01bb15c677997d0ec9973d3a98e0efae7b8e299a
BL_genes.md
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| 1 | -# BL genes |
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| 2 | - |
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| 3 | -## Origins of BL genes |
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| 4 | -```mermaid |
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| 5 | 1 | --- |
| 6 | -config: |
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| 7 | - sankey: |
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| 8 | - showValues: false |
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| 9 | - linkColor: target |
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| 10 | - width: 800 |
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| 11 | - height: 1000 |
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| 12 | - nodeAlignment: right |
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| 2 | +title: 'BL 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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| 13 | 6 | --- |
| 14 | -sankey-beta |
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| 15 | -Grande 2019, BL Tier 1, 9 |
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| 16 | -Grande 2019, BL Tier 2, 4 |
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| 17 | -Richter 2012, BL Tier 1, 5 |
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| 18 | -Burkhardt 2022, BL Tier 2, 25 |
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| 19 | -Schmitz 2012, BL Tier 1, 3 |
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| 20 | -Schmitz 2012, BL Tier 2, 16 |
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| 21 | -Love 2012, BL Tier 1, 3 |
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| 22 | -Love 2012, BL Tier 2, 56 |
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| 23 | -Muppidi 2014, BL Tier 1, 1 |
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| 24 | -Muppidi 2014, BL Tier 2, 2 |
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| 25 | -Panea 2019, BL Tier 1, 4 |
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| 26 | -Panea 2019, BL Tier 2, 46 |
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| 27 | -Thomas 2023, BL Tier 1, 2 |
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| 28 | -Thomas 2023, BL Tier 2, 3 |
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| 29 | -BL, panel, 25 |
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| 30 | -panel, Burkhardt 2022, 25 |
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| 31 | -BL, WGS, 13 |
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| 32 | -WGS, Grande 2019, 13 |
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| 33 | -BL, RNA-seq/WGS/exome, 5 |
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| 34 | -RNA-seq/WGS/exome, Richter 2012, 5 |
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| 35 | -BL, exome, 59 |
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| 36 | -exome, Love 2012, 59 |
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| 37 | -BL, RNA-seq, 19 |
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| 38 | -RNA-seq, Schmitz 2012, 19 |
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| 39 | -BL, Sanger, 3 |
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| 40 | -Sanger, Muppidi 2014, 3 |
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| 41 | -BL, RNA-seq/exome, 50 |
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| 42 | -RNA-seq/exome, Panea 2019, 50 |
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| 43 | -BL, WGS, 5 |
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| 44 | -WGS, Thomas 2023, 5 |
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| 45 | -``` |
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| 7 | + |
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| 8 | +## Origins of BL genes |
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| 9 | + |
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| 10 | + |
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| 11 | + |
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| 46 | 12 | ## Tier 1 BL genes |
| 47 | 13 | |
| 48 | 14 | ### *29 total* |
| 49 | 15 | |
| 50 | -| Gene | Tier | Relevant references | |
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| 51 | -|:------------------:|:-------:|:---------------------------------------------------------------------------------------------------| |
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| 52 | -| [ARID1A](ARID1A) | 1 | Rossi et al. 2012; Wienand et al. 2019; Zhang et al. 2013; Love et al. 2012; Krysiak et al. 2017 | |
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| 53 | -| [BCL7A](BCL7A) | 1, aSHM | Krysiak et al. 2017; Arthur et al. 2018; Grande et al. 2019; Reichel et al. 2015 | |
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| 54 | -| [BMP7](BMP7) | 1 | Panea et al. 2019 | |
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| 55 | -| [CCND3](CCND3) | 1 | Desch et al. 2020; Richter et al. 2012; Jallades et al. 2017; Morin et al. 2011 | |
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| 56 | -| [CHD8](CHD8) | 1 | Reddy et al. 2017; Grande et al. 2019 | |
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| 57 | -| [DDX3X](DDX3X) | 1 | Schmitz et al. 2012, 2018; Mottok et al. 2019 | |
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| 58 | -| [EIF4A1](EIF4A1) | 1 | Panea et al. 2019 | |
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| 59 | -| [EPPK1](EPPK1) | 1 | Panea et al. 2019 | |
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| 60 | -| [FBXO11](FBXO11) | 1 | Hübschmann et al. 2021; Parry et al. 2013; Richter et al. 2012 | |
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| 61 | -| [FOXO1](FOXO1) | 1 | Schmitz et al. 2012; Morin et al. 2011; Duns et al. 2021 | |
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| 62 | -| [GNA13](GNA13) | 1 | Reichel et al. 2015; Love et al. 2012; Morin et al. 2011 | |
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| 63 | -| [GNAI2](GNAI2) | 1 | Grande et al. 2019; Morin et al. 2013 | |
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| 64 | -| [HNRNPU](HNRNPU) | 1, aSHM | Panea et al. 2019; Reddy et al. 2017 | |
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| 65 | -| [ID3](ID3) | 1 | Schmitz et al. 2012; Spina et al. 2016; Richter et al. 2012 | |
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| 66 | -| [KMT2D](KMT2D) | 1 | Desch et al. 2020; Rossi et al. 2012; Morin et al. 2011; Beà et al. 2013; Grande et al. 2019 | |
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| 67 | -| [MYC](MYC) | 1, aSHM | Johnston and Carroll 1992; L. Pasqualucci et al. 2001; Duns et al. 2021; Jallades et al. 2017 | |
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| 68 | -| [P2RY8](P2RY8) | 1 | Muppidi et al. 2014; Lohr et al. 2012 | |
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| 69 | -| [PHF6](PHF6) | 1 | Thomas et al. 2023; Reddy et al. 2017 | |
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| 70 | -| [PTEN](PTEN) | 1 | Love et al. 2012 | |
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| 71 | -| [RFX7](RFX7) | 1 | Grande et al. 2019 | |
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| 72 | -| [RHOA](RHOA) | 1 | Richter et al. 2012 | |
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| 73 | -| [SIN3A](SIN3A) | 1 | Grande et al. 2019; Rossi et al. 2012 | |
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| 74 | -| [SMARCA4](SMARCA4) | 1 | Richter et al. 2012; Nadeu et al. 2020; Zhang et al. 2013; Krysiak et al. 2017 | |
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| 75 | -| [TCF3](TCF3) | 1 | Schmitz et al. 2012 | |
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| 76 | -| [TCL1A](TCL1A) | 1, aSHM | Grande et al. 2019 | |
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| 77 | -| [TFAP4](TFAP4) | 1 | Grande et al. 2019 | |
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| 78 | -| [TP53](TP53) | 1 | Rossi et al. 2012; Wilda et al. 2004; Tiacci et al. 2018; Beà et al. 2013; Morin et al. 2011 | |
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| 79 | -| [USP7](USP7) | 1 | Grande et al. 2019 | |
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| 80 | -| [WNK1](WNK1) | 1 | Hübschmann et al. 2021; Thomas et al. 2023; Jallades et al. 2017 | |
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| 16 | +|Gene|Tier| Relevant references| |
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| 17 | +|:-:|:-:|:-| |
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| 18 | +|[ARID1A](ARID1A)|1|[@wienandGenomicAnalysesFlowsorted2019b; @loveGeneticLandscapeMutations2012; @zhangGeneticHeterogeneityDiffuse2013; @rossiCodingGenomeSplenic2012c; @krysiakRecurrentSomaticMutations2017b]| |
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| 19 | +|[BCL7A](BCL7A)|1, aSHM|[@grandeGenomewideDiscoverySomatic2019; @reichelFlowSortingExome2015a; @krysiakRecurrentSomaticMutations2017b; @arthurGenomewideDiscoverySomatic2018]| |
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| 20 | +|[BMP7](BMP7)|1|[@paneaWholeGenomeLandscape2019]| |
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| 21 | +|[CCND3](CCND3)|1|[@deschGenotypingCirculatingTumor2020; @richterRecurrentMutationID32012a; @jalladesExomeSequencingIdentifies2017; @morinFrequentMutationHistonemodifying2011]| |
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| 22 | +|[CHD8](CHD8)|1|[@grandeGenomewideDiscoverySomatic2019; @reddyGeneticFunctionalDrivers2017]| |
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| 23 | +|[DDX3X](DDX3X)|1|[@mottokIntegrativeGenomicAnalysis2019b; @schmitzBurkittLymphomaPathogenesis2012; @schmitzGeneticsPathogenesisDiffuse2018a]| |
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| 24 | +|[EIF4A1](EIF4A1)|1|[@paneaWholeGenomeLandscape2019]| |
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| 25 | +|[EPPK1](EPPK1)|1|[@paneaWholeGenomeLandscape2019]| |
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| 26 | +|[FBXO11](FBXO11)|1|[@parryWholeExomeSequencing2013; @hubschmannMutationalMechanismsShaping2021b; @richterRecurrentMutationID32012a]| |
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| 27 | +|[FOXO1](FOXO1)|1|[@dunsCharacterizationDLBCLPMBL2021b; @morinFrequentMutationHistonemodifying2011; @schmitzBurkittLymphomaPathogenesis2012]| |
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| 28 | +|[GNA13](GNA13)|1|[@morinFrequentMutationHistonemodifying2011; @reichelFlowSortingExome2015a; @loveGeneticLandscapeMutations2012]| |
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| 29 | +|[GNAI2](GNAI2)|1|[@grandeGenomewideDiscoverySomatic2019; @morinMutationalStructuralAnalysis2013]| |
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| 30 | +|[HNRNPU](HNRNPU)|1, aSHM|[@reddyGeneticFunctionalDrivers2017; @paneaWholeGenomeLandscape2019]| |
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| 31 | +|[ID3](ID3)|1|[@schmitzBurkittLymphomaPathogenesis2012; @spinaGeneticsNodalMarginal2016b; @richterRecurrentMutationID32012a]| |
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| 32 | +|[KMT2D](KMT2D)|1|[@morinFrequentMutationHistonemodifying2011; @rossiCodingGenomeSplenic2012c; @deschGenotypingCirculatingTumor2020; @grandeGenomewideDiscoverySomatic2019; @beaLandscapeSomaticMutations2013]| |
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| 33 | +|[MYC](MYC)|1, aSHM|[@dunsCharacterizationDLBCLPMBL2021b; @jalladesExomeSequencingIdentifies2017; @johnstonCmycHypermutationBurkitt1992; @pasqualucciHypermutationMultipleProtooncogenes2001a]| |
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| 34 | +|[P2RY8](P2RY8)|1|[@muppidiLossSignalingGa132014b; @lohrDiscoveryPrioritizationSomatic2012a]| |
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| 35 | +|[PHF6](PHF6)|1|[@thomasGeneticSubgroupsInform2023; @reddyGeneticFunctionalDrivers2017]| |
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| 36 | +|[PTEN](PTEN)|1|[@loveGeneticLandscapeMutations2012]| |
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| 37 | +|[RFX7](RFX7)|1|[@grandeGenomewideDiscoverySomatic2019]| |
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| 38 | +|[RHOA](RHOA)|1|[@richterRecurrentMutationID32012a]| |
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| 39 | +|[SIN3A](SIN3A)|1|[@rossiCodingGenomeSplenic2012c; @grandeGenomewideDiscoverySomatic2019]| |
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| 40 | +|[SMARCA4](SMARCA4)|1|[@krysiakRecurrentSomaticMutations2017b; @zhangGeneticHeterogeneityDiffuse2013; @nadeuGenomicEpigenomicInsights2020b; @richterRecurrentMutationID32012a]| |
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| 41 | +|[TCF3](TCF3)|1|[@schmitzBurkittLymphomaPathogenesis2012]| |
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| 42 | +|[TCL1A](TCL1A)|1, aSHM|[@grandeGenomewideDiscoverySomatic2019]| |
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| 43 | +|[TFAP4](TFAP4)|1|[@grandeGenomewideDiscoverySomatic2019]| |
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| 44 | +|[TP53](TP53)|1|[@rossiCodingGenomeSplenic2012c; @morinFrequentMutationHistonemodifying2011; @tiacciPervasiveMutationsJAKSTAT2018b; @beaLandscapeSomaticMutations2013; @wildaInactivationARFMDM2p53Pathway2004]| |
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| 45 | +|[USP7](USP7)|1|[@grandeGenomewideDiscoverySomatic2019]| |
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| 46 | +|[WNK1](WNK1)|1|[@hubschmannMutationalMechanismsShaping2021b; @thomasGeneticSubgroupsInform2023; @jalladesExomeSequencingIdentifies2017]| |
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| 81 | 47 | |
| 82 | 48 | ## Tier 2 BL genes |
| 83 | 49 | |
| 84 | 50 | ### *157 total* |
| 85 | 51 | |
| 86 | -| Gene | Tier | Relevant references | |
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| 87 | -|:----------------------:|:-------:|:--------------------------------------------------------------------------------------------------------| |
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| 88 | -| [ACAD9](ACAD9) | 2 | Love et al. 2012 | |
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| 89 | -| [ACE](ACE) | 2 | Love et al. 2012 | |
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| 90 | -| [ADAMTS5](ADAMTS5) | 2 | Burkhardt et al. 2022 | |
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| 91 | -| [ADNP](ADNP) | 2 | Burkhardt et al. 2022 | |
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| 92 | -| [AGO4](AGO4) | 2 | Burkhardt et al. 2022 | |
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| 93 | -| [ALPK2](ALPK2) | 2 | Panea et al. 2019 | |
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| 94 | -| [ARHGEF1](ARHGEF1) | 2 | Muppidi et al. 2014 | |
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| 95 | -| [ATP2C2](ATP2C2) | 2 | Love et al. 2012 | |
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| 96 | -| [BACH2](BACH2) | 2, aSHM | Grande et al. 2019 | |
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| 97 | -| [BCL2](BCL2) | 2, aSHM | Sarkozy et al. 2021; Tanaka et al. 1992; Burkhardt et al. 2022; Morin et al. 2011 | |
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| 98 | -| [BCL6](BCL6) | 2, aSHM | Love et al. 2012; Morin et al. 2011 | |
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| 99 | -| [BRAF](BRAF) | 2 | Tiacci et al. 2011; Love et al. 2012 | |
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| 100 | -| [BRD4](BRD4) | 2 | Love et al. 2012 | |
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| 101 | -| [BTG1](BTG1) | 2, aSHM | Sarkozy et al. 2021; Burkhardt et al. 2022; Morin et al. 2011 | |
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| 102 | -| [BTG2](BTG2) | 2, aSHM | Love et al. 2012; Morin et al. 2011 | |
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| 103 | -| [C16orf48](C16orf48) | 2 | Schmitz et al. 2012 | |
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| 104 | -| [C6orf27](C6orf27) | 2 | Love et al. 2012 | |
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| 105 | -| [CAD](CAD) | 2 | Love et al. 2012 | |
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| 106 | -| [CARD11](CARD11) | 2 | Wu et al. 2016; Panea et al. 2019; Morin et al. 2011; Yan et al. 2012; Lenz et al. 2008 | |
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| 107 | -| [CARD4](CARD4) | 2 | Love et al. 2012 | |
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| 108 | -| [CCNF](CCNF) | 2 | Abate et al. 2015 | |
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| 109 | -| [CCT6B](CCT6B) | 2 | Love et al. 2012 | |
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| 110 | -| [CD79A](CD79A) | 2 | Burkhardt et al. 2022; Rossi et al. 2012 | |
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| 111 | -| [CD79B](CD79B) | 2 | Morin et al. 2011; Panea et al. 2019 | |
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| 112 | -| [CD83](CD83) | 2, aSHM | Russler-Germain et al. 2023; Morin et al. 2013; Duns et al. 2021; Panea et al. 2019 | |
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| 113 | -| [CDC73](CDC73) | 2 | Reddy et al. 2017; Love et al. 2012 | |
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| 114 | -| [CDH17](CDH17) | 2 | Love et al. 2012 | |
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| 115 | -| [CDKN2A](CDKN2A) | 2 | Morin et al. 2013; Spina et al. 2016; Grande et al. 2019 | |
