f8f005c7982006dd801fe213fadfef3dae9825ce
DLBCL_genes_temp.md
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| 1 | ---- |
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| 2 | -title: 'DLBCL genes' |
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| 3 | -bibliography: 'morinlab.bib' |
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| 4 | -csl: 'NLM.csl' |
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| 5 | -link-citations: true |
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| 6 | ---- |
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| 7 | - |
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| 8 | -# DLBCL genes |
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| 9 | - |
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| 10 | -## Origins of DLBCL genes |
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| 11 | - |
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| 12 | -## Tier 1 DLBCL genes |
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| 13 | - |
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| 14 | -### *128 total* |
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| 15 | - |
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| 16 | -|Gene|Tier| Relevant references| |
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| 17 | -|:-:|:-:|:-| |
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| 18 | -|[ACTB](ACTB)|1, aSHM|[@wienandGenomicAnalysesFlowsorted2019b; @lohrDiscoveryPrioritizationSomatic2012a]| |
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| 19 | -|[ACTG1](ACTG1)|1, aSHM|[@spinaGeneticsNodalMarginal2016b; @deschGenotypingCirculatingTumor2020; @hubschmannMutationalMechanismsShaping2021b]| |
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| 20 | -|[ARID1A](ARID1A)|1|[@rossiCodingGenomeSplenic2012c; @wienandGenomicAnalysesFlowsorted2019b; @loveGeneticLandscapeMutations2012; @zhangGeneticHeterogeneityDiffuse2013; @krysiakRecurrentSomaticMutations2017b]| |
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| 21 | -|[ATM](ATM)|1|[@braggioGenomicAnalysisMarginal2012; @beaLandscapeSomaticMutations2013; @reddyGeneticFunctionalDrivers2017]| |
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| 22 | -|[B2M](B2M)|1|[@pararajalingamCodingNoncodingDrivers2020; @reichelFlowSortingExome2015a; @morinFrequentMutationHistonemodifying2011]| |
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| 23 | -|[BCL10](BCL10)|1|[@morinFrequentMutationHistonemodifying2011; @russler-germainMutationsAssociatedProgression2023b; @spinaGeneticsNodalMarginal2016b]| |
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| 24 | -|[BCL2](BCL2)|1, aSHM|[@sarkozyMutationalLandscapeGray2021a; @tanakaFrequentIncidenceSomatic1992; @burkhardtClinicalRelevanceMolecular2022b; @morinFrequentMutationHistonemodifying2011]| |
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| 25 | -|[BCL6](BCL6)|1, aSHM|[@morinFrequentMutationHistonemodifying2011; @loveGeneticLandscapeMutations2012]| |
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| 26 | -|[BCL7A](BCL7A)|1, aSHM|[@reichelFlowSortingExome2015a; @krysiakRecurrentSomaticMutations2017b; @arthurGenomewideDiscoverySomatic2018; @grandeGenomewideDiscoverySomatic2019]| |
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| 27 | -|[BIRC6](BIRC6)|1|[@reddyGeneticFunctionalDrivers2017; @sarkozyMutationalLandscapeGray2021a]| |
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| 28 | -|[BRAF](BRAF)|1|[@loveGeneticLandscapeMutations2012; @tiacciBRAFMutationsHairycell2011a]| |
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| 29 | -|[BTG1](BTG1)|1, aSHM|[@morinFrequentMutationHistonemodifying2011; @burkhardtClinicalRelevanceMolecular2022b; @sarkozyMutationalLandscapeGray2021a]| |
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| 30 | -|[BTG2](BTG2)|1, aSHM|[@morinFrequentMutationHistonemodifying2011; @loveGeneticLandscapeMutations2012]| |
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| 31 | -|[BTK](BTK)|1|[@krysiakRecurrentSomaticMutations2017b; @albuquerqueEnhancingKnowledgeDiscovery2017a]| |
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| 32 | -|[CARD11](CARD11)|1|[@wuGeneticHeterogeneityPrimary2016; @paneaWholeGenomeLandscape2019; @lenzOncogenicCARD11Mutations2008; @yanBCRTLRSignaling2012a; @morinFrequentMutationHistonemodifying2011]| |
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| 33 | -|[CCND3](CCND3)|1|[@jalladesExomeSequencingIdentifies2017; @richterRecurrentMutationID32012a; @deschGenotypingCirculatingTumor2020; @morinFrequentMutationHistonemodifying2011]| |
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| 34 | -|[CD58](CD58)|1|[@morinFrequentMutationHistonemodifying2011; @schneiderAlterationsCD58Gene2015a]| |
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| 35 | -|[CD70](CD70)|1|[@russler-germainMutationsAssociatedProgression2023b; @morinFrequentMutationHistonemodifying2011]| |
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| 36 | -|[CD79B](CD79B)|1|[@morinFrequentMutationHistonemodifying2011; @paneaWholeGenomeLandscape2019]| |
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| 37 | -|[CD83](CD83)|1, aSHM|[@russler-germainMutationsAssociatedProgression2023b; @morinMutationalStructuralAnalysis2013; @dunsCharacterizationDLBCLPMBL2021b; @paneaWholeGenomeLandscape2019]| |
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| 38 | -|[CDKN2A](CDKN2A)|1|[@grandeGenomewideDiscoverySomatic2019; @spinaGeneticsNodalMarginal2016b; @morinMutationalStructuralAnalysis2013]| |
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| 39 | -|[CIITA](CIITA)|1, aSHM|[@mottokGenomicAlterationsCIITA2015b; @morinFrequentMutationHistonemodifying2011]| |
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| 40 | -|[CREBBP](CREBBP)|1|[@dunsCharacterizationDLBCLPMBL2021b; @pasqualucciInactivatingMutationsAcetyltransferase2011a; @loveGeneticLandscapeMutations2012; @parryWholeExomeSequencing2013]| |
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| 41 | -|[CXCR4](CXCR4)|1, aSHM|[@khodabakhshiRecurrentTargetsAberrant2012; @paneaWholeGenomeLandscape2019; @krysiakRecurrentSomaticMutations2017b]| |
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| 42 | -|[CXCR5](CXCR5)|1|[@schmitzGeneticsPathogenesisDiffuse2018a; @mottokIntegrativeGenomicAnalysis2019b]| |
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| 43 | -|[DDX3X](DDX3X)|1|[@schmitzBurkittLymphomaPathogenesis2012; @mottokIntegrativeGenomicAnalysis2019b; @schmitzGeneticsPathogenesisDiffuse2018a]| |
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| 44 | -|[DTX1](DTX1)|1, aSHM|[@paneaWholeGenomeLandscape2019; @gomezUltraDeepSequencingReveals2023; @schmitzGeneticsPathogenesisDiffuse2018a; @rossiCodingGenomeSplenic2012c]| |
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| 45 | -|[DUSP2](DUSP2)|1, aSHM|[@dunsCharacterizationDLBCLPMBL2021b; @morinMutationalStructuralAnalysis2013]| |
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| 46 | -|[EBF1](EBF1)|1, aSHM|[@reichelFlowSortingExome2015a; @bohleRoleEarlyBcell2013; @thomasGeneticSubgroupsInform2023]| |
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| 47 | -|[EEF1A1](EEF1A1)|1|[@hubschmannMutationalMechanismsShaping2021b; @reichelFlowSortingExome2015a]| |
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| 48 | -|[EP300](EP300)|1|[@rossiCodingGenomeSplenic2012c; @paneaWholeGenomeLandscape2019; @pasqualucciInactivatingMutationsAcetyltransferase2011a]| |
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| 49 | -|[ETS1](ETS1)|1, aSHM|[@paneaWholeGenomeLandscape2019; @morinFrequentMutationHistonemodifying2011]| |
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| 50 | -|[ETV6](ETV6)|1, aSHM|[@arthurGenomewideDiscoverySomatic2018]| |
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| 51 | -|[EZH2](EZH2)|1|[@morinSomaticMutationsAltering2010a; @mottokIntegrativeGenomicAnalysis2019b; @loveGeneticLandscapeMutations2012]| |
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| 52 | -|[FAS](FAS)|1|[@schollMutationsRegionFAS2007; @spinaGeneticsNodalMarginal2016b]| |
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| 53 | -|[FBXO11](FBXO11)|1|[@richterRecurrentMutationID32012a; @hubschmannMutationalMechanismsShaping2021b; @parryWholeExomeSequencing2013]| |
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| 54 | -|[FBXW7](FBXW7)|1|[@zhangGeneticHeterogeneityDiffuse2013]| |
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| 55 | -|[FOXO1](FOXO1)|1|[@schmitzBurkittLymphomaPathogenesis2012; @morinFrequentMutationHistonemodifying2011; @dunsCharacterizationDLBCLPMBL2021b]| |
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| 56 | -|[GNA13](GNA13)|1|[@loveGeneticLandscapeMutations2012; @morinFrequentMutationHistonemodifying2011; @reichelFlowSortingExome2015a]| |
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| 57 | -|[GNAI2](GNAI2)|1|[@grandeGenomewideDiscoverySomatic2019; @morinMutationalStructuralAnalysis2013]| |
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| 58 | -|[GRB2](GRB2)|1|[@paneaWholeGenomeLandscape2019; @pasqualucciAnalysisCodingGenome2011]| |
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| 59 | -|[GRHPR](GRHPR)|1, aSHM|[@arthurGenomewideDiscoverySomatic2018]| |
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| 60 | -|[HIST1H1B](HIST1H1B)|1, aSHM|[@krysiakRecurrentSomaticMutations2017b; @sarkozyMutationalLandscapeGray2021a; @chapuyMolecularSubtypesDiffuse2018b]| |
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| 61 | -|[HIST1H1C](HIST1H1C)|1, aSHM|[@morinFrequentMutationHistonemodifying2011; @paneaWholeGenomeLandscape2019]| |
