MCL_genes.md
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### *23 total*
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-|Gene|Summary| First MCL study | Other entities | QC result |
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-|:-:|:--:|:-:|:-|:-|
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-|[ATM](ATM)|Tier 1 GE[@beaLandscapeSomaticMutations2013], FE[@camachoATMGeneInactivation2002]|[Bea et al](papers/beaLandscapeSomaticMutations2013)|[@braggioGenomicAnalysisMarginal2012; @reddyGeneticFunctionalDrivers2017]||
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-|[BIRC3](BIRC3)|Tier 1 GE[@beaLandscapeSomaticMutations2013], aSHM|[Bea et al](papers/beaLandscapeSomaticMutations2013)|[@arthurGenomewideDiscoverySomatic2018; @dunsCharacterizationDLBCLPMBL2021; @rossiAlterationBIRC3Multiple2011]||
20
-|[CARD11](CARD11)|Tier 1 GE[@wuGeneticHeterogeneityPrimary2016], FE[@lenzOncogenicCARD11Mutations2008]|[Wu et al](papers/wuGeneticHeterogeneityPrimary2016)|[@lenzOncogenicCARD11Mutations2008; @morinFrequentMutationHistonemodifying2011; @yanBCRTLRSignaling2012]||
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-|[CCND1](CCND1)|Tier 1 GE[@beaLandscapeSomaticMutations2013]|[Bea et al](papers/beaLandscapeSomaticMutations2013)|||
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-|[DAZAP1](DAZAP1)|Tier 1 GE[@pararajalingamCodingNoncodingDrivers2020]|[Pararajalingam et al](papers/pararajalingamCodingNoncodingDrivers2020)|||
23
-|[EWSR1](EWSR1)|Tier 1 GE[@pararajalingamCodingNoncodingDrivers2020]|[Pararajalingam et al](papers/pararajalingamCodingNoncodingDrivers2020)|||
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-|[HNRNPH1](HNRNPH1)|Tier 1 GE[@pararajalingamCodingNoncodingDrivers2020]|[Pararajalingam et al](papers/pararajalingamCodingNoncodingDrivers2020)|||
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-|[KMT2D](KMT2D)|Tier 1 GE[@beaLandscapeSomaticMutations2013], FE[@zhangDisruptionKMT2DPerturbs2015]|[Bea et al](papers/beaLandscapeSomaticMutations2013)|[@deschGenotypingCirculatingTumor2020; @grandeGenomewideDiscoverySomatic2019; @morinFrequentMutationHistonemodifying2011; @rossiCodingGenomeSplenic2012]||
26
-|[MEF2B](MEF2B)|Tier 1 GE[@beaLandscapeSomaticMutations2013], FE[@ponMEF2BMutationsNonHodgkin2015], aSHM|[Bea et al](papers/beaLandscapeSomaticMutations2013)|[@morinFrequentMutationHistonemodifying2011]||
27
-|[NFKBIE](NFKBIE)|Tier 1 GE[@pararajalingamCodingNoncodingDrivers2020], FE[@mansouriFunctionalLossIkBe2015]|[Pararajalingam et al](papers/pararajalingamCodingNoncodingDrivers2020)|[@mansouriFrequentNFKBIEDeletions2016; @morinGeneticLandscapesRelapsed2016]||
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-|[NOTCH1](NOTCH1)|Tier 1 GE[@beaLandscapeSomaticMutations2013], FE[@ryanCellRegulomeLinks2017]|[Bea et al](papers/beaLandscapeSomaticMutations2013)|[@loveGeneticLandscapeMutations2012; @pasqualucciAnalysisCodingGenome2011; @rossiCodingGenomeSplenic2012]||
29
-|[NOTCH2](NOTCH2)|Tier 1 GE[@beaLandscapeSomaticMutations2013], FE[@leeGainoffunctionMutationsCopy2009]|[Bea et al](papers/beaLandscapeSomaticMutations2013)|[@rossiCodingGenomeSplenic2012; @zhangGeneticHeterogeneityDiffuse2013]||
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-|[NSD2](NSD2)|Tier 1 GE[@beaLandscapeSomaticMutations2013]|[Bea et al](papers/beaLandscapeSomaticMutations2013)|[@zhangGeneticHeterogeneityDiffuse2013]||
