CYP2A6.md
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@@ -42,6 +42,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
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## CYP2A6 Expression
43 43
![image](images/gene_expression/CYP2A6_by_pathology.svg)
44 44
<!-- ORIGIN: russler-germainMutationsAssociatedProgression2023a -->
45
-<!-- FL: russler-germainMutationsAssociatedProgression2023a -->
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+<!-- FL: russler-germainMutationsAssociatedProgression2023b -->
46 46
## References
47 47
1. Russler-Germain DA, Krysiak K, Ramirez CA, Mosior M, Watkins MP, Gomez F, Skidmore ZL, Trani L, Gao F, Geyer S, Cashen A, Mehta-Shah N, Kahl B, Bartlett N, Alderuccio J, Lossos I, Ondrejka S, Hsi E, Martin P, Leonard J, Griffith M, Griffith O, Fehniger T. Mutations associated with progression in follicular lymphoma predict inferior outcomes at diagnosis: Alliance A151303. Blood Advances. 2023;7:5524–5539.
DLBCL_genes_temp.md
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@@ -0,0 +1,345 @@
1
+---
2
+title: DLBCL genes
3
+csl: 'chicago-author-date.csl'
4
+bibliography: 'morinlab.bib'
5
+---
6
+# DLBCL genes
7
+## Origins of DLBCL genes![sankey](DLBCL_sankey-1.svg)
8
+## Tier 1 DLBCL genes
9
+### *128 total*
10
+|Gene|Tier| Relevant references|
11
+|:-:|:-:|:-|
12
+|[ACTB](ACTB)|1, aSHM|[@wienandGenomicAnalysesFlowsorted2019b; @lohrDiscoveryPrioritizationSomatic2012a]|
13
+|[ACTG1](ACTG1)|1, aSHM|[@spinaGeneticsNodalMarginal2016b; @deschGenotypingCirculatingTumor2020; @hubschmannMutationalMechanismsShaping2021b]|
14
+|[ARID1A](ARID1A)|1|[@rossiCodingGenomeSplenic2012c; @wienandGenomicAnalysesFlowsorted2019b; @loveGeneticLandscapeMutations2012; @zhangGeneticHeterogeneityDiffuse2013; @krysiakRecurrentSomaticMutations2017b]|
15
+|[ATM](ATM)|1|[@braggioGenomicAnalysisMarginal2012; @beaLandscapeSomaticMutations2013; @reddyGeneticFunctionalDrivers2017]|
16
+|[B2M](B2M)|1|[@pararajalingamCodingNoncodingDrivers2020; @reichelFlowSortingExome2015a; @morinFrequentMutationHistonemodifying2011]|
17
+|[BCL10](BCL10)|1|[@morinFrequentMutationHistonemodifying2011; @russler-germainMutationsAssociatedProgression2023b; @spinaGeneticsNodalMarginal2016b]|
18
+|[BCL2](BCL2)|1, aSHM|[@sarkozyMutationalLandscapeGray2021a; @tanakaFrequentIncidenceSomatic1992; @burkhardtClinicalRelevanceMolecular2022b; @morinFrequentMutationHistonemodifying2011]|
19
+|[BCL6](BCL6)|1, aSHM|[@morinFrequentMutationHistonemodifying2011; @loveGeneticLandscapeMutations2012]|
20
+|[BCL7A](BCL7A)|1, aSHM|[@reichelFlowSortingExome2015a; @krysiakRecurrentSomaticMutations2017b; @arthurGenomewideDiscoverySomatic2018; @grandeGenomewideDiscoverySomatic2019]|
21
+|[BIRC6](BIRC6)|1|[@reddyGeneticFunctionalDrivers2017; @sarkozyMutationalLandscapeGray2021a]|
22
+|[BRAF](BRAF)|1|[@loveGeneticLandscapeMutations2012; @tiacciBRAFMutationsHairycell2011a]|
23
+|[BTG1](BTG1)|1, aSHM|[@morinFrequentMutationHistonemodifying2011; @burkhardtClinicalRelevanceMolecular2022b; @sarkozyMutationalLandscapeGray2021a]|
24
+|[BTG2](BTG2)|1, aSHM|[@morinFrequentMutationHistonemodifying2011; @loveGeneticLandscapeMutations2012]|
25
+|[BTK](BTK)|1|[@krysiakRecurrentSomaticMutations2017b; @albuquerqueEnhancingKnowledgeDiscovery2017a]|
26
+|[CARD11](CARD11)|1|[@wuGeneticHeterogeneityPrimary2016; @paneaWholeGenomeLandscape2019; @lenzOncogenicCARD11Mutations2008; @yanBCRTLRSignaling2012a; @morinFrequentMutationHistonemodifying2011]|
27
+|[CCND3](CCND3)|1|[@jalladesExomeSequencingIdentifies2017; @richterRecurrentMutationID32012a; @deschGenotypingCirculatingTumor2020; @morinFrequentMutationHistonemodifying2011]|
28