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| 116 | -| [CDKN2C](CDKN2C) | 2 | Thomas et al. 2023 | |
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| 117 | -| [CHD4](CHD4) | 2 | Burkhardt et al. 2022 | |
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| 118 | -| [COL4A2](COL4A2) | 2 | Love et al. 2012 | |
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| 119 | -| [CPXM2](CPXM2) | 2 | Burkhardt et al. 2022 | |
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| 120 | -| [CREBBP](CREBBP) | 2 | Parry et al. 2013; Love et al. 2012; Laura Pasqualucci, Dominguez-Sola, et al. 2011; Duns et al. 2021 | |
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| 121 | -| [CTCF](CTCF) | 2 | Panea et al. 2019 | |
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| 122 | -| [CXCR4](CXCR4) | 2, aSHM | Krysiak et al. 2017; Panea et al. 2019; Khodabakhshi et al. 2012 | |
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| 123 | -| [CYB5D1](CYB5D1) | 2 | Love et al. 2012 | |
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| 124 | -| [CYP4F22](CYP4F22) | 2 | Love et al. 2012 | |
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| 125 | -| [DHCR7](DHCR7) | 2 | Schmitz et al. 2012 | |
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| 126 | -| [DLGAP1](DLGAP1) | 2 | Love et al. 2012 | |
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| 127 | -| [DNMT1](DNMT1) | 2 | Panea et al. 2019 | |
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| 128 | -| [DTX1](DTX1) | 2, aSHM | Gomez et al. 2023; Panea et al. 2019; Schmitz et al. 2018; Rossi et al. 2012 | |
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| 129 | -| [E2F2](E2F2) | 2 | Burkhardt et al. 2022 | |
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| 130 | -| [EBF1](EBF1) | 2, aSHM | Reichel et al. 2015; Bohle et al. 2013; Thomas et al. 2023 | |
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| 131 | -| [EDNRB](EDNRB) | 2 | Burkhardt et al. 2022 | |
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| 132 | -| [EHD1](EHD1) | 2 | Thomas et al. 2023 | |
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| 133 | -| [EIF2C4](EIF2C4) | 2 | Love et al. 2012 | |
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| 134 | -| [ELP2](ELP2) | 2 | Schmitz et al. 2012 | |
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| 135 | -| [EML2](EML2) | 2 | Love et al. 2012 | |
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| 136 | -| [ENTPD3](ENTPD3) | 2 | Love et al. 2012 | |
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| 137 | -| [EP300](EP300) | 2 | Panea et al. 2019; Rossi et al. 2012; Laura Pasqualucci, Dominguez-Sola, et al. 2011 | |
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| 138 | -| [EPHB2](EPHB2) | 2 | Love et al. 2012 | |
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| 139 | -| [ERAP1](ERAP1) | 2 | Burkhardt et al. 2022 | |
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| 140 | -| [ETS1](ETS1) | 2, aSHM | Morin et al. 2011; Panea et al. 2019 | |
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| 141 | -| [EXOSC6](EXOSC6) | 2 | Schmitz et al. 2012 | |
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| 142 | -| [EZH2](EZH2) | 2 | Mottok et al. 2019; Love et al. 2012; Morin et al. 2010 | |
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| 143 | -| [FAM129B](FAM129B) | 2 | Love et al. 2012 | |
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| 144 | -| [FGFR3](FGFR3) | 2 | Love et al. 2012 | |
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| 145 | -| [FLYWCH1](FLYWCH1) | 2 | Schmitz et al. 2012 | |
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| 146 | -| [FTCD](FTCD) | 2 | Love et al. 2012 | |
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| 147 | -| [FZD3](FZD3) | 2 | Panea et al. 2019 | |
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| 148 | -| [GGTLA4](GGTLA4) | 2 | Love et al. 2012 | |
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| 149 | -| [GRB2](GRB2) | 2 | Panea et al. 2019; Laura Pasqualucci, Trifonov, et al. 2011 | |
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| 150 | -| [GRIK5](GRIK5) | 2 | Love et al. 2012 | |
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| 151 | -| [GTSE1](GTSE1) | 2 | Schmitz et al. 2012 | |
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| 152 | -| [HIST1H1C](HIST1H1C) | 2, aSHM | Panea et al. 2019; Morin et al. 2011 | |
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| 153 | -| [HIST1H1E](HIST1H1E) | 2, aSHM | Morin et al. 2013; Reichel et al. 2015; Grande et al. 2019; Krysiak et al. 2017 | |
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| 154 | -| [HIST1H2AG](HIST1H2AG) | 2, aSHM | Krysiak et al. 2017; Panea et al. 2019; Morin et al. 2013; Rossi et al. 2012 | |
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| 155 | -| [HIST1H2AM](HIST1H2AM) | 2, aSHM | Krysiak et al. 2017; Panea et al. 2019 | |
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| 156 | -| [HIST1H2BK](HIST1H2BK) | 2, aSHM | Rossi et al. 2012; Panea et al. 2019 | |
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| 157 | -| [HIST1H3D](HIST1H3D) | 2, aSHM | Panea et al. 2019 | |
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| 158 | -| [HIST1H3H](HIST1H3H) | 2, aSHM | Panea et al. 2019 | |
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| 159 | -| [HIST1H3I](HIST1H3I) | 2, aSHM | Panea et al. 2019; Krysiak et al. 2017 | |
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| 160 | -| [HIST1H3J](HIST1H3J) | 2, aSHM | Panea et al. 2019 | |
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| 161 | -| [HIST1H4J](HIST1H4J) | 2, aSHM | Mottok et al. 2019; Panea et al. 2019 | |
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| 162 | -| [HLA-A](HLA-A) | 2 | Desch et al. 2020 | |
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| 163 | -| [HLA-B](HLA-B) | 2 | Wienand et al. 2019 | |
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| 164 | -| [HLA-DMB](HLA-DMB) | 2 | | |
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| 165 | -| [HLA-DQB1](HLA-DQB1) | 2 | Burkhardt et al. 2022 | |
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| 166 | -| [ICK](ICK) | 2 | Love et al. 2012 | |
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| 167 | -| [IGLL5](IGLL5) | 2, aSHM | Russler-Germain et al. 2023; Panea et al. 2019; Desch et al. 2020 | |
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| 168 | -| [IKZF3](IKZF3) | 2, aSHM | Morin et al. 2013; Panea et al. 2019 | |
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| 169 | -| [IRF8](IRF8) | 2, aSHM | Mottok et al. 2019; Morin et al. 2011; Panea et al. 2019 | |
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| 170 | -| [ITPR3](ITPR3) | 2 | Tiacci et al. 2018; Love et al. 2012 | |
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| 171 | -| [KANK2](KANK2) | 2 | Schmitz et al. 2012 | |
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| 172 | -| [KCNK10](KCNK10) | 2 | Panea et al. 2019 | |
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| 173 | -| [KIFC3](KIFC3) | 2 | Love et al. 2012 | |
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| 174 | -| [KLHL26](KLHL26) | 2 | Burkhardt et al. 2022 | |
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| 175 | -| [KLHL6](KLHL6) | 2, aSHM | Ganapathi et al. 2016; Panea et al. 2019; Morin et al. 2011 | |
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| 176 | -| [KMT2C](KMT2C) | 2 | Zhang et al. 2013; Zhou et al. 2019; Sarkozy et al. 2021; Zhang et al. 2014 | |
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| 177 | -| [LTB](LTB) | 2, aSHM | Panea et al. 2019; Chapuy et al. 2018; Desch et al. 2020 | |
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| 178 | -| [MAP3K6](MAP3K6) | 2 | Love et al. 2012 | |
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| 179 | -| [MCL1](MCL1) | 2 | Reddy et al. 2017; Duns et al. 2021; Panea et al. 2019 | |
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| 180 | -| [MIR142](MIR142) | 2, aSHM | Grande et al. 2019; Kwanhian et al. 2012 | |
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| 181 | -| [MKI67](MKI67) | 2 | Russler-Germain et al. 2023; Schmitz et al. 2012 | |
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| 182 | -| [MME](MME) | 2 | Panea et al. 2019 | |
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| 183 | -| [MTOR](MTOR) | 2 | Panea et al. 2019; Zhang et al. 2013 | |
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| 184 | -| [MYH10](MYH10) | 2 | Love et al. 2012 | |
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| 185 | -| [MYO18A](MYO18A) | 2 | Schmitz et al. 2012 | |
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| 186 | -| [NBEAL1](NBEAL1) | 2 | Love et al. 2012 | |
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| 187 | -| [NCOR2](NCOR2) | 2 | Spina et al. 2016; Sarkozy et al. 2021; Schmitz et al. 2012 | |
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| 188 | -| [NOA1](NOA1) | 2 | Burkhardt et al. 2022 | |
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| 189 | -| [NOTCH1](NOTCH1) | 2 | Love et al. 2012; Laura Pasqualucci, Trifonov, et al. 2011; Beà et al. 2013; Rossi et al. 2012 | |
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| 190 | -| [NOTCH2](NOTCH2) | 2 | Rossi et al. 2012; Panea et al. 2019; Trøen et al. 2008; Beà et al. 2013 | |
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| 191 | -| [NRXN2](NRXN2) | 2 | Love et al. 2012 | |
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| 192 | -| [P2RY2](P2RY2) | 2 | Love et al. 2012 | |
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| 193 | -| [PABPC4L](PABPC4L) | 2 | Panea et al. 2019 | |
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| 194 | -| [PC](PC) | 2 | Love et al. 2012 | |
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| 195 | -| [PCBP1](PCBP1) | 2 | Schmitz et al. 2012 | |
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| 196 | -| [PCDHA11](PCDHA11) | 2 | Panea et al. 2019 | |
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| 197 | -| [PDCD11](PDCD11) | 2 | Schmitz et al. 2012 | |
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| 198 | -| [PDZRN3](PDZRN3) | 2 | Panea et al. 2019 | |
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| 199 | -| [PIK3R1](PIK3R1) | 2 | Zhang et al. 2013; Panea et al. 2019 | |
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| 200 | -| [PIM1](PIM1) | 2, aSHM | Burkhardt et al. 2022; Duns et al. 2021; L. Pasqualucci et al. 2001 | |
|
| 201 | -| [PLCG2](PLCG2) | 2 | Panea et al. 2019 | |
|
| 202 | -| [POLRMT](POLRMT) | 2 | Love et al. 2012 | |
|
| 203 | -| [POR](POR) | 2 | Love et al. 2012 | |
|
| 204 | -| [PPP6R2](PPP6R2) | 2 | Burkhardt et al. 2022 | |
|
| 205 | -| [PREX1](PREX1) | 2 | Burkhardt et al. 2022 | |
|
| 206 | -| [PRSS22](PRSS22) | 2 | Love et al. 2012 | |
|
| 207 | -| [PTPRN](PTPRN) | 2 | Love et al. 2012 | |
|
| 208 | -| [PXDNL](PXDNL) | 2 | Panea et al. 2019 | |
|
| 209 | -| [RAC2](RAC2) | 2 | Hübschmann et al. 2021; Panea et al. 2019 | |
|
| 210 | -| [RANBP6](RANBP6) | 2 | Love et al. 2012 | |
|
| 211 | -| [RBP3](RBP3) | 2 | Love et al. 2012 | |
|
| 212 | -| [RET](RET) | 2 | Love et al. 2012 | |
|
| 213 | -| [REV3L](REV3L) | 2 | Burkhardt et al. 2022 | |
|
| 214 | -| [RNF144B](RNF144B) | 2 | Panea et al. 2019 | |
|
| 215 | -| [RPL10](RPL10) | 2 | Burkhardt et al. 2022 | |
|
| 216 | -| [S1PR2](S1PR2) | 2, aSHM | Morin et al. 2011; Muppidi et al. 2014 | |
|
| 217 | -| [SAL3](SAL3) | 2 | Burkhardt et al. 2022 | |
|
| 218 | -| [SALL3](SALL3) | 2 | Love et al. 2012; Zhang et al. 2014 | |
|
| 219 | -| [SAPS2](SAPS2) | 2 | Love et al. 2012 | |
|
| 220 | -| [SBF1](SBF1) | 2 | Love et al. 2012 | |
|
| 221 | -| [SF3B1](SF3B1) | 2 | Love et al. 2012 | |
|
| 222 | -| [SHANK1](SHANK1) | 2 | Love et al. 2012 | |
|
| 223 | -| [SLC29A2](SLC29A2) | 2 | Love et al. 2012 | |
|
| 224 | -| [SNTB2](SNTB2) | 2 | Panea et al. 2019 | |
|
| 225 | -| [SP3](SP3) | 2 | Panea et al. 2019 | |
|
| 226 | -| [SYNCRIP](SYNCRIP) | 2 | Panea et al. 2019 | |
|
| 227 | -| [SYNGAP1](SYNGAP1) | 2 | Love et al. 2012 | |
|
| 228 | -| [TBC1D9B](TBC1D9B) | 2 | Love et al. 2012 | |
|
| 229 | -| [TET2](TET2) | 2 | Albuquerque et al. 2017; Panea et al. 2019 | |
|
| 230 | -| [TIGD6](TIGD6) | 2 | Love et al. 2012 | |
|
| 231 | -| [TOP2A](TOP2A) | 2 | Schmitz et al. 2012 | |
|
| 232 | -| [TPST2](TPST2) | 2 | Love et al. 2012 | |
|
| 233 | -| [TTN](TTN) | 2 | Burkhardt et al. 2022 | |
|
| 234 | -| [VWA7](VWA7) | 2 | Burkhardt et al. 2022 | |
|
| 235 | -| [WDR7](WDR7) | 2 | Panea et al. 2019 | |
|
| 236 | -| [WDR90](WDR90) | 2 | Schmitz et al. 2012 | |
|
| 237 | -| [WHAMM](WHAMM) | 2 | Schmitz et al. 2012 | |
|
| 238 | -| [WNK2](WNK2) | 2 | Panea et al. 2019 | |
|
| 239 | -| [YY1AP1](YY1AP1) | 2 | Schmitz et al. 2012 | |
|
| 240 | -| [ZAN](ZAN) | 2 | Burkhardt et al. 2022 | |
|
| 241 | -| [ZBTB7A](ZBTB7A) | 2 | Burkhardt et al. 2022; Reddy et al. 2017 | |
|
| 242 | -| [ZFP36L1](ZFP36L1) | 2, aSHM | Morin et al. 2011; Reichel et al. 2015; Panea et al. 2019 | |
|
| 243 | -| [ZNF229](ZNF229) | 2 | Love et al. 2012 | |
|
| 244 | -| [ZNF85](ZNF85) | 2 | Burkhardt et al. 2022 | |
|
| 245 | - |
|
| 246 | -# References |
|
| 247 | - |
|
| 248 | -<div id="refs" class="references csl-bib-body hanging-indent"> |
|
| 249 | - |
|
| 250 | -<div id="ref-abateDistinctViralMutational2015a" class="csl-entry"> |
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| 251 | - |
|
| 252 | -Abate, F., M. Ambrosio, L. Mundo, M. Laginestra, F. Fuligni, M. Rossi, |
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| 253 | -Sakellarios Zairis, et al. 2015. “Distinct Viral and Mutational Spectrum |
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| 254 | -of Endemic Burkitt Lymphoma.” *PLoS Pathogens* 11. |
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| 255 | -<https://doi.org/10.1371/journal.ppat.1005158>. |
|
| 256 | - |
|
| 257 | -</div> |
|
| 258 | - |
|
| 259 | -<div id="ref-albuquerqueEnhancingKnowledgeDiscovery2017a" |
|
| 260 | -class="csl-entry"> |
|
| 261 | - |
|
| 262 | -Albuquerque, Marco A., Bruno M. Grande, Elie J. Ritch, Prasath |
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| 263 | -Pararajalingam, Selin Jessa, Martin Krzywinski, Jasleen K. Grewal, |
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| 264 | -Sohrab P. Shah, Paul C. Boutros, and Ryan D. Morin. 2017. “Enhancing |
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| 265 | -Knowledge Discovery from Cancer Genomics Data with Galaxy.” |
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| 266 | -*GigaScience* 6 5: 1–13. <https://doi.org/10.1093/gigascience/gix015>. |
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| 267 | - |
|
| 268 | -</div> |
|
| 269 | - |
|
| 270 | -<div id="ref-arthurGenomewideDiscoverySomatic2018" class="csl-entry"> |
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| 271 | - |
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| 272 | -Arthur, Sarah E., Aixiang Jiang, Bruno M. Grande, Miguel Alcaide, Razvan |
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| 273 | -Cojocaru, Christopher K. Rushton, Anja Mottok, et al. 2018. “Genome-Wide |
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| 274 | -Discovery of Somatic Regulatory Variants in Diffuse Large <span |
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| 275 | -class="nocase">B-cell</span> Lymphoma.” *Nature Communications* 9 1: |
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| 276 | -4001. <https://doi.org/10.1038/s41467-018-06354-3>. |
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| 277 | - |
|
| 278 | -</div> |
|
| 279 | - |
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| 280 | -<div id="ref-beaLandscapeSomaticMutations2013" class="csl-entry"> |
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| 281 | - |
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| 282 | -Beà, Sílvia, Rafael Valdés-Mas, Alba Navarro, Itziar Salaverria, David |
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| 283 | -Martín-Garcia, Pedro Jares, Eva Giné, et al. 2013. “Landscape of Somatic |
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| 284 | -Mutations and Clonal Evolution in Mantle Cell Lymphoma.” *Proceedings of |
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| 285 | -the National Academy of Sciences* 110 45: 18250–55. |
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| 286 | -<https://doi.org/10.1073/pnas.1314608110>. |
|
| 287 | - |
|
| 288 | -</div> |
|
| 289 | - |
|
| 290 | -<div id="ref-bohleRoleEarlyBcell2013" class="csl-entry"> |
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| 291 | - |
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| 292 | -Bohle, V., C. Döring, M.-L. Hansmann, and R. Küppers. 2013. “Role of |
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| 293 | -Early <span class="nocase">B-cell</span> Factor 1 EBF1 in Hodgkin |
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| 294 | -Lymphoma.” *Leukemia* 27 3: 671–79. |
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| 295 | -<https://doi.org/10.1038/leu.2012.280>. |
|
| 296 | - |
|
| 297 | -</div> |
|
| 298 | - |
|
| 299 | -<div id="ref-burkhardtClinicalRelevanceMolecular2022b" |
|
| 300 | -class="csl-entry"> |
|
| 301 | - |
|
| 302 | -Burkhardt, Birgit, Ulf Michgehl, Jonas Rohde, Tabea Erdmann, Philipp |
|
| 303 | -Berning, Katrin Reutter, Marius Rohde, et al. 2022. “Clinical Relevance |
