssociatedProgression2023b 37563306 KLF2 2 TRUE drevalGeneticSubdivisionsFollicular2023 NA +LAPTM5 2 PASS 4 hubschmannMutationalMechanismsShaping2021b 33953289 LTB 2 TRUE drevalGeneticSubdivisionsFollicular2023 NA +MAGEC1 2 russler-germainMutationsAssociatedProgression2023b 37563306 +MAP7D1 2 russler-germainMutationsAssociatedProgression2023b 37563306 MEF2C 2 TRUE NA NA +MGEA5 2 PASS 3 hubschmannMutationalMechanismsShaping2021b 33953289 +MKI67 2 russler-germainMutationsAssociatedProgression2023b 37493986 +MYCBP2 2 PASS 4 hubschmannMutationalMechanismsShaping2021b 33953289 MYD88 2 drevalGeneticSubdivisionsFollicular2023 NA +NFKBIA 2 russler-germainMutationsAssociatedProgression2023b 37493986 +OR8H2 2 russler-germainMutationsAssociatedProgression2023b 37493986 P2RY8 2 drevalGeneticSubdivisionsFollicular2023 NA +PDS5B 2 PASS 3 hubschmannMutationalMechanismsShaping2021b 33953289 +PPP4C 2 PASS 4 hubschmannMutationalMechanismsShaping2021b 33953289 +PRKDC 2 hubschmannMutationalMechanismsShaping2021b 33953289 PTPRD 2 drevalGeneticSubdivisionsFollicular2023 NA +PZP 2 russler-germainMutationsAssociatedProgression2023b 37493986 +RBM6 2 hubschmannMutationalMechanismsShaping2021b 33953289 S1PR2 2 TRUE drevalGeneticSubdivisionsFollicular2023 NA +SHROOM3 2 russler-germainMutationsAssociatedProgression2023b 37493986 +SRRM2 2 russler-germainMutationsAssociatedProgression2023b 37493986 +STAB2 2 russler-germainMutationsAssociatedProgression2023b 37493986 +TMEM30A 2 morinFrequentMutationHistonemodifying2011 21796119 +TPP1 2 hubschmannMutationalMechanismsShaping2021b 33953289 +XIRP2 2 russler-germainMutationsAssociatedProgression2023b 37493986 ZC3H12A 2 NA NA -Gene Tier aSHM QC Mean Variant Quality citekey PMID MutationEffect Mutation-PMID \ No newline at end of file +ZNF608 2 krysiakRecurrentSomaticMutations2017b 28064239 \ No newline at end of file