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| 62 | -|[HIST1H1D](HIST1H1D)|1, aSHM|[@krysiakRecurrentSomaticMutations2017b; @jalladesExomeSequencingIdentifies2017; @morinMutationalStructuralAnalysis2013]| |
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| 63 | -|[HIST1H1E](HIST1H1E)|1, aSHM|[@morinMutationalStructuralAnalysis2013; @reichelFlowSortingExome2015a; @grandeGenomewideDiscoverySomatic2019; @krysiakRecurrentSomaticMutations2017b]| |
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| 64 | -|[HIST1H2AC](HIST1H2AC)|1, aSHM|[@krysiakRecurrentSomaticMutations2017b; @morinMutationalStructuralAnalysis2013]| |
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| 65 | -|[HIST1H2AM](HIST1H2AM)|1, aSHM|[@paneaWholeGenomeLandscape2019; @krysiakRecurrentSomaticMutations2017b]| |
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| 66 | -|[HIST1H2BC](HIST1H2BC)|1, aSHM|[@krysiakRecurrentSomaticMutations2017b; @mottokIntegrativeGenomicAnalysis2019b; @reddyGeneticFunctionalDrivers2017]| |
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| 67 | -|[HIST1H2BK](HIST1H2BK)|1, aSHM|[@paneaWholeGenomeLandscape2019; @rossiCodingGenomeSplenic2012c]| |
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| 68 | -|[HIST1H3B](HIST1H3B)|1, aSHM|[@zhangGeneticHeterogeneityDiffuse2013; @reichelFlowSortingExome2015a]| |
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| 69 | -|[HIST2H2BE](HIST2H2BE)|1, aSHM|[@schmitzGeneticsPathogenesisDiffuse2018a]| |
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| 70 | -|[HLA-A](HLA-A)|1|[@deschGenotypingCirculatingTumor2020]| |
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| 71 | -|[HLA-B](HLA-B)|1|[@wienandGenomicAnalysesFlowsorted2019b]| |
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| 72 | -|[HLA-C](HLA-C)|1|[@gomezUltraDeepSequencingReveals2023]| |
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| 73 | -|[HLA-DMB](HLA-DMB)|1|| |
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| 74 | -|[HNRNPU](HNRNPU)|1, aSHM|[@paneaWholeGenomeLandscape2019; @reddyGeneticFunctionalDrivers2017]| |
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| 75 | -|[HVCN1](HVCN1)|1|[@krysiakRecurrentSomaticMutations2017b]| |
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| 76 | -|[IKZF3](IKZF3)|1|[@morinMutationalStructuralAnalysis2013; @paneaWholeGenomeLandscape2019]| |
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| 77 | -|[IL4R](IL4R)|1, aSHM|[@dunsCharacterizationDLBCLPMBL2021b; @viganoSomaticIL4RMutations2018b]| |
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| 78 | -|[IRF4](IRF4)|1, aSHM|[@mottokIntegrativeGenomicAnalysis2019b; @morinFrequentMutationHistonemodifying2011]| |
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| 79 | -|[IRF8](IRF8)|1, aSHM|[@paneaWholeGenomeLandscape2019; @morinFrequentMutationHistonemodifying2011; @mottokIntegrativeGenomicAnalysis2019b]| |
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| 80 | -|[ITPKB](ITPKB)|1, aSHM|[@schmitzGeneticsPathogenesisDiffuse2018a; @reichelFlowSortingExome2015a]| |
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| 81 | -|[KLF2](KLF2)|1, aSHM|[@deschGenotypingCirculatingTumor2020; @jalladesExomeSequencingIdentifies2017; @pasqualucciAnalysisCodingGenome2011]| |
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| 82 | -|[KLHL14](KLHL14)|1|[@zhangGeneticHeterogeneityDiffuse2013]| |
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| 83 | -|[KLHL6](KLHL6)|1, aSHM|[@paneaWholeGenomeLandscape2019; @ganapathiGeneticLandscapeDural2016; @morinFrequentMutationHistonemodifying2011]| |
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| 84 | -|[KMT2C](KMT2C)|1|[@zhangGenomicLandscapeMantle2014; @sarkozyMutationalLandscapeGray2021a; @zhouSporadicEndemicBurkitt2019; @zhangGeneticHeterogeneityDiffuse2013]| |
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| 85 | -|[KMT2D](KMT2D)|1|[@deschGenotypingCirculatingTumor2020; @rossiCodingGenomeSplenic2012c; @grandeGenomewideDiscoverySomatic2019; @morinFrequentMutationHistonemodifying2011; @beaLandscapeSomaticMutations2013]| |
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| 86 | -|[KRAS](KRAS)|1|[@lohrDiscoveryPrioritizationSomatic2012a]| |
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| 87 | -|[LCOR](LCOR)|1|[@arthurGenomewideDiscoverySomatic2018]| |
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| 88 | -|[LTB](LTB)|1, aSHM|[@deschGenotypingCirculatingTumor2020; @chapuyMolecularSubtypesDiffuse2018b; @paneaWholeGenomeLandscape2019]| |
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| 89 | -|[MEF2B](MEF2B)|1, aSHM|[@beaLandscapeSomaticMutations2013; @morinFrequentMutationHistonemodifying2011]| |
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| 90 | -|[MEF2C](MEF2C)|1, aSHM|[@arthurGenomewideDiscoverySomatic2018]| |
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| 91 | -|[MGA](MGA)|1|[@jalladesExomeSequencingIdentifies2017; @zhangGeneticHeterogeneityDiffuse2013]| |
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| 92 | -|[MPEG1](MPEG1)|1|[@morinMutationalStructuralAnalysis2013]| |
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| 93 | -|[MS4A1](MS4A1)|1, aSHM|[@rushtonGeneticEvolutionaryPatterns2020; @mottokIntegrativeGenomicAnalysis2019b]| |
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| 94 | -|[MTOR](MTOR)|1|[@zhangGeneticHeterogeneityDiffuse2013; @paneaWholeGenomeLandscape2019]| |
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| 95 | -|[MYC](MYC)|1, aSHM|[@pasqualucciHypermutationMultipleProtooncogenes2001a; @jalladesExomeSequencingIdentifies2017; @dunsCharacterizationDLBCLPMBL2021b; @johnstonCmycHypermutationBurkitt1992]| |
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| 96 | -|[MYD88](MYD88)|1|[@yanBCRTLRSignaling2012a; @ngoOncogenicallyActiveMYD882011a]| |
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| 97 | -|[NFKBIA](NFKBIA)|1|[@lakeMutationsNFKBIAEncoding2009; @wienandGenomicAnalysesFlowsorted2019b; @russler-germainMutationsAssociatedProgression2023b]| |
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| 98 | -|[NFKBIE](NFKBIE)|1|[@morinGeneticLandscapesRelapsed2016; @pararajalingamCodingNoncodingDrivers2020; @mansouriFrequentNFKBIEDeletions2016]| |
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| 99 | -|[NFKBIZ](NFKBIZ)|1, noncoding|[@morinGeneticLandscapesRelapsed2016]| |
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| 100 | -|[NOL9](NOL9)|1, aSHM|[@spinaGeneticsNodalMarginal2016b; @schmitzGeneticsPathogenesisDiffuse2018a]| |
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| 101 | -|[NOTCH1](NOTCH1)|1|[@beaLandscapeSomaticMutations2013; @pasqualucciAnalysisCodingGenome2011; @loveGeneticLandscapeMutations2012; @rossiCodingGenomeSplenic2012c]| |
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| 102 | -|[NOTCH2](NOTCH2)|1|[@rossiCodingGenomeSplenic2012c; @paneaWholeGenomeLandscape2019; @beaLandscapeSomaticMutations2013; @troenNOTCH2MutationsMarginal2008]| |
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| 103 | -|[OSBPL10](OSBPL10)|1, aSHM|[@arthurGenomewideDiscoverySomatic2018]| |
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| 104 | -|[P2RY8](P2RY8)|1|[@muppidiLossSignalingGa132014b; @lohrDiscoveryPrioritizationSomatic2012a]| |
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| 105 | -|[PIM1](PIM1)|1, aSHM|[@pasqualucciHypermutationMultipleProtooncogenes2001a; @dunsCharacterizationDLBCLPMBL2021b; @burkhardtClinicalRelevanceMolecular2022b]| |
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| 106 | -|[PIM2](PIM2)|1, aSHM|[@arthurGenomewideDiscoverySomatic2018; @reichelFlowSortingExome2015a]| |
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| 107 | -|[POU2AF1](POU2AF1)|1, aSHM|[@krysiakRecurrentSomaticMutations2017b]| |
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| 108 | -|[POU2F2](POU2F2)|1|[@krysiakRecurrentSomaticMutations2017b; @zhangGeneticHeterogeneityDiffuse2013]| |
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| 109 | -|[PRDM1](PRDM1)|1|[@pasqualucciInactivationPRDM1BLIMP12006a]| |
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| 110 | -|[PTEN](PTEN)|1|[@loveGeneticLandscapeMutations2012]| |
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| 111 | -|[PTPRD](PTPRD)|1|[@spinaGeneticsNodalMarginal2016b]| |
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| 112 | -|[RB1](RB1)|1|[@zhangGenomicLandscapeMantle2014; @morinMutationalStructuralAnalysis2013]| |
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| 113 | -|[RFX7](RFX7)|1|[@grandeGenomewideDiscoverySomatic2019]| |
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| 114 | -|[RHOA](RHOA)|1|[@richterRecurrentMutationID32012a]| |
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| 115 | -|[RRAGC](RRAGC)|1|[@okosunRecurrentMTORC1activatingRRAGC2016a]| |
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| 116 | -|[S1PR2](S1PR2)|1, aSHM|[@morinFrequentMutationHistonemodifying2011; @muppidiLossSignalingGa132014b]| |
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| 117 | -|[SETD1B](SETD1B)|1|[@reddyGeneticFunctionalDrivers2017]| |
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| 118 | -|[SF3B1](SF3B1)|1|[@loveGeneticLandscapeMutations2012]| |
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| 119 | -|[SGK1](SGK1)|1, aSHM|[@dunsCharacterizationDLBCLPMBL2021b; @morinFrequentMutationHistonemodifying2011]| |
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| 120 | -|[SIN3A](SIN3A)|1|[@grandeGenomewideDiscoverySomatic2019; @rossiCodingGenomeSplenic2012c]| |
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| 121 | -|[SMARCA4](SMARCA4)|1|[@zhangGeneticHeterogeneityDiffuse2013; @nadeuGenomicEpigenomicInsights2020b; @krysiakRecurrentSomaticMutations2017b; @richterRecurrentMutationID32012a]| |