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| 304 | -of Molecular Characteristics in Burkitt Lymphoma Differs According to |
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| 305 | -Age.” *Nature Communications* 13 1: 3881. |
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| 306 | -<https://doi.org/10.1038/s41467-022-31355-8>. |
|
| 307 | - |
|
| 308 | -</div> |
|
| 309 | - |
|
| 310 | -<div id="ref-chapuyMolecularSubtypesDiffuse2018b" class="csl-entry"> |
|
| 311 | - |
|
| 312 | -Chapuy, Bjoern, Chip Stewart, Andrew J. Dunford, Jaegil Kim, Atanas |
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| 313 | -Kamburov, Robert A. Redd, Mike S. Lawrence, et al. 2018. “Molecular |
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| 314 | -Subtypes of Diffuse Large B Cell Lymphoma Are Associated with Distinct |
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| 315 | -Pathogenic Mechanisms and Outcomes.” *Nature Medicine* 24 5: 679–90. |
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| 316 | -<https://doi.org/10.1038/s41591-018-0016-8>. |
|
| 317 | - |
|
| 318 | -</div> |
|
| 319 | - |
|
| 320 | -<div id="ref-deschGenotypingCirculatingTumor2020" class="csl-entry"> |
|
| 321 | - |
|
| 322 | -Desch, Ann-Kathrin, Kristin Hartung, Ante Botzen, Alexander Brobeil, |
|
| 323 | -Mathias Rummel, Lars Kurch, Thomas Georgi, et al. 2020. “Genotyping |
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| 324 | -Circulating Tumor DNA of Pediatric Hodgkin Lymphoma.” *Leukemia* 34 1: |
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| 325 | -151–66. <https://doi.org/10.1038/s41375-019-0541-6>. |
|
| 326 | - |
|
| 327 | -</div> |
|
| 328 | - |
|
| 329 | -<div id="ref-dunsCharacterizationDLBCLPMBL2021b" class="csl-entry"> |
|
| 330 | - |
|
| 331 | -Duns, Gerben, Elena Viganò, Daisuke Ennishi, Clementine Sarkozy, Stacy |
|
| 332 | -S. Hung, Elizabeth Chavez, Katsuyoshi Takata, et al. 2021. |
|
| 333 | -“Characterization of DLBCL with a PMBL Gene Expression Signature.” |
|
| 334 | -*Blood* 138 2: 136–48. <https://doi.org/10.1182/blood.2020007683>. |
|
| 335 | - |
|
| 336 | -</div> |
|
| 337 | - |
|
| 338 | -<div id="ref-ganapathiGeneticLandscapeDural2016" class="csl-entry"> |
|
| 339 | - |
|
| 340 | -Ganapathi, Karthik A., Vaidehi Jobanputra, Fabio Iwamoto, Preti Jain, |
|
| 341 | -Jinli Chen, Luciano Cascione, Odelia Nahum, et al. 2016. “The Genetic |
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| 342 | -Landscape of Dural Marginal Zone Lymphomas.” *Oncotarget* 7 28: |
|
| 343 | -43052–61. <https://doi.org/10.18632/oncotarget.9678>. |
|
| 344 | - |
|
| 345 | -</div> |
|
| 346 | - |
|
| 347 | -<div id="ref-gomezUltraDeepSequencingReveals2023" class="csl-entry"> |
|
| 348 | - |
|
| 349 | -Gomez, Felicia, Bryan Fisk, Joshua F. McMichael, Matthew Mosior, |
|
| 350 | -Jennifer A. Foltz, Zachary L. Skidmore, Eric J. Duncavage, et al. 2023. |
|
| 351 | -“Ultra-Deep Sequencing Reveals the Mutational Landscape of Classical |
|
| 352 | -Hodgkin Lymphoma.” *Cancer Research Communications* 3 11: 2312–30. |
|
| 353 | -<https://doi.org/10.1158/2767-9764.CRC-23-0140>. |
|
| 354 | - |
|
| 355 | -</div> |
|
| 356 | - |
|
| 357 | -<div id="ref-grandeGenomewideDiscoverySomatic2019" class="csl-entry"> |
|
| 358 | - |
|
| 359 | -Grande, Bruno M., Daniela S. Gerhard, Aixiang Jiang, Nicholas B. Griner, |
|
| 360 | -Jeremy S. Abramson, Thomas B. Alexander, Hilary Allen, et al. 2019. |
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| 361 | -“Genome-Wide Discovery of Somatic Coding and Noncoding Mutations in |
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| 362 | -Pediatric Endemic and Sporadic Burkitt Lymphoma.” *Blood* 133 12: |
|
| 363 | -1313–24. <https://doi.org/10.1182/blood-2018-09-871418>. |
|
| 364 | - |
|
| 365 | -</div> |
|
| 366 | - |
|
| 367 | -<div id="ref-hubschmannMutationalMechanismsShaping2021b" |
|
| 368 | -class="csl-entry"> |
|
| 369 | - |
|
| 370 | -Hübschmann, Daniel, Kortine Kleinheinz, Rabea Wagener, Stephan H. |
|
| 371 | -Bernhart, Cristina López, Umut H. Toprak, Stephanie Sungalee, et al. |
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| 372 | -2021. “Mutational Mechanisms Shaping the Coding and Noncoding Genome of |
|
| 373 | -Germinal Center Derived <span class="nocase">B-cell</span> Lymphomas.” |
|
| 374 | -*Leukemia* 35 7: 2002–16. |
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| 375 | -<https://doi.org/10.1038/s41375-021-01251-z>. |
|
| 376 | - |
|
| 377 | -</div> |
|
| 378 | - |
|
| 379 | -<div id="ref-jalladesExomeSequencingIdentifies2017" class="csl-entry"> |
|
| 380 | - |
|
| 381 | -Jallades, Laurent, Lucile Baseggio, Pierre Sujobert, Sarah Huet, Kaddour |
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| 382 | -Chabane, Evelyne Callet-Bauchu, Aurélie Verney, et al. 2017. “Exome |
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| 383 | -Sequencing Identifies Recurrent BCOR Alterations and the Absence of |
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| 384 | -KLF2, TNFAIP3 and MYD88 Mutations in Splenic Diffuse Red Pulp Small |
|
| 385 | -<span class="nocase">B-cell</span> Lymphoma.” *Haematologica* 102 10: |
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| 386 | -1758–66. <https://doi.org/10.3324/haematol.2016.160192>. |
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| 387 | - |
|
| 388 | -</div> |
|
| 389 | - |
|
| 390 | -<div id="ref-johnstonCmycHypermutationBurkitt1992" class="csl-entry"> |
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| 391 | - |
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| 392 | -Johnston, J. M., and W. L. Carroll. 1992. “C-Myc Hypermutation in |
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| 393 | -Burkitt’s Lymphoma.” *Leukemia & Lymphoma* 8 6: 431–39. |
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| 394 | -<https://doi.org/10.3109/10428199209051025>. |
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| 395 | - |
|
| 396 | -</div> |
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| 397 | - |
|
| 398 | -<div id="ref-khodabakhshiRecurrentTargetsAberrant2012" |
|
| 399 | -class="csl-entry"> |
|
| 400 | - |
|
| 401 | -Khodabakhshi, Alireza Hadj, Ryan D. Morin, Anthony P. Fejes, Andrew J. |
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| 402 | -Mungall, Karen L. Mungall, Madison Bolger-Munro, Nathalie A. Johnson, et |
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| 403 | -al. 2012. “Recurrent Targets of Aberrant Somatic Hypermutation in |
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| 404 | -Lymphoma.” *Oncotarget* 3 11: 1308–19. |
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| 405 | -<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3717795/>. |
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| 406 | - |
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| 407 | -</div> |
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| 408 | - |
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| 409 | -<div id="ref-krysiakRecurrentSomaticMutations2017b" class="csl-entry"> |
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| 410 | - |
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| 411 | -Krysiak, Kilannin, Felicia Gomez, Brian S. White, Matthew Matlock, |
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| 412 | -Christopher A. Miller, Lee Trani, Catrina C. Fronick, et al. 2017. |
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| 413 | -“Recurrent Somatic Mutations Affecting <span |
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| 414 | -class="nocase">B-cell</span> Receptor Signaling Pathway Genes in |
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| 415 | -Follicular Lymphoma.” *Blood* 129 4: 473–83. |
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| 416 | -<https://doi.org/10.1182/blood-2016-07-729954>. |
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| 417 | - |
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| 418 | -</div> |
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| 419 | - |
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| 420 | -<div id="ref-kwanhianMicroRNA142Mutated202012b" class="csl-entry"> |
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| 421 | - |
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| 422 | -Kwanhian, Wiyada, Dido Lenze, Julia Alles, Natalie Motsch, Stephanie |
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| 423 | -Barth, Celina Döll, Jochen Imig, et al. 2012. “MicroRNA-142 Is Mutated |
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| 424 | -in about 20% of Diffuse Large <span class="nocase">B-cell</span> |
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| 425 | -Lymphoma.” *Cancer Medicine* 1 2: 141–55. |
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| 426 | -<https://doi.org/10.1002/cam4.29>. |
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| 427 | - |
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| 428 | -</div> |
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| 429 | - |
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| 430 | -<div id="ref-lenzOncogenicCARD11Mutations2008" class="csl-entry"> |
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| 432 | -Lenz, Georg, R Eric Davis, Vu N Ngo, Lloyd Lam, Thaddeus C George, |
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| 433 | -George W Wright, Sandeep S Dave, et al. 2008. “Oncogenic CARD11 |
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| 434 | -Mutations in Human Diffuse Large B Cell Lymphoma.” *Science* 319 5870: |
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| 435 | -1676–79. |
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| 436 | - |
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| 437 | -</div> |
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| 438 | - |
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| 439 | -<div id="ref-lohrDiscoveryPrioritizationSomatic2012a" class="csl-entry"> |
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| 440 | - |
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| 441 | -Lohr, Jens G., Petar Stojanov, Michael S. Lawrence, Daniel Auclair, |
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| 443 | -“Discovery and Prioritization of Somatic Mutations in Diffuse Large |
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| 444 | -<span class="nocase">B-cell</span> Lymphoma DLBCL by Whole-Exome |
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| 445 | -Sequencing.” *Proceedings of the National Academy of Sciences of the |
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| 447 | -<https://doi.org/10.1073/pnas.1121343109>. |
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| 448 | - |
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| 450 | - |
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| 451 | -<div id="ref-loveGeneticLandscapeMutations2012" class="csl-entry"> |
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| 454 | -Miles, Kristy L. Richards, et al. 2012. “The Genetic Landscape of |
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| 455 | -Mutations in Burkitt Lymphoma.” *Nature Genetics* 44 12: 1321–25. |
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| 456 | -<https://doi.org/10.1038/ng.2468>. |
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| 457 | - |
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| 458 | -</div> |
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| 459 | - |
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| 460 | -<div id="ref-morinSomaticMutationsAltering2010a" class="csl-entry"> |
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| 461 | - |
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| 462 | -Morin, Ryan D., Nathalie A. Johnson, Tesa M. Severson, Andrew J. |
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| 463 | -Mungall, Jianghong An, Rodrigo Goya, Jessica E. Paul, et al. 2010. |
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| 464 | -“Somatic Mutations Altering EZH2 Tyr641 in Follicular and Diffuse |
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| 466 | -Origin.” *Nature Genetics* 42 2: 181–85. |
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| 467 | -<https://doi.org/10.1038/ng.518>. |
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| 468 | - |
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| 469 | -</div> |
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| 470 | - |
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| 471 | -<div id="ref-morinFrequentMutationHistonemodifying2011" |
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| 472 | -class="csl-entry"> |
|
| 473 | - |
|
| 474 | -Morin, Ryan D., Maria Mendez-Lago, Andrew J. Mungall, Rodrigo Goya, |
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| 475 | -Karen L. Mungall, Richard D. Corbett, Nathalie A. Johnson, et al. 2011. |
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| 476 | -“Frequent Mutation of Histone-Modifying Genes in Non-Hodgkin Lymphoma.” |
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| 477 | -*Nature* 476 7360: 298–303. <https://doi.org/10.1038/nature10351>. |
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| 478 | - |
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| 479 | -</div> |
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| 480 | - |
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| 481 | -<div id="ref-morinMutationalStructuralAnalysis2013" class="csl-entry"> |
|
| 482 | - |
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| 483 | -Morin, Ryan D., Karen Mungall, Erin Pleasance, Andrew J. Mungall, |
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| 484 | -Rodrigo Goya, Ryan D. Huff, David W. Scott, et al. 2013. “Mutational and |
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| 485 | -Structural Analysis of Diffuse Large <span class="nocase">B-cell</span> |
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| 486 | -Lymphoma Using Whole-Genome Sequencing.” *Blood* 122 7: 1256–65. |
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| 487 | -<https://doi.org/10.1182/blood-2013-02-483727>. |
|
| 488 | - |
|
| 489 | -</div> |
|
| 490 | - |
|
| 491 | -<div id="ref-mottokIntegrativeGenomicAnalysis2019b" class="csl-entry"> |
|
| 492 | - |
|
| 493 | -Mottok, Anja, Stacy S. Hung, Elizabeth A. Chavez, Bruce Woolcock, Adèle |
|
| 494 | -Telenius, Lauren C. Chong, Barbara Meissner, et al. 2019. “Integrative |
|
| 495 | -Genomic Analysis Identifies Key Pathogenic Mechanisms in Primary |
|
| 496 | -Mediastinal Large <span class="nocase">B-cell</span> Lymphoma.” *Blood* |
|
| 497 | -134 10: 802–13. <https://doi.org/10.1182/blood.2019001126>. |
|
| 498 | - |
|
| 499 | -</div> |
|
| 52 | +|Gene|Tier| Relevant references| |
|
| 53 | +|:-:|:-:|:-| |
|
| 54 | +|[ACAD9](ACAD9)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 55 | +|[ACE](ACE)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 56 | +|[ADAMTS5](ADAMTS5)|2|[@burkhardtClinicalRelevanceMolecular2022b]| |
|
| 57 | +|[ADNP](ADNP)|2|[@burkhardtClinicalRelevanceMolecular2022b]| |
|
| 58 | +|[AGO4](AGO4)|2|[@burkhardtClinicalRelevanceMolecular2022b]| |
|
| 59 | +|[ALPK2](ALPK2)|2|[@paneaWholeGenomeLandscape2019]| |
|
| 60 | +|[ARHGEF1](ARHGEF1)|2|[@muppidiLossSignalingGa132014b]| |
|
| 61 | +|[ATP2C2](ATP2C2)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 62 | +|[BACH2](BACH2)|2, aSHM|[@grandeGenomewideDiscoverySomatic2019]| |
|
| 63 | +|[BCL2](BCL2)|2, aSHM|[@tanakaFrequentIncidenceSomatic1992; @burkhardtClinicalRelevanceMolecular2022b; @sarkozyMutationalLandscapeGray2021a; @morinFrequentMutationHistonemodifying2011]| |
|
| 64 | +|[BCL6](BCL6)|2, aSHM|[@morinFrequentMutationHistonemodifying2011; @loveGeneticLandscapeMutations2012]| |
|
| 65 | +|[BRAF](BRAF)|2|[@tiacciBRAFMutationsHairycell2011a; @loveGeneticLandscapeMutations2012]| |
|
| 66 | +|[BRD4](BRD4)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 67 | +|[BTG1](BTG1)|2, aSHM|[@sarkozyMutationalLandscapeGray2021a; @morinFrequentMutationHistonemodifying2011; @burkhardtClinicalRelevanceMolecular2022b]| |
|
| 68 | +|[BTG2](BTG2)|2, aSHM|[@morinFrequentMutationHistonemodifying2011; @loveGeneticLandscapeMutations2012]| |
|
| 69 | +|[C16orf48](C16orf48)|2|[@schmitzBurkittLymphomaPathogenesis2012]| |
|
| 70 | +|[C6orf27](C6orf27)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 71 | +|[CAD](CAD)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 72 | +|[CARD11](CARD11)|2|[@lenzOncogenicCARD11Mutations2008; @paneaWholeGenomeLandscape2019; @wuGeneticHeterogeneityPrimary2016; @morinFrequentMutationHistonemodifying2011; @yanBCRTLRSignaling2012a]| |
|
| 73 | +|[CARD4](CARD4)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 74 | +|[CCNF](CCNF)|2|[@abateDistinctViralMutational2015a]| |
|
| 75 | +|[CCT6B](CCT6B)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 76 | +|[CD79A](CD79A)|2|[@burkhardtClinicalRelevanceMolecular2022b; @rossiCodingGenomeSplenic2012c]| |
|
| 77 | +|[CD79B](CD79B)|2|[@morinFrequentMutationHistonemodifying2011; @paneaWholeGenomeLandscape2019]| |
|
| 78 | +|[CD83](CD83)|2, aSHM|[@morinMutationalStructuralAnalysis2013; @russler-germainMutationsAssociatedProgression2023b; @dunsCharacterizationDLBCLPMBL2021b; @paneaWholeGenomeLandscape2019]| |
|
| 79 | +|[CDC73](CDC73)|2|[@reddyGeneticFunctionalDrivers2017; @loveGeneticLandscapeMutations2012]| |
|