+|[CD58](CD58)|1|[@morinFrequentMutationHistonemodifying2011; @schneiderAlterationsCD58Gene2015a]|
29
+|[CD70](CD70)|1|[@russler-germainMutationsAssociatedProgression2023b; @morinFrequentMutationHistonemodifying2011]|
30
+|[CD79B](CD79B)|1|[@morinFrequentMutationHistonemodifying2011; @paneaWholeGenomeLandscape2019]|
31
+|[CD83](CD83)|1, aSHM|[@russler-germainMutationsAssociatedProgression2023b; @morinMutationalStructuralAnalysis2013; @dunsCharacterizationDLBCLPMBL2021b; @paneaWholeGenomeLandscape2019]|
32
+|[CDKN2A](CDKN2A)|1|[@grandeGenomewideDiscoverySomatic2019; @spinaGeneticsNodalMarginal2016b; @morinMutationalStructuralAnalysis2013]|
33
+|[CIITA](CIITA)|1, aSHM|[@mottokGenomicAlterationsCIITA2015b; @morinFrequentMutationHistonemodifying2011]|
34
+|[CREBBP](CREBBP)|1|[@dunsCharacterizationDLBCLPMBL2021b; @pasqualucciInactivatingMutationsAcetyltransferase2011a; @loveGeneticLandscapeMutations2012; @parryWholeExomeSequencing2013]|
35
+|[CXCR4](CXCR4)|1, aSHM|[@khodabakhshiRecurrentTargetsAberrant2012; @paneaWholeGenomeLandscape2019; @krysiakRecurrentSomaticMutations2017b]|
36
+|[CXCR5](CXCR5)|1|[@schmitzGeneticsPathogenesisDiffuse2018a; @mottokIntegrativeGenomicAnalysis2019b]|
37
+|[DDX3X](DDX3X)|1|[@schmitzBurkittLymphomaPathogenesis2012; @mottokIntegrativeGenomicAnalysis2019b; @schmitzGeneticsPathogenesisDiffuse2018a]|
38
+|[DTX1](DTX1)|1, aSHM|[@paneaWholeGenomeLandscape2019; @gomezUltraDeepSequencingReveals2023; @schmitzGeneticsPathogenesisDiffuse2018a; @rossiCodingGenomeSplenic2012c]|
39
+|[DUSP2](DUSP2)|1, aSHM|[@dunsCharacterizationDLBCLPMBL2021b; @morinMutationalStructuralAnalysis2013]|
40
+|[EBF1](EBF1)|1, aSHM|[@reichelFlowSortingExome2015a; @bohleRoleEarlyBcell2013; @thomasGeneticSubgroupsInform2023]|
41
+|[EEF1A1](EEF1A1)|1|[@hubschmannMutationalMechanismsShaping2021b; @reichelFlowSortingExome2015a]|
42
+|[EP300](EP300)|1|[@rossiCodingGenomeSplenic2012c; @paneaWholeGenomeLandscape2019; @pasqualucciInactivatingMutationsAcetyltransferase2011a]|
43
+|[ETS1](ETS1)|1, aSHM|[@paneaWholeGenomeLandscape2019; @morinFrequentMutationHistonemodifying2011]|
44
+|[ETV6](ETV6)|1, aSHM|[@arthurGenomewideDiscoverySomatic2018]|
45
+|[EZH2](EZH2)|1|[@morinSomaticMutationsAltering2010a; @mottokIntegrativeGenomicAnalysis2019b; @loveGeneticLandscapeMutations2012]|
46
+|[FAS](FAS)|1|[@schollMutationsRegionFAS2007; @spinaGeneticsNodalMarginal2016b]|
47
+|[FBXO11](FBXO11)|1|[@richterRecurrentMutationID32012a; @hubschmannMutationalMechanismsShaping2021b; @parryWholeExomeSequencing2013]|
48
+|[FBXW7](FBXW7)|1|[@zhangGeneticHeterogeneityDiffuse2013]|
49
+|[FOXO1](FOXO1)|1|[@schmitzBurkittLymphomaPathogenesis2012; @morinFrequentMutationHistonemodifying2011; @dunsCharacterizationDLBCLPMBL2021b]|
50
+|[GNA13](GNA13)|1|[@loveGeneticLandscapeMutations2012; @morinFrequentMutationHistonemodifying2011; @reichelFlowSortingExome2015a]|
51
+|[GNAI2](GNAI2)|1|[@grandeGenomewideDiscoverySomatic2019; @morinMutationalStructuralAnalysis2013]|
52
+|[GRB2](GRB2)|1|[@paneaWholeGenomeLandscape2019; @pasqualucciAnalysisCodingGenome2011]|
53
+|[GRHPR](GRHPR)|1, aSHM|[@arthurGenomewideDiscoverySomatic2018]|
54
+|[HIST1H1B](HIST1H1B)|1, aSHM|[@krysiakRecurrentSomaticMutations2017b; @sarkozyMutationalLandscapeGray2021a; @chapuyMolecularSubtypesDiffuse2018b]|
55
+|[HIST1H1C](HIST1H1C)|1, aSHM|[@morinFrequentMutationHistonemodifying2011; @paneaWholeGenomeLandscape2019]|
56
+|[HIST1H1D](HIST1H1D)|1, aSHM|[@krysiakRecurrentSomaticMutations2017b; @jalladesExomeSequencingIdentifies2017; @morinMutationalStructuralAnalysis2013]|
57
+|[HIST1H1E](HIST1H1E)|1, aSHM|[@morinMutationalStructuralAnalysis2013; @reichelFlowSortingExome2015a; @grandeGenomewideDiscoverySomatic2019; @krysiakRecurrentSomaticMutations2017b]|