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| 122 | -|[SOCS1](SOCS1)|1, aSHM|[@wenigerMutationsTumorSuppressor2006a; @morinFrequentMutationHistonemodifying2011]| |
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| 123 | -|[SPEN](SPEN)|1|[@sarkozyMutationalLandscapeGray2021a; @rossiCodingGenomeSplenic2012c]| |
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| 124 | -|[STAT3](STAT3)|1|[@ohgamiSTAT3MutationsAre2014]| |
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| 125 | -|[STAT6](STAT6)|1|[@yildizActivatingSTAT6Mutations2015c; @ritzRecurrentMutationsSTAT62009a]| |
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| 126 | -|[TAF1](TAF1)|1|[@spinaGeneticsNodalMarginal2016b; @morinMutationalStructuralAnalysis2013]| |
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| 127 | -|[TBL1XR1](TBL1XR1)|1|[@rossiCodingGenomeSplenic2012c; @mareschalWholeExomeSequencing2016]| |
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| 128 | -|[TET2](TET2)|1|[@albuquerqueEnhancingKnowledgeDiscovery2017a; @paneaWholeGenomeLandscape2019]| |
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| 129 | -|[TMEM30A](TMEM30A)|1|[@morinFrequentMutationHistonemodifying2011]| |
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| 130 | -|[TMSB4X](TMSB4X)|1, aSHM|[@albuquerqueEnhancingKnowledgeDiscovery2017a]| |
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| 131 | -|[TNFAIP3](TNFAIP3)|1|[@schmitzTNFAIP3A20Tumor2009a; @rossiAlterationBIRC3Multiple2011a; @compagnoMutationsMultipleGenes2009a]| |
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| 132 | -|[TNFRSF14](TNFRSF14)|1|[@cheungAcquiredTNFRSF14Mutations2010a; @spinaGeneticsNodalMarginal2016b]| |
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| 133 | -|[TOX](TOX)|1|[@reddyGeneticFunctionalDrivers2017]| |
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| 134 | -|[TP53](TP53)|1|[@wildaInactivationARFMDM2p53Pathway2004; @rossiCodingGenomeSplenic2012c; @tiacciPervasiveMutationsJAKSTAT2018b; @beaLandscapeSomaticMutations2013; @morinFrequentMutationHistonemodifying2011]| |
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| 135 | -|[TRRAP](TRRAP)|1|[@rossiCodingGenomeSplenic2012c; @parryWholeExomeSequencing2013]| |
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| 136 | -|[UBE2A](UBE2A)|1|[@reddyGeneticFunctionalDrivers2017; @reichelFlowSortingExome2015a]| |
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| 137 | -|[UNC5C](UNC5C)|1|| |
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| 138 | -|[USP7](USP7)|1|[@grandeGenomewideDiscoverySomatic2019]| |
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| 139 | -|[VPS13B](VPS13B)|1|| |
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| 140 | -|[WEE1](WEE1)|1|[@schmitzGeneticsPathogenesisDiffuse2018a; @reichelFlowSortingExome2015a]| |
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| 141 | -|[XPO1](XPO1)|1|[@jardinRecurrentMutationsExportin2016a; @mareschalWholeExomeSequencing2016]| |
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| 142 | -|[ZC3H12A](ZC3H12A)|1|[@arthurGenomewideDiscoverySomatic2018]| |
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| 143 | -|[ZFP36L1](ZFP36L1)|1, aSHM|[@morinFrequentMutationHistonemodifying2011; @reichelFlowSortingExome2015a; @paneaWholeGenomeLandscape2019]| |
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| 144 | -|[ZNF292](ZNF292)|1|[@zhangGeneticHeterogeneityDiffuse2013]| |
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| 145 | -|[ZNF608](ZNF608)|1, aSHM|[@zhangGeneticHeterogeneityDiffuse2013; @krysiakRecurrentSomaticMutations2017b]| |
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| 146 | - |
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| 147 | -## Tier 2 DLBCL genes |
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| 148 | -### *198 total* |
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| 149 | -|Gene|Tier| Relevant references| |
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| 150 | -|:-:|:-:|:-| |
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| 151 | -|[ABI3BP](ABI3BP)|2|[@morinMutationalStructuralAnalysis2013]| |
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| 152 | -|[ADAMTS1](ADAMTS1)|2|[@hubschmannMutationalMechanismsShaping2021b]| |
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| 153 | -|[AICDA](AICDA)|2, aSHM|[@arthurGenomewideDiscoverySomatic2018]| |
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| 154 | -|[ANKRD12](ANKRD12)|2|[@hubschmannMutationalMechanismsShaping2021b]| |
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| 155 | -|[ANKRD17](ANKRD17)|2|[@reddyGeneticFunctionalDrivers2017]| |
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| 156 | -|[ARID1B](ARID1B)|2|[@reddyGeneticFunctionalDrivers2017]| |
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| 157 | -|[ARID5B](ARID5B)|2|[@reddyGeneticFunctionalDrivers2017; @gomezUltraDeepSequencingReveals2023]| |
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| 158 | -|[ATR](ATR)|2|[@reddyGeneticFunctionalDrivers2017]| |
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| 159 | -|[BCL11A](BCL11A)|2, aSHM|| |
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| 160 | -|[BCOR](BCOR)|2|[@nadeuGenomicEpigenomicInsights2020b; @jalladesExomeSequencingIdentifies2017]| |
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| 161 | -|[BCR](BCR)|2, aSHM|| |
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| 162 | -|[BIRC3](BIRC3)|2, aSHM|[@dunsCharacterizationDLBCLPMBL2021b; @rossiAlterationBIRC3Multiple2011a; @arthurGenomewideDiscoverySomatic2018; @beaLandscapeSomaticMutations2013]| |
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| 163 | -|[BLK](BLK)|2, aSHM|| |
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| 164 | -|[BRINP3](BRINP3)|2|[@reddyGeneticFunctionalDrivers2017]| |
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| 165 | -|[BTBD3](BTBD3)|2|[@reddyGeneticFunctionalDrivers2017]| |
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| 166 | -|[CADPS2](CADPS2)|2|[@hubschmannMutationalMechanismsShaping2021b]| |
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| 167 | -|[CASP8](CASP8)|2|[@reddyGeneticFunctionalDrivers2017]| |
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| 168 | -|[CBLB](CBLB)|2|[@reddyGeneticFunctionalDrivers2017]| |
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| 169 | -|[CCL4](CCL4)|2|[@chapuyMolecularSubtypesDiffuse2018b]| |
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| 170 | -|[CD22](CD22)|2|[@reddyGeneticFunctionalDrivers2017]| |
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| 171 | -|[CD274](CD274)|2|[@morinFrequentMutationHistonemodifying2011]| |
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| 172 | -|[CD36](CD36)|2|[@pasqualucciAnalysisCodingGenome2011]| |
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| 173 | -|[CD44](CD44)|2, aSHM|[@arthurGenomewideDiscoverySomatic2018]| |
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| 174 | -|[CD74](CD74)|2, aSHM|[@arthurGenomewideDiscoverySomatic2018]| |
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| 175 | -|[CDC73](CDC73)|2|[@reddyGeneticFunctionalDrivers2017; @loveGeneticLandscapeMutations2012]| |
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| 176 | -|[CDH9](CDH9)|2|[@morinMutationalStructuralAnalysis2013]| |
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| 177 | -|[CHD1](CHD1)|2|[@reddyGeneticFunctionalDrivers2017]| |
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| 178 | -|[CHD8](CHD8)|2|[@grandeGenomewideDiscoverySomatic2019; @reddyGeneticFunctionalDrivers2017]| |
|
| 179 | -|[CHST2](CHST2)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 180 | -|[CNOT2](CNOT2)|2|[@hubschmannMutationalMechanismsShaping2021b]| |
|
| 181 | -|[CNTNAP5](CNTNAP5)|2|[@morinMutationalStructuralAnalysis2013]| |
|
| 182 | -|[COQ7](COQ7)|2|[@chapuyMolecularSubtypesDiffuse2018b]| |
|
| 183 | -|[CRIP1](CRIP1)|2|[@chapuyMolecularSubtypesDiffuse2018b]| |
|
| 184 | -|[DAZAP1](DAZAP1)|2|[@pararajalingamCodingNoncodingDrivers2020]| |
|
| 185 | -|[DCAF6](DCAF6)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 186 | -|[DDX10](DDX10)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 187 | -|[DHX16](DHX16)|2|[@hubschmannMutationalMechanismsShaping2021b]| |
|
| 188 | -|[DICER1](DICER1)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 189 | -|[DNAH5](DNAH5)|2|[@morinMutationalStructuralAnalysis2013; @jalladesExomeSequencingIdentifies2017]| |
|
| 190 | -|[DNM2](DNM2)|2|[@hubschmannMutationalMechanismsShaping2021b]| |
|
| 191 | -|[DNMT3A](DNMT3A)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 192 | -|[DOCK1](DOCK1)|2|[@chapuyMolecularSubtypesDiffuse2018b]| |
|
| 193 | -|[DSG4](DSG4)|2|[@morinMutationalStructuralAnalysis2013]| |
|
| 194 | -|[EIF2AK3](EIF2AK3)|2, aSHM|| |
|
| 195 | -|[EZR](EZR)|2, aSHM|[@deschGenotypingCirculatingTumor2020]| |
|
| 196 | -|[FAM102A](FAM102A)|2, aSHM|| |
|
| 197 | -|[FAM38B](FAM38B)|2|[@morinMutationalStructuralAnalysis2013]| |
|
| 198 | -|[FANK1](FANK1)|2, aSHM|| |
|
| 199 | -|[FAT4](FAT4)|2|[@parryWholeExomeSequencing2013; @morinMutationalStructuralAnalysis2013; @zhangGenomicLandscapeMantle2014]| |
|
| 200 | -|[FCRL3](FCRL3)|2, aSHM|| |
|
| 201 | -|[FNBP1](FNBP1)|2, aSHM|| |
|
| 202 | -|[FNDC1](FNDC1)|2|[@morinMutationalStructuralAnalysis2013]| |
|
| 203 | -|[FOXC1](FOXC1)|2|[@schmitzGeneticsPathogenesisDiffuse2018a]| |
|
| 204 | -|[FOXP1](FOXP1)|2, aSHM|[@reddyGeneticFunctionalDrivers2017]| |
|
| 205 | -|[FUBP1](FUBP1)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 206 | -|[FUT5](FUT5)|2|[@chapuyMolecularSubtypesDiffuse2018b]| |
|
| 207 | -|[GABRA2](GABRA2)|2|[@chapuyMolecularSubtypesDiffuse2018b]| |
|