| 80 | +|[CDH17](CDH17)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 81 | +|[CDKN2A](CDKN2A)|2|[@grandeGenomewideDiscoverySomatic2019; @spinaGeneticsNodalMarginal2016b; @morinMutationalStructuralAnalysis2013]| |
|
| 82 | +|[CDKN2C](CDKN2C)|2|[@thomasGeneticSubgroupsInform2023]| |
|
| 83 | +|[CHD4](CHD4)|2|[@burkhardtClinicalRelevanceMolecular2022b]| |
|
| 84 | +|[COL4A2](COL4A2)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 85 | +|[CPXM2](CPXM2)|2|[@burkhardtClinicalRelevanceMolecular2022b]| |
|
| 86 | +|[CREBBP](CREBBP)|2|[@pasqualucciInactivatingMutationsAcetyltransferase2011a; @loveGeneticLandscapeMutations2012; @parryWholeExomeSequencing2013; @dunsCharacterizationDLBCLPMBL2021b]| |
|
| 87 | +|[CTCF](CTCF)|2|[@paneaWholeGenomeLandscape2019]| |
|
| 88 | +|[CXCR4](CXCR4)|2, aSHM|[@khodabakhshiRecurrentTargetsAberrant2012; @krysiakRecurrentSomaticMutations2017b; @paneaWholeGenomeLandscape2019]| |
|
| 89 | +|[CYB5D1](CYB5D1)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 90 | +|[CYP4F22](CYP4F22)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 91 | +|[DHCR7](DHCR7)|2|[@schmitzBurkittLymphomaPathogenesis2012]| |
|
| 92 | +|[DLGAP1](DLGAP1)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 93 | +|[DNMT1](DNMT1)|2|[@paneaWholeGenomeLandscape2019]| |
|
| 94 | +|[DTX1](DTX1)|2, aSHM|[@gomezUltraDeepSequencingReveals2023; @schmitzGeneticsPathogenesisDiffuse2018a; @paneaWholeGenomeLandscape2019; @rossiCodingGenomeSplenic2012c]| |
|
| 95 | +|[E2F2](E2F2)|2|[@burkhardtClinicalRelevanceMolecular2022b]| |
|
| 96 | +|[EBF1](EBF1)|2, aSHM|[@reichelFlowSortingExome2015a; @bohleRoleEarlyBcell2013; @thomasGeneticSubgroupsInform2023]| |
|
| 97 | +|[EDNRB](EDNRB)|2|[@burkhardtClinicalRelevanceMolecular2022b]| |
|
| 98 | +|[EHD1](EHD1)|2|[@thomasGeneticSubgroupsInform2023]| |
|
| 99 | +|[EIF2C4](EIF2C4)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 100 | +|[ELP2](ELP2)|2|[@schmitzBurkittLymphomaPathogenesis2012]| |
|
| 101 | +|[EML2](EML2)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 102 | +|[ENTPD3](ENTPD3)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 103 | +|[EP300](EP300)|2|[@paneaWholeGenomeLandscape2019; @rossiCodingGenomeSplenic2012c; @pasqualucciInactivatingMutationsAcetyltransferase2011a]| |
|
| 104 | +|[EPHB2](EPHB2)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 105 | +|[ERAP1](ERAP1)|2|[@burkhardtClinicalRelevanceMolecular2022b]| |
|
| 106 | +|[ETS1](ETS1)|2, aSHM|[@paneaWholeGenomeLandscape2019; @morinFrequentMutationHistonemodifying2011]| |
|
| 107 | +|[EXOSC6](EXOSC6)|2|[@schmitzBurkittLymphomaPathogenesis2012]| |
|
| 108 | +|[EZH2](EZH2)|2|[@mottokIntegrativeGenomicAnalysis2019b; @morinSomaticMutationsAltering2010a; @loveGeneticLandscapeMutations2012]| |
|
| 109 | +|[FAM129B](FAM129B)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 110 | +|[FGFR3](FGFR3)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 111 | +|[FLYWCH1](FLYWCH1)|2|[@schmitzBurkittLymphomaPathogenesis2012]| |
|
| 112 | +|[FTCD](FTCD)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 113 | +|[FZD3](FZD3)|2|[@paneaWholeGenomeLandscape2019]| |
|
| 114 | +|[GGTLA4](GGTLA4)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 115 | +|[GRB2](GRB2)|2|[@paneaWholeGenomeLandscape2019; @pasqualucciAnalysisCodingGenome2011]| |
|
| 116 | +|[GRIK5](GRIK5)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 117 | +|[GTSE1](GTSE1)|2|[@schmitzBurkittLymphomaPathogenesis2012]| |
|
| 118 | +|[HIST1H1C](HIST1H1C)|2, aSHM|[@paneaWholeGenomeLandscape2019; @morinFrequentMutationHistonemodifying2011]| |
|
| 119 | +|[HIST1H1E](HIST1H1E)|2, aSHM|[@grandeGenomewideDiscoverySomatic2019; @reichelFlowSortingExome2015a; @morinMutationalStructuralAnalysis2013; @krysiakRecurrentSomaticMutations2017b]| |
|
| 120 | +|[HIST1H2AG](HIST1H2AG)|2, aSHM|[@morinMutationalStructuralAnalysis2013; @rossiCodingGenomeSplenic2012c; @krysiakRecurrentSomaticMutations2017b; @paneaWholeGenomeLandscape2019]| |
|
| 121 | +|[HIST1H2AM](HIST1H2AM)|2, aSHM|[@paneaWholeGenomeLandscape2019; @krysiakRecurrentSomaticMutations2017b]| |
|
| 122 | +|[HIST1H2BK](HIST1H2BK)|2, aSHM|[@rossiCodingGenomeSplenic2012c; @paneaWholeGenomeLandscape2019]| |
|
| 123 | +|[HIST1H3D](HIST1H3D)|2, aSHM|[@paneaWholeGenomeLandscape2019]| |
|
| 124 | +|[HIST1H3H](HIST1H3H)|2, aSHM|[@paneaWholeGenomeLandscape2019]| |
|
| 125 | +|[HIST1H3I](HIST1H3I)|2, aSHM|[@paneaWholeGenomeLandscape2019; @krysiakRecurrentSomaticMutations2017b]| |
|
| 126 | +|[HIST1H3J](HIST1H3J)|2, aSHM|[@paneaWholeGenomeLandscape2019]| |
|
| 127 | +|[HIST1H4J](HIST1H4J)|2, aSHM|[@mottokIntegrativeGenomicAnalysis2019b; @paneaWholeGenomeLandscape2019]| |
|
| 128 | +|[HLA-A](HLA-A)|2|[@deschGenotypingCirculatingTumor2020]| |
|
| 129 | +|[HLA-B](HLA-B)|2|[@wienandGenomicAnalysesFlowsorted2019b]| |
|
| 130 | +|[HLA-DMB](HLA-DMB)|2|| |
|
| 131 | +|[HLA-DQB1](HLA-DQB1)|2|[@burkhardtClinicalRelevanceMolecular2022b]| |
|
| 132 | +|[ICK](ICK)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 133 | +|[IGLL5](IGLL5)|2, aSHM|[@deschGenotypingCirculatingTumor2020; @russler-germainMutationsAssociatedProgression2023b; @paneaWholeGenomeLandscape2019]| |
|
| 134 | +|[IKZF3](IKZF3)|2, aSHM|[@morinMutationalStructuralAnalysis2013; @paneaWholeGenomeLandscape2019]| |
|
| 135 | +|[IRF8](IRF8)|2, aSHM|[@mottokIntegrativeGenomicAnalysis2019b; @morinFrequentMutationHistonemodifying2011; @paneaWholeGenomeLandscape2019]| |
|
| 136 | +|[ITPR3](ITPR3)|2|[@tiacciPervasiveMutationsJAKSTAT2018b; @loveGeneticLandscapeMutations2012]| |
|
| 137 | +|[KANK2](KANK2)|2|[@schmitzBurkittLymphomaPathogenesis2012]| |
|
| 138 | +|[KCNK10](KCNK10)|2|[@paneaWholeGenomeLandscape2019]| |
|
| 139 | +|[KIFC3](KIFC3)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 140 | +|[KLHL26](KLHL26)|2|[@burkhardtClinicalRelevanceMolecular2022b]| |
|
| 141 | +|[KLHL6](KLHL6)|2, aSHM|[@paneaWholeGenomeLandscape2019; @morinFrequentMutationHistonemodifying2011; @ganapathiGeneticLandscapeDural2016]| |
|
| 142 | +|[KMT2C](KMT2C)|2|[@zhouSporadicEndemicBurkitt2019; @zhangGenomicLandscapeMantle2014; @zhangGeneticHeterogeneityDiffuse2013; @sarkozyMutationalLandscapeGray2021a]| |
|
| 143 | +|[LTB](LTB)|2, aSHM|[@deschGenotypingCirculatingTumor2020; @chapuyMolecularSubtypesDiffuse2018b; @paneaWholeGenomeLandscape2019]| |
|
| 144 | +|[MAP3K6](MAP3K6)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 145 | +|[MCL1](MCL1)|2|[@reddyGeneticFunctionalDrivers2017; @dunsCharacterizationDLBCLPMBL2021b; @paneaWholeGenomeLandscape2019]| |
|
| 146 | +|[MIR142](MIR142)|2, aSHM|[@kwanhianMicroRNA142Mutated202012b; @grandeGenomewideDiscoverySomatic2019]| |
|
| 147 | +|[MKI67](MKI67)|2|[@schmitzBurkittLymphomaPathogenesis2012; @russler-germainMutationsAssociatedProgression2023b]| |
|
| 148 | +|[MME](MME)|2|[@paneaWholeGenomeLandscape2019]| |
|
| 149 | +|[MTOR](MTOR)|2|[@paneaWholeGenomeLandscape2019; @zhangGeneticHeterogeneityDiffuse2013]| |
|
| 150 | +|[MYH10](MYH10)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 151 | +|[MYO18A](MYO18A)|2|[@schmitzBurkittLymphomaPathogenesis2012]| |
|
| 152 | +|[NBEAL1](NBEAL1)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 153 | +|[NCOR2](NCOR2)|2|[@sarkozyMutationalLandscapeGray2021a; @spinaGeneticsNodalMarginal2016b; @schmitzBurkittLymphomaPathogenesis2012]| |
|
| 154 | +|[NOA1](NOA1)|2|[@burkhardtClinicalRelevanceMolecular2022b]| |
|
| 155 | +|[NOTCH1](NOTCH1)|2|[@rossiCodingGenomeSplenic2012c; @pasqualucciAnalysisCodingGenome2011; @beaLandscapeSomaticMutations2013; @loveGeneticLandscapeMutations2012]| |
|
| 156 | +|[NOTCH2](NOTCH2)|2|[@troenNOTCH2MutationsMarginal2008; @rossiCodingGenomeSplenic2012c; @paneaWholeGenomeLandscape2019; @beaLandscapeSomaticMutations2013]| |
|
| 157 | +|[NRXN2](NRXN2)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 158 | +|[P2RY2](P2RY2)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 159 | +|[PABPC4L](PABPC4L)|2|[@paneaWholeGenomeLandscape2019]| |
|
| 160 | +|[PC](PC)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 161 | +|[PCBP1](PCBP1)|2|[@schmitzBurkittLymphomaPathogenesis2012]| |
|
| 162 | +|[PCDHA11](PCDHA11)|2|[@paneaWholeGenomeLandscape2019]| |
|
| 163 | +|[PDCD11](PDCD11)|2|[@schmitzBurkittLymphomaPathogenesis2012]| |
|
| 164 | +|[PDZRN3](PDZRN3)|2|[@paneaWholeGenomeLandscape2019]| |
|
| 165 | +|[PIK3R1](PIK3R1)|2|[@paneaWholeGenomeLandscape2019; @zhangGeneticHeterogeneityDiffuse2013]| |
|
| 166 | +|[PIM1](PIM1)|2, aSHM|[@pasqualucciHypermutationMultipleProtooncogenes2001a; @dunsCharacterizationDLBCLPMBL2021b; @burkhardtClinicalRelevanceMolecular2022b]| |
|
| 167 | +|[PLCG2](PLCG2)|2|[@paneaWholeGenomeLandscape2019]| |
|
| 168 | +|[POLRMT](POLRMT)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 169 | +|[POR](POR)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 170 | +|[PPP6R2](PPP6R2)|2|[@burkhardtClinicalRelevanceMolecular2022b]| |
|
| 171 | +|[PREX1](PREX1)|2|[@burkhardtClinicalRelevanceMolecular2022b]| |
|
| 172 | +|[PRSS22](PRSS22)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 173 | +|[PTPRN](PTPRN)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 174 | +|[PXDNL](PXDNL)|2|[@paneaWholeGenomeLandscape2019]| |
|
| 175 | +|[RAC2](RAC2)|2|[@hubschmannMutationalMechanismsShaping2021b; @paneaWholeGenomeLandscape2019]| |
|
| 176 | +|[RANBP6](RANBP6)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 177 | +|[RBP3](RBP3)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 178 | +|[RET](RET)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 179 | +|[REV3L](REV3L)|2|[@burkhardtClinicalRelevanceMolecular2022b]| |
|
| 180 | +|[RNF144B](RNF144B)|2|[@paneaWholeGenomeLandscape2019]| |
|
| 181 | +|[RPL10](RPL10)|2|[@burkhardtClinicalRelevanceMolecular2022b]| |
|
| 182 | +|[S1PR2](S1PR2)|2, aSHM|[@morinFrequentMutationHistonemodifying2011; @muppidiLossSignalingGa132014b]| |
|
| 183 | +|[SAL3](SAL3)|2|[@burkhardtClinicalRelevanceMolecular2022b]| |
|
| 184 | +|[SALL3](SALL3)|2|[@loveGeneticLandscapeMutations2012; @zhangGenomicLandscapeMantle2014]| |
|
| 185 | +|[SAPS2](SAPS2)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 186 | +|[SBF1](SBF1)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 187 | +|[SF3B1](SF3B1)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 188 | +|[SHANK1](SHANK1)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 189 | +|[SLC29A2](SLC29A2)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 190 | +|[SNTB2](SNTB2)|2|[@paneaWholeGenomeLandscape2019]| |
|
| 191 | +|[SP3](SP3)|2|[@paneaWholeGenomeLandscape2019]| |
|
| 192 | +|[SYNCRIP](SYNCRIP)|2|[@paneaWholeGenomeLandscape2019]| |
|
| 193 | +|[SYNGAP1](SYNGAP1)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 194 | +|[TBC1D9B](TBC1D9B)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 195 | +|[TET2](TET2)|2|[@paneaWholeGenomeLandscape2019; @albuquerqueEnhancingKnowledgeDiscovery2017a]| |
|
| 196 | +|[TIGD6](TIGD6)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 197 | +|[TOP2A](TOP2A)|2|[@schmitzBurkittLymphomaPathogenesis2012]| |
|
| 198 | +|[TPST2](TPST2)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 199 | +|[TTN](TTN)|2|[@burkhardtClinicalRelevanceMolecular2022b]| |
|
| 200 | +|[VWA7](VWA7)|2|[@burkhardtClinicalRelevanceMolecular2022b]| |
|
| 201 | +|[WDR7](WDR7)|2|[@paneaWholeGenomeLandscape2019]| |
|
| 202 | +|[WDR90](WDR90)|2|[@schmitzBurkittLymphomaPathogenesis2012]| |
|
| 203 | +|[WHAMM](WHAMM)|2|[@schmitzBurkittLymphomaPathogenesis2012]| |
|
| 204 | +|[WNK2](WNK2)|2|[@paneaWholeGenomeLandscape2019]| |
|
| 205 | +|[YY1AP1](YY1AP1)|2|[@schmitzBurkittLymphomaPathogenesis2012]| |
|
| 206 | +|[ZAN](ZAN)|2|[@burkhardtClinicalRelevanceMolecular2022b]| |
|
| 207 | +|[ZBTB7A](ZBTB7A)|2|[@burkhardtClinicalRelevanceMolecular2022b; @reddyGeneticFunctionalDrivers2017]| |
|
| 208 | +|[ZFP36L1](ZFP36L1)|2, aSHM|[@morinFrequentMutationHistonemodifying2011; @paneaWholeGenomeLandscape2019; @reichelFlowSortingExome2015a]| |
|
| 209 | +|[ZNF229](ZNF229)|2|[@loveGeneticLandscapeMutations2012]| |
|
| 210 | +|[ZNF85](ZNF85)|2|[@burkhardtClinicalRelevanceMolecular2022b]| |
|
| 500 | 211 | |
| 501 | -<div id="ref-muppidiLossSignalingGa132014b" class="csl-entry"> |
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| 502 | 212 | |
| 503 | -Muppidi, J., R. Schmitz, Jesse A. Green, Jesse A. Green, Wenming Xiao, |
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| 504 | -Adrien B. Larsen, S. Braun, et al. 2014. “Loss of Signaling via Gα13 in |
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| 505 | -Germinal Center B Cell-Derived Lymphoma.” *Nature* 516: 254–58. |
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| 506 | -<https://doi.org/10.1038/nature13765>. |
|
| 507 | - |
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| 508 | -</div> |
|
| 509 | - |
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| 510 | -<div id="ref-nadeuGenomicEpigenomicInsights2020b" class="csl-entry"> |
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| 511 | - |
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| 512 | -Nadeu, F., D. Martín-García, G. Clot, A. Díaz-Navarro, M. Duran-Ferrer, |
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| 513 | -A. Navarro, Roser Vilarrasa-Blasi, et al. 2020. “Genomic and Epigenomic |
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| 514 | -Insights into the Origin, Pathogenesis and Clinical Behavior of Mantle |
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| 515 | -Cell Lymphoma Subtypes.” *Blood*. |
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| 516 | -<https://doi.org/10.1182/blood.2020005289>. |
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| 517 | - |
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| 518 | -</div> |
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| 519 | - |
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| 520 | -<div id="ref-paneaWholeGenomeLandscape2019" class="csl-entry"> |
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| 521 | - |
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| 522 | -Panea, R., C. Love, Jennifer R. Shingleton, Anupama Reddy, J. Bailey, A. |
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| 523 | -Moormann, J. Otieno, et al. 2019. “The Whole Genome Landscape of Burkitt |
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| 524 | -Lymphoma Subtypes.” *Blood*. <https://doi.org/10.1182/blood.2019001880>. |
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| 525 | - |
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| 526 | -</div> |
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| 527 | - |
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| 528 | -<div id="ref-parryWholeExomeSequencing2013" class="csl-entry"> |
|
| 529 | - |
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| 530 | -Parry, Marina, Matthew J. J. Rose-Zerilli, Jane Gibson, Sarah Ennis, |
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| 531 | -Renata Walewska, Jade Forster, Helen Parker, et al. 2013. “Whole Exome |
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| 532 | -Sequencing Identifies Novel Recurrently Mutated Genes in Patients with |
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| 533 | -Splenic Marginal Zone Lymphoma.” *PloS One* 8 12: e83244. |
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| 534 | -<https://doi.org/10.1371/journal.pone.0083244>. |
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| 535 | - |
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| 536 | -</div> |
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| 537 | - |
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| 538 | -<div id="ref-pasqualucciInactivatingMutationsAcetyltransferase2011a" |
|
| 539 | -class="csl-entry"> |
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| 540 | - |
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| 541 | -Pasqualucci, Laura, David Dominguez-Sola, Annalisa Chiarenza, Giulia |
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| 542 | -Fabbri, Adina Grunn, Vladimir Trifonov, Lawryn H. Kasper, et al. 2011. |
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| 543 | -“Inactivating Mutations of Acetyltransferase Genes in <span |
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| 544 | -class="nocase">B-cell</span> Lymphoma.” *Nature* 471 7337: 189–95. |
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| 545 | -<https://doi.org/10.1038/nature09730>. |
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| 546 | - |
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| 547 | -</div> |
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| 548 | - |
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| 549 | -<div id="ref-pasqualucciAnalysisCodingGenome2011" class="csl-entry"> |
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| 550 | - |
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| 551 | -Pasqualucci, Laura, Vladimir Trifonov, Giulia Fabbri, Jing Ma, Davide |
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| 552 | -Rossi, Annalisa Chiarenza, Victoria A. Wells, et al. 2011. “Analysis of |
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| 553 | -the Coding Genome of Diffuse Large <span class="nocase">B-cell</span> |
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| 554 | -Lymphoma.” *Nature Genetics* 43 9: 830–37. |
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| 555 | -<https://doi.org/10.1038/ng.892>. |
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| 556 | - |
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| 557 | -</div> |
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| 558 | - |