58
+|[HIST1H2AC](HIST1H2AC)|1, aSHM|[@krysiakRecurrentSomaticMutations2017b; @morinMutationalStructuralAnalysis2013]|
59
+|[HIST1H2AM](HIST1H2AM)|1, aSHM|[@paneaWholeGenomeLandscape2019; @krysiakRecurrentSomaticMutations2017b]|
60
+|[HIST1H2BC](HIST1H2BC)|1, aSHM|[@krysiakRecurrentSomaticMutations2017b; @mottokIntegrativeGenomicAnalysis2019b; @reddyGeneticFunctionalDrivers2017]|
61
+|[HIST1H2BK](HIST1H2BK)|1, aSHM|[@paneaWholeGenomeLandscape2019; @rossiCodingGenomeSplenic2012c]|
62
+|[HIST1H3B](HIST1H3B)|1, aSHM|[@zhangGeneticHeterogeneityDiffuse2013; @reichelFlowSortingExome2015a]|
63
+|[HIST2H2BE](HIST2H2BE)|1, aSHM|[@schmitzGeneticsPathogenesisDiffuse2018a]|
64
+|[HLA-A](HLA-A)|1|[@deschGenotypingCirculatingTumor2020]|
65
+|[HLA-B](HLA-B)|1|[@wienandGenomicAnalysesFlowsorted2019b]|
66
+|[HLA-C](HLA-C)|1|[@gomezUltraDeepSequencingReveals2023]|
67
+|[HLA-DMB](HLA-DMB)|1||
68
+|[HNRNPU](HNRNPU)|1, aSHM|[@paneaWholeGenomeLandscape2019; @reddyGeneticFunctionalDrivers2017]|
69
+|[HVCN1](HVCN1)|1|[@krysiakRecurrentSomaticMutations2017b]|
70
+|[IKZF3](IKZF3)|1|[@morinMutationalStructuralAnalysis2013; @paneaWholeGenomeLandscape2019]|
71
+|[IL4R](IL4R)|1, aSHM|[@dunsCharacterizationDLBCLPMBL2021b; @viganoSomaticIL4RMutations2018b]|
72
+|[IRF4](IRF4)|1, aSHM|[@mottokIntegrativeGenomicAnalysis2019b; @morinFrequentMutationHistonemodifying2011]|
73
+|[IRF8](IRF8)|1, aSHM|[@paneaWholeGenomeLandscape2019; @morinFrequentMutationHistonemodifying2011; @mottokIntegrativeGenomicAnalysis2019b]|
74
+|[ITPKB](ITPKB)|1, aSHM|[@schmitzGeneticsPathogenesisDiffuse2018a; @reichelFlowSortingExome2015a]|
75
+|[KLF2](KLF2)|1, aSHM|[@deschGenotypingCirculatingTumor2020; @jalladesExomeSequencingIdentifies2017; @pasqualucciAnalysisCodingGenome2011]|
76
+|[KLHL14](KLHL14)|1|[@zhangGeneticHeterogeneityDiffuse2013]|
77
+|[KLHL6](KLHL6)|1, aSHM|[@paneaWholeGenomeLandscape2019; @ganapathiGeneticLandscapeDural2016; @morinFrequentMutationHistonemodifying2011]|
78
+|[KMT2C](KMT2C)|1|[@zhangGenomicLandscapeMantle2014; @sarkozyMutationalLandscapeGray2021a; @zhouSporadicEndemicBurkitt2019; @zhangGeneticHeterogeneityDiffuse2013]|
79
+|[KMT2D](KMT2D)|1|[@deschGenotypingCirculatingTumor2020; @rossiCodingGenomeSplenic2012c; @grandeGenomewideDiscoverySomatic2019; @morinFrequentMutationHistonemodifying2011; @beaLandscapeSomaticMutations2013]|
80
+|[KRAS](KRAS)|1|[@lohrDiscoveryPrioritizationSomatic2012a]|
81
+|[LCOR](LCOR)|1|[@arthurGenomewideDiscoverySomatic2018]|
82
+|[LTB](LTB)|1, aSHM|[@deschGenotypingCirculatingTumor2020; @chapuyMolecularSubtypesDiffuse2018b; @paneaWholeGenomeLandscape2019]|
83
+|[MEF2B](MEF2B)|1, aSHM|[@beaLandscapeSomaticMutations2013; @morinFrequentMutationHistonemodifying2011]|
84
+|[MEF2C](MEF2C)|1, aSHM|[@arthurGenomewideDiscoverySomatic2018]|
85
+|[MGA](MGA)|1|[@jalladesExomeSequencingIdentifies2017; @zhangGeneticHeterogeneityDiffuse2013]|
86
+|[MPEG1](MPEG1)|1|[@morinMutationalStructuralAnalysis2013]|
87
+|[MS4A1](MS4A1)|1, aSHM|[@rushtonGeneticEvolutionaryPatterns2020; @mottokIntegrativeGenomicAnalysis2019b]|
88
+|[MTOR](MTOR)|1|[@zhangGeneticHeterogeneityDiffuse2013; @paneaWholeGenomeLandscape2019]|
89
+|[MYC](MYC)|1, aSHM|[@pasqualucciHypermutationMultipleProtooncogenes2001a; @jalladesExomeSequencingIdentifies2017; @dunsCharacterizationDLBCLPMBL2021b; @johnstonCmycHypermutationBurkitt1992]|
90
+|[MYD88](MYD88)|1|[@yanBCRTLRSignaling2012a; @ngoOncogenicallyActiveMYD882011a]|
91
+|[NFKBIA](NFKBIA)|1|[@lakeMutationsNFKBIAEncoding2009; @wienandGenomicAnalysesFlowsorted2019b; @russler-germainMutationsAssociatedProgression2023b]|
92