| 208 | -|[GAK](GAK)|2|[@hubschmannMutationalMechanismsShaping2021b]| |
|
| 209 | -|[GNAS](GNAS)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 210 | -|[GOLGA5](GOLGA5)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 211 | -|[GPC5](GPC5)|2|[@schmitzGeneticsPathogenesisDiffuse2018a]| |
|
| 212 | -|[GSG2](GSG2)|2|[@schmitzGeneticsPathogenesisDiffuse2018a]| |
|
| 213 | -|[HDAC7](HDAC7)|2|[@morinMutationalStructuralAnalysis2013]| |
|
| 214 | -|[HIST1H2AG](HIST1H2AG)|2, aSHM|[@morinMutationalStructuralAnalysis2013; @rossiCodingGenomeSplenic2012c; @paneaWholeGenomeLandscape2019; @krysiakRecurrentSomaticMutations2017b]| |
|
| 215 | -|[HLA-DMA](HLA-DMA)|2|| |
|
| 216 | -|[HLA-DQA1](HLA-DQA1)|2|[@hubschmannMutationalMechanismsShaping2021b]| |
|
| 217 | -|[HNF1B](HNF1B)|2|[@pasqualucciAnalysisCodingGenome2011]| |
|
| 218 | -|[HNRNPD](HNRNPD)|2|| |
|
| 219 | -|[HNRNPH1](HNRNPH1)|2, noncoding|[@pararajalingamCodingNoncodingDrivers2020]| |
|
| 220 | -|[HRAS](HRAS)|2|[@jalladesExomeSequencingIdentifies2017; @reddyGeneticFunctionalDrivers2017]| |
|
| 221 | -|[ID3](ID3)|2|[@richterRecurrentMutationID32012a; @spinaGeneticsNodalMarginal2016b; @schmitzBurkittLymphomaPathogenesis2012]| |
|
| 222 | -|[IER2](IER2)|2|[@morinMutationalStructuralAnalysis2013]| |
|
| 223 | -|[IFNGR1](IFNGR1)|2|[@morinMutationalStructuralAnalysis2013]| |
|
| 224 | -|[IGLL5](IGLL5)|2, aSHM|[@russler-germainMutationsAssociatedProgression2023b; @deschGenotypingCirculatingTumor2020; @paneaWholeGenomeLandscape2019]| |
|
| 225 | -|[IKBKB](IKBKB)|2|[@reddyGeneticFunctionalDrivers2017; @rossiAlterationBIRC3Multiple2011a; @wienandGenomicAnalysesFlowsorted2019b]| |
|
| 226 | -|[IKBKE](IKBKE)|2|[@hubschmannMutationalMechanismsShaping2021b]| |
|
| 227 | -|[IL16](IL16)|2|| |
|
| 228 | -|[IL6](IL6)|2|[@chapuyMolecularSubtypesDiffuse2018b]| |
|
| 229 | -|[INO80](INO80)|2|[@zhangGeneticHeterogeneityDiffuse2013]| |
|
| 230 | -|[IRAG2](IRAG2)|2, aSHM|| |
|
| 231 | -|[IRF1](IRF1)|2, aSHM|[@hubschmannMutationalMechanismsShaping2021b]| |
|
| 232 | -|[JAK1](JAK1)|2|[@zhangGeneticHeterogeneityDiffuse2013; @mottokIntegrativeGenomicAnalysis2019b]| |
|
| 233 | -|[JAK3](JAK3)|2|[@zhangGeneticHeterogeneityDiffuse2013]| |
|
| 234 | -|[JUNB](JUNB)|2|[@reddyGeneticFunctionalDrivers2017; @mottokIntegrativeGenomicAnalysis2019b]| |
|
| 235 | -|[KCMF1](KCMF1)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 236 | -|[KLHL21](KLHL21)|2|[@schmitzGeneticsPathogenesisDiffuse2018a]| |
|
| 237 | -|[LAMA5](LAMA5)|2|[@schmitzGeneticsPathogenesisDiffuse2018a]| |
|
| 238 | -|[LAPTM5](LAPTM5)|2, aSHM|[@hubschmannMutationalMechanismsShaping2021b]| |
|
| 239 | -|[LIN54](LIN54)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 240 | -|[LPP](LPP)|2, aSHM|[@arthurGenomewideDiscoverySomatic2018]| |
|
| 241 | -|[LRP12](LRP12)|2|[@hubschmannMutationalMechanismsShaping2021b]| |
|
| 242 | -|[LRRN3](LRRN3)|2|[@sarkozyMutationalLandscapeGray2021a; @morinMutationalStructuralAnalysis2013]| |
|
| 243 | -|[LYN](LYN)|2|[@chapuyMolecularSubtypesDiffuse2018b]| |
|
| 244 | -|[MAGT1](MAGT1)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 245 | -|[MALAT1](MALAT1)|2, aSHM|[@arthurGenomewideDiscoverySomatic2018]| |
|
| 246 | -|[MAP2K1](MAP2K1)|2|[@shinBRAFV600EMAP2K12015; @louissaintPediatrictypeNodalFollicular2016a]| |
|
| 247 | -|[MAP4K4](MAP4K4)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 248 | -|[MARK1](MARK1)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 249 | -|[MCL1](MCL1)|2|[@paneaWholeGenomeLandscape2019; @reddyGeneticFunctionalDrivers2017; @dunsCharacterizationDLBCLPMBL2021b]| |
|
| 250 | -|[MECOM](MECOM)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 251 | -|[MET](MET)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 252 | -|[MIR142](MIR142)|2, aSHM|[@grandeGenomewideDiscoverySomatic2019; @kwanhianMicroRNA142Mutated202012b]| |
|
| 253 | -|[MIR155HG](MIR155HG)|2, aSHM|| |
|
| 254 | -|[MPDZ](MPDZ)|2|[@reichelFlowSortingExome2015a; @morinMutationalStructuralAnalysis2013]| |
|
| 255 | -|[MSH2](MSH2)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 256 | -|[MSH6](MSH6)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 257 | -|[MYB](MYB)|2|[@reddyGeneticFunctionalDrivers2017; @deschGenotypingCirculatingTumor2020]| |
|
| 258 | -|[MYBPC2](MYBPC2)|2|[@schmitzGeneticsPathogenesisDiffuse2018a]| |
|
| 259 | -|[MYO1E](MYO1E)|2, aSHM|| |
|
| 260 | -|[MYOM2](MYOM2)|2|[@pasqualucciAnalysisCodingGenome2011]| |
|
| 261 | -|[N2RF2](N2RF2)|2|[@hubschmannMutationalMechanismsShaping2021b]| |
|
| 262 | -|[NANOG](NANOG)|2|[@chapuyMolecularSubtypesDiffuse2018b]| |
|
| 263 | -|[NAV1](NAV1)|2|[@chapuyMolecularSubtypesDiffuse2018b]| |
|
| 264 | -|[NCOA3](NCOA3)|2, aSHM|| |
|
| 265 | -|[NCOR1](NCOR1)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 266 | -|[NCOR2](NCOR2)|2|[@schmitzBurkittLymphomaPathogenesis2012; @spinaGeneticsNodalMarginal2016b; @sarkozyMutationalLandscapeGray2021a]| |
|
| 267 | -|[NEAT1](NEAT1)|2, aSHM|[@arthurGenomewideDiscoverySomatic2018]| |
|
| 268 | -|[NF1](NF1)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 269 | -|[NFKB1](NFKB1)|2|| |
|
| 270 | -|[NFKB2](NFKB2)|2|[@reddyGeneticFunctionalDrivers2017; @mottokIntegrativeGenomicAnalysis2019b]| |
|
| 271 | -|[NLRC5](NLRC5)|2|| |
|
| 272 | -|[NLRP5](NLRP5)|2|[@morinMutationalStructuralAnalysis2013]| |
|
| 273 | -|[NLRP8](NLRP8)|2|[@chapuyMolecularSubtypesDiffuse2018b]| |
|
| 274 | -|[ODZ3](ODZ3)|2|[@morinMutationalStructuralAnalysis2013]| |
|
| 275 | -|[P2RX5](P2RX5)|2, aSHM|[@morinMutationalStructuralAnalysis2013]| |
|
| 276 | -|[PAPOLG](PAPOLG)|2|[@schmitzGeneticsPathogenesisDiffuse2018a]| |
|
| 277 | -|[PASK](PASK)|2|[@morinMutationalStructuralAnalysis2013]| |
|
| 278 | -|[PAX5](PAX5)|2, aSHM|[@pasqualucciHypermutationMultipleProtooncogenes2001a]| |
|
| 279 | -|[PCBP1](PCBP1)|2|[@schmitzBurkittLymphomaPathogenesis2012]| |
|
| 280 | -|[PCDHB11](PCDHB11)|2|[@morinMutationalStructuralAnalysis2013]| |
|
| 281 | -|[PCLO](PCLO)|2|[@lohrDiscoveryPrioritizationSomatic2012a]| |
|
| 282 | -|[PDE4DIP](PDE4DIP)|2|[@chapuyMolecularSubtypesDiffuse2018b]| |
|
| 283 | -|[PDS5B](PDS5B)|2|[@hubschmannMutationalMechanismsShaping2021b; @morinMutationalStructuralAnalysis2013]| |
|
| 284 | -|[PHF6](PHF6)|2|[@reddyGeneticFunctionalDrivers2017; @thomasGeneticSubgroupsInform2023]| |
|
| 285 | -|[PIK3CD](PIK3CD)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 286 | -|[PIK3R1](PIK3R1)|2|[@zhangGeneticHeterogeneityDiffuse2013; @paneaWholeGenomeLandscape2019]| |
|
| 287 | -|[PKD1](PKD1)|2|[@morinMutationalStructuralAnalysis2013]| |
|
| 288 | -|[PNPO](PNPO)|2|[@hubschmannMutationalMechanismsShaping2021b]| |
|
| 289 | -|[POGZ](POGZ)|2|[@morinMutationalStructuralAnalysis2013]| |
|
| 290 | -|[PPP1R9B](PPP1R9B)|2|| |
|
| 291 | -|[PRKCB](PRKCB)|2|[@morinMutationalStructuralAnalysis2013]| |
|
| 292 | -|[PRKDC](PRKDC)|2|[@hubschmannMutationalMechanismsShaping2021b; @schmitzGeneticsPathogenesisDiffuse2018a]| |
|
| 293 | -|[PRPS1](PRPS1)|2|[@chapuyMolecularSubtypesDiffuse2018b]| |
|
| 294 | -|[PTMA](PTMA)|2, aSHM|| |
|
| 295 | -|[PTPN1](PTPN1)|2, aSHM|[@gunawardanaRecurrentSomaticMutations2014c]| |
|
| 296 | -|[PTPN23](PTPN23)|2|[@morinMutationalStructuralAnalysis2013]| |
|
| 297 | -|[PTPN6](PTPN6)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 298 | -|[PTPRK](PTPRK)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 299 | -|[RAC2](RAC2)|2|[@hubschmannMutationalMechanismsShaping2021b; @paneaWholeGenomeLandscape2019]| |
|
| 300 | -|[RAD9A](RAD9A)|2|[@chapuyMolecularSubtypesDiffuse2018b]| |
|
| 301 | -|[RARA](RARA)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 302 | -|[RCC](RCC)|2, aSHM|| |
|
| 303 | -|[RFTN1](RFTN1)|2, aSHM|[@dunsCharacterizationDLBCLPMBL2021b; @arthurGenomewideDiscoverySomatic2018]| |
|
| 304 | -|[RFXAP](RFXAP)|2|| |
|
| 305 | -|[RHEX](RHEX)|2, aSHM|| |
|
| 306 | -|[RHOH](RHOH)|2, aSHM|[@pasqualucciHypermutationMultipleProtooncogenes2001a]| |
|
| 307 | -|[RUBCNL](RUBCNL)|2, aSHM|| |
|
| 308 | -|[RUNX1](RUNX1)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 309 | -|[SAMD9L](SAMD9L)|2|[@morinMutationalStructuralAnalysis2013]| |
|
| 310 | -|[SARM1](SARM1)|2|[@morinMutationalStructuralAnalysis2013]| |
|
| 311 | -|[SEL1L3](SEL1L3)|2, aSHM|| |
|
| 312 | -|[SEPTIN9](SEPTIN9)|2, aSHM|| |
|
| 313 | -|[SERPINA9](SERPINA9)|2, aSHM|[@arthurGenomewideDiscoverySomatic2018]| |
|
| 314 | -|[SETD2](SETD2)|2|[@zhangGeneticHeterogeneityDiffuse2013]| |
|
| 315 | -|[SETD5](SETD5)|2|[@reddyGeneticFunctionalDrivers2017; @tiacciPervasiveMutationsJAKSTAT2018b]| |
|
| 316 | -|[SIAH2](SIAH2)|2|[@reichelFlowSortingExome2015a; @hubschmannMutationalMechanismsShaping2021b]| |
|
| 317 | -|[SLC34A2](SLC34A2)|2|[@hubschmannMutationalMechanismsShaping2021b]| |
|
| 318 | -|[SMEK1](SMEK1)|2|[@chapuyMolecularSubtypesDiffuse2018b]| |
|
| 319 | -|[SRRM2](SRRM2)|2|[@russler-germainMutationsAssociatedProgression2023b; @morinMutationalStructuralAnalysis2013]| |
|
| 320 | -|[ST6GAL1](ST6GAL1)|2, aSHM|[@arthurGenomewideDiscoverySomatic2018]| |
|
| 321 | -|[STAT5B](STAT5B)|2|[@zhangGeneticHeterogeneityDiffuse2013; @tiacciPervasiveMutationsJAKSTAT2018b]| |
|
| 322 | -|[SYK](SYK)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 323 | -|[SYPL1](SYPL1)|2|[@morinMutationalStructuralAnalysis2013]| |
|
| 324 | -|[TAP1](TAP1)|2|[@schmitzGeneticsPathogenesisDiffuse2018a]| |
|
| 325 | -|[TBC1D4](TBC1D4)|2, aSHM|[@arthurGenomewideDiscoverySomatic2018]| |
|
| 326 | -|[TCL1A](TCL1A)|2, aSHM|[@grandeGenomewideDiscoverySomatic2019]| |
|
| 327 | -|[TGFBR2](TGFBR2)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 328 | -|[TIPARP](TIPARP)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 329 | -|[TLR2](TLR2)|2|[@chapuyMolecularSubtypesDiffuse2018b; @beaLandscapeSomaticMutations2013]| |
