4b8627491368fd5802825b78095776dc91e0d519
MCL_genes.md
| ... | ... | @@ -13,31 +13,31 @@ link-citations: true |
| 13 | 13 | |
| 14 | 14 | ### *23 total* |
| 15 | 15 | |
| 16 | -|Gene|Summary| First MCL study | Other entities | QC result | |
|
| 17 | -|:-:|:--:|:-:|:-|:-| |
|
| 18 | -|[ATM](ATM)|Tier 1 GE[@beaLandscapeSomaticMutations2013], FE[@camachoATMGeneInactivation2002]|[Bea et al](papers/beaLandscapeSomaticMutations2013)|[@braggioGenomicAnalysisMarginal2012; @reddyGeneticFunctionalDrivers2017]|| |
|
| 19 | -|[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]|| |
|
| 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 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]|| |
|
| 28 | -|[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]|| |
|
| 30 | -|[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)||| |
|
| 37 | -|[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]|| |
|
| 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]| |
|
| 28 | +|[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]| |
|
| 30 | +|[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)|| |
|
| 37 | +|[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]| |
|
| 41 | 41 | |
| 42 | 42 | ## Tier 2, low-confidence MCL genes |
| 43 | 43 |