+|[NFKBIE](NFKBIE)|1|[@morinGeneticLandscapesRelapsed2016; @pararajalingamCodingNoncodingDrivers2020; @mansouriFrequentNFKBIEDeletions2016]|
93
+|[NFKBIZ](NFKBIZ)|1, noncoding|[@morinGeneticLandscapesRelapsed2016]|
94
+|[NOL9](NOL9)|1, aSHM|[@spinaGeneticsNodalMarginal2016b; @schmitzGeneticsPathogenesisDiffuse2018a]|
95
+|[NOTCH1](NOTCH1)|1|[@beaLandscapeSomaticMutations2013; @pasqualucciAnalysisCodingGenome2011; @loveGeneticLandscapeMutations2012; @rossiCodingGenomeSplenic2012c]|
96
+|[NOTCH2](NOTCH2)|1|[@rossiCodingGenomeSplenic2012c; @paneaWholeGenomeLandscape2019; @beaLandscapeSomaticMutations2013; @troenNOTCH2MutationsMarginal2008]|
97
+|[OSBPL10](OSBPL10)|1, aSHM|[@arthurGenomewideDiscoverySomatic2018]|
98
+|[P2RY8](P2RY8)|1|[@muppidiLossSignalingGa132014b; @lohrDiscoveryPrioritizationSomatic2012a]|
99
+|[PIM1](PIM1)|1, aSHM|[@pasqualucciHypermutationMultipleProtooncogenes2001a; @dunsCharacterizationDLBCLPMBL2021b; @burkhardtClinicalRelevanceMolecular2022b]|
100
+|[PIM2](PIM2)|1, aSHM|[@arthurGenomewideDiscoverySomatic2018; @reichelFlowSortingExome2015a]|
101
+|[POU2AF1](POU2AF1)|1, aSHM|[@krysiakRecurrentSomaticMutations2017b]|
102
+|[POU2F2](POU2F2)|1|[@krysiakRecurrentSomaticMutations2017b; @zhangGeneticHeterogeneityDiffuse2013]|
103
+|[PRDM1](PRDM1)|1|[@pasqualucciInactivationPRDM1BLIMP12006a]|
104
+|[PTEN](PTEN)|1|[@loveGeneticLandscapeMutations2012]|
105
+|[PTPRD](PTPRD)|1|[@spinaGeneticsNodalMarginal2016b]|
106
+|[RB1](RB1)|1|[@zhangGenomicLandscapeMantle2014; @morinMutationalStructuralAnalysis2013]|
107
+|[RFX7](RFX7)|1|[@grandeGenomewideDiscoverySomatic2019]|
108
+|[RHOA](RHOA)|1|[@richterRecurrentMutationID32012a]|
109
+|[RRAGC](RRAGC)|1|[@okosunRecurrentMTORC1activatingRRAGC2016a]|
110
+|[S1PR2](S1PR2)|1, aSHM|[@morinFrequentMutationHistonemodifying2011; @muppidiLossSignalingGa132014b]|
111
+|[SETD1B](SETD1B)|1|[@reddyGeneticFunctionalDrivers2017]|
112
+|[SF3B1](SF3B1)|1|[@loveGeneticLandscapeMutations2012]|
113
+|[SGK1](SGK1)|1, aSHM|[@dunsCharacterizationDLBCLPMBL2021b; @morinFrequentMutationHistonemodifying2011]|
114
+|[SIN3A](SIN3A)|1|[@grandeGenomewideDiscoverySomatic2019; @rossiCodingGenomeSplenic2012c]|
115
+|[SMARCA4](SMARCA4)|1|[@zhangGeneticHeterogeneityDiffuse2013; @nadeuGenomicEpigenomicInsights2020b; @krysiakRecurrentSomaticMutations2017b; @richterRecurrentMutationID32012a]|
116
+|[SOCS1](SOCS1)|1, aSHM|[@wenigerMutationsTumorSuppressor2006a; @morinFrequentMutationHistonemodifying2011]|
117
+|[SPEN](SPEN)|1|[@sarkozyMutationalLandscapeGray2021a; @rossiCodingGenomeSplenic2012c]|
118
+|[STAT3](STAT3)|1|[@ohgamiSTAT3MutationsAre2014]|
119
+|[STAT6](STAT6)|1|[@yildizActivatingSTAT6Mutations2015c; @ritzRecurrentMutationsSTAT62009a]|
120
+|[TAF1](TAF1)|1|[@spinaGeneticsNodalMarginal2016b; @morinMutationalStructuralAnalysis2013]|
121
+|[TBL1XR1](TBL1XR1)|1|[@rossiCodingGenomeSplenic2012c; @mareschalWholeExomeSequencing2016]|
122
+|[TET2](TET2)|1|[@albuquerqueEnhancingKnowledgeDiscovery2017a; @paneaWholeGenomeLandscape2019]|
123
+|[TMEM30A](TMEM30A)|1|[@morinFrequentMutationHistonemodifying2011]|
124
+|[TMSB4X](TMSB4X)|1, aSHM|[@albuquerqueEnhancingKnowledgeDiscovery2017a]|
125
+|[TNFAIP3](TNFAIP3)|1|[@schmitzTNFAIP3A20Tumor2009a; @rossiAlterationBIRC3Multiple2011a; @compagnoMutationsMultipleGenes2009a]|
126
+|[TNFRSF14](TNFRSF14)|1|[@cheungAcquiredTNFRSF14Mutations2010a; @spinaGeneticsNodalMarginal2016b]|
127
+|[TOX](TOX)|1|[@reddyGeneticFunctionalDrivers2017]|
128
+|[TP53](TP53)|1|[@wildaInactivationARFMDM2p53Pathway2004; @rossiCodingGenomeSplenic2012c; @tiacciPervasiveMutationsJAKSTAT2018b; @beaLandscapeSomaticMutations2013; @morinFrequentMutationHistonemodifying2011]|
129
+|[TRRAP](TRRAP)|1|[@rossiCodingGenomeSplenic2012c; @parryWholeExomeSequencing2013]|