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| 559 | -<div id="ref-pasqualucciHypermutationMultipleProtooncogenes2001a" |
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| 560 | -class="csl-entry"> |
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| 561 | - |
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| 562 | -Pasqualucci, L., P. Neumeister, T. Goossens, G. Nanjangud, R. S. |
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| 563 | -Chaganti, R. Küppers, and R. Dalla-Favera. 2001. “Hypermutation of |
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| 564 | -Multiple Proto-Oncogenes in <span class="nocase">B-cell</span> Diffuse |
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| 565 | -Large-Cell Lymphomas.” *Nature* 412 6844: 341–46. |
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| 566 | -<https://doi.org/10.1038/35085588>. |
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| 567 | - |
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| 568 | -</div> |
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| 569 | - |
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| 570 | -<div id="ref-reddyGeneticFunctionalDrivers2017" class="csl-entry"> |
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| 571 | - |
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| 572 | -Reddy, Anupama, Jenny Zhang, Nicholas S Davis, Andrea B Moffitt, |
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| 573 | -Cassandra L Love, Alexander Waldrop, Sirpa Leppa, et al. 2017. “Genetic |
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| 574 | -and Functional Drivers of Diffuse Large B Cell Lymphoma.” *Cell* 171 |
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| 575 | -2: 481–494.e15. |
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| 576 | - |
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| 577 | -</div> |
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| 578 | - |
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| 579 | -<div id="ref-reichelFlowSortingExome2015a" class="csl-entry"> |
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| 580 | - |
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| 581 | -Reichel, Jonathan, Amy Chadburn, Paul G. Rubinstein, Lisa Giulino-Roth, |
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| 582 | -Wayne Tam, Yifang Liu, Rafael Gaiolla, et al. 2015. “Flow Sorting and |
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| 583 | -Exome Sequencing Reveal the Oncogenome of Primary Hodgkin and |
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| 584 | -Reed-Sternberg Cells.” *Blood* 125 7: 1061–72. |
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| 585 | -<https://doi.org/10.1182/blood-2014-11-610436>. |
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| 586 | - |
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| 587 | -</div> |
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| 588 | - |
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| 589 | -<div id="ref-richterRecurrentMutationID32012a" class="csl-entry"> |
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| 590 | - |
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| 591 | -Richter, Julia, Matthias Schlesner, Steve Hoffmann, Markus Kreuz, Ellen |
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| 592 | -Leich, Birgit Burkhardt, Maciej Rosolowski, et al. 2012. “Recurrent |
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| 593 | -Mutation of the ID3 Gene in Burkitt Lymphoma Identified by Integrated |
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| 594 | -Genome, Exome and Transcriptome Sequencing.” *Nature Genetics* 44 12: |
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| 595 | -1316–20. <https://doi.org/10.1038/ng.2469>. |
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| 213 | +# References |
DLBCL_genes.md
| ... | ... | @@ -1,1220 +1,353 @@ |
| 1 | -# DLBCL genes |
|
| 1 | +--- |
|
| 2 | +title: 'DLBCL genes' |
|
| 3 | +bibliography: 'morinlab.bib' |
|
| 4 | +csl: 'NLM.csl' |
|
| 5 | +link-citations: true |
|
| 6 | +--- |
|
| 2 | 7 | |
| 3 | 8 | ## Origins of DLBCL genes |
| 4 | 9 | |
| 5 | -```mermaid |
|
| 6 | ---- |
|
| 7 | -config: |
|
| 8 | - sankey: |
|
| 9 | - showValues: false |
|
| 10 | - linkColor: target |
|
| 11 | - width: 800 |
|
| 12 | - height: 1000 |
|
| 13 | - nodeAlignment: right |
|
| 14 | ---- |
|
| 15 | -sankey-beta |
|
| 16 | -Morin 2013, DLBCL Tier 1, 11 |
|
| 17 | -Morin 2013, DLBCL Tier 2, 29 |
|
| 18 | -Morin 2016, DLBCL Tier 1, 2 |
|
| 19 | -Mareschal 2016, DLBCL Tier 1, 2 |
|
| 20 | -Arthur 2018, DLBCL Tier 1, 8 |
|
| 21 | -Arthur 2018, DLBCL Tier 2, 12 |
|
| 22 | -Pasqualucci 2001, DLBCL Tier 1, 2 |
|
| 23 | -Pasqualucci 2001, DLBCL Tier 2, 2 |
|
| 24 | -Albuquerque 2017, DLBCL Tier 1, 3 |
|
| 25 | -Lohr 2012, DLBCL Tier 1, 3 |
|
| 26 | -Lohr 2012, DLBCL Tier 2, 1 |
|
| 27 | -Schmitz 2018, DLBCL Tier 1, 7 |
|
| 28 | -Schmitz 2018, DLBCL Tier 2, 9 |
|
| 29 | -Zhang 2013, DLBCL Tier 1, 11 |
|
| 30 | -Zhang 2013, DLBCL Tier 2, 8 |
|
| 31 | -Morin 2011, DLBCL Tier 1, 24 |
|
| 32 | -Morin 2011, DLBCL Tier 2, 1 |
|
| 33 | -Reddy 2017, DLBCL Tier 1, 7 |
|
| 34 | -Reddy 2017, DLBCL Tier 2, 53 |
|
| 35 | -Pasqualucci 2011, DLBCL Tier 1, 3 |
|
| 36 | -Pasqualucci 2011, DLBCL Tier 2, 4 |
|
| 37 | -Chapuy 2018, DLBCL Tier 1, 2 |
|
| 38 | -Chapuy 2018, DLBCL Tier 2, 17 |
|
| 39 | -Pasqualucci 2011, DLBCL Tier 1, 2 |
|
| 40 | -Hubschmann 2021, DLBCL Tier 1, 3 |
|
| 41 | -Hubschmann 2021, DLBCL Tier 2, 20 |
|
| 42 | -Pararajalingam 2020, DLBCL Tier 2, 2 |
|
| 43 | -DLBCL, Sanger, 4 |
|
| 44 | -Sanger, Pasqualucci 2001, 4 |
|
| 45 | -DLBCL, exome, 2 |
|
| 46 | -exome, Mareschal 2016, 2 |
|
| 47 | -DLBCL, WGS, 20 |
|
| 48 | -WGS, Arthur 2018, 20 |
|
| 49 | -DLBCL, exome, 2 |
|
| 50 | -exome, Morin 2016, 2 |
|
| 51 | -DLBCL, WGS, 40 |
|
| 52 | -WGS, Morin 2013, 40 |
|
| 53 | -DLBCL, exome, 3 |
|
| 54 | -exome, Albuquerque 2017, 3 |
|
| 55 | -DLBCL, exome, 4 |
|
| 56 | -exome, Lohr 2012, 4 |
|
| 57 | -DLBCL, exome, 60 |
|
| 58 | -exome, Reddy 2017, 60 |
|
| 59 | -DLBCL, exome, 16 |
|
| 60 | -exome, Schmitz 2018, 16 |
|
| 61 | -DLBCL, exome, 19 |
|
| 62 | -exome, Zhang 2013, 19 |
|
| 63 | -DLBCL, RNA-seq/WGS, 25 |
|
| 64 | -RNA-seq/WGS, Morin 2011, 25 |
|
| 65 | -DLBCL, exome, 2 |
|
| 66 | -exome, Pasqualucci 2011, 2 |
|
| 67 | -DLBCL, WGS/exome, 2 |
|
| 68 | -WGS/exome, Pararajalingam 2020, 2 |
|
| 69 | -DLBCL, WGS, 23 |
|
| 70 | -WGS, Hubschmann 2021, 23 |
|
| 71 | -DLBCL, exome, 19 |
|
| 72 | -exome, Chapuy 2018, 19 |
|
| 73 | -DLBCL, exome, 7 |
|
| 74 | -exome, Pasqualucci 2011, 7 |
|
| 75 | -``` |
|
| 10 | + |
|
| 76 | 11 | |
| 77 | 12 | ## Tier 1 DLBCL genes |
| 78 | 13 | |
| 79 | 14 | ### *128 total* |
| 80 | 15 | |
| 81 | -| Gene | Tier | Relevant references | |
|
| 82 | -|:----------------------:|:------------:|:--------------------------------------------------------------------------------------------------------| |
|
| 83 | -| [ACTB](ACTB) | 1, aSHM | Wienand et al. 2019; Lohr et al. 2012 | |
|
| 84 | -| [ACTG1](ACTG1) | 1, aSHM | Spina et al. 2016; Desch et al. 2020; Hübschmann et al. 2021 | |
|
| 85 | -| [ARID1A](ARID1A) | 1 | Rossi et al. 2012; Wienand et al. 2019; Love et al. 2012; Zhang et al. 2013; Krysiak et al. 2017 | |
|
| 86 | -| [ATM](ATM) | 1 | Braggio et al. 2012; Beà et al. 2013; Reddy et al. 2017 | |
|
| 87 | -| [B2M](B2M) | 1 | Pararajalingam et al. 2020; Reichel et al. 2015; Morin et al. 2011 | |
|
| 88 | -| [BCL10](BCL10) | 1 | Morin et al. 2011; Russler-Germain et al. 2023; Spina et al. 2016 | |
|
| 89 | -| [BCL2](BCL2) | 1, aSHM | Sarkozy et al. 2021; Tanaka et al. 1992; Burkhardt et al. 2022; Morin et al. 2011 | |
|
| 90 | -| [BCL6](BCL6) | 1, aSHM | Morin et al. 2011; Love et al. 2012 | |
|
| 91 | -| [BCL7A](BCL7A) | 1, aSHM | Reichel et al. 2015; Krysiak et al. 2017; Arthur et al. 2018; Grande et al. 2019 | |
|
| 92 | -| [BIRC6](BIRC6) | 1 | Reddy et al. 2017; Sarkozy et al. 2021 | |
|
| 93 | -| [BRAF](BRAF) | 1 | Love et al. 2012; Tiacci et al. 2011 | |
|
| 94 | -| [BTG1](BTG1) | 1, aSHM | Morin et al. 2011; Burkhardt et al. 2022; Sarkozy et al. 2021 | |
|
| 95 | -| [BTG2](BTG2) | 1, aSHM | Morin et al. 2011; Love et al. 2012 | |
|
| 96 | -| [BTK](BTK) | 1 | Krysiak et al. 2017; Albuquerque et al. 2017 | |
|
| 97 | -| [CARD11](CARD11) | 1 | Wu et al. 2016; Panea et al. 2019; Lenz et al. 2008; Yan et al. 2012; Morin et al. 2011 | |
|
| 98 | -| [CCND3](CCND3) | 1 | Jallades et al. 2017; Richter et al. 2012; Desch et al. 2020; Morin et al. 2011 | |
|
| 99 | -| [CD58](CD58) | 1 | Morin et al. 2011; Schneider et al. 2015 | |
|
| 100 | -| [CD70](CD70) | 1 | Russler-Germain et al. 2023; Morin et al. 2011 | |
|
| 101 | -| [CD79B](CD79B) | 1 | Morin et al. 2011; Panea et al. 2019 | |
|
| 102 | -| [CD83](CD83) | 1, aSHM | Russler-Germain et al. 2023; Morin et al. 2013; Duns et al. 2021; Panea et al. 2019 | |
|
| 103 | -| [CDKN2A](CDKN2A) | 1 | Grande et al. 2019; Spina et al. 2016; Morin et al. 2013 | |
|
| 104 | -| [CIITA](CIITA) | 1, aSHM | Mottok et al. 2015; Morin et al. 2011 | |
|
| 105 | -| [CREBBP](CREBBP) | 1 | Duns et al. 2021; Laura Pasqualucci, Dominguez-Sola, et al. 2011; Love et al. 2012; Parry et al. 2013 | |
|
| 106 | -| [CXCR4](CXCR4) | 1, aSHM | Khodabakhshi et al. 2012; Panea et al. 2019; Krysiak et al. 2017 | |
|
| 107 | -| [CXCR5](CXCR5) | 1 | Schmitz et al. 2018; Mottok et al. 2019 | |
|
| 108 | -| [DDX3X](DDX3X) | 1 | Schmitz et al. 2012, 2018; Mottok et al. 2019 | |
|
| 109 | -| [DTX1](DTX1) | 1, aSHM | Panea et al. 2019; Gomez et al. 2023; Schmitz et al. 2018; Rossi et al. 2012 | |
|
| 110 | -| [DUSP2](DUSP2) | 1, aSHM | Duns et al. 2021; Morin et al. 2013 | |
|
| 111 | -| [EBF1](EBF1) | 1, aSHM | Reichel et al. 2015; Bohle et al. 2013; Thomas et al. 2023 | |
|
| 112 | -| [EEF1A1](EEF1A1) | 1 | Hübschmann et al. 2021; Reichel et al. 2015 | |
|
| 113 | -| [EP300](EP300) | 1 | Rossi et al. 2012; Panea et al. 2019; Laura Pasqualucci, Dominguez-Sola, et al. 2011 | |
|
| 114 | -| [ETS1](ETS1) | 1, aSHM | Panea et al. 2019; Morin et al. 2011 | |
|
| 115 | -| [ETV6](ETV6) | 1, aSHM | Arthur et al. 2018 | |
|
| 116 | -| [EZH2](EZH2) | 1 | Morin et al. 2010; Mottok et al. 2019; Love et al. 2012 | |
|
| 117 | -| [FAS](FAS) | 1 | Scholl et al. 2007; Spina et al. 2016 | |
|
| 118 | -| [FBXO11](FBXO11) | 1 | Richter et al. 2012; Hübschmann et al. 2021; Parry et al. 2013 | |
|
| 119 | -| [FBXW7](FBXW7) | 1 | Zhang et al. 2013 | |
|
| 120 | -| [FOXO1](FOXO1) | 1 | Schmitz et al. 2012; Morin et al. 2011; Duns et al. 2021 | |
|
| 121 | -| [GNA13](GNA13) | 1 | Love et al. 2012; Morin et al. 2011; Reichel et al. 2015 | |
|
| 122 | -| [GNAI2](GNAI2) | 1 | Grande et al. 2019; Morin et al. 2013 | |
|
| 123 | -| [GRB2](GRB2) | 1 | Panea et al. 2019; Laura Pasqualucci, Trifonov, et al. 2011 | |
|
| 124 | -| [GRHPR](GRHPR) | 1, aSHM | Arthur et al. 2018 | |
|
| 125 | -| [HIST1H1B](HIST1H1B) | 1, aSHM | Krysiak et al. 2017; Sarkozy et al. 2021; Chapuy et al. 2018 | |
|
| 126 | -| [HIST1H1C](HIST1H1C) | 1, aSHM | Morin et al. 2011; Panea et al. 2019 | |
|
| 127 | -| [HIST1H1D](HIST1H1D) | 1, aSHM | Krysiak et al. 2017; Jallades et al. 2017; Morin et al. 2013 | |
|
| 128 | -| [HIST1H1E](HIST1H1E) | 1, aSHM | Morin et al. 2013; Reichel et al. 2015; Grande et al. 2019; Krysiak et al. 2017 | |
|
| 129 | -| [HIST1H2AC](HIST1H2AC) | 1, aSHM | Krysiak et al. 2017; Morin et al. 2013 | |
|
| 130 | -| [HIST1H2AM](HIST1H2AM) | 1, aSHM | Panea et al. 2019; Krysiak et al. 2017 | |
|
| 131 | -| [HIST1H2BC](HIST1H2BC) | 1, aSHM | Krysiak et al. 2017; Mottok et al. 2019; Reddy et al. 2017 | |
|
| 132 | -| [HIST1H2BK](HIST1H2BK) | 1, aSHM | Panea et al. 2019; Rossi et al. 2012 | |
|
| 133 | -| [HIST1H3B](HIST1H3B) | 1, aSHM | Zhang et al. 2013; Reichel et al. 2015 | |
|
| 134 | -| [HIST2H2BE](HIST2H2BE) | 1, aSHM | Schmitz et al. 2018 | |
|
| 135 | -| [HLA-A](HLA-A) | 1 | Desch et al. 2020 | |
|
| 136 | -| [HLA-B](HLA-B) | 1 | Wienand et al. 2019 | |
|
| 137 | -| [HLA-C](HLA-C) | 1 | Gomez et al. 2023 | |
|
| 138 | -| [HLA-DMB](HLA-DMB) | 1 | | |
|
| 139 | -| [HNRNPU](HNRNPU) | 1, aSHM | Panea et al. 2019; Reddy et al. 2017 | |
|
| 140 | -| [HVCN1](HVCN1) | 1 | Krysiak et al. 2017 | |
|
| 141 | -| [IKZF3](IKZF3) | 1 | Morin et al. 2013; Panea et al. 2019 | |
|
| 142 | -| [IL4R](IL4R) | 1, aSHM | Duns et al. 2021; Viganò et al. 2018 | |
|
| 143 | -| [IRF4](IRF4) | 1, aSHM | Mottok et al. 2019; Morin et al. 2011 | |
|
| 144 | -| [IRF8](IRF8) | 1, aSHM | Panea et al. 2019; Morin et al. 2011; Mottok et al. 2019 | |
|
| 145 | -| [ITPKB](ITPKB) | 1, aSHM | Schmitz et al. 2018; Reichel et al. 2015 | |
|
| 146 | -| [KLF2](KLF2) | 1, aSHM | Desch et al. 2020; Jallades et al. 2017; Laura Pasqualucci, Trifonov, et al. 2011 | |
|
| 147 | -| [KLHL14](KLHL14) | 1 | Zhang et al. 2013 | |
|
| 148 | -| [KLHL6](KLHL6) | 1, aSHM | Panea et al. 2019; Ganapathi et al. 2016; Morin et al. 2011 | |
|
| 149 | -| [KMT2C](KMT2C) | 1 | Zhang et al. 2014; Sarkozy et al. 2021; Zhou et al. 2019; Zhang et al. 2013 | |
|
| 150 | -| [KMT2D](KMT2D) | 1 | Desch et al. 2020; Rossi et al. 2012; Grande et al. 2019; Morin et al. 2011; Beà et al. 2013 | |
|
| 151 | -| [KRAS](KRAS) | 1 | Lohr et al. 2012 | |
|
| 152 | -| [LCOR](LCOR) | 1 | Arthur et al. 2018 | |
|
| 153 | -| [LTB](LTB) | 1, aSHM | Desch et al. 2020; Chapuy et al. 2018; Panea et al. 2019 | |
|
| 154 | -| [MEF2B](MEF2B) | 1, aSHM | Beà et al. 2013; Morin et al. 2011 | |
|
| 155 | -| [MEF2C](MEF2C) | 1, aSHM | Arthur et al. 2018 | |
|
| 156 | -| [MGA](MGA) | 1 | Jallades et al. 2017; Zhang et al. 2013 | |
|
| 157 | -| [MPEG1](MPEG1) | 1 | Morin et al. 2013 | |
|
| 158 | -| [MS4A1](MS4A1) | 1, aSHM | Rushton et al. 2020; Mottok et al. 2019 | |
|
| 159 | -| [MTOR](MTOR) | 1 | Zhang et al. 2013; Panea et al. 2019 | |
|
| 160 | -| [MYC](MYC) | 1, aSHM | L. Pasqualucci et al. 2001; Jallades et al. 2017; Duns et al. 2021; Johnston and Carroll 1992 | |
|
| 161 | -| [MYD88](MYD88) | 1 | Yan et al. 2012; Ngo et al. 2011 | |
|
| 162 | -| [NFKBIA](NFKBIA) | 1 | Lake et al. 2009; Wienand et al. 2019; Russler-Germain et al. 2023 | |
|
| 163 | -| [NFKBIE](NFKBIE) | 1 | Morin et al. 2016; Pararajalingam et al. 2020; Mansouri et al. 2016 | |
|
| 164 | -| [NFKBIZ](NFKBIZ) | 1, noncoding | Morin et al. 2016 | |
|
| 165 | -| [NOL9](NOL9) | 1, aSHM | Spina et al. 2016; Schmitz et al. 2018 | |
|
| 166 | -| [NOTCH1](NOTCH1) | 1 | Beà et al. 2013; Laura Pasqualucci, Trifonov, et al. 2011; Love et al. 2012; Rossi et al. 2012 | |
|
| 167 | -| [NOTCH2](NOTCH2) | 1 | Rossi et al. 2012; Panea et al. 2019; Beà et al. 2013; Trøen et al. 2008 | |
|
| 168 | -| [OSBPL10](OSBPL10) | 1, aSHM | Arthur et al. 2018 | |
|
| 169 | -| [P2RY8](P2RY8) | 1 | Muppidi et al. 2014; Lohr et al. 2012 | |
|
| 170 | -| [PIM1](PIM1) | 1, aSHM | L. Pasqualucci et al. 2001; Duns et al. 2021; Burkhardt et al. 2022 | |
|
| 171 | -| [PIM2](PIM2) | 1, aSHM | Arthur et al. 2018; Reichel et al. 2015 | |
|
| 172 | -| [POU2AF1](POU2AF1) | 1, aSHM | Krysiak et al. 2017 | |
|
| 173 | -| [POU2F2](POU2F2) | 1 | Krysiak et al. 2017; Zhang et al. 2013 | |
|
| 174 | -| [PRDM1](PRDM1) | 1 | Laura Pasqualucci et al. 2006 | |
|
| 175 | -| [PTEN](PTEN) | 1 | Love et al. 2012 | |
|
| 176 | -| [PTPRD](PTPRD) | 1 | Spina et al. 2016 | |
|
| 177 | -| [RB1](RB1) | 1 | Zhang et al. 2014; Morin et al. 2013 | |
|
| 178 | -| [RFX7](RFX7) | 1 | Grande et al. 2019 | |
|
| 179 | -| [RHOA](RHOA) | 1 | Richter et al. 2012 | |
|
| 180 | -| [RRAGC](RRAGC) | 1 | Okosun et al. 2016 | |
|
| 181 | -| [S1PR2](S1PR2) | 1, aSHM | Morin et al. 2011; Muppidi et al. 2014 | |
|
| 182 | -| [SETD1B](SETD1B) | 1 | Reddy et al. 2017 | |
|
| 183 | -| [SF3B1](SF3B1) | 1 | Love et al. 2012 | |
|
| 184 | -| [SGK1](SGK1) | 1, aSHM | Duns et al. 2021; Morin et al. 2011 | |
|
| 185 | -| [SIN3A](SIN3A) | 1 | Grande et al. 2019; Rossi et al. 2012 | |
|
| 186 | -| [SMARCA4](SMARCA4) | 1 | Zhang et al. 2013; Nadeu et al. 2020; Krysiak et al. 2017; Richter et al. 2012 | |
|
| 187 | -| [SOCS1](SOCS1) | 1, aSHM | Weniger et al. 2006; Morin et al. 2011 | |
|
| 188 | -| [SPEN](SPEN) | 1 | Sarkozy et al. 2021; Rossi et al. 2012 | |
|
| 189 | -| [STAT3](STAT3) | 1 | Ohgami et al. 2014 | |
|
| 190 | -| [STAT6](STAT6) | 1 | Yildiz et al. 2015; Ritz et al. 2009 | |
|
| 191 | -| [TAF1](TAF1) | 1 | Spina et al. 2016; Morin et al. 2013 | |
|
| 192 | -| [TBL1XR1](TBL1XR1) | 1 | Rossi et al. 2012; Mareschal et al. 2016 | |
|
| 193 | -| [TET2](TET2) | 1 | Albuquerque et al. 2017; Panea et al. 2019 | |
|
| 194 | -| [TMEM30A](TMEM30A) | 1 | Morin et al. 2011 | |
|
| 195 | -| [TMSB4X](TMSB4X) | 1, aSHM | Albuquerque et al. 2017 | |
|
| 196 | -| [TNFAIP3](TNFAIP3) | 1 | Schmitz et al. 2009; Rossi et al. 2011; Compagno et al. 2009 | |
|
| 197 | -| [TNFRSF14](TNFRSF14) | 1 | Cheung et al. 2010; Spina et al. 2016 | |
|
| 198 | -| [TOX](TOX) | 1 | Reddy et al. 2017 | |
|
| 199 | -| [TP53](TP53) | 1 | Wilda et al. 2004; Rossi et al. 2012; Tiacci et al. 2018; Beà et al. 2013; Morin et al. 2011 | |
|
| 200 | -| [TRRAP](TRRAP) | 1 | Rossi et al. 2012; Parry et al. 2013 | |
|
| 201 | -| [UBE2A](UBE2A) | 1 | Reddy et al. 2017; Reichel et al. 2015 | |
|
| 202 | -| [UNC5C](UNC5C) | 1 | | |
|
| 203 | -| [USP7](USP7) | 1 | Grande et al. 2019 | |
|
| 204 | -| [VPS13B](VPS13B) | 1 | | |
|
| 205 | -| [WEE1](WEE1) | 1 | Schmitz et al. 2018; Reichel et al. 2015 | |
|
| 206 | -| [XPO1](XPO1) | 1 | Jardin et al. 2016; Mareschal et al. 2016 | |
|
| 207 | -| [ZC3H12A](ZC3H12A) | 1 | Arthur et al. 2018 | |