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-|[POT1](POT1)|Tier 1 GE[@zhangGenomicLandscapeMantle2014]|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)|||
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-|[RB1](RB1)|Tier 1 GE[@zhangGenomicLandscapeMantle2014], FE[@pinyolInactivationRB1Mantlecell2007]|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)|[@morinMutationalStructuralAnalysis2013]||
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-|[S1PR1](S1PR1)|Tier 1 GE[@pararajalingamCodingNoncodingDrivers2020]|[Pararajalingam et al](papers/pararajalingamCodingNoncodingDrivers2020)|[@lohrDiscoveryPrioritizationSomatic2012]||
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-|[SMARCA4](SMARCA4)|Tier 1 GE[@nadeuGenomicEpigenomicInsights2020], FE[@fernandoFunctionalCharacterizationSMARCA42020]|[Nadeu et al](papers/nadeuGenomicEpigenomicInsights2020)|[@krysiakRecurrentSomaticMutations2017; @reddyGeneticFunctionalDrivers2017; @richterRecurrentMutationID32012]||
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-|[SP140](SP140)|Tier 1 GE[@beaLandscapeSomaticMutations2013]|[Bea et al](papers/beaLandscapeSomaticMutations2013)|||
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-|[SYNE1](SYNE1)|Tier 1 GE[@nadeuGenomicEpigenomicInsights2020]|[Nadeu et al](papers/nadeuGenomicEpigenomicInsights2020)|||
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-|[TERT](TERT)|Tier 1 GE[@nadeuGenomicEpigenomicInsights2020]|[Nadeu et al](papers/nadeuGenomicEpigenomicInsights2020)|||
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-|[TLR2](TLR2)|Tier 1 GE[@beaLandscapeSomaticMutations2013]|[Bea et al](papers/beaLandscapeSomaticMutations2013)|[@chapuyMolecularSubtypesDiffuse2018]||
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-|[TP53](TP53)|Tier 1 GE[@beaLandscapeSomaticMutations2013], FE[@katoUnderstandingFunctionstructureFunctionmutation2003]|[Bea et al](papers/beaLandscapeSomaticMutations2013)|[@morinFrequentMutationHistonemodifying2011; @rossiCodingGenomeSplenic2012; @tiacciPervasiveMutationsJAKSTAT2018; @wildaInactivationARFMDM2p53Pathway2004]||
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-|[UBR5](UBR5)|Tier 1 GE[@pararajalingamCodingNoncodingDrivers2020]|[Pararajalingam et al](papers/pararajalingamCodingNoncodingDrivers2020)|[@albuquerqueEnhancingKnowledgeDiscovery2017]||
16
+|Gene|Status| First MCL study | Other lists |
17
+|:-:|:--:|:-:|:-|
18
+|[ATM](ATM)|MCL Tier 1|[Bea et al](papers/beaLandscapeSomaticMutations2013)|[@braggioGenomicAnalysisMarginal2012; @reddyGeneticFunctionalDrivers2017]|
19
+|[BIRC3](BIRC3)|MCL Tier 1 |[Bea et al](papers/beaLandscapeSomaticMutations2013)|[@arthurGenomewideDiscoverySomatic2018; @dunsCharacterizationDLBCLPMBL2021; @rossiAlterationBIRC3Multiple2011]|
20
+|[CARD11](CARD11)|MCL Tier 1 |[Wu et al](papers/wuGeneticHeterogeneityPrimary2016)|[@lenzOncogenicCARD11Mutations2008; @morinFrequentMutationHistonemodifying2011; @yanBCRTLRSignaling2012]|
21
+|[CCND1](CCND1)|Tier 1 GE[@beaLandscapeSomaticMutations2013]|[Bea et al](papers/beaLandscapeSomaticMutations2013)||
22
+|[DAZAP1](DAZAP1)|Tier 1 GE[@pararajalingamCodingNoncodingDrivers2020]|[Pararajalingam et al](papers/pararajalingamCodingNoncodingDrivers2020)||
23
+|[EWSR1](EWSR1)|Tier 1 GE[@pararajalingamCodingNoncodingDrivers2020]|[Pararajalingam et al](papers/pararajalingamCodingNoncodingDrivers2020)||