|
| 330 | -|[TRAF3](TRAF3)|2|[@rossiAlterationBIRC3Multiple2011a; @ottoGeneticLesionsTRAF32012a; @pasqualucciAnalysisCodingGenome2011]| |
|
| 331 | -|[TRAF6](TRAF6)|2|[@hubschmannMutationalMechanismsShaping2021b]| |
|
| 332 | -|[TRIP12](TRIP12)|2|| |
|
| 333 | -|[UBE2J1](UBE2J1)|2, aSHM|| |
|
| 334 | -|[UBR5](UBR5)|2|[@pararajalingamCodingNoncodingDrivers2020; @zhangGeneticHeterogeneityDiffuse2013]| |
|
| 335 | -|[UNC5B](UNC5B)|2|[@hubschmannMutationalMechanismsShaping2021b]| |
|
| 336 | -|[UNC5D](UNC5D)|2|| |
|
| 337 | -|[WAC](WAC)|2|[@rossiCodingGenomeSplenic2012c; @reddyGeneticFunctionalDrivers2017]| |
|
| 338 | -|[WDFY3](WDFY3)|2|[@morinMutationalStructuralAnalysis2013]| |
|
| 339 | -|[WNK1](WNK1)|2|[@hubschmannMutationalMechanismsShaping2021b; @thomasGeneticSubgroupsInform2023; @jalladesExomeSequencingIdentifies2017]| |
|
| 340 | -|[XBP1](XBP1)|2, aSHM|| |
|
| 341 | -|[YY1](YY1)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 342 | -|[ZBTB7A](ZBTB7A)|2|[@burkhardtClinicalRelevanceMolecular2022b; @reddyGeneticFunctionalDrivers2017]| |
|
| 343 | -|[ZCCHC7](ZCCHC7)|2, aSHM|[@arthurGenomewideDiscoverySomatic2018]| |
|
| 344 | -|[ZEB2](ZEB2)|2|[@zhangGeneticHeterogeneityDiffuse2013]| |
|
| 345 | -|[ZFAT](ZFAT)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 346 | -|[ZFX](ZFX)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 347 | -|[ZNF217](ZNF217)|2|[@hubschmannMutationalMechanismsShaping2021b; @reichelFlowSortingExome2015a]| |
|
| 348 | -|[ZNF423](ZNF423)|2|[@chapuyMolecularSubtypesDiffuse2018b]| |
|
| 349 | - |
|
| 350 | - |
|
| 351 | -# References |
VAX1.md
| ... | ... | @@ -0,0 +1,31 @@ |
| 1 | +--- |
|
| 2 | +bibliography: 'morinlab.bib' |
|
| 3 | +csl: 'NLM.csl' |
|
| 4 | +link-citations: true |
|
| 5 | +--- |
|
| 6 | + |
|
| 7 | +# VAX1 |
|
| 8 | + |
|
| 9 | +## History |
|
| 10 | + |
|
| 11 | +```mermaid |
|
| 12 | +%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
|
| 13 | +timeline |
|
| 14 | + title Publication timing |
|
| 15 | + 2012-03-06 : Lohr : DLBCL |
|
| 16 | +``` |
|
| 17 | + |
|
| 18 | + |
|
| 19 | +## Relevance tier by entity |
|
| 20 | + |
|
| 21 | +|Entity|Tier|Description| |
|
| 22 | +|:------:|:----:|--------------------------------------| |
|
| 23 | +||2|relevance in DLBCL not firmly established[@lohrDiscoveryPrioritizationSomatic2012]| |
|
| 24 | + |
|
| 25 | + |
|
| 26 | + |
|
| 27 | + |
|
| 28 | + |
|
| 29 | +## References |
|
| 30 | + |
|
| 31 | + |
ZWILCH.md
| ... | ... | @@ -23,10 +23,6 @@ timeline |
| 23 | 23 | ||2|relevance in DLBCL not firmly established[@pasqualucciAnalysisCodingGenome2011]| |
| 24 | 24 | |
| 25 | 25 | |
| 26 | -## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
|
| 27 | - |
|
| 28 | -|Entity|source |frequency (%)| |
|
| 29 | -|:------:|:----:|:----:| |
|
| 30 | 26 | |
| 31 | 27 | |
| 32 | 28 | ## References |
config_test.rb
| ... | ... | @@ -1,288 +0,0 @@ |
| 1 | - # Launch Gollum using a specific git adapter. See https://github.com/gollum/gollum/wiki/Git-adapters |
|
| 2 | - # Default: rugged |
|
| 3 | - # |
|
| 4 | - # Equivalent to --adapter [ADAPTER] |
|
| 5 | - |
|
| 6 | -require 'gollum/app' |
|
| 7 | -require 'pandoc-ruby' |
|
| 8 | - |
|
| 9 | - module Gollum |
|
| 10 | - # to require 'my_adapter': |
|
| 11 | - Gollum::GIT_ADAPTER = "my" |
|
| 12 | - end |
|
| 13 | - |
|
| 14 | - wiki_options = { |
|
| 15 | - |
|
| 16 | - ############################################################################## |
|
| 17 | - #----------------------------------------------------------------------------- |
|
| 18 | - |
|
| 19 | - #----------------------------------------------------------------------------- |
|
| 20 | - # Enable file uploads. If set to 'dir', Gollum will store all uploads in the |
|
| 21 | - # /uploads/ directory in repository root. If set to 'page', Gollum will |
|
| 22 | - # store each upload at the currently edited page. |
|
| 23 | - # Default: false |
|
| 24 | - |
|
| 25 | - # Equivalent to --allow-uploads dir |
|
| 26 | - #allow_uploads: true, |
|
| 27 | - |
|
| 28 | - # Equivalent to --allow-uploads page |
|
| 29 | - #allow_uploads: true, |
|
| 30 | - #per_page_uploads: true, |
|
| 31 | - |
|
| 32 | - #----------------------------------------------------------------------------- |
|
| 33 | - # Set the path to look for static assets. |
|
| 34 | - # |
|
| 35 | - # Equivalent to --assets [PATH] |
|
| 36 | - |
|
| 37 | - #static_assets_path: [PATH] |
|
| 38 | - |
|
| 39 | - #----------------------------------------------------------------------------- |
|
| 40 | - # Tell Gollum that the git repository should be treated as bare. |
|
| 41 | - # |
|
| 42 | - # Equivalent to --bare |
|
| 43 | - |
|
| 44 | - #repo_is_bare: true, |
|
| 45 | - |
|
| 46 | - #----------------------------------------------------------------------------- |
|
| 47 | - # Specify the leading portion of all Gollum URLs (path info). Setting this to |
|
| 48 | - # /wiki will make the wiki accessible under http://localhost:4567/wiki/. |
|
| 49 | - # Default: / |
|
| 50 | - # |
|
| 51 | - # Equivalent to --base-path [PATH] |
|
| 52 | - |
|
| 53 | - #base_path: [PATH], |
|
| 54 | - |
|
| 55 | - #----------------------------------------------------------------------------- |
|
| 56 | - # Enable support for annotations using CriticMarkup. |
|
| 57 | - # |
|
| 58 | - # Equivalent to --critic-markup |
|
| 59 | - |
|
| 60 | - #critic_markup: true, |
|
| 61 | - |
|
| 62 | - #----------------------------------------------------------------------------- |
|
| 63 | - # Tell Gollum to inject custom CSS into each page. Uses custom.css from wiki |
|
| 64 | - # root |
|
| 65 | - # |
|
| 66 | - # Equivalent to --css |
|
| 67 | - |
|
| 68 | - css: true, |
|
| 69 | - |
|
| 70 | - #----------------------------------------------------------------------------- |
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| 71 | - # What should the default keybinding be on the edit page? Note: the editor will anyway remember the last choice the user made, so this is only to specify the default. |
|
| 72 | - |
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| 73 | - #default_keybinding: vim |
|
| 74 | - #default_keybinding: emacs |
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| 75 | - |
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| 76 | - #----------------------------------------------------------------------------- |
|
| 77 | - # Parse and interpret emoji tags (e.g. :heart:) except when the leading colon |
|
| 78 | - # is backslashed (e.g. \:heart:). |
|
| 79 | - # |
|
| 80 | - # Equivalent to --emoji |
|
| 81 | - |
|
| 82 | - #emoji: true, |
|
| 83 | - |
|
| 84 | - #----------------------------------------------------------------------------- |
|
| 85 | - # Tell Gollum to use the first <h1> as page title. |
|
| 86 | - # |
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| 87 | - # Equivalent to --h1-title |
|
| 88 | - |
|
| 89 | - h1_title: true, |
|
| 90 | - |
|
| 91 | - #----------------------------------------------------------------------------- |
|
| 92 | - # Specify the hostname or IP address to listen on. |
|
| 93 | - # Default: '0.0.0.0'. |
|
| 94 | - # |
|
| 95 | - # Equivalent to --host [HOST] |
|
| 96 | - |
|
| 97 | - # ??? |
|
| 98 | - |
|
| 99 | - #----------------------------------------------------------------------------- |
|
| 100 | - # Launch Gollum in "console mode", with a predefined API. |
|
| 101 | - # |
|
| 102 | - # Equivalent to --irb |
|
| 103 | - |
|
| 104 | - # ??? |
|
| 105 | - |
|
| 106 | - #----------------------------------------------------------------------------- |
|
| 107 | - # Tell Gollum to inject custom JS into each page. Uses custom.js from wiki |
|
| 108 | - # root. |
|
| 109 | - # |
|
| 110 | - # Equivalent to --js |
|
| 111 | - |
|
| 112 | - #js: true, |
|
| 113 | - |
|
| 114 | - #----------------------------------------------------------------------------- |
|
| 115 | - # Compatibility with 4.x |
|
| 116 | - # https://github.com/gollum/gollum/wiki/5.0-release-notes#compatibility-option |
|
| 117 | - # |
|
| 118 | - # Internal links resolve case-insensitively, will treat spaces as hyphens, and |
|
| 119 | - # will match the first page found with a certain filename, anywhere in the |
|
| 120 | - # repository. Provides compatibility with Gollum 4.x. |
|
| 121 | - # |
|
| 122 | - # Equivalent to --lenient-tag-lookup |
|
| 123 | - |
|
| 124 | - #hyphened_tag_lookup: true, |
|
| 125 | - #case_insensitive_tag_lookup: true, |
|
| 126 | - #global_tag_lookup: true, |
|
| 127 | - |
|
| 128 | - #----------------------------------------------------------------------------- |
|
| 129 | - # Use the browser's local timezone instead of the server's timezone for displaying dates. |
|
| 130 | - |
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| 131 | - #show_local_time: true |
|
| 132 | - |
|
| 133 | - #----------------------------------------------------------------------------- |
|
| 134 | - # Equivalent to --math. Set math parsing to either mathjax or katex (default) |
|
| 135 | - |
|
| 136 | - #math: :mathjax, |
|
| 137 | - #math: :katex, |
|
| 138 | - |
|
| 139 | - #----------------------------------------------------------------------------- |
|
| 140 | - # Specify path to a custom MathJax configuration. |
|
| 141 | - # Default: mathjax.config.js file from repository root. |
|
| 142 | - # |
|
| 143 | - # Equivalent to --mathjax-config [FILE] |
|
| 144 | - |
|
| 145 | - #mathjax_config: [FILE], |
|
| 146 | - |
|
| 147 | - #----------------------------------------------------------------------------- |
|
| 148 | - # Do not render metadata tables in pages. |
|
| 149 | - # |
|
| 150 | - # Equivalent to --no-display-metadata |
|
| 151 | - |