|
| 208 | -| [ZFP36L1](ZFP36L1) | 1, aSHM | Morin et al. 2011; Reichel et al. 2015; Panea et al. 2019 | |
|
| 209 | -| [ZNF292](ZNF292) | 1 | Zhang et al. 2013 | |
|
| 210 | -| [ZNF608](ZNF608) | 1, aSHM | Zhang et al. 2013; Krysiak et al. 2017 | |
|
| 16 | +|Gene|Tier| Relevant references| |
|
| 17 | +|:-:|:-:|:-| |
|
| 18 | +|[ACTB](ACTB)|1, aSHM|[@lohrDiscoveryPrioritizationSomatic2012a; @wienandGenomicAnalysesFlowsorted2019b]| |
|
| 19 | +|[ACTG1](ACTG1)|1, aSHM|[@deschGenotypingCirculatingTumor2020; @spinaGeneticsNodalMarginal2016b; @hubschmannMutationalMechanismsShaping2021b]| |
|
| 20 | +|[ARID1A](ARID1A)|1|[@zhangGeneticHeterogeneityDiffuse2013; @rossiCodingGenomeSplenic2012c; @krysiakRecurrentSomaticMutations2017b; @wienandGenomicAnalysesFlowsorted2019b; @loveGeneticLandscapeMutations2012]| |
|
| 21 | +|[ATM](ATM)|1|[@beaLandscapeSomaticMutations2013; @braggioGenomicAnalysisMarginal2012; @reddyGeneticFunctionalDrivers2017]| |
|
| 22 | +|[B2M](B2M)|1|[@morinFrequentMutationHistonemodifying2011; @reichelFlowSortingExome2015a; @pararajalingamCodingNoncodingDrivers2020]| |
|
| 23 | +|[BCL10](BCL10)|1|[@russler-germainMutationsAssociatedProgression2023b; @morinFrequentMutationHistonemodifying2011; @spinaGeneticsNodalMarginal2016b]| |
|
| 24 | +|[BCL2](BCL2)|1, aSHM|[@sarkozyMutationalLandscapeGray2021a; @morinFrequentMutationHistonemodifying2011; @tanakaFrequentIncidenceSomatic1992; @burkhardtClinicalRelevanceMolecular2022b]| |
|
| 25 | +|[BCL6](BCL6)|1, aSHM|[@morinFrequentMutationHistonemodifying2011; @loveGeneticLandscapeMutations2012]| |
|
| 26 | +|[BCL7A](BCL7A)|1, aSHM|[@arthurGenomewideDiscoverySomatic2018; @krysiakRecurrentSomaticMutations2017b; @reichelFlowSortingExome2015a; @grandeGenomewideDiscoverySomatic2019]| |
|
| 27 | +|[BIRC6](BIRC6)|1|[@sarkozyMutationalLandscapeGray2021a; @reddyGeneticFunctionalDrivers2017]| |
|
| 28 | +|[BRAF](BRAF)|1|[@loveGeneticLandscapeMutations2012; @tiacciBRAFMutationsHairycell2011a]| |
|
| 29 | +|[BTG1](BTG1)|1, aSHM|[@burkhardtClinicalRelevanceMolecular2022b; @morinFrequentMutationHistonemodifying2011; @sarkozyMutationalLandscapeGray2021a]| |
|
| 30 | +|[BTG2](BTG2)|1, aSHM|[@loveGeneticLandscapeMutations2012; @morinFrequentMutationHistonemodifying2011]| |
|
| 31 | +|[BTK](BTK)|1|[@krysiakRecurrentSomaticMutations2017b; @albuquerqueEnhancingKnowledgeDiscovery2017a]| |
|
| 32 | +|[CARD11](CARD11)|1|[@morinFrequentMutationHistonemodifying2011; @wuGeneticHeterogeneityPrimary2016; @paneaWholeGenomeLandscape2019; @lenzOncogenicCARD11Mutations2008; @yanBCRTLRSignaling2012a]| |
|
| 33 | +|[CCND3](CCND3)|1|[@jalladesExomeSequencingIdentifies2017; @morinFrequentMutationHistonemodifying2011; @richterRecurrentMutationID32012a; @deschGenotypingCirculatingTumor2020]| |
|
| 34 | +|[CD58](CD58)|1|[@morinFrequentMutationHistonemodifying2011; @schneiderAlterationsCD58Gene2015a]| |
|
| 35 | +|[CD70](CD70)|1|[@russler-germainMutationsAssociatedProgression2023b; @morinFrequentMutationHistonemodifying2011]| |
|
| 36 | +|[CD79B](CD79B)|1|[@paneaWholeGenomeLandscape2019; @morinFrequentMutationHistonemodifying2011]| |
|
| 37 | +|[CD83](CD83)|1, aSHM|[@dunsCharacterizationDLBCLPMBL2021b; @paneaWholeGenomeLandscape2019; @russler-germainMutationsAssociatedProgression2023b; @morinMutationalStructuralAnalysis2013]| |
|
| 38 | +|[CDKN2A](CDKN2A)|1|[@morinMutationalStructuralAnalysis2013; @spinaGeneticsNodalMarginal2016b; @grandeGenomewideDiscoverySomatic2019]| |
|
| 39 | +|[CIITA](CIITA)|1, aSHM|[@mottokGenomicAlterationsCIITA2015b; @morinFrequentMutationHistonemodifying2011]| |
|
| 40 | +|[CREBBP](CREBBP)|1|[@dunsCharacterizationDLBCLPMBL2021b; @parryWholeExomeSequencing2013; @loveGeneticLandscapeMutations2012; @pasqualucciInactivatingMutationsAcetyltransferase2011a]| |
|
| 41 | +|[CXCR4](CXCR4)|1, aSHM|[@krysiakRecurrentSomaticMutations2017b; @paneaWholeGenomeLandscape2019; @khodabakhshiRecurrentTargetsAberrant2012]| |
|
| 42 | +|[CXCR5](CXCR5)|1|[@schmitzGeneticsPathogenesisDiffuse2018a; @mottokIntegrativeGenomicAnalysis2019b]| |
|
| 43 | +|[DDX3X](DDX3X)|1|[@schmitzBurkittLymphomaPathogenesis2012; @schmitzGeneticsPathogenesisDiffuse2018a; @mottokIntegrativeGenomicAnalysis2019b]| |
|
| 44 | +|[DTX1](DTX1)|1, aSHM|[@schmitzGeneticsPathogenesisDiffuse2018a; @gomezUltraDeepSequencingReveals2023; @rossiCodingGenomeSplenic2012c; @paneaWholeGenomeLandscape2019]| |
|
| 45 | +|[DUSP2](DUSP2)|1, aSHM|[@dunsCharacterizationDLBCLPMBL2021b; @morinMutationalStructuralAnalysis2013]| |
|
| 46 | +|[EBF1](EBF1)|1, aSHM|[@reichelFlowSortingExome2015a; @bohleRoleEarlyBcell2013; @thomasGeneticSubgroupsInform2023]| |
|
| 47 | +|[EEF1A1](EEF1A1)|1|[@hubschmannMutationalMechanismsShaping2021b; @reichelFlowSortingExome2015a]| |
|
| 48 | +|[EP300](EP300)|1|[@rossiCodingGenomeSplenic2012c; @paneaWholeGenomeLandscape2019; @pasqualucciInactivatingMutationsAcetyltransferase2011a]| |
|
| 49 | +|[ETS1](ETS1)|1, aSHM|[@paneaWholeGenomeLandscape2019; @morinFrequentMutationHistonemodifying2011]| |
|
| 50 | +|[ETV6](ETV6)|1, aSHM|[@arthurGenomewideDiscoverySomatic2018]| |
|
| 51 | +|[EZH2](EZH2)|1|[@loveGeneticLandscapeMutations2012; @morinSomaticMutationsAltering2010a; @mottokIntegrativeGenomicAnalysis2019b]| |
|
| 52 | +|[FAS](FAS)|1|[@spinaGeneticsNodalMarginal2016b; @schollMutationsRegionFAS2007]| |
|
| 53 | +|[FBXO11](FBXO11)|1|[@parryWholeExomeSequencing2013; @hubschmannMutationalMechanismsShaping2021b; @richterRecurrentMutationID32012a]| |
|
| 54 | +|[FBXW7](FBXW7)|1|[@zhangGeneticHeterogeneityDiffuse2013]| |
|
| 55 | +|[FOXO1](FOXO1)|1|[@schmitzBurkittLymphomaPathogenesis2012; @dunsCharacterizationDLBCLPMBL2021b; @morinFrequentMutationHistonemodifying2011]| |
|
| 56 | +|[GNA13](GNA13)|1|[@morinFrequentMutationHistonemodifying2011; @loveGeneticLandscapeMutations2012; @reichelFlowSortingExome2015a]| |
|
| 57 | +|[GNAI2](GNAI2)|1|[@morinMutationalStructuralAnalysis2013; @grandeGenomewideDiscoverySomatic2019]| |
|
| 58 | +|[GRB2](GRB2)|1|[@paneaWholeGenomeLandscape2019; @pasqualucciAnalysisCodingGenome2011]| |
|
| 59 | +|[GRHPR](GRHPR)|1, aSHM|[@arthurGenomewideDiscoverySomatic2018]| |
|
| 60 | +|[HIST1H1B](HIST1H1B)|1, aSHM|[@chapuyMolecularSubtypesDiffuse2018b; @sarkozyMutationalLandscapeGray2021a; @krysiakRecurrentSomaticMutations2017b]| |
|
| 61 | +|[HIST1H1C](HIST1H1C)|1, aSHM|[@morinFrequentMutationHistonemodifying2011; @paneaWholeGenomeLandscape2019]| |
|
| 62 | +|[HIST1H1D](HIST1H1D)|1, aSHM|[@krysiakRecurrentSomaticMutations2017b; @jalladesExomeSequencingIdentifies2017; @morinMutationalStructuralAnalysis2013]| |
|
| 63 | +|[HIST1H1E](HIST1H1E)|1, aSHM|[@grandeGenomewideDiscoverySomatic2019; @morinMutationalStructuralAnalysis2013; @reichelFlowSortingExome2015a; @krysiakRecurrentSomaticMutations2017b]| |
|
| 64 | +|[HIST1H2AC](HIST1H2AC)|1, aSHM|[@morinMutationalStructuralAnalysis2013; @krysiakRecurrentSomaticMutations2017b]| |
|
| 65 | +|[HIST1H2AM](HIST1H2AM)|1, aSHM|[@paneaWholeGenomeLandscape2019; @krysiakRecurrentSomaticMutations2017b]| |
|
| 66 | +|[HIST1H2BC](HIST1H2BC)|1, aSHM|[@mottokIntegrativeGenomicAnalysis2019b; @reddyGeneticFunctionalDrivers2017; @krysiakRecurrentSomaticMutations2017b]| |
|
| 67 | +|[HIST1H2BK](HIST1H2BK)|1, aSHM|[@rossiCodingGenomeSplenic2012c; @paneaWholeGenomeLandscape2019]| |
|
| 68 | +|[HIST1H3B](HIST1H3B)|1, aSHM|[@reichelFlowSortingExome2015a; @zhangGeneticHeterogeneityDiffuse2013]| |
|
| 69 | +|[HIST2H2BE](HIST2H2BE)|1, aSHM|[@schmitzGeneticsPathogenesisDiffuse2018a]| |
|
| 70 | +|[HLA-A](HLA-A)|1|[@deschGenotypingCirculatingTumor2020]| |
|
| 71 | +|[HLA-B](HLA-B)|1|[@wienandGenomicAnalysesFlowsorted2019b]| |
|
| 72 | +|[HLA-C](HLA-C)|1|[@gomezUltraDeepSequencingReveals2023]| |
|
| 73 | +|[HLA-DMB](HLA-DMB)|1|| |
|
| 74 | +|[HNRNPU](HNRNPU)|1, aSHM|[@reddyGeneticFunctionalDrivers2017; @paneaWholeGenomeLandscape2019]| |
|
| 75 | +|[HVCN1](HVCN1)|1|[@krysiakRecurrentSomaticMutations2017b]| |
|
| 76 | +|[IKZF3](IKZF3)|1|[@morinMutationalStructuralAnalysis2013; @paneaWholeGenomeLandscape2019]| |
|
| 77 | +|[IL4R](IL4R)|1, aSHM|[@dunsCharacterizationDLBCLPMBL2021b; @viganoSomaticIL4RMutations2018b]| |
|
| 78 | +|[IRF4](IRF4)|1, aSHM|[@mottokIntegrativeGenomicAnalysis2019b; @morinFrequentMutationHistonemodifying2011]| |
|
| 79 | +|[IRF8](IRF8)|1, aSHM|[@paneaWholeGenomeLandscape2019; @mottokIntegrativeGenomicAnalysis2019b; @morinFrequentMutationHistonemodifying2011]| |
|
| 80 | +|[ITPKB](ITPKB)|1, aSHM|[@schmitzGeneticsPathogenesisDiffuse2018a; @reichelFlowSortingExome2015a]| |
|
| 81 | +|[KLF2](KLF2)|1, aSHM|[@jalladesExomeSequencingIdentifies2017; @deschGenotypingCirculatingTumor2020; @pasqualucciAnalysisCodingGenome2011]| |
|
| 82 | +|[KLHL14](KLHL14)|1|[@zhangGeneticHeterogeneityDiffuse2013]| |
|
| 83 | +|[KLHL6](KLHL6)|1, aSHM|[@morinFrequentMutationHistonemodifying2011; @paneaWholeGenomeLandscape2019; @ganapathiGeneticLandscapeDural2016]| |
|
| 84 | +|[KMT2C](KMT2C)|1|[@zhangGeneticHeterogeneityDiffuse2013; @sarkozyMutationalLandscapeGray2021a; @zhangGenomicLandscapeMantle2014; @zhouSporadicEndemicBurkitt2019]| |
|
| 85 | +|[KMT2D](KMT2D)|1|[@grandeGenomewideDiscoverySomatic2019; @beaLandscapeSomaticMutations2013; @deschGenotypingCirculatingTumor2020; @rossiCodingGenomeSplenic2012c; @morinFrequentMutationHistonemodifying2011]| |
|
| 86 | +|[KRAS](KRAS)|1|[@lohrDiscoveryPrioritizationSomatic2012a]| |
|
| 87 | +|[LCOR](LCOR)|1|[@arthurGenomewideDiscoverySomatic2018]| |
|
| 88 | +|[LTB](LTB)|1, aSHM|[@paneaWholeGenomeLandscape2019; @chapuyMolecularSubtypesDiffuse2018b; @deschGenotypingCirculatingTumor2020]| |
|
| 89 | +|[MEF2B](MEF2B)|1, aSHM|[@morinFrequentMutationHistonemodifying2011; @beaLandscapeSomaticMutations2013]| |
|
| 90 | +|[MEF2C](MEF2C)|1, aSHM|[@arthurGenomewideDiscoverySomatic2018]| |
|
| 91 | +|[MGA](MGA)|1|[@jalladesExomeSequencingIdentifies2017; @zhangGeneticHeterogeneityDiffuse2013]| |
|
| 92 | +|[MPEG1](MPEG1)|1|[@morinMutationalStructuralAnalysis2013]| |
|
| 93 | +|[MS4A1](MS4A1)|1, aSHM|[@mottokIntegrativeGenomicAnalysis2019b; @rushtonGeneticEvolutionaryPatterns2020]| |
|
| 94 | +|[MTOR](MTOR)|1|[@paneaWholeGenomeLandscape2019; @zhangGeneticHeterogeneityDiffuse2013]| |
|
| 95 | +|[MYC](MYC)|1, aSHM|[@jalladesExomeSequencingIdentifies2017; @johnstonCmycHypermutationBurkitt1992; @dunsCharacterizationDLBCLPMBL2021b; @pasqualucciHypermutationMultipleProtooncogenes2001a]| |
|
| 96 | +|[MYD88](MYD88)|1|[@ngoOncogenicallyActiveMYD882011a; @yanBCRTLRSignaling2012a]| |
|
| 97 | +|[NFKBIA](NFKBIA)|1|[@wienandGenomicAnalysesFlowsorted2019b; @lakeMutationsNFKBIAEncoding2009; @russler-germainMutationsAssociatedProgression2023b]| |
|
| 98 | +|[NFKBIE](NFKBIE)|1|[@mansouriFrequentNFKBIEDeletions2016; @morinGeneticLandscapesRelapsed2016; @pararajalingamCodingNoncodingDrivers2020]| |
|
| 99 | +|[NFKBIZ](NFKBIZ)|1, noncoding|[@morinGeneticLandscapesRelapsed2016]| |
|
| 100 | +|[NOL9](NOL9)|1, aSHM|[@spinaGeneticsNodalMarginal2016b; @schmitzGeneticsPathogenesisDiffuse2018a]| |
|
| 101 | +|[NOTCH1](NOTCH1)|1|[@rossiCodingGenomeSplenic2012c; @loveGeneticLandscapeMutations2012; @beaLandscapeSomaticMutations2013; @pasqualucciAnalysisCodingGenome2011]| |
|
| 102 | +|[NOTCH2](NOTCH2)|1|[@troenNOTCH2MutationsMarginal2008; @rossiCodingGenomeSplenic2012c; @paneaWholeGenomeLandscape2019; @beaLandscapeSomaticMutations2013]| |
|
| 103 | +|[OSBPL10](OSBPL10)|1, aSHM|[@arthurGenomewideDiscoverySomatic2018]| |
|
| 104 | +|[P2RY8](P2RY8)|1|[@lohrDiscoveryPrioritizationSomatic2012a; @muppidiLossSignalingGa132014b]| |
|
| 105 | +|[PIM1](PIM1)|1, aSHM|[@dunsCharacterizationDLBCLPMBL2021b; @pasqualucciHypermutationMultipleProtooncogenes2001a; @burkhardtClinicalRelevanceMolecular2022b]| |
|
| 106 | +|[PIM2](PIM2)|1, aSHM|[@arthurGenomewideDiscoverySomatic2018; @reichelFlowSortingExome2015a]| |
|
| 107 | +|[POU2AF1](POU2AF1)|1, aSHM|[@krysiakRecurrentSomaticMutations2017b]| |
|
| 108 | +|[POU2F2](POU2F2)|1|[@zhangGeneticHeterogeneityDiffuse2013; @krysiakRecurrentSomaticMutations2017b]| |
|
| 109 | +|[PRDM1](PRDM1)|1|[@pasqualucciInactivationPRDM1BLIMP12006a]| |
|
| 110 | +|[PTEN](PTEN)|1|[@loveGeneticLandscapeMutations2012]| |
|
| 111 | +|[PTPRD](PTPRD)|1|[@spinaGeneticsNodalMarginal2016b]| |
|
| 112 | +|[RB1](RB1)|1|[@zhangGenomicLandscapeMantle2014; @morinMutationalStructuralAnalysis2013]| |
|
| 113 | +|[RFX7](RFX7)|1|[@grandeGenomewideDiscoverySomatic2019]| |
|
| 114 | +|[RHOA](RHOA)|1|[@richterRecurrentMutationID32012a]| |
|
| 115 | +|[RRAGC](RRAGC)|1|[@okosunRecurrentMTORC1activatingRRAGC2016a]| |
|
| 116 | +|[S1PR2](S1PR2)|1, aSHM|[@morinFrequentMutationHistonemodifying2011; @muppidiLossSignalingGa132014b]| |
|
| 117 | +|[SETD1B](SETD1B)|1|[@reddyGeneticFunctionalDrivers2017]| |
|
| 118 | +|[SF3B1](SF3B1)|1|[@loveGeneticLandscapeMutations2012]| |
|
| 119 | +|[SGK1](SGK1)|1, aSHM|[@dunsCharacterizationDLBCLPMBL2021b; @morinFrequentMutationHistonemodifying2011]| |
|
| 120 | +|[SIN3A](SIN3A)|1|[@grandeGenomewideDiscoverySomatic2019; @rossiCodingGenomeSplenic2012c]| |
|
| 121 | +|[SMARCA4](SMARCA4)|1|[@zhangGeneticHeterogeneityDiffuse2013; @krysiakRecurrentSomaticMutations2017b; @nadeuGenomicEpigenomicInsights2020b; @richterRecurrentMutationID32012a]| |
|
| 122 | +|[SOCS1](SOCS1)|1, aSHM|[@morinFrequentMutationHistonemodifying2011; @wenigerMutationsTumorSuppressor2006a]| |
|
| 123 | +|[SPEN](SPEN)|1|[@rossiCodingGenomeSplenic2012c; @sarkozyMutationalLandscapeGray2021a]| |
|
| 124 | +|[STAT3](STAT3)|1|[@ohgamiSTAT3MutationsAre2014]| |
|
| 125 | +|[STAT6](STAT6)|1|[@yildizActivatingSTAT6Mutations2015c; @ritzRecurrentMutationsSTAT62009a]| |
|
| 126 | +|[TAF1](TAF1)|1|[@spinaGeneticsNodalMarginal2016b; @morinMutationalStructuralAnalysis2013]| |
|
| 127 | +|[TBL1XR1](TBL1XR1)|1|[@rossiCodingGenomeSplenic2012c; @mareschalWholeExomeSequencing2016]| |
|
| 128 | +|[TET2](TET2)|1|[@paneaWholeGenomeLandscape2019; @albuquerqueEnhancingKnowledgeDiscovery2017a]| |
|
| 129 | +|[TMEM30A](TMEM30A)|1|[@morinFrequentMutationHistonemodifying2011]| |
|
| 130 | +|[TMSB4X](TMSB4X)|1, aSHM|[@albuquerqueEnhancingKnowledgeDiscovery2017a]| |
|
| 131 | +|[TNFAIP3](TNFAIP3)|1|[@compagnoMutationsMultipleGenes2009a; @rossiAlterationBIRC3Multiple2011a; @schmitzTNFAIP3A20Tumor2009a]| |
|
| 132 | +|[TNFRSF14](TNFRSF14)|1|[@cheungAcquiredTNFRSF14Mutations2010a; @spinaGeneticsNodalMarginal2016b]| |
|
| 133 | +|[TOX](TOX)|1|[@reddyGeneticFunctionalDrivers2017]| |
|
| 134 | +|[TP53](TP53)|1|[@wildaInactivationARFMDM2p53Pathway2004; @beaLandscapeSomaticMutations2013; @tiacciPervasiveMutationsJAKSTAT2018b; @morinFrequentMutationHistonemodifying2011; @rossiCodingGenomeSplenic2012c]| |
|
| 135 | +|[TRRAP](TRRAP)|1|[@rossiCodingGenomeSplenic2012c; @parryWholeExomeSequencing2013]| |
|
| 136 | +|[UBE2A](UBE2A)|1|[@reichelFlowSortingExome2015a; @reddyGeneticFunctionalDrivers2017]| |
|
| 137 | +|[UNC5C](UNC5C)|1|| |
|
| 138 | +|[USP7](USP7)|1|[@grandeGenomewideDiscoverySomatic2019]| |
|
| 139 | +|[VPS13B](VPS13B)|1|| |
|
| 140 | +|[WEE1](WEE1)|1|[@reichelFlowSortingExome2015a; @schmitzGeneticsPathogenesisDiffuse2018a]| |
|
| 141 | +|[XPO1](XPO1)|1|[@mareschalWholeExomeSequencing2016; @jardinRecurrentMutationsExportin2016a]| |
|
| 142 | +|[ZC3H12A](ZC3H12A)|1|[@arthurGenomewideDiscoverySomatic2018]| |
|
| 143 | +|[ZFP36L1](ZFP36L1)|1, aSHM|[@reichelFlowSortingExome2015a; @paneaWholeGenomeLandscape2019; @morinFrequentMutationHistonemodifying2011]| |
|
| 144 | +|[ZNF292](ZNF292)|1|[@zhangGeneticHeterogeneityDiffuse2013]| |
|
| 145 | +|[ZNF608](ZNF608)|1, aSHM|[@krysiakRecurrentSomaticMutations2017b; @zhangGeneticHeterogeneityDiffuse2013]| |
|
| 211 | 146 | |
| 212 | 147 | ## Tier 2 DLBCL genes |
| 213 | 148 | |
| 214 | 149 | ### *198 total* |
| 215 | 150 | |
| 216 | -| Gene | Tier | Relevant references | |
|
| 217 | -|:----------------------:|:------------:|:--------------------------------------------------------------------------------| |
|
| 218 | -| [ABI3BP](ABI3BP) | 2 | Morin et al. 2013 | |
|
| 219 | -| [ADAMTS1](ADAMTS1) | 2 | Hübschmann et al. 2021 | |
|
| 220 | -| [AICDA](AICDA) | 2, aSHM | Arthur et al. 2018 | |
|
| 221 | -| [ANKRD12](ANKRD12) | 2 | Hübschmann et al. 2021 | |
|
| 222 | -| [ANKRD17](ANKRD17) | 2 | Reddy et al. 2017 | |
|
| 223 | -| [ARID1B](ARID1B) | 2 | Reddy et al. 2017 | |
|
| 224 | -| [ARID5B](ARID5B) | 2 | Reddy et al. 2017; Gomez et al. 2023 | |
|
| 225 | -| [ATR](ATR) | 2 | Reddy et al. 2017 | |
|
| 226 | -| [BCL11A](BCL11A) | 2, aSHM | | |
|
| 227 | -| [BCOR](BCOR) | 2 | Nadeu et al. 2020; Jallades et al. 2017 | |
|
| 228 | -| [BCR](BCR) | 2, aSHM | | |
|
| 229 | -| [BIRC3](BIRC3) | 2, aSHM | Duns et al. 2021; Rossi et al. 2011; Arthur et al. 2018; Beà et al. 2013 | |
|
| 230 | -| [BLK](BLK) | 2, aSHM | | |
|
| 231 | -| [BRINP3](BRINP3) | 2 | Reddy et al. 2017 | |
|
| 232 | -| [BTBD3](BTBD3) | 2 | Reddy et al. 2017 | |
|
| 233 | -| [CADPS2](CADPS2) | 2 | Hübschmann et al. 2021 | |
|
| 234 | -| [CASP8](CASP8) | 2 | Reddy et al. 2017 | |
|
| 235 | -| [CBLB](CBLB) | 2 | Reddy et al. 2017 | |
|
| 236 | -| [CCL4](CCL4) | 2 | Chapuy et al. 2018 | |
|
| 237 | -| [CD22](CD22) | 2 | Reddy et al. 2017 | |
|
| 238 | -| [CD274](CD274) | 2 | Morin et al. 2011 | |
|
| 239 | -| [CD36](CD36) | 2 | Laura Pasqualucci, Trifonov, et al. 2011 | |
|
| 240 | -| [CD44](CD44) | 2, aSHM | Arthur et al. 2018 | |
|
| 241 | -| [CD74](CD74) | 2, aSHM | Arthur et al. 2018 | |
|
| 242 | -| [CDC73](CDC73) | 2 | Reddy et al. 2017; Love et al. 2012 | |
|
| 243 | -| [CDH9](CDH9) | 2 | Morin et al. 2013 | |
|
| 244 | -| [CHD1](CHD1) | 2 | Reddy et al. 2017 | |
|
| 245 | -| [CHD8](CHD8) | 2 | Grande et al. 2019; Reddy et al. 2017 | |