24
+|[HNRNPH1](HNRNPH1)|Tier 1 GE[@pararajalingamCodingNoncodingDrivers2020]|[Pararajalingam et al](papers/pararajalingamCodingNoncodingDrivers2020)||
25
+|[KMT2D](KMT2D)|Tier 1 |[Bea et al](papers/beaLandscapeSomaticMutations2013)|[@deschGenotypingCirculatingTumor2020; @grandeGenomewideDiscoverySomatic2019; @morinFrequentMutationHistonemodifying2011; @rossiCodingGenomeSplenic2012]|
26
+|[MEF2B](MEF2B)|MCL Tier 1 |[Bea et al](papers/beaLandscapeSomaticMutations2013)|[@morinFrequentMutationHistonemodifying2011]|
27
+|[NFKBIE](NFKBIE)|MCL Tier 1 |[Pararajalingam et al](papers/pararajalingamCodingNoncodingDrivers2020)|[@mansouriFrequentNFKBIEDeletions2016; @morinGeneticLandscapesRelapsed2016]|
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+|[NOTCH1](NOTCH1)|MCL Tier 1 |[Bea et al](papers/beaLandscapeSomaticMutations2013)|[@loveGeneticLandscapeMutations2012; @pasqualucciAnalysisCodingGenome2011; @rossiCodingGenomeSplenic2012]|
29
+|[NOTCH2](NOTCH2)|MCL Tier 1 |[Bea et al](papers/beaLandscapeSomaticMutations2013)|[@rossiCodingGenomeSplenic2012; @zhangGeneticHeterogeneityDiffuse2013]|
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+|[NSD2](NSD2)|Tier 1 GE[@beaLandscapeSomaticMutations2013]|[Bea et al](papers/beaLandscapeSomaticMutations2013)|[@zhangGeneticHeterogeneityDiffuse2013]|
31
+|[POT1](POT1)|Tier 1 GE[@zhangGenomicLandscapeMantle2014]|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)||
32
+|[RB1](RB1)|Tier 1 GE[@zhangGenomicLandscapeMantle2014], FE[@pinyolInactivationRB1Mantlecell2007]|[Zhang et al](papers/zhangGenomicLandscapeMantle2014)|[@morinMutationalStructuralAnalysis2013]|
33
+|[S1PR1](S1PR1)|Tier 1 GE[@pararajalingamCodingNoncodingDrivers2020]|[Pararajalingam et al](papers/pararajalingamCodingNoncodingDrivers2020)|[@lohrDiscoveryPrioritizationSomatic2012]|
34
+|[SMARCA4](SMARCA4)|Tier 1 GE[@nadeuGenomicEpigenomicInsights2020], FE[@fernandoFunctionalCharacterizationSMARCA42020]|[Nadeu et al](papers/nadeuGenomicEpigenomicInsights2020)|[@krysiakRecurrentSomaticMutations2017; @reddyGeneticFunctionalDrivers2017; @richterRecurrentMutationID32012]|
35
+|[SP140](SP140)|Tier 1 GE[@beaLandscapeSomaticMutations2013]|[Bea et al](papers/beaLandscapeSomaticMutations2013)||
36
+|[SYNE1](SYNE1)|Tier 1 GE[@nadeuGenomicEpigenomicInsights2020]|[Nadeu et al](papers/nadeuGenomicEpigenomicInsights2020)||
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+|[TERT](TERT)|Tier 1 GE[@nadeuGenomicEpigenomicInsights2020]|[Nadeu et al](papers/nadeuGenomicEpigenomicInsights2020)||
38
+|[TLR2](TLR2)|Tier 1 GE[@beaLandscapeSomaticMutations2013]|[Bea et al](papers/beaLandscapeSomaticMutations2013)|[@chapuyMolecularSubtypesDiffuse2018]|
39
+|[TP53](TP53)|Tier 1 GE[@beaLandscapeSomaticMutations2013], FE[@katoUnderstandingFunctionstructureFunctionmutation2003]|[Bea et al](papers/beaLandscapeSomaticMutations2013)|[@morinFrequentMutationHistonemodifying2011; @rossiCodingGenomeSplenic2012; @tiacciPervasiveMutationsJAKSTAT2018; @wildaInactivationARFMDM2p53Pathway2004]|
40
+|[UBR5](UBR5)|Tier 1 GE[@pararajalingamCodingNoncodingDrivers2020]|[Pararajalingam et al](papers/pararajalingamCodingNoncodingDrivers2020)|[@albuquerqueEnhancingKnowledgeDiscovery2017]|
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## Tier 2, low-confidence MCL genes
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