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| 152 | - display_metadata: false, |
|
| 153 | - |
|
| 154 | - #----------------------------------------------------------------------------- |
|
| 155 | - # Disable the feature of editing pages. |
|
| 156 | - # Default: true |
|
| 157 | - # |
|
| 158 | - # Equivalent to --no-edit |
|
| 159 | - |
|
| 160 | - allow_editing: false, |
|
| 161 | - |
|
| 162 | - #----------------------------------------------------------------------------- |
|
| 163 | - # Specify the subdirectory for all pages. If set, Gollum will only serve pages |
|
| 164 | - # from this directory and its subdirectories. |
|
| 165 | - # Default: repository root. |
|
| 166 | - # |
|
| 167 | - # Equivalent to --page-file-dir [PATH] |
|
| 168 | - |
|
| 169 | - #page_file_dir: [PATH], |
|
| 170 | - |
|
| 171 | - #----------------------------------------------------------------------------- |
|
| 172 | - # Follow pages across renames in the History view. You may set this to `false` to improve performance on wikis with very large histories. |
|
| 173 | - # Default: true. |
|
| 174 | - |
|
| 175 | - #follow_renames: true, |
|
| 176 | - |
|
| 177 | - #----------------------------------------------------------------------------- |
|
| 178 | - # Specify the port to bind Gollum with. |
|
| 179 | - # Default: 4567. |
|
| 180 | - # |
|
| 181 | - # Equivalent to --port [PORT] |
|
| 182 | - |
|
| 183 | - # ??? |
|
| 184 | - |
|
| 185 | - #----------------------------------------------------------------------------- |
|
| 186 | - # Specify the git branch to serve. |
|
| 187 | - # Default: master. |
|
| 188 | - # |
|
| 189 | - # Equivalent to --ref [REF] |
|
| 190 | - |
|
| 191 | - #ref: [REF], |
|
| 192 | - |
|
| 193 | - #----------------------------------------------------------------------------- |
|
| 194 | - # Use static assets. |
|
| 195 | - # Defaults to false in development/test, true in |
|
| 196 | - # production/staging. |
|
| 197 | - |
|
| 198 | - # Equivalent to --static |
|
| 199 | - #static: true, |
|
| 200 | - |
|
| 201 | - # Equivalent to --no-static |
|
| 202 | - #static: false, |
|
| 203 | - |
|
| 204 | - #----------------------------------------------------------------------------- |
|
| 205 | - # Specify custom mustache template directory. |
|
| 206 | - # |
|
| 207 | - # Equivalent to --template-dir [PATH] |
|
| 208 | - |
|
| 209 | - #template_dir: [PATH], |
|
| 210 | - |
|
| 211 | - #----------------------------------------------------------------------------- |
|
| 212 | - # Use _Template in root as a template for new pages. Must be committed. |
|
| 213 | - # |
|
| 214 | - # Equivalent to --template-page |
|
| 215 | - |
|
| 216 | - #template_page: true, |
|
| 217 | - |
|
| 218 | - #----------------------------------------------------------------------------- |
|
| 219 | - # Tell Gollum to use specific user icons for history view. Can be set to |
|
| 220 | - # gravatar, identicon or none. |
|
| 221 | - # Default: none. |
|
| 222 | - # |
|
| 223 | - # Equivalent to --user-icons [MODE] |
|
| 224 | - |
|
| 225 | - #user_icons: [MODE], |
|
| 226 | - |
|
| 227 | - ############################################################################## |
|
| 228 | - # Metadata (front matter) |
|
| 229 | - |
|
| 230 | - #----------------------------------------------------------------------------- |
|
| 231 | - # Header counting |
|
| 232 | - # Default: false |
|
| 233 | - # Can also be a pre-defined counter. See |
|
| 234 | - # https://www.w3.org/TR/css-counter-styles-3/#predefined-counters |
|
| 235 | - |
|
| 236 | - #header_enum: false, |
|
| 237 | - #header_enum: 'decimal-leading-zero', |
|
| 238 | - |
|
| 239 | - #----------------------------------------------------------------------------- |
|
| 240 | - # Global metadata. Arbitrary metadata that will be applied to each page. |
|
| 241 | - |
|
| 242 | - #metadata: { |
|
| 243 | - # monkeyboys: 'are loose in the facility' |
|
| 244 | - #}, |
|
| 245 | - |
|
| 246 | - ############################################################################## |
|
| 247 | - # Tips |
|
| 248 | - |
|
| 249 | - #----------------------------------------------------------------------------- |
|
| 250 | - # Force table of contents tag ([[_TOC_]]) into each page. |
|
| 251 | - # ??? How to set the level in the configuration file? |
|
| 252 | - # https://github.com/gollum/gollum/wiki#table-of-contents-toc-tag |
|
| 253 | - # Default: false |
|
| 254 | - |
|
| 255 | - #universal_toc: false, |
|
| 256 | - |
|
| 257 | - #----------------------------------------------------------------------------- |
|
| 258 | - # Move the sidebar to the left of the page |
|
| 259 | - # https://github.com/gollum/gollum/issues/1450#issuecomment-599124384 |
|
| 260 | - |
|
| 261 | - #sidebar: :left, |
|
| 262 | - |
|
| 263 | - #----------------------------------------------------------------------------- |
|
| 264 | - # Change the home page name |
|
| 265 | - # https://github.com/gollum/gollum/issues/1569#issuecomment-633033895 |
|
| 266 | - |
|
| 267 | - #index_page: 'index', |
|
| 268 | - |
|
| 269 | - #----------------------------------------------------------------------------- |
|
| 270 | - # Change the number of changes in the rss feed |
|
| 271 | - |
|
| 272 | - #pagination_count: 15 |
|
| 273 | - } |
|
| 274 | - |
|
| 275 | - #------------------------------------------------------------------------------- |
|
| 276 | - # Change default markup |
|
| 277 | - #Precious::App.set(:default_markup, :asciidoc) |
|
| 278 | - |
|
| 279 | - Precious::App.set(:wiki_options, wiki_options) |
|
| 280 | - |
|
| 281 | -Precious::App.set(:markdown, { |
|
| 282 | - :extensions => { |
|
| 283 | - 'md' => 'markdown' |
|
| 284 | - }, |
|
| 285 | - :format => lambda { |content| |
|
| 286 | - PandocRuby.convert(content, from: :markdown, to: :html) |
|
| 287 | - } |
|
| 288 | -}) |
test_FL_genes.md
| ... | ... | @@ -1,143 +0,0 @@ |
| 1 | ---- |
|
| 2 | -title: 'FL genes' |
|
| 3 | -bibliography: 'morinlab.bib' |
|
| 4 | -csl: 'NLM.csl' |
|
| 5 | -link-citations: true |
|
| 6 | ---- |
|
| 7 | - |
|
| 8 | -## Origins of FL genes |
|
| 9 | - |
|
| 10 | - |
|
| 11 | - |
|
| 12 | -## Tier 1 FL genes |
|
| 13 | - |
|
| 14 | -### *66 total* |
|
| 15 | - |
|
| 16 | -|Gene|Tier| First FL evidence | Other entities | |
|
| 17 | -|:-:|:-:|:-|:-| |
|
| 18 | -|[ACTB](ACTB)|1, aSHM||[@lohrDiscoveryPrioritizationSomatic2012a; @wienandGenomicAnalysesFlowsorted2019b]| |
|
| 19 | -|[ARID1A](ARID1A)|1|[Study Page](papers/krysiakRecurrentSomaticMutations2017b)[@krysiakRecurrentSomaticMutations2017b]|[@wienandGenomicAnalysesFlowsorted2019b; @rossiCodingGenomeSplenic2012c; @zhangGeneticHeterogeneityDiffuse2013; @loveGeneticLandscapeMutations2012]| |
|
| 20 | -|[ATP6AP1](ATP6AP1)|1|[Study Page](papers/okosunRecurrentMTORC1activatingRRAGC2016a)[@okosunRecurrentMTORC1activatingRRAGC2016a]|| |
|
| 21 | -|[ATP6V1B2](ATP6V1B2)|1|[Study Page](papers/okosunRecurrentMTORC1activatingRRAGC2016a)[@okosunRecurrentMTORC1activatingRRAGC2016a]|| |
|
| 22 | -|[B2M](B2M)|1|[Study Page](papers/morinFrequentMutationHistonemodifying2011)[@morinFrequentMutationHistonemodifying2011]|[@pararajalingamCodingNoncodingDrivers2020; @reichelFlowSortingExome2015a]| |
|
| 23 | -|[BCL2](BCL2)|1, aSHM|[Study Page](papers/morinFrequentMutationHistonemodifying2011)[@morinFrequentMutationHistonemodifying2011]|[@tanakaFrequentIncidenceSomatic1992; @burkhardtClinicalRelevanceMolecular2022b; @sarkozyMutationalLandscapeGray2021a]| |
|
| 24 | -|[BCL6](BCL6)|1, aSHM||[@loveGeneticLandscapeMutations2012; @morinFrequentMutationHistonemodifying2011]| |
|
| 25 | -|[BCL7A](BCL7A)|1, aSHM|[Study Page](papers/krysiakRecurrentSomaticMutations2017b)[@krysiakRecurrentSomaticMutations2017b]|[@grandeGenomewideDiscoverySomatic2019; @arthurGenomewideDiscoverySomatic2018; @reichelFlowSortingExome2015a]| |
|
| 26 | -|[BIRC6](BIRC6)|1||[@sarkozyMutationalLandscapeGray2021a; @reddyGeneticFunctionalDrivers2017]| |
|
| 27 | -|[BTG1](BTG1)|1, aSHM||[@sarkozyMutationalLandscapeGray2021a; @morinFrequentMutationHistonemodifying2011; @burkhardtClinicalRelevanceMolecular2022b]| |
|
| 28 | -|[BTG2](BTG2)|1, aSHM|[Study Page](papers/morinFrequentMutationHistonemodifying2011)[@morinFrequentMutationHistonemodifying2011]|[@loveGeneticLandscapeMutations2012]| |
|
| 29 | -|[BTK](BTK)|1|[Study Page](papers/krysiakRecurrentSomaticMutations2017b)[@krysiakRecurrentSomaticMutations2017b]|[@albuquerqueEnhancingKnowledgeDiscovery2017a]| |
|
| 30 | -|[CARD11](CARD11)|1|[Study Page](papers/morinFrequentMutationHistonemodifying2011)[@morinFrequentMutationHistonemodifying2011]|[@lenzOncogenicCARD11Mutations2008; @paneaWholeGenomeLandscape2019; @wuGeneticHeterogeneityPrimary2016; @yanBCRTLRSignaling2012a]| |
|
| 31 | -|[CCND3](CCND3)|1|[Study Page](papers/morinFrequentMutationHistonemodifying2011)[@morinFrequentMutationHistonemodifying2011]|[@richterRecurrentMutationID32012a; @jalladesExomeSequencingIdentifies2017; @deschGenotypingCirculatingTumor2020]| |
|
| 32 | -|[CD83](CD83)|1, aSHM|[Study Page](papers/russler-germainMutationsAssociatedProgression2023b)[@russler-germainMutationsAssociatedProgression2023b]|[@paneaWholeGenomeLandscape2019; @dunsCharacterizationDLBCLPMBL2021b; @morinMutationalStructuralAnalysis2013]| |
|
| 33 | -|[CREBBP](CREBBP)|1|[Study Page](papers/pasqualucciInactivatingMutationsAcetyltransferase2011a)[@pasqualucciInactivatingMutationsAcetyltransferase2011a]|[@dunsCharacterizationDLBCLPMBL2021b; @parryWholeExomeSequencing2013; @loveGeneticLandscapeMutations2012]| |
|
| 34 | -|[CTSS](CTSS)|1|[Study Page](papers/barariaCathepsinAlterationsInduce2020c)[@barariaCathepsinAlterationsInduce2020c]|| |
|