130
+|[UBE2A](UBE2A)|1|[@reddyGeneticFunctionalDrivers2017; @reichelFlowSortingExome2015a]|
131
+|[UNC5C](UNC5C)|1||
132
+|[USP7](USP7)|1|[@grandeGenomewideDiscoverySomatic2019]|
133
+|[VPS13B](VPS13B)|1||
134
+|[WEE1](WEE1)|1|[@schmitzGeneticsPathogenesisDiffuse2018a; @reichelFlowSortingExome2015a]|
135
+|[XPO1](XPO1)|1|[@jardinRecurrentMutationsExportin2016a; @mareschalWholeExomeSequencing2016]|
136
+|[ZC3H12A](ZC3H12A)|1|[@arthurGenomewideDiscoverySomatic2018]|
137
+|[ZFP36L1](ZFP36L1)|1, aSHM|[@morinFrequentMutationHistonemodifying2011; @reichelFlowSortingExome2015a; @paneaWholeGenomeLandscape2019]|
138
+|[ZNF292](ZNF292)|1|[@zhangGeneticHeterogeneityDiffuse2013]|
139
+|[ZNF608](ZNF608)|1, aSHM|[@zhangGeneticHeterogeneityDiffuse2013; @krysiakRecurrentSomaticMutations2017b]|
140
+
141
+## Tier 2 DLBCL genes
142
+### *198 total*
143
+|Gene|Tier| Relevant references|
144
+|:-:|:-:|:-|
145
+|[ABI3BP](ABI3BP)|2|[@morinMutationalStructuralAnalysis2013]|
146
+|[ADAMTS1](ADAMTS1)|2|[@hubschmannMutationalMechanismsShaping2021b]|
147
+|[AICDA](AICDA)|2, aSHM|[@arthurGenomewideDiscoverySomatic2018]|
148
+|[ANKRD12](ANKRD12)|2|[@hubschmannMutationalMechanismsShaping2021b]|
149
+|[ANKRD17](ANKRD17)|2|[@reddyGeneticFunctionalDrivers2017]|
150
+|[ARID1B](ARID1B)|2|[@reddyGeneticFunctionalDrivers2017]|
151
+|[ARID5B](ARID5B)|2|[@reddyGeneticFunctionalDrivers2017; @gomezUltraDeepSequencingReveals2023]|
152
+|[ATR](ATR)|2|[@reddyGeneticFunctionalDrivers2017]|
153
+|[BCL11A](BCL11A)|2, aSHM||
154
+|[BCOR](BCOR)|2|[@nadeuGenomicEpigenomicInsights2020b; @jalladesExomeSequencingIdentifies2017]|
155
+|[BCR](BCR)|2, aSHM||
156
+|[BIRC3](BIRC3)|2, aSHM|[@dunsCharacterizationDLBCLPMBL2021b; @rossiAlterationBIRC3Multiple2011a; @arthurGenomewideDiscoverySomatic2018; @beaLandscapeSomaticMutations2013]|
157
+|[BLK](BLK)|2, aSHM||
158
+|[BRINP3](BRINP3)|2|[@reddyGeneticFunctionalDrivers2017]|
159
+|[BTBD3](BTBD3)|2|[@reddyGeneticFunctionalDrivers2017]|
160
+|[CADPS2](CADPS2)|2|[@hubschmannMutationalMechanismsShaping2021b]|
161
+|[CASP8](CASP8)|2|[@reddyGeneticFunctionalDrivers2017]|
162
+|[CBLB](CBLB)|2|[@reddyGeneticFunctionalDrivers2017]|
163
+|[CCL4](CCL4)|2|[@chapuyMolecularSubtypesDiffuse2018b]|
164
+|[CD22](CD22)|2|[@reddyGeneticFunctionalDrivers2017]|
165
+|[CD274](CD274)|2|[@morinFrequentMutationHistonemodifying2011]|
166
+|[CD36](CD36)|2|[@pasqualucciAnalysisCodingGenome2011]|
167
+|[CD44](CD44)|2, aSHM|[@arthurGenomewideDiscoverySomatic2018]|
168
+|[CD74](CD74)|2, aSHM|[@arthurGenomewideDiscoverySomatic2018]|
169
+|[CDC73](CDC73)|2|[@reddyGeneticFunctionalDrivers2017; @loveGeneticLandscapeMutations2012]|
170
+|[CDH9](CDH9)|2|[@morinMutationalStructuralAnalysis2013]|
171
+|[CHD1](CHD1)|2|[@reddyGeneticFunctionalDrivers2017]|
172
+|[CHD8](CHD8)|2|[@grandeGenomewideDiscoverySomatic2019; @reddyGeneticFunctionalDrivers2017]|
173
+|[CHST2](CHST2)|2|[@reddyGeneticFunctionalDrivers2017]|
174
+|[CNOT2](CNOT2)|2|[@hubschmannMutationalMechanismsShaping2021b]|
175
+|[CNTNAP5](CNTNAP5)|2|[@morinMutationalStructuralAnalysis2013]|
176
+|[COQ7](COQ7)|2|[@chapuyMolecularSubtypesDiffuse2018b]|
177
+|[CRIP1](CRIP1)|2|[@chapuyMolecularSubtypesDiffuse2018b]|
178
+|[DAZAP1](DAZAP1)|2|[@pararajalingamCodingNoncodingDrivers2020]|
179
+|[DCAF6](DCAF6)|2|[@reddyGeneticFunctionalDrivers2017]|
180
+|[DDX10](DDX10)|2|[@reddyGeneticFunctionalDrivers2017]|
181
+|[DHX16](DHX16)|2|[@hubschmannMutationalMechanismsShaping2021b]|
182
+|[DICER1](DICER1)|2|[@reddyGeneticFunctionalDrivers2017]|
183
+|[DNAH5](DNAH5)|2|[@morinMutationalStructuralAnalysis2013; @jalladesExomeSequencingIdentifies2017]|
184
+|[DNM2](DNM2)|2|[@hubschmannMutationalMechanismsShaping2021b]|