|
| 246 | -| [CHST2](CHST2) | 2 | Reddy et al. 2017 | |
|
| 247 | -| [CNOT2](CNOT2) | 2 | Hübschmann et al. 2021 | |
|
| 248 | -| [CNTNAP5](CNTNAP5) | 2 | Morin et al. 2013 | |
|
| 249 | -| [COQ7](COQ7) | 2 | Chapuy et al. 2018 | |
|
| 250 | -| [CRIP1](CRIP1) | 2 | Chapuy et al. 2018 | |
|
| 251 | -| [DAZAP1](DAZAP1) | 2 | Pararajalingam et al. 2020 | |
|
| 252 | -| [DCAF6](DCAF6) | 2 | Reddy et al. 2017 | |
|
| 253 | -| [DDX10](DDX10) | 2 | Reddy et al. 2017 | |
|
| 254 | -| [DHX16](DHX16) | 2 | Hübschmann et al. 2021 | |
|
| 255 | -| [DICER1](DICER1) | 2 | Reddy et al. 2017 | |
|
| 256 | -| [DNAH5](DNAH5) | 2 | Morin et al. 2013; Jallades et al. 2017 | |
|
| 257 | -| [DNM2](DNM2) | 2 | Hübschmann et al. 2021 | |
|
| 258 | -| [DNMT3A](DNMT3A) | 2 | Reddy et al. 2017 | |
|
| 259 | -| [DOCK1](DOCK1) | 2 | Chapuy et al. 2018 | |
|
| 260 | -| [DSG4](DSG4) | 2 | Morin et al. 2013 | |
|
| 261 | -| [EIF2AK3](EIF2AK3) | 2, aSHM | | |
|
| 262 | -| [EZR](EZR) | 2, aSHM | Desch et al. 2020 | |
|
| 263 | -| [FAM102A](FAM102A) | 2, aSHM | | |
|
| 264 | -| [FAM38B](FAM38B) | 2 | Morin et al. 2013 | |
|
| 265 | -| [FANK1](FANK1) | 2, aSHM | | |
|
| 266 | -| [FAT4](FAT4) | 2 | Parry et al. 2013; Morin et al. 2013; Zhang et al. 2014 | |
|
| 267 | -| [FCRL3](FCRL3) | 2, aSHM | | |
|
| 268 | -| [FNBP1](FNBP1) | 2, aSHM | | |
|
| 269 | -| [FNDC1](FNDC1) | 2 | Morin et al. 2013 | |
|
| 270 | -| [FOXC1](FOXC1) | 2 | Schmitz et al. 2018 | |
|
| 271 | -| [FOXP1](FOXP1) | 2, aSHM | Reddy et al. 2017 | |
|
| 272 | -| [FUBP1](FUBP1) | 2 | Reddy et al. 2017 | |
|
| 273 | -| [FUT5](FUT5) | 2 | Chapuy et al. 2018 | |
|
| 274 | -| [GABRA2](GABRA2) | 2 | Chapuy et al. 2018 | |
|
| 275 | -| [GAK](GAK) | 2 | Hübschmann et al. 2021 | |
|
| 276 | -| [GNAS](GNAS) | 2 | Reddy et al. 2017 | |
|
| 277 | -| [GOLGA5](GOLGA5) | 2 | Reddy et al. 2017 | |
|
| 278 | -| [GPC5](GPC5) | 2 | Schmitz et al. 2018 | |
|
| 279 | -| [GSG2](GSG2) | 2 | Schmitz et al. 2018 | |
|
| 280 | -| [HDAC7](HDAC7) | 2 | Morin et al. 2013 | |
|
| 281 | -| [HIST1H2AG](HIST1H2AG) | 2, aSHM | Morin et al. 2013; Rossi et al. 2012; Panea et al. 2019; Krysiak et al. 2017 | |
|
| 282 | -| [HLA-DMA](HLA-DMA) | 2 | | |
|
| 283 | -| [HLA-DQA1](HLA-DQA1) | 2 | Hübschmann et al. 2021 | |
|
| 284 | -| [HNF1B](HNF1B) | 2 | Laura Pasqualucci, Trifonov, et al. 2011 | |
|
| 285 | -| [HNRNPD](HNRNPD) | 2 | | |
|
| 286 | -| [HNRNPH1](HNRNPH1) | 2, noncoding | Pararajalingam et al. 2020 | |
|
| 287 | -| [HRAS](HRAS) | 2 | Jallades et al. 2017; Reddy et al. 2017 | |
|
| 288 | -| [ID3](ID3) | 2 | Richter et al. 2012; Spina et al. 2016; Schmitz et al. 2012 | |
|
| 289 | -| [IER2](IER2) | 2 | Morin et al. 2013 | |
|
| 290 | -| [IFNGR1](IFNGR1) | 2 | Morin et al. 2013 | |
|
| 291 | -| [IGLL5](IGLL5) | 2, aSHM | Russler-Germain et al. 2023; Desch et al. 2020; Panea et al. 2019 | |
|
| 292 | -| [IKBKB](IKBKB) | 2 | Reddy et al. 2017; Rossi et al. 2011; Wienand et al. 2019 | |
|
| 293 | -| [IKBKE](IKBKE) | 2 | Hübschmann et al. 2021 | |
|
| 294 | -| [IL16](IL16) | 2 | | |
|
| 295 | -| [IL6](IL6) | 2 | Chapuy et al. 2018 | |
|
| 296 | -| [INO80](INO80) | 2 | Zhang et al. 2013 | |
|
| 297 | -| [IRAG2](IRAG2) | 2, aSHM | | |
|
| 298 | -| [IRF1](IRF1) | 2, aSHM | Hübschmann et al. 2021 | |
|
| 299 | -| [JAK1](JAK1) | 2 | Zhang et al. 2013; Mottok et al. 2019 | |
|
| 300 | -| [JAK3](JAK3) | 2 | Zhang et al. 2013 | |
|
| 301 | -| [JUNB](JUNB) | 2 | Reddy et al. 2017; Mottok et al. 2019 | |
|
| 302 | -| [KCMF1](KCMF1) | 2 | Reddy et al. 2017 | |
|
| 303 | -| [KLHL21](KLHL21) | 2 | Schmitz et al. 2018 | |
|
| 304 | -| [LAMA5](LAMA5) | 2 | Schmitz et al. 2018 | |
|
| 305 | -| [LAPTM5](LAPTM5) | 2, aSHM | Hübschmann et al. 2021 | |
|
| 306 | -| [LIN54](LIN54) | 2 | Reddy et al. 2017 | |
|
| 307 | -| [LPP](LPP) | 2, aSHM | Arthur et al. 2018 | |
|
| 308 | -| [LRP12](LRP12) | 2 | Hübschmann et al. 2021 | |
|
| 309 | -| [LRRN3](LRRN3) | 2 | Sarkozy et al. 2021; Morin et al. 2013 | |
|
| 310 | -| [LYN](LYN) | 2 | Chapuy et al. 2018 | |
|
| 311 | -| [MAGT1](MAGT1) | 2 | Reddy et al. 2017 | |
|
| 312 | -| [MALAT1](MALAT1) | 2, aSHM | Arthur et al. 2018 | |
|
| 313 | -| [MAP2K1](MAP2K1) | 2 | Shin et al. 2015; Louissaint et al. 2016 | |
|
| 314 | -| [MAP4K4](MAP4K4) | 2 | Reddy et al. 2017 | |
|
| 315 | -| [MARK1](MARK1) | 2 | Reddy et al. 2017 | |
|
| 316 | -| [MCL1](MCL1) | 2 | Panea et al. 2019; Reddy et al. 2017; Duns et al. 2021 | |
|
| 317 | -| [MECOM](MECOM) | 2 | Reddy et al. 2017 | |
|
| 318 | -| [MET](MET) | 2 | Reddy et al. 2017 | |
|
| 319 | -| [MIR142](MIR142) | 2, aSHM | Grande et al. 2019; Kwanhian et al. 2012 | |
|
| 320 | -| [MIR155HG](MIR155HG) | 2, aSHM | | |
|
| 321 | -| [MPDZ](MPDZ) | 2 | Reichel et al. 2015; Morin et al. 2013 | |
|
| 322 | -| [MSH2](MSH2) | 2 | Reddy et al. 2017 | |
|
| 323 | -| [MSH6](MSH6) | 2 | Reddy et al. 2017 | |
|
| 324 | -| [MYB](MYB) | 2 | Reddy et al. 2017; Desch et al. 2020 | |
|
| 325 | -| [MYBPC2](MYBPC2) | 2 | Schmitz et al. 2018 | |
|
| 326 | -| [MYO1E](MYO1E) | 2, aSHM | | |
|
| 327 | -| [MYOM2](MYOM2) | 2 | Laura Pasqualucci, Trifonov, et al. 2011 | |
|
| 328 | -| [N2RF2](N2RF2) | 2 | Hübschmann et al. 2021 | |
|
| 329 | -| [NANOG](NANOG) | 2 | Chapuy et al. 2018 | |
|
| 330 | -| [NAV1](NAV1) | 2 | Chapuy et al. 2018 | |
|
| 331 | -| [NCOA3](NCOA3) | 2, aSHM | | |
|
| 332 | -| [NCOR1](NCOR1) | 2 | Reddy et al. 2017 | |
|
| 333 | -| [NCOR2](NCOR2) | 2 | Schmitz et al. 2012; Spina et al. 2016; Sarkozy et al. 2021 | |
|
| 334 | -| [NEAT1](NEAT1) | 2, aSHM | Arthur et al. 2018 | |
|
| 335 | -| [NF1](NF1) | 2 | Reddy et al. 2017 | |
|
| 336 | -| [NFKB1](NFKB1) | 2 | | |
|
| 337 | -| [NFKB2](NFKB2) | 2 | Reddy et al. 2017; Mottok et al. 2019 | |
|
| 338 | -| [NLRC5](NLRC5) | 2 | | |
|
| 339 | -| [NLRP5](NLRP5) | 2 | Morin et al. 2013 | |
|
| 340 | -| [NLRP8](NLRP8) | 2 | Chapuy et al. 2018 | |
|
| 341 | -| [ODZ3](ODZ3) | 2 | Morin et al. 2013 | |
|
| 342 | -| [P2RX5](P2RX5) | 2, aSHM | Morin et al. 2013 | |
|
| 343 | -| [PAPOLG](PAPOLG) | 2 | Schmitz et al. 2018 | |
|
| 344 | -| [PASK](PASK) | 2 | Morin et al. 2013 | |
|
| 345 | -| [PAX5](PAX5) | 2, aSHM | L. Pasqualucci et al. 2001 | |
|
| 346 | -| [PCBP1](PCBP1) | 2 | Schmitz et al. 2012 | |
|
| 347 | -| [PCDHB11](PCDHB11) | 2 | Morin et al. 2013 | |
|
| 348 | -| [PCLO](PCLO) | 2 | Lohr et al. 2012 | |
|
| 349 | -| [PDE4DIP](PDE4DIP) | 2 | Chapuy et al. 2018 | |
|
| 350 | -| [PDS5B](PDS5B) | 2 | Hübschmann et al. 2021; Morin et al. 2013 | |
|
| 351 | -| [PHF6](PHF6) | 2 | Reddy et al. 2017; Thomas et al. 2023 | |
|
| 352 | -| [PIK3CD](PIK3CD) | 2 | Reddy et al. 2017 | |
|
| 353 | -| [PIK3R1](PIK3R1) | 2 | Zhang et al. 2013; Panea et al. 2019 | |
|
| 354 | -| [PKD1](PKD1) | 2 | Morin et al. 2013 | |
|
| 355 | -| [PNPO](PNPO) | 2 | Hübschmann et al. 2021 | |
|
| 356 | -| [POGZ](POGZ) | 2 | Morin et al. 2013 | |
|
| 357 | -| [PPP1R9B](PPP1R9B) | 2 | | |
|
| 358 | -| [PRKCB](PRKCB) | 2 | Morin et al. 2013 | |
|
| 359 | -| [PRKDC](PRKDC) | 2 | Hübschmann et al. 2021; Schmitz et al. 2018 | |
|
| 360 | -| [PRPS1](PRPS1) | 2 | Chapuy et al. 2018 | |
|
| 361 | -| [PTMA](PTMA) | 2, aSHM | | |
|
| 362 | -| [PTPN1](PTPN1) | 2, aSHM | Gunawardana et al. 2014 | |
|
| 363 | -| [PTPN23](PTPN23) | 2 | Morin et al. 2013 | |
|
| 364 | -| [PTPN6](PTPN6) | 2 | Reddy et al. 2017 | |
|
| 365 | -| [PTPRK](PTPRK) | 2 | Reddy et al. 2017 | |
|
| 366 | -| [RAC2](RAC2) | 2 | Hübschmann et al. 2021; Panea et al. 2019 | |
|
| 367 | -| [RAD9A](RAD9A) | 2 | Chapuy et al. 2018 | |
|
| 368 | -| [RARA](RARA) | 2 | Reddy et al. 2017 | |
|
| 369 | -| [RCC](RCC) | 2, aSHM | | |
|
| 370 | -| [RFTN1](RFTN1) | 2, aSHM | Duns et al. 2021; Arthur et al. 2018 | |
|
| 371 | -| [RFXAP](RFXAP) | 2 | | |
|
| 372 | -| [RHEX](RHEX) | 2, aSHM | | |
|
| 373 | -| [RHOH](RHOH) | 2, aSHM | L. Pasqualucci et al. 2001 | |
|
| 374 | -| [RUBCNL](RUBCNL) | 2, aSHM | | |
|
| 375 | -| [RUNX1](RUNX1) | 2 | Reddy et al. 2017 | |
|
| 376 | -| [SAMD9L](SAMD9L) | 2 | Morin et al. 2013 | |
|
| 377 | -| [SARM1](SARM1) | 2 | Morin et al. 2013 | |
|
| 378 | -| [SEL1L3](SEL1L3) | 2, aSHM | | |
|
| 379 | -| [SEPTIN9](SEPTIN9) | 2, aSHM | | |
|
| 380 | -| [SERPINA9](SERPINA9) | 2, aSHM | Arthur et al. 2018 | |
|
| 381 | -| [SETD2](SETD2) | 2 | Zhang et al. 2013 | |
|
| 382 | -| [SETD5](SETD5) | 2 | Reddy et al. 2017; Tiacci et al. 2018 | |
|
| 383 | -| [SIAH2](SIAH2) | 2 | Reichel et al. 2015; Hübschmann et al. 2021 | |
|
| 384 | -| [SLC34A2](SLC34A2) | 2 | Hübschmann et al. 2021 | |
|
| 385 | -| [SMEK1](SMEK1) | 2 | Chapuy et al. 2018 | |
|
| 386 | -| [SRRM2](SRRM2) | 2 | Russler-Germain et al. 2023; Morin et al. 2013 | |
|
| 387 | -| [ST6GAL1](ST6GAL1) | 2, aSHM | Arthur et al. 2018 | |
|
| 388 | -| [STAT5B](STAT5B) | 2 | Zhang et al. 2013; Tiacci et al. 2018 | |
|
| 389 | -| [SYK](SYK) | 2 | Reddy et al. 2017 | |
|
| 390 | -| [SYPL1](SYPL1) | 2 | Morin et al. 2013 | |
|
| 391 | -| [TAP1](TAP1) | 2 | Schmitz et al. 2018 | |
|
| 392 | -| [TBC1D4](TBC1D4) | 2, aSHM | Arthur et al. 2018 | |
|
| 393 | -| [TCL1A](TCL1A) | 2, aSHM | Grande et al. 2019 | |
|
| 394 | -| [TGFBR2](TGFBR2) | 2 | Reddy et al. 2017 | |
|
| 395 | -| [TIPARP](TIPARP) | 2 | Reddy et al. 2017 | |
|
| 396 | -| [TLR2](TLR2) | 2 | Chapuy et al. 2018; Beà et al. 2013 | |
|
| 397 | -| [TRAF3](TRAF3) | 2 | Rossi et al. 2011; Otto et al. 2012; Laura Pasqualucci, Trifonov, et al. 2011 | |
|
| 398 | -| [TRAF6](TRAF6) | 2 | Hübschmann et al. 2021 | |
|
| 399 | -| [TRIP12](TRIP12) | 2 | | |
|
| 400 | -| [UBE2J1](UBE2J1) | 2, aSHM | | |
|
| 401 | -| [UBR5](UBR5) | 2 | Pararajalingam et al. 2020; Zhang et al. 2013 | |
|
| 402 | -| [UNC5B](UNC5B) | 2 | Hübschmann et al. 2021 | |
|
| 403 | -| [UNC5D](UNC5D) | 2 | | |
|
| 404 | -| [WAC](WAC) | 2 | Rossi et al. 2012; Reddy et al. 2017 | |
|
| 405 | -| [WDFY3](WDFY3) | 2 | Morin et al. 2013 | |
|
| 406 | -| [WNK1](WNK1) | 2 | Hübschmann et al. 2021; Thomas et al. 2023; Jallades et al. 2017 | |
|
| 407 | -| [XBP1](XBP1) | 2, aSHM | | |
|
| 408 | -| [YY1](YY1) | 2 | Reddy et al. 2017 | |
|
| 409 | -| [ZBTB7A](ZBTB7A) | 2 | Burkhardt et al. 2022; Reddy et al. 2017 | |
|
| 410 | -| [ZCCHC7](ZCCHC7) | 2, aSHM | Arthur et al. 2018 | |
|
| 411 | -| [ZEB2](ZEB2) | 2 | Zhang et al. 2013 | |
|
| 412 | -| [ZFAT](ZFAT) | 2 | Reddy et al. 2017 | |
|
| 413 | -| [ZFX](ZFX) | 2 | Reddy et al. 2017 | |
|
| 414 | -| [ZNF217](ZNF217) | 2 | Hübschmann et al. 2021; Reichel et al. 2015 | |
|
| 415 | -| [ZNF423](ZNF423) | 2 | Chapuy et al. 2018 | |
|
| 416 | - |
|
| 417 | -# References |
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| 418 | - |
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| 419 | -<div id="refs" class="references csl-bib-body hanging-indent"> |
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| 420 | - |
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| 421 | -<div id="ref-albuquerqueEnhancingKnowledgeDiscovery2017a" |
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| 422 | -class="csl-entry"> |
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| 423 | - |
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| 424 | -Albuquerque, Marco A., Bruno M. Grande, Elie J. Ritch, Prasath |
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| 429 | - |
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| 430 | -</div> |
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| 431 | - |
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| 432 | -<div id="ref-arthurGenomewideDiscoverySomatic2018" class="csl-entry"> |
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| 433 | - |
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| 434 | -Arthur, Sarah E., Aixiang Jiang, Bruno M. Grande, Miguel Alcaide, Razvan |
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| 439 | - |
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| 440 | -</div> |
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| 441 | - |
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| 443 | - |
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| 444 | -Beà, Sílvia, Rafael Valdés-Mas, Alba Navarro, Itziar Salaverria, David |
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| 449 | - |
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| 450 | -</div> |
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| 451 | - |
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| 452 | -<div id="ref-bohleRoleEarlyBcell2013" class="csl-entry"> |
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| 453 | - |
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| 454 | -Bohle, V., C. Döring, M.-L. Hansmann, and R. Küppers. 2013. “Role of |
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| 458 | - |
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| 459 | -</div> |
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| 460 | - |
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| 461 | -<div id="ref-braggioGenomicAnalysisMarginal2012" class="csl-entry"> |
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| 462 | - |
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| 463 | -Braggio, Esteban, Ahmet Dogan, Jonathan J. Keats, Wee J. Chng, Gaofeng |
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| 464 | -Huang, Julie M. Matthews, Matthew J. Maurer, et al. 2012. “Genomic |
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| 465 | -Analysis of Marginal Zone and Lymphoplasmacytic Lymphomas Identified |
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| 469 | - |
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| 470 | -</div> |
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| 471 | - |
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| 472 | -<div id="ref-burkhardtClinicalRelevanceMolecular2022b" |
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| 473 | -class="csl-entry"> |
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| 474 | - |
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| 475 | -Burkhardt, Birgit, Ulf Michgehl, Jonas Rohde, Tabea Erdmann, Philipp |
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| 476 | -Berning, Katrin Reutter, Marius Rohde, et al. 2022. “Clinical Relevance |
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| 477 | -of Molecular Characteristics in Burkitt Lymphoma Differs According to |
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| 478 | -Age.” *Nature Communications* 13 1: 3881. |
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| 479 | -<https://doi.org/10.1038/s41467-022-31355-8>. |
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| 480 | - |
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| 481 | -</div> |
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| 482 | - |
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| 483 | -<div id="ref-chapuyMolecularSubtypesDiffuse2018b" class="csl-entry"> |
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| 484 | - |
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| 485 | -Chapuy, Bjoern, Chip Stewart, Andrew J. Dunford, Jaegil Kim, Atanas |
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| 486 | -Kamburov, Robert A. Redd, Mike S. Lawrence, et al. 2018. “Molecular |
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| 487 | -Subtypes of Diffuse Large B Cell Lymphoma Are Associated with Distinct |
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| 488 | -Pathogenic Mechanisms and Outcomes.” *Nature Medicine* 24 5: 679–90. |
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| 489 | -<https://doi.org/10.1038/s41591-018-0016-8>. |
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| 490 | - |
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| 491 | -</div> |
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| 492 | - |
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| 493 | -<div id="ref-cheungAcquiredTNFRSF14Mutations2010a" class="csl-entry"> |
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| 494 | - |
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| 495 | -Cheung, K.-John J., Nathalie A. Johnson, Joslynn G. Affleck, Tesa |
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| 496 | -Severson, Christian Steidl, Susana Ben-Neriah, Jacqueline Schein, et al. |
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| 497 | -2010. “Acquired TNFRSF14 Mutations in Follicular Lymphoma Are Associated |
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| 498 | -with Worse Prognosis.” *Cancer Research* 70 22: 9166–74. |
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| 499 | -<https://doi.org/10.1158/0008-5472.CAN-10-2460>. |
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| 500 | - |
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| 501 | -</div> |
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| 502 | - |
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| 503 | -<div id="ref-compagnoMutationsMultipleGenes2009a" class="csl-entry"> |
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| 504 | - |
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| 505 | -Compagno, Mara, Wei Keat Lim, Adina Grunn, Subhadra V. Nandula, Manisha |
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| 506 | -Brahmachary, Qiong Shen, Francesco Bertoni, et al. 2009. “Mutations of |
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| 507 | -Multiple Genes Cause Deregulation of <span |
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| 508 | -class="nocase">NF-kappaB</span> in Diffuse Large <span |
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| 509 | -class="nocase">B-cell</span> Lymphoma.” *Nature* 459 7247: 717–21. |