| 35 | -|[DTX1](DTX1)|1, aSHM||[@schmitzGeneticsPathogenesisDiffuse2018a; @gomezUltraDeepSequencingReveals2023; @loveGeneticLandscapeMutations2012; @rossiCodingGenomeSplenic2012c]| |
|
| 36 | -|[EBF1](EBF1)|1, aSHM||[@reichelFlowSortingExome2015a; @bohleRoleEarlyBcell2013; @thomasGeneticSubgroupsInform2023]| |
|
| 37 | -|[EEF1A1](EEF1A1)|1|[Study Page](papers/hubschmannMutationalMechanismsShaping2021b)[@hubschmannMutationalMechanismsShaping2021b]|[@reichelFlowSortingExome2015a]| |
|
| 38 | -|[EP300](EP300)|1|[Study Page](papers/pasqualucciInactivatingMutationsAcetyltransferase2011a)[@pasqualucciInactivatingMutationsAcetyltransferase2011a]|[@paneaWholeGenomeLandscape2019; @rossiCodingGenomeSplenic2012c]| |
|
| 39 | -|[EZH2](EZH2)|1|[Study Page](papers/morinSomaticMutationsAltering2010a)[@morinSomaticMutationsAltering2010a]|[@mottokIntegrativeGenomicAnalysis2019b; @loveGeneticLandscapeMutations2012]| |
|
| 40 | -|[FAS](FAS)|1||[@schollMutationsRegionFAS2007; @spinaGeneticsNodalMarginal2016b]| |
|
| 41 | -|[FOXO1](FOXO1)|1|[Study Page](papers/morinFrequentMutationHistonemodifying2011)[@morinFrequentMutationHistonemodifying2011]|[@dunsCharacterizationDLBCLPMBL2021b; @schmitzBurkittLymphomaPathogenesis2012]| |
|
| 42 | -|[GNA13](GNA13)|1|[Study Page](papers/morinFrequentMutationHistonemodifying2011)[@morinFrequentMutationHistonemodifying2011]|[@reichelFlowSortingExome2015a; @loveGeneticLandscapeMutations2012]| |
|
| 43 | -|[GNAI2](GNAI2)|1||[@morinMutationalStructuralAnalysis2013; @grandeGenomewideDiscoverySomatic2019]| |
|
| 44 | -|[HIST1H1B](HIST1H1B)|1, aSHM|[Study Page](papers/krysiakRecurrentSomaticMutations2017b)[@krysiakRecurrentSomaticMutations2017b]|[@chapuyMolecularSubtypesDiffuse2018b; @sarkozyMutationalLandscapeGray2021a]| |
|
| 45 | -|[HIST1H1C](HIST1H1C)|1, aSHM|[Study Page](papers/morinFrequentMutationHistonemodifying2011)[@morinFrequentMutationHistonemodifying2011]|[@paneaWholeGenomeLandscape2019]| |
|
| 46 | -|[HIST1H1D](HIST1H1D)|1, aSHM|[Study Page](papers/krysiakRecurrentSomaticMutations2017b)[@krysiakRecurrentSomaticMutations2017b]|[@morinMutationalStructuralAnalysis2013; @jalladesExomeSequencingIdentifies2017]| |
|
| 47 | -|[HIST1H1E](HIST1H1E)|1, aSHM|[Study Page](papers/krysiakRecurrentSomaticMutations2017b)[@krysiakRecurrentSomaticMutations2017b]|[@grandeGenomewideDiscoverySomatic2019; @lohrDiscoveryPrioritizationSomatic2012a; @reichelFlowSortingExome2015a]| |
|
| 48 | -|[HIST1H2AC](HIST1H2AC)|1, aSHM|[Study Page](papers/krysiakRecurrentSomaticMutations2017b)[@krysiakRecurrentSomaticMutations2017b]|[@morinMutationalStructuralAnalysis2013]| |
|
| 49 | -|[HIST1H2AG](HIST1H2AG)|1, aSHM|[Study Page](papers/krysiakRecurrentSomaticMutations2017b)[@krysiakRecurrentSomaticMutations2017b]|[@morinMutationalStructuralAnalysis2013; @rossiCodingGenomeSplenic2012c; @paneaWholeGenomeLandscape2019]| |
|
| 50 | -|[HIST1H2AM](HIST1H2AM)|1, aSHM|[Study Page](papers/krysiakRecurrentSomaticMutations2017b)[@krysiakRecurrentSomaticMutations2017b]|[@paneaWholeGenomeLandscape2019]| |
|
| 51 | -|[HIST1H2BC](HIST1H2BC)|1, aSHM|[Study Page](papers/krysiakRecurrentSomaticMutations2017b)[@krysiakRecurrentSomaticMutations2017b]|[@lohrDiscoveryPrioritizationSomatic2012a; @mottokIntegrativeGenomicAnalysis2019b]| |
|
| 52 | -|[HIST1H2BD](HIST1H2BD)|1, aSHM|[Study Page](papers/krysiakRecurrentSomaticMutations2017b)[@krysiakRecurrentSomaticMutations2017b]|| |
|
| 53 | -|[HIST1H2BG](HIST1H2BG)|1, aSHM|[Study Page](papers/krysiakRecurrentSomaticMutations2017b)[@krysiakRecurrentSomaticMutations2017b]|| |
|
| 54 | -|[HIST1H3B](HIST1H3B)|1, aSHM||[@reichelFlowSortingExome2015a; @lohrDiscoveryPrioritizationSomatic2012a]| |
|
| 55 | -|[HIST1H3G](HIST1H3G)|1, aSHM|[Study Page](papers/krysiakRecurrentSomaticMutations2017b)[@krysiakRecurrentSomaticMutations2017b]|| |
|
| 56 | -|[HVCN1](HVCN1)|1|[Study Page](papers/krysiakRecurrentSomaticMutations2017b)[@krysiakRecurrentSomaticMutations2017b]|| |
|
| 57 | -|[IRF4](IRF4)|1, aSHM||[@morinFrequentMutationHistonemodifying2011; @mottokIntegrativeGenomicAnalysis2019b]| |
|
| 58 | -|[IRF8](IRF8)|1, aSHM|[Study Page](papers/morinFrequentMutationHistonemodifying2011)[@morinFrequentMutationHistonemodifying2011]|[@paneaWholeGenomeLandscape2019; @mottokIntegrativeGenomicAnalysis2019b]| |
|
| 59 | -|[ITPKB](ITPKB)|1, aSHM||[@reichelFlowSortingExome2015a; @schmitzGeneticsPathogenesisDiffuse2018a]| |
|
| 60 | -|[KLF2](KLF2)|1, aSHM||[@jalladesExomeSequencingIdentifies2017; @pasqualucciAnalysisCodingGenome2011; @deschGenotypingCirculatingTumor2020]| |
|
| 61 | -|[KLHL6](KLHL6)|1, aSHM|[Study Page](papers/morinFrequentMutationHistonemodifying2011)[@morinFrequentMutationHistonemodifying2011]|[@paneaWholeGenomeLandscape2019; @ganapathiGeneticLandscapeDural2016]| |
|
| 62 | -|[KMT2D](KMT2D)|1|[Study Page](papers/morinFrequentMutationHistonemodifying2011)[@morinFrequentMutationHistonemodifying2011]|[@beaLandscapeSomaticMutations2013; @rossiCodingGenomeSplenic2012c; @grandeGenomewideDiscoverySomatic2019; @deschGenotypingCirculatingTumor2020]| |
|
| 63 | -|[LTB](LTB)|1, aSHM||[@paneaWholeGenomeLandscape2019; @deschGenotypingCirculatingTumor2020; @chapuyMolecularSubtypesDiffuse2018b]| |
|
| 64 | -|[MAP2K1](MAP2K1)|1|[Study Page](papers/louissaintPediatrictypeNodalFollicular2016a)[@louissaintPediatrictypeNodalFollicular2016a]|[@shinBRAFV600EMAP2K12015]| |
|
| 65 | -|[MEF2B](MEF2B)|1, aSHM|[Study Page](papers/morinFrequentMutationHistonemodifying2011)[@morinFrequentMutationHistonemodifying2011]|[@beaLandscapeSomaticMutations2013]| |
|
| 66 | -|[MEF2C](MEF2C)|1, aSHM||[@arthurGenomewideDiscoverySomatic2018]| |
|
| 67 | -|[PCLO](PCLO)|1||[@lohrDiscoveryPrioritizationSomatic2012a]| |
|
| 68 | -|[PIM1](PIM1)|1, aSHM||[@dunsCharacterizationDLBCLPMBL2021b; @pasqualucciHypermutationMultipleProtooncogenes2001a; @burkhardtClinicalRelevanceMolecular2022b]| |
|
| 69 | -|[POU2AF1](POU2AF1)|1|[Study Page](papers/krysiakRecurrentSomaticMutations2017b)[@krysiakRecurrentSomaticMutations2017b]|| |
|
| 70 | -|[POU2F2](POU2F2)|1|[Study Page](papers/krysiakRecurrentSomaticMutations2017b)[@krysiakRecurrentSomaticMutations2017b]|[@lohrDiscoveryPrioritizationSomatic2012a]| |
|
| 71 | -|[PTPRD](PTPRD)|1||[@spinaGeneticsNodalMarginal2016b]| |
|
| 72 | -|[RRAGC](RRAGC)|1||[@okosunRecurrentMTORC1activatingRRAGC2016a]| |
|
| 73 | -|[S1PR2](S1PR2)|1, aSHM||[@muppidiLossSignalingGa132014b; @morinFrequentMutationHistonemodifying2011]| |
|
| 74 | -|[SGK1](SGK1)|1, aSHM|[Study Page](papers/morinFrequentMutationHistonemodifying2011)[@morinFrequentMutationHistonemodifying2011]|[@dunsCharacterizationDLBCLPMBL2021b]| |
|
| 75 | -|[SMARCA4](SMARCA4)|1|[Study Page](papers/krysiakRecurrentSomaticMutations2017b)[@krysiakRecurrentSomaticMutations2017b]|[@richterRecurrentMutationID32012a; @nadeuGenomicEpigenomicInsights2020b; @lohrDiscoveryPrioritizationSomatic2012a]| |
|
| 76 | -|[SOCS1](SOCS1)|1, aSHM||[@morinFrequentMutationHistonemodifying2011; @wenigerMutationsTumorSuppressor2006a]| |
|
| 77 | -|[STAT6](STAT6)|1|[Study Page](papers/yildizActivatingSTAT6Mutations2015c)[@yildizActivatingSTAT6Mutations2015c]|[@ritzRecurrentMutationsSTAT62009a]| |
|
| 78 | -|[TBL1XR1](TBL1XR1)|1||[@lohrDiscoveryPrioritizationSomatic2012a; @rossiCodingGenomeSplenic2012c]| |
|
| 79 | -|[TMSB4X](TMSB4X)|1, aSHM||[@albuquerqueEnhancingKnowledgeDiscovery2017a]| |
|
| 80 | -|[TNFAIP3](TNFAIP3)|1||[@rossiAlterationBIRC3Multiple2011a; @compagnoMutationsMultipleGenes2009a; @schmitzTNFAIP3A20Tumor2009a]| |
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| 81 | -|[TNFRSF14](TNFRSF14)|1|[Study Page](papers/cheungAcquiredTNFRSF14Mutations2010a)[@cheungAcquiredTNFRSF14Mutations2010a]|[@spinaGeneticsNodalMarginal2016b; @morinFrequentMutationHistonemodifying2011]| |
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| 82 | -|[TP53](TP53)|1|[Study Page](papers/morinFrequentMutationHistonemodifying2011)[@morinFrequentMutationHistonemodifying2011]|[@rossiCodingGenomeSplenic2012c; @beaLandscapeSomaticMutations2013; @tiacciPervasiveMutationsJAKSTAT2018b; @wildaInactivationARFMDM2p53Pathway2004; @lohrDiscoveryPrioritizationSomatic2012a]| |
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| 83 | -|[VMA21](VMA21)|1|[Study Page](papers/hubschmannMutationalMechanismsShaping2021b)[@hubschmannMutationalMechanismsShaping2021b]|| |
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| 84 | - |
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| 85 | -## Tier 2 FL genes |
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| 86 | - |
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| 87 | -### *50 total* |
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| 88 | - |
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| 89 | -|Gene|Tier| First FL evidence | Other entities | |
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| 90 | -|:-:|:-:|:-|:-| |
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| 91 | -|[ABL2](ABL2)|2|[Study Page](papers/russler-germainMutationsAssociatedProgression2023b)[@russler-germainMutationsAssociatedProgression2023b]|| |
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| 92 | -|[ACTG1](ACTG1)|2, aSHM|[Study Page](papers/hubschmannMutationalMechanismsShaping2021b)[@hubschmannMutationalMechanismsShaping2021b]|[@spinaGeneticsNodalMarginal2016b; @deschGenotypingCirculatingTumor2020]| |
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| 93 | -|[ATP6V1A](ATP6V1A)|2|[Study Page](papers/hubschmannMutationalMechanismsShaping2021b)[@hubschmannMutationalMechanismsShaping2021b]|| |
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| 94 | -|[BCL10](BCL10)|2|[Study Page](papers/russler-germainMutationsAssociatedProgression2023b)[@russler-germainMutationsAssociatedProgression2023b]|[@spinaGeneticsNodalMarginal2016b; @morinFrequentMutationHistonemodifying2011]| |