185
+|[DNMT3A](DNMT3A)|2|[@reddyGeneticFunctionalDrivers2017]|
186
+|[DOCK1](DOCK1)|2|[@chapuyMolecularSubtypesDiffuse2018b]|
187
+|[DSG4](DSG4)|2|[@morinMutationalStructuralAnalysis2013]|
188
+|[EIF2AK3](EIF2AK3)|2, aSHM||
189
+|[EZR](EZR)|2, aSHM|[@deschGenotypingCirculatingTumor2020]|
190
+|[FAM102A](FAM102A)|2, aSHM||
191
+|[FAM38B](FAM38B)|2|[@morinMutationalStructuralAnalysis2013]|
192
+|[FANK1](FANK1)|2, aSHM||
193
+|[FAT4](FAT4)|2|[@parryWholeExomeSequencing2013; @morinMutationalStructuralAnalysis2013; @zhangGenomicLandscapeMantle2014]|
194
+|[FCRL3](FCRL3)|2, aSHM||
195
+|[FNBP1](FNBP1)|2, aSHM||
196
+|[FNDC1](FNDC1)|2|[@morinMutationalStructuralAnalysis2013]|
197
+|[FOXC1](FOXC1)|2|[@schmitzGeneticsPathogenesisDiffuse2018a]|
198
+|[FOXP1](FOXP1)|2, aSHM|[@reddyGeneticFunctionalDrivers2017]|
199
+|[FUBP1](FUBP1)|2|[@reddyGeneticFunctionalDrivers2017]|
200
+|[FUT5](FUT5)|2|[@chapuyMolecularSubtypesDiffuse2018b]|
201
+|[GABRA2](GABRA2)|2|[@chapuyMolecularSubtypesDiffuse2018b]|
202
+|[GAK](GAK)|2|[@hubschmannMutationalMechanismsShaping2021b]|
203
+|[GNAS](GNAS)|2|[@reddyGeneticFunctionalDrivers2017]|
204
+|[GOLGA5](GOLGA5)|2|[@reddyGeneticFunctionalDrivers2017]|
205
+|[GPC5](GPC5)|2|[@schmitzGeneticsPathogenesisDiffuse2018a]|
206
+|[GSG2](GSG2)|2|[@schmitzGeneticsPathogenesisDiffuse2018a]|
207
+|[HDAC7](HDAC7)|2|[@morinMutationalStructuralAnalysis2013]|
208
+|[HIST1H2AG](HIST1H2AG)|2, aSHM|[@morinMutationalStructuralAnalysis2013; @rossiCodingGenomeSplenic2012c; @paneaWholeGenomeLandscape2019; @krysiakRecurrentSomaticMutations2017b]|
209
+|[HLA-DMA](HLA-DMA)|2||
210
+|[HLA-DQA1](HLA-DQA1)|2|[@hubschmannMutationalMechanismsShaping2021b]|
211
+|[HNF1B](HNF1B)|2|[@pasqualucciAnalysisCodingGenome2011]|
212
+|[HNRNPD](HNRNPD)|2||
213
+|[HNRNPH1](HNRNPH1)|2, noncoding|[@pararajalingamCodingNoncodingDrivers2020]|
214
+|[HRAS](HRAS)|2|[@jalladesExomeSequencingIdentifies2017; @reddyGeneticFunctionalDrivers2017]|
215
+|[ID3](ID3)|2|[@richterRecurrentMutationID32012a; @spinaGeneticsNodalMarginal2016b; @schmitzBurkittLymphomaPathogenesis2012]|
216
+|[IER2](IER2)|2|[@morinMutationalStructuralAnalysis2013]|
217
+|[IFNGR1](IFNGR1)|2|[@morinMutationalStructuralAnalysis2013]|
218
+|[IGLL5](IGLL5)|2, aSHM|[@russler-germainMutationsAssociatedProgression2023b; @deschGenotypingCirculatingTumor2020; @paneaWholeGenomeLandscape2019]|
219
+|[IKBKB](IKBKB)|2|[@reddyGeneticFunctionalDrivers2017; @rossiAlterationBIRC3Multiple2011a; @wienandGenomicAnalysesFlowsorted2019b]|
220
+|[IKBKE](IKBKE)|2|[@hubschmannMutationalMechanismsShaping2021b]|
221
+|[IL16](IL16)|2||
222
+|[IL6](IL6)|2|[@chapuyMolecularSubtypesDiffuse2018b]|
223
+|[INO80](INO80)|2|[@zhangGeneticHeterogeneityDiffuse2013]|
224
+|[IRAG2](IRAG2)|2, aSHM||
225
+|[IRF1](IRF1)|2, aSHM|[@hubschmannMutationalMechanismsShaping2021b]|
226
+|[JAK1](JAK1)|2|[@zhangGeneticHeterogeneityDiffuse2013; @mottokIntegrativeGenomicAnalysis2019b]|
227
+|[JAK3](JAK3)|2|[@zhangGeneticHeterogeneityDiffuse2013]|
228
+|[JUNB](JUNB)|2|[@reddyGeneticFunctionalDrivers2017; @mottokIntegrativeGenomicAnalysis2019b]|
229
+|[KCMF1](KCMF1)|2|[@reddyGeneticFunctionalDrivers2017]|
230
+|[KLHL21](KLHL21)|2|[@schmitzGeneticsPathogenesisDiffuse2018a]|
231
+|[LAMA5](LAMA5)|2|[@schmitzGeneticsPathogenesisDiffuse2018a]|
232
+|[LAPTM5](LAPTM5)|2, aSHM|[@hubschmannMutationalMechanismsShaping2021b]|
233
+|[LIN54](LIN54)|2|[@reddyGeneticFunctionalDrivers2017]|
234
+|[LPP](LPP)|2, aSHM|[@arthurGenomewideDiscoverySomatic2018]|
235
+|[LRP12](LRP12)|2|[@hubschmannMutationalMechanismsShaping2021b]|
236
+|[LRRN3](LRRN3)|2|[@sarkozyMutationalLandscapeGray2021a; @morinMutationalStructuralAnalysis2013]|
237