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| 510 | -<https://doi.org/10.1038/nature07968>. |
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| 511 | - |
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| 512 | -</div> |
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| 513 | - |
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| 514 | -<div id="ref-deschGenotypingCirculatingTumor2020" class="csl-entry"> |
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| 515 | - |
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| 516 | -Desch, Ann-Kathrin, Kristin Hartung, Ante Botzen, Alexander Brobeil, |
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| 517 | -Mathias Rummel, Lars Kurch, Thomas Georgi, et al. 2020. “Genotyping |
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| 518 | -Circulating Tumor DNA of Pediatric Hodgkin Lymphoma.” *Leukemia* 34 1: |
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| 519 | -151–66. <https://doi.org/10.1038/s41375-019-0541-6>. |
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| 520 | - |
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| 521 | -</div> |
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| 522 | - |
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| 523 | -<div id="ref-dunsCharacterizationDLBCLPMBL2021b" class="csl-entry"> |
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| 524 | - |
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| 525 | -Duns, Gerben, Elena Viganò, Daisuke Ennishi, Clementine Sarkozy, Stacy |
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| 526 | -S. Hung, Elizabeth Chavez, Katsuyoshi Takata, et al. 2021. |
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| 527 | -“Characterization of DLBCL with a PMBL Gene Expression Signature.” |
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| 528 | -*Blood* 138 2: 136–48. <https://doi.org/10.1182/blood.2020007683>. |
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| 529 | - |
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| 530 | -</div> |
|
| 531 | - |
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| 532 | -<div id="ref-ganapathiGeneticLandscapeDural2016" class="csl-entry"> |
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| 533 | - |
|
| 534 | -Ganapathi, Karthik A., Vaidehi Jobanputra, Fabio Iwamoto, Preti Jain, |
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| 535 | -Jinli Chen, Luciano Cascione, Odelia Nahum, et al. 2016. “The Genetic |
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| 536 | -Landscape of Dural Marginal Zone Lymphomas.” *Oncotarget* 7 28: |
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| 537 | -43052–61. <https://doi.org/10.18632/oncotarget.9678>. |
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| 538 | - |
|
| 539 | -</div> |
|
| 540 | - |
|
| 541 | -<div id="ref-gomezUltraDeepSequencingReveals2023" class="csl-entry"> |
|
| 542 | - |
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| 543 | -Gomez, Felicia, Bryan Fisk, Joshua F. McMichael, Matthew Mosior, |
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| 544 | -Jennifer A. Foltz, Zachary L. Skidmore, Eric J. Duncavage, et al. 2023. |
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| 545 | -“Ultra-Deep Sequencing Reveals the Mutational Landscape of Classical |
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| 546 | -Hodgkin Lymphoma.” *Cancer Research Communications* 3 11: 2312–30. |
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| 547 | -<https://doi.org/10.1158/2767-9764.CRC-23-0140>. |
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| 548 | - |
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| 549 | -</div> |
|
| 550 | - |
|
| 551 | -<div id="ref-grandeGenomewideDiscoverySomatic2019" class="csl-entry"> |
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| 552 | - |
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| 553 | -Grande, Bruno M., Daniela S. Gerhard, Aixiang Jiang, Nicholas B. Griner, |
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| 554 | -Jeremy S. Abramson, Thomas B. Alexander, Hilary Allen, et al. 2019. |
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| 555 | -“Genome-Wide Discovery of Somatic Coding and Noncoding Mutations in |
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| 556 | -Pediatric Endemic and Sporadic Burkitt Lymphoma.” *Blood* 133 12: |
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| 557 | -1313–24. <https://doi.org/10.1182/blood-2018-09-871418>. |
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| 558 | - |
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| 559 | -</div> |
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| 560 | - |
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| 561 | -<div id="ref-gunawardanaRecurrentSomaticMutations2014c" |
|
| 562 | -class="csl-entry"> |
|
| 563 | - |
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| 564 | -Gunawardana, Jay, Fong Chun Chan, Adèle Telenius, Bruce Woolcock, Robert |
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| 565 | -Kridel, King L. Tan, Susana Ben-Neriah, et al. 2014. “Recurrent Somatic |
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| 566 | -Mutations of PTPN1 in Primary Mediastinal B Cell Lymphoma and Hodgkin |
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| 567 | -Lymphoma.” *Nature Genetics* 46 4: 329–35. |
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| 568 | -<https://doi.org/10.1038/ng.2900>. |
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| 569 | - |
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| 570 | -</div> |
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| 571 | - |
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| 572 | -<div id="ref-hubschmannMutationalMechanismsShaping2021b" |
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| 573 | -class="csl-entry"> |
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| 574 | - |
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| 575 | -Hübschmann, Daniel, Kortine Kleinheinz, Rabea Wagener, Stephan H. |
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| 576 | -Bernhart, Cristina López, Umut H. Toprak, Stephanie Sungalee, et al. |
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| 577 | -2021. “Mutational Mechanisms Shaping the Coding and Noncoding Genome of |
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| 578 | -Germinal Center Derived <span class="nocase">B-cell</span> Lymphomas.” |
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| 579 | -*Leukemia* 35 7: 2002–16. |
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| 580 | -<https://doi.org/10.1038/s41375-021-01251-z>. |
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| 581 | - |
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| 582 | -</div> |
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| 583 | - |
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| 584 | -<div id="ref-jalladesExomeSequencingIdentifies2017" class="csl-entry"> |
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| 585 | - |
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| 586 | -Jallades, Laurent, Lucile Baseggio, Pierre Sujobert, Sarah Huet, Kaddour |
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| 588 | -Sequencing Identifies Recurrent BCOR Alterations and the Absence of |
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| 589 | -KLF2, TNFAIP3 and MYD88 Mutations in Splenic Diffuse Red Pulp Small |
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| 590 | -<span class="nocase">B-cell</span> Lymphoma.” *Haematologica* 102 10: |
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| 591 | -1758–66. <https://doi.org/10.3324/haematol.2016.160192>. |
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| 592 | - |
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| 599 | -Mutations of the Exportin 1 Gene XPO1 and Their Impact on Selective |
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| 600 | -Inhibitor of Nuclear Export Compounds Sensitivity in Primary Mediastinal |
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| 602 | -Hematology* 91 9: 923–30. <https://doi.org/10.1002/ajh.24451>. |
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| 603 | - |
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| 650 | -NFKBIA, Encoding IkappaB Alpha, Are a Recurrent Finding in Classical |
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| 667 | - |
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| 670 | -“Discovery and Prioritization of Somatic Mutations in Diffuse Large |
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| 675 | - |
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| 681 | -Louissaint, Abner, Kristian T. Schafernak, Julia T. Geyer, Alexandra E. |
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| 752 | - |
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| 753 | -Morin, Ryan D., Karen Mungall, Erin Pleasance, Andrew J. Mungall, |
|
| 754 | -Rodrigo Goya, Ryan D. Huff, David W. Scott, et al. 2013. “Mutational and |
|
| 755 | -Structural Analysis of Diffuse Large <span class="nocase">B-cell</span> |
|
| 756 | -Lymphoma Using Whole-Genome Sequencing.” *Blood* 122 7: 1256–65. |
|
| 757 | -<https://doi.org/10.1182/blood-2013-02-483727>. |
|
| 758 | - |
|
| 759 | -</div> |
|
| 760 | - |
|
| 761 | -<div id="ref-mottokIntegrativeGenomicAnalysis2019b" class="csl-entry"> |
|
| 762 | - |
|
| 763 | -Mottok, Anja, Stacy S. Hung, Elizabeth A. Chavez, Bruce Woolcock, Adèle |
|
| 764 | -Telenius, Lauren C. Chong, Barbara Meissner, et al. 2019. “Integrative |
|
| 765 | -Genomic Analysis Identifies Key Pathogenic Mechanisms in Primary |
|
| 766 | -Mediastinal Large <span class="nocase">B-cell</span> Lymphoma.” *Blood* |
|
| 767 | -134 10: 802–13. <https://doi.org/10.1182/blood.2019001126>. |
|
| 768 | - |
|
| 769 | -</div> |
|
| 770 | - |
|
| 771 | -<div id="ref-mottokGenomicAlterationsCIITA2015b" class="csl-entry"> |
|
| 772 | - |
|
| 773 | -Mottok, Anja, Bruce Woolcock, Fong Chun Chan, King Mong Tong, Lauren |
|
| 774 | -Chong, Pedro Farinha, Adèle Telenius, et al. 2015. “Genomic Alterations |
|
| 775 | -in CIITA Are Frequent in Primary Mediastinal Large B Cell Lymphoma and |
|
| 776 | -Are Associated with Diminished MHC Class II Expression.” *Cell Reports* |
|
| 777 | -13 7: 1418–31. <https://doi.org/10.1016/j.celrep.2015.10.008>. |
|
| 778 | - |
|
| 779 | -</div> |
|
| 780 | - |
|
| 781 | -<div id="ref-muppidiLossSignalingGa132014b" class="csl-entry"> |
|
| 782 | - |
|
| 783 | -Muppidi, J., R. Schmitz, Jesse A. Green, Jesse A. Green, Wenming Xiao, |
|
| 784 | -Adrien B. Larsen, S. Braun, et al. 2014. “Loss of Signaling via Gα13 in |
|
| 785 | -Germinal Center B Cell-Derived Lymphoma.” *Nature* 516: 254–58. |
|
| 786 | -<https://doi.org/10.1038/nature13765>. |
|
| 787 | - |
|
| 788 | -</div> |
|
| 789 | - |
|
| 790 | -<div id="ref-nadeuGenomicEpigenomicInsights2020b" class="csl-entry"> |
|
| 791 | - |
|
| 792 | -Nadeu, F., D. Martín-García, G. Clot, A. Díaz-Navarro, M. Duran-Ferrer, |
|
| 793 | -A. Navarro, Roser Vilarrasa-Blasi, et al. 2020. “Genomic and Epigenomic |
|
| 794 | -Insights into the Origin, Pathogenesis and Clinical Behavior of Mantle |
|
| 795 | -Cell Lymphoma Subtypes.” *Blood*. |
|
| 796 | -<https://doi.org/10.1182/blood.2020005289>. |
|
| 797 | - |
|
| 798 | -</div> |
|
| 799 | - |
|
| 800 | -<div id="ref-ngoOncogenicallyActiveMYD882011a" class="csl-entry"> |
|
| 801 | - |
|
| 802 | -Ngo, Vu N., Ryan M. Young, Roland Schmitz, Sameer Jhavar, Wenming Xiao, |
|
| 803 | -Kian-Huat Lim, Holger Kohlhammer, et al. 2011. “Oncogenically Active |
|
| 804 | -MYD88 Mutations in Human Lymphoma.” *Nature* 470 7332: 115–19. |
|
| 805 | -<https://doi.org/10.1038/nature09671>. |
|
| 806 | - |
|
| 807 | -</div> |
|
| 808 | - |
|
| 809 | -<div id="ref-ohgamiSTAT3MutationsAre2014" class="csl-entry"> |
|
| 151 | +|Gene|Tier| Relevant references| |
|
| 152 | +|:-:|:-:|:-| |
|
| 153 | +|[ABI3BP](ABI3BP)|2|[@morinMutationalStructuralAnalysis2013]| |
|
| 154 | +|[ADAMTS1](ADAMTS1)|2|[@hubschmannMutationalMechanismsShaping2021b]| |
|
| 155 | +|[AICDA](AICDA)|2, aSHM|[@arthurGenomewideDiscoverySomatic2018]| |
|
| 156 | +|[ANKRD12](ANKRD12)|2|[@hubschmannMutationalMechanismsShaping2021b]| |
|
| 157 | +|[ANKRD17](ANKRD17)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 158 | +|[ARID1B](ARID1B)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 159 | +|[ARID5B](ARID5B)|2|[@gomezUltraDeepSequencingReveals2023; @reddyGeneticFunctionalDrivers2017]| |
|
| 160 | +|[ATR](ATR)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 161 | +|[BCL11A](BCL11A)|2, aSHM|| |
|
| 162 | +|[BCOR](BCOR)|2|[@nadeuGenomicEpigenomicInsights2020b; @jalladesExomeSequencingIdentifies2017]| |
|
| 163 | +|[BCR](BCR)|2, aSHM|| |
|
| 164 | +|[BIRC3](BIRC3)|2, aSHM|[@dunsCharacterizationDLBCLPMBL2021b; @arthurGenomewideDiscoverySomatic2018; @beaLandscapeSomaticMutations2013; @rossiAlterationBIRC3Multiple2011a]| |
|
| 165 | +|[BLK](BLK)|2, aSHM|| |
|
| 166 | +|[BRINP3](BRINP3)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 167 | +|[BTBD3](BTBD3)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 168 | +|[CADPS2](CADPS2)|2|[@hubschmannMutationalMechanismsShaping2021b]| |
|
| 169 | +|[CASP8](CASP8)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 170 | +|[CBLB](CBLB)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 171 | +|[CCL4](CCL4)|2|[@chapuyMolecularSubtypesDiffuse2018b]| |
|
| 172 | +|[CD22](CD22)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 173 | +|[CD274](CD274)|2|[@morinFrequentMutationHistonemodifying2011]| |
|
| 174 | +|[CD36](CD36)|2|[@pasqualucciAnalysisCodingGenome2011]| |
|
| 175 | +|[CD44](CD44)|2, aSHM|[@arthurGenomewideDiscoverySomatic2018]| |
|
| 176 | +|[CD74](CD74)|2, aSHM|[@arthurGenomewideDiscoverySomatic2018]| |
|
| 177 | +|[CDC73](CDC73)|2|[@reddyGeneticFunctionalDrivers2017; @loveGeneticLandscapeMutations2012]| |
|
| 178 | +|[CDH9](CDH9)|2|[@morinMutationalStructuralAnalysis2013]| |
|
| 179 | +|[CHD1](CHD1)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 180 | +|[CHD8](CHD8)|2|[@reddyGeneticFunctionalDrivers2017; @grandeGenomewideDiscoverySomatic2019]| |
|
| 181 | +|[CHST2](CHST2)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 182 | +|[CNOT2](CNOT2)|2|[@hubschmannMutationalMechanismsShaping2021b]| |
|
| 183 | +|[CNTNAP5](CNTNAP5)|2|[@morinMutationalStructuralAnalysis2013]| |
|
| 184 | +|[COQ7](COQ7)|2|[@chapuyMolecularSubtypesDiffuse2018b]| |
|
| 185 | +|[CRIP1](CRIP1)|2|[@chapuyMolecularSubtypesDiffuse2018b]| |
|
| 186 | +|[DAZAP1](DAZAP1)|2|[@pararajalingamCodingNoncodingDrivers2020]| |
|
| 187 | +|[DCAF6](DCAF6)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 188 | +|[DDX10](DDX10)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 189 | +|[DHX16](DHX16)|2|[@hubschmannMutationalMechanismsShaping2021b]| |
|
| 190 | +|[DICER1](DICER1)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 191 | +|[DNAH5](DNAH5)|2|[@jalladesExomeSequencingIdentifies2017; @morinMutationalStructuralAnalysis2013]| |
|
| 192 | +|[DNM2](DNM2)|2|[@hubschmannMutationalMechanismsShaping2021b]| |
|
| 193 | +|[DNMT3A](DNMT3A)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 194 | +|[DOCK1](DOCK1)|2|[@chapuyMolecularSubtypesDiffuse2018b]| |
|
| 195 | +|[DSG4](DSG4)|2|[@morinMutationalStructuralAnalysis2013]| |
|
| 196 | +|[EIF2AK3](EIF2AK3)|2, aSHM|| |
|
| 197 | +|[EZR](EZR)|2, aSHM|[@deschGenotypingCirculatingTumor2020]| |
|
| 198 | +|[FAM102A](FAM102A)|2, aSHM|| |
|
| 199 | +|[FAM38B](FAM38B)|2|[@morinMutationalStructuralAnalysis2013]| |
|
| 200 | +|[FANK1](FANK1)|2, aSHM|| |
|
| 201 | +|[FAT4](FAT4)|2|[@zhangGenomicLandscapeMantle2014; @morinMutationalStructuralAnalysis2013; @parryWholeExomeSequencing2013]| |
|
| 202 | +|[FCRL3](FCRL3)|2, aSHM|| |
|
| 203 | +|[FNBP1](FNBP1)|2, aSHM|| |
|
| 204 | +|[FNDC1](FNDC1)|2|[@morinMutationalStructuralAnalysis2013]| |
|
| 205 | +|[FOXC1](FOXC1)|2|[@schmitzGeneticsPathogenesisDiffuse2018a]| |
|
| 206 | +|[FOXP1](FOXP1)|2, aSHM|[@reddyGeneticFunctionalDrivers2017]| |
|
| 207 | +|[FUBP1](FUBP1)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 208 | +|[FUT5](FUT5)|2|[@chapuyMolecularSubtypesDiffuse2018b]| |
|
| 209 | +|[GABRA2](GABRA2)|2|[@chapuyMolecularSubtypesDiffuse2018b]| |
|
| 210 | +|[GAK](GAK)|2|[@hubschmannMutationalMechanismsShaping2021b]| |
|
| 211 | +|[GNAS](GNAS)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 212 | +|[GOLGA5](GOLGA5)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 213 | +|[GPC5](GPC5)|2|[@schmitzGeneticsPathogenesisDiffuse2018a]| |
|
| 214 | +|[GSG2](GSG2)|2|[@schmitzGeneticsPathogenesisDiffuse2018a]| |
|
| 215 | +|[HDAC7](HDAC7)|2|[@morinMutationalStructuralAnalysis2013]| |
|
| 216 | +|[HIST1H2AG](HIST1H2AG)|2, aSHM|[@morinMutationalStructuralAnalysis2013; @paneaWholeGenomeLandscape2019; @krysiakRecurrentSomaticMutations2017b; @rossiCodingGenomeSplenic2012c]| |
|
| 217 | +|[HLA-DMA](HLA-DMA)|2|| |
|
| 218 | +|[HLA-DQA1](HLA-DQA1)|2|[@hubschmannMutationalMechanismsShaping2021b]| |
|
| 219 | +|[HNF1B](HNF1B)|2|[@pasqualucciAnalysisCodingGenome2011]| |
|
| 220 | +|[HNRNPD](HNRNPD)|2|| |
|
| 221 | +|[HNRNPH1](HNRNPH1)|2, noncoding|[@pararajalingamCodingNoncodingDrivers2020]| |
|
| 222 | +|[HRAS](HRAS)|2|[@jalladesExomeSequencingIdentifies2017; @reddyGeneticFunctionalDrivers2017]| |
|
| 223 | +|[ID3](ID3)|2|[@spinaGeneticsNodalMarginal2016b; @richterRecurrentMutationID