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| 95 | -|[CD70](CD70)|2|[Study Page](papers/russler-germainMutationsAssociatedProgression2023b)[@russler-germainMutationsAssociatedProgression2023b]|[@morinFrequentMutationHistonemodifying2011]| |
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| 96 | -|[CD79B](CD79B)|2||[@morinFrequentMutationHistonemodifying2011; @paneaWholeGenomeLandscape2019]| |
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| 97 | -|[CDC42BPB](CDC42BPB)|2|[Study Page](papers/hubschmannMutationalMechanismsShaping2021b)[@hubschmannMutationalMechanismsShaping2021b]|[@spinaGeneticsNodalMarginal2016b]| |
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| 98 | -|[CILP](CILP)|2|[Study Page](papers/russler-germainMutationsAssociatedProgression2023b)[@russler-germainMutationsAssociatedProgression2023b]|| |
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| 99 | -|[CPNE8](CPNE8)|2|[Study Page](papers/hubschmannMutationalMechanismsShaping2021b)[@hubschmannMutationalMechanismsShaping2021b]|| |
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| 100 | -|[CXCR4](CXCR4)|2, aSHM|[Study Page](papers/krysiakRecurrentSomaticMutations2017b)[@krysiakRecurrentSomaticMutations2017b]|[@paneaWholeGenomeLandscape2019; @khodabakhshiRecurrentTargetsAberrant2012]| |
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| 101 | -|[CYP2A6](CYP2A6)|2|[Study Page](papers/russler-germainMutationsAssociatedProgression2023b)[@russler-germainMutationsAssociatedProgression2023b]|| |
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| 102 | -|[DDX3X](DDX3X)|2||[@schmitzGeneticsPathogenesisDiffuse2018a; @mottokIntegrativeGenomicAnalysis2019b; @schmitzBurkittLymphomaPathogenesis2012]| |
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| 103 | -|[DHX15](DHX15)|2|[Study Page](papers/hubschmannMutationalMechanismsShaping2021b)[@hubschmannMutationalMechanismsShaping2021b]|| |
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| 104 | -|[DUSP2](DUSP2)|2, aSHM||[@dunsCharacterizationDLBCLPMBL2021b; @lohrDiscoveryPrioritizationSomatic2012a]| |
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| 105 | -|[EGR1](EGR1)|2|[Study Page](papers/krysiakRecurrentSomaticMutations2017b)[@krysiakRecurrentSomaticMutations2017b]|[@rossiCodingGenomeSplenic2012c; @reichelFlowSortingExome2015a]| |
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| 106 | -|[FZR1](FZR1)|2|[Study Page](papers/hubschmannMutationalMechanismsShaping2021b)[@hubschmannMutationalMechanismsShaping2021b]|| |
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| 107 | -|[GBP7](GBP7)|2|[Study Page](papers/russler-germainMutationsAssociatedProgression2023b)[@russler-germainMutationsAssociatedProgression2023b]|| |
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| 108 | -|[GRM6](GRM6)|2|[Study Page](papers/russler-germainMutationsAssociatedProgression2023b)[@russler-germainMutationsAssociatedProgression2023b]|| |
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| 109 | -|[HIST1H2BM](HIST1H2BM)|2, aSHM|[Study Page](papers/krysiakRecurrentSomaticMutations2017b)[@krysiakRecurrentSomaticMutations2017b]|| |
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| 110 | -|[HIST1H3I](HIST1H3I)|2, aSHM|[Study Page](papers/krysiakRecurrentSomaticMutations2017b)[@krysiakRecurrentSomaticMutations2017b]|[@paneaWholeGenomeLandscape2019]| |
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| 111 | -|[HLA-B](HLA-B)|2||[@lohrDiscoveryPrioritizationSomatic2012a; @wienandGenomicAnalysesFlowsorted2019b]| |
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| 112 | -|[HNRNPD](HNRNPD)|2||| |
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| 113 | -|[IGLL5](IGLL5)|2, aSHM|[Study Page](papers/russler-germainMutationsAssociatedProgression2023b)[@russler-germainMutationsAssociatedProgression2023b]|[@deschGenotypingCirculatingTumor2020; @paneaWholeGenomeLandscape2019]| |
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| 114 | -|[JUP](JUP)|2|[Study Page](papers/hubschmannMutationalMechanismsShaping2021b)[@hubschmannMutationalMechanismsShaping2021b]|| |
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| 115 | -|[KIR3DL1](KIR3DL1)|2|[Study Page](papers/russler-germainMutationsAssociatedProgression2023b)[@russler-germainMutationsAssociatedProgression2023b]|| |
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| 116 | -|[LAPTM5](LAPTM5)|2|[Study Page](papers/hubschmannMutationalMechanismsShaping2021b)[@hubschmannMutationalMechanismsShaping2021b]|| |
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| 117 | -|[MAGEC1](MAGEC1)|2|[Study Page](papers/russler-germainMutationsAssociatedProgression2023b)[@russler-germainMutationsAssociatedProgression2023b]|| |
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| 118 | -|[MAP7D1](MAP7D1)|2|[Study Page](papers/russler-germainMutationsAssociatedProgression2023b)[@russler-germainMutationsAssociatedProgression2023b]|| |
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| 119 | -|[MGEA5](MGEA5)|2|[Study Page](papers/hubschmannMutationalMechanismsShaping2021b)[@hubschmannMutationalMechanismsShaping2021b]|| |
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| 120 | -|[MKI67](MKI67)|2|[Study Page](papers/russler-germainMutationsAssociatedProgression2023b)[@russler-germainMutationsAssociatedProgression2023b]|[@schmitzBurkittLymphomaPathogenesis2012]| |
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| 121 | -|[MYC](MYC)|2, aSHM||[@pasqualucciHypermutationMultipleProtooncogenes2001a; @jalladesExomeSequencingIdentifies2017; @johnstonCmycHypermutationBurkitt1992; @dunsCharacterizationDLBCLPMBL2021b]| |
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| 122 | -|[MYCBP2](MYCBP2)|2|[Study Page](papers/hubschmannMutationalMechanismsShaping2021b)[@hubschmannMutationalMechanismsShaping2021b]|| |
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| 123 | -|[MYD88](MYD88)|2||[@yanBCRTLRSignaling2012a; @ngoOncogenicallyActiveMYD882011a]| |
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| 124 | -|[NFKBIA](NFKBIA)|2|[Study Page](papers/russler-germainMutationsAssociatedProgression2023b)[@russler-germainMutationsAssociatedProgression2023b]|[@wienandGenomicAnalysesFlowsorted2019b; @lakeMutationsNFKBIAEncoding2009]| |
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| 125 | -|[OR8H2](OR8H2)|2|[Study Page](papers/russler-germainMutationsAssociatedProgression2023b)[@russler-germainMutationsAssociatedProgression2023b]|| |
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| 126 | -|[P2RY8](P2RY8)|2||[@muppidiLossSignalingGa132014b; @lohrDiscoveryPrioritizationSomatic2012a]| |
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| 127 | -|[PDS5B](PDS5B)|2|[Study Page](papers/hubschmannMutationalMechanismsShaping2021b)[@hubschmannMutationalMechanismsShaping2021b]|[@morinMutationalStructuralAnalysis2013]| |
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| 128 | -|[PPP4C](PPP4C)|2|[Study Page](papers/hubschmannMutationalMechanismsShaping2021b)[@hubschmannMutationalMechanismsShaping2021b]|| |
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| 129 | -|[PRKDC](PRKDC)|2|[Study Page](papers/hubschmannMutationalMechanismsShaping2021b)[@hubschmannMutationalMechanismsShaping2021b]|[@schmitzGeneticsPathogenesisDiffuse2018a]| |
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| 130 | -|[PZP](PZP)|2|[Study Page](papers/russler-germainMutationsAssociatedProgression2023b)[@russler-germainMutationsAssociatedProgression2023b]|| |
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| 131 | -|[RBM6](RBM6)|2|[Study Page](papers/hubschmannMutationalMechanismsShaping2021b)[@hubschmannMutationalMechanismsShaping2021b]|| |
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| 132 | -|[SESN1](SESN1)|2|[Study Page](papers/oricchioGeneticEpigeneticInactivation2017b)[@oricchioGeneticEpigeneticInactivation2017b]|| |
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| 133 | -|[SHROOM3](SHROOM3)|2|[Study Page](papers/russler-germainMutationsAssociatedProgression2023b)[@russler-germainMutationsAssociatedProgression2023b]|| |
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| 134 | -|[SRRM2](SRRM2)|2|[Study Page](papers/russler-germainMutationsAssociatedProgression2023b)[@russler-germainMutationsAssociatedProgression2023b]|[@morinMutationalStructuralAnalysis2013]| |
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| 135 | -|[STAB2](STAB2)|2|[Study Page](papers/russler-germainMutationsAssociatedProgression2023b)[@russler-germainMutationsAssociatedProgression2023b]|| |
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| 136 | -|[TMEM30A](TMEM30A)|2|[Study Page](papers/morinFrequentMutationHistonemodifying2011)[@morinFrequentMutationHistonemodifying2011]|| |
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| 137 | -|[TPP1](TPP1)|2|[Study Page](papers/hubschmannMutationalMechanismsShaping2021b)[@hubschmannMutationalMechanismsShaping2021b]|| |
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| 138 | -|[XIRP2](XIRP2)|2|[Study Page](papers/russler-germainMutationsAssociatedProgression2023b)[@russler-germainMutationsAssociatedProgression2023b]|| |
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| 139 | -|[ZC3H12A](ZC3H12A)|2||[@arthurGenomewideDiscoverySomatic2018]| |
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| 140 | -|[ZNF608](ZNF608)|2|[Study Page](papers/krysiakRecurrentSomaticMutations2017b)[@krysiakRecurrentSomaticMutations2017b]|[@zhangGeneticHeterogeneityDiffuse2013]| |
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| 141 | - |
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| 142 | - |
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| 143 | -# References |