+|[LYN](LYN)|2|[@chapuyMolecularSubtypesDiffuse2018b]|
238
+|[MAGT1](MAGT1)|2|[@reddyGeneticFunctionalDrivers2017]|
239
+|[MALAT1](MALAT1)|2, aSHM|[@arthurGenomewideDiscoverySomatic2018]|
240
+|[MAP2K1](MAP2K1)|2|[@shinBRAFV600EMAP2K12015; @louissaintPediatrictypeNodalFollicular2016a]|
241
+|[MAP4K4](MAP4K4)|2|[@reddyGeneticFunctionalDrivers2017]|
242
+|[MARK1](MARK1)|2|[@reddyGeneticFunctionalDrivers2017]|
243
+|[MCL1](MCL1)|2|[@paneaWholeGenomeLandscape2019; @reddyGeneticFunctionalDrivers2017; @dunsCharacterizationDLBCLPMBL2021b]|
244
+|[MECOM](MECOM)|2|[@reddyGeneticFunctionalDrivers2017]|
245
+|[MET](MET)|2|[@reddyGeneticFunctionalDrivers2017]|
246
+|[MIR142](MIR142)|2, aSHM|[@grandeGenomewideDiscoverySomatic2019; @kwanhianMicroRNA142Mutated202012b]|
247
+|[MIR155HG](MIR155HG)|2, aSHM||
248
+|[MPDZ](MPDZ)|2|[@reichelFlowSortingExome2015a; @morinMutationalStructuralAnalysis2013]|
249
+|[MSH2](MSH2)|2|[@reddyGeneticFunctionalDrivers2017]|
250
+|[MSH6](MSH6)|2|[@reddyGeneticFunctionalDrivers2017]|
251
+|[MYB](MYB)|2|[@reddyGeneticFunctionalDrivers2017; @deschGenotypingCirculatingTumor2020]|
252
+|[MYBPC2](MYBPC2)|2|[@schmitzGeneticsPathogenesisDiffuse2018a]|
253
+|[MYO1E](MYO1E)|2, aSHM||
254
+|[MYOM2](MYOM2)|2|[@pasqualucciAnalysisCodingGenome2011]|
255
+|[N2RF2](N2RF2)|2|[@hubschmannMutationalMechanismsShaping2021b]|
256
+|[NANOG](NANOG)|2|[@chapuyMolecularSubtypesDiffuse2018b]|
257
+|[NAV1](NAV1)|2|[@chapuyMolecularSubtypesDiffuse2018b]|
258
+|[NCOA3](NCOA3)|2, aSHM||
259
+|[NCOR1](NCOR1)|2|[@reddyGeneticFunctionalDrivers2017]|
260
+|[NCOR2](NCOR2)|2|[@schmitzBurkittLymphomaPathogenesis2012; @spinaGeneticsNodalMarginal2016b; @sarkozyMutationalLandscapeGray2021a]|
261
+|[NEAT1](NEAT1)|2, aSHM|[@arthurGenomewideDiscoverySomatic2018]|
262
+|[NF1](NF1)|2|[@reddyGeneticFunctionalDrivers2017]|
263
+|[NFKB1](NFKB1)|2||
264
+|[NFKB2](NFKB2)|2|[@reddyGeneticFunctionalDrivers2017; @mottokIntegrativeGenomicAnalysis2019b]|
265
+|[NLRC5](NLRC5)|2||
266
+|[NLRP5](NLRP5)|2|[@morinMutationalStructuralAnalysis2013]|
267
+|[NLRP8](NLRP8)|2|[@chapuyMolecularSubtypesDiffuse2018b]|
268
+|[ODZ3](ODZ3)|2|[@morinMutationalStructuralAnalysis2013]|
269
+|[P2RX5](P2RX5)|2, aSHM|[@morinMutationalStructuralAnalysis2013]|
270
+|[PAPOLG](PAPOLG)|2|[@schmitzGeneticsPathogenesisDiffuse2018a]|
271
+|[PASK](PASK)|2|[@morinMutationalStructuralAnalysis2013]|
272
+|[PAX5](PAX5)|2, aSHM|[@pasqualucciHypermutationMultipleProtooncogenes2001a]|
273
+|[PCBP1](PCBP1)|2|[@schmitzBurkittLymphomaPathogenesis2012]|
274
+|[PCDHB11](PCDHB11)|2|[@morinMutationalStructuralAnalysis2013]|
275
+|[PCLO](PCLO)|2|[@lohrDiscoveryPrioritizationSomatic2012a]|
276
+|[PDE4DIP](PDE4DIP)|2|[@chapuyMolecularSubtypesDiffuse2018b]|
277
+|[PDS5B](PDS5B)|2|[@hubschmannMutationalMechanismsShaping2021b; @morinMutationalStructuralAnalysis2013]|
278
+|[PHF6](PHF6)|2|[@reddyGeneticFunctionalDrivers2017; @thomasGeneticSubgroupsInform2023]|
279
+|[PIK3CD](PIK3CD)|2|[@reddyGeneticFunctionalDrivers2017]|
280
+|[PIK3R1](PIK3R1)|2|[@zhangGeneticHeterogeneityDiffuse2013; @paneaWholeGenomeLandscape2019]|
281
+|[PKD1](PKD1)|2|[@morinMutationalStructuralAnalysis2013]|
282
+|[PNPO](PNPO)|2|[@hubschmannMutationalMechanismsShaping2021b]|
283
+|[POGZ](POGZ)|2|[@morinMutationalStructuralAnalysis2013]|
284
+|[PPP1R9B](PPP1R9B)|2||
285
+|[PRKCB](PRKCB)|2|[@morinMutationalStructuralAnalysis2013]|
286
+|[PRKDC](PRKDC)|2|[@hubschmannMutationalMechanismsShaping2021b; @schmitzGeneticsPathogenesisDiffuse2018a]|
287
+|[PRPS1](PRPS1)|2|[@chapuyMolecularSubtypesDiffuse2018b]|
288
+|[PTMA](PTMA)|2, aSHM||
289
+|[PTPN1](PTPN1)|2, aSHM|[@gunawardanaRecurrentSomaticMutations2014c]|
290
+|[PTPN23](PTPN23)|2|[@morinMutationalStructuralAnalysis2013]|
291
+|[PTPN6](PTPN6)|2|[@reddyGeneticFunctionalDrivers2017]|
292
+|[PTPRK](PTPRK)|2|[@reddyGeneticFunctionalDrivers2017]|
293
+|[RAC2](RAC2)|2|[@hubschmannMutationalMechanismsShaping2021b; @paneaWholeGenomeLandscape2019]|
294
+|[RAD9A](RAD9A)|2|[@chapuyMolecularSubtypesDiffuse2018b]|
295
+|[RARA](RARA)|2|[@reddyGeneticFunctionalDrivers2017]|
296
+|[RCC](RCC)|2, aSHM||
297
+|[RFTN1](RFTN1)|2, aSHM|[@dunsCharacterizationDLBCLPMBL2021b; @arthurGenomewideDiscoverySomatic2018]|
298
+|[RFXAP](RFXAP)|2||
299
+|[RHEX](RHEX)|2, aSHM||
300
+|[RHOH](RHOH)|2, aSHM|[@pasqualucciHypermutationMultipleProtooncogenes2001a]|
301
+|[RUBCNL](RUBCNL)|2, aSHM||
302
+|[RUNX1](RUNX1)|2|[@reddyGeneticFunctionalDrivers2017]|
303
+|[SAMD9L](SAMD9L)|2|[@morinMutationalStructuralAnalysis2013]|
304
+|[SARM1](SARM1)|2|[@morinMutationalStructuralAnalysis2013]|
305
+|[SEL1L3](SEL1L3)|2, aSHM||
306
+|[SEPTIN9](SEPTIN9)|2, aSHM||
307
+|[SERPINA9](SERPINA9)|2, aSHM|[@arthurGenomewideDiscoverySomatic2018]|
308
+|[SETD2](SETD2)|2|[@zhangGeneticHeterogeneityDiffuse2013]|
309
+|[SETD5](SETD5)|2|[@reddyGeneticFunctionalDrivers2017; @tiacciPervasiveMutationsJAKSTAT2018b]|
310
+|[SIAH2](SIAH2)|2|[@reichelFlowSortingExome2015a; @hubschmannMutationalMechanismsShaping2021b]|
311
+|[SLC34A2](SLC34A2)|2|[@hubschmannMutationalMechanismsShaping2021b]|
312
+|[SMEK1](SMEK1)|2|[@chapuyMolecularSubtypesDiffuse2018b]|
313
+|[SRRM2](SRRM2)|2|[@russler-germainMutationsAssociatedProgression2023b; @morinMutationalStructuralAnalysis2013]|
314
+|[ST6GAL1](ST6GAL1)|2, aSHM|[@arthurGenomewideDiscoverySomatic2018]|
315
+|[STAT5B](STAT5B)|2|[@zhangGeneticHeterogeneityDiffuse2013; @tiacciPervasiveMutationsJAKSTAT2018b]|
316
+|[SYK](SYK)|2|[@reddyGeneticFunctionalDrivers2017]|
317
+|[SYPL1](SYPL1)|2|[@morinMutationalStructuralAnalysis2013]|
318
+|[TAP1](TAP1)|2|[@schmitzGeneticsPathogenesisDiffuse2018a]|
319
+|[TBC1D4](TBC1D4)|2, aSHM|[@arthurGenomewideDiscoverySomatic2018]|
320
+|[TCL1A](TCL1A)|2, aSHM|[@grandeGenomewideDiscoverySomatic2019]|
321
+|[TGFBR2](TGFBR2)|2|[@reddyGeneticFunctionalDrivers2017]|
322
+|[TIPARP](TIPARP)|2|[@reddyGeneticFunctionalDrivers2017]|
323
+|[TLR2](TLR2)|2|[@chapuyMolecularSubtypesDiffuse2018b; @beaLandscapeSomaticMutations2013]|
324
+|[TRAF3](TRAF3)|2|[@rossiAlterationBIRC3Multiple2011a; @ottoGeneticLesionsTRAF32012a; @pasqualucciAnalysisCodingGenome2011]|
325
+|[TRAF6](TRAF6)|2|[@hubschmannMutationalMechanismsShaping2021b]|
326
+|[TRIP12](TRIP12)|2||
327
+|[UBE2J1](UBE2J1)|2, aSHM||
328
+|[UBR5](UBR5)|2|[@pararajalingamCodingNoncodingDrivers2020; @zhangGeneticHeterogeneityDiffuse2013]|
329
+|[UNC5B](UNC5B)|2|[@hubschmannMutationalMechanismsShaping2021b]|
330
+|[UNC5D](UNC5D)|2||
331
+|[WAC](WAC)|2|[@rossiCodingGenomeSplenic2012c; @reddyGeneticFunctionalDrivers2017]|
332
+|[WDFY3](WDFY3)|2|[@morinMutationalStructuralAnalysis2013]|
333
+|[WNK1](WNK1)|2|[@hubschmannMutationalMechanismsShaping2021b; @thomasGeneticSubgroupsInform2023; @jalladesExomeSequencingIdentifies2017]|
334
+|[XBP1](XBP1)|2, aSHM||
335
+|[YY1](YY1)|2|[@reddyGeneticFunctionalDrivers2017]|
336
+|[ZBTB7A](ZBTB7A)|2|[@burkhardtClinicalRelevanceMolecular2022b; @reddyGeneticFunctionalDrivers2017]|
337
+|[ZCCHC7](ZCCHC7)|2, aSHM|[@arthurGenomewideDiscoverySomatic2018]|
338
+|[ZEB2](ZEB2)|2|[@zhangGeneticHeterogeneityDiffuse2013]|
339
+|[ZFAT](ZFAT)|2|[@reddyGeneticFunctionalDrivers2017]|
340
+|[ZFX](ZFX)|2|[@reddyGeneticFunctionalDrivers2017]|
341
+|[ZNF217](ZNF217)|2|[@hubschmannMutationalMechanismsShaping2021b; @reichelFlowSortingExome2015a]|
342
+|[ZNF423](ZNF423)|2|[@chapuyMolecularSubtypesDiffuse2018b]|
343
+
344
+
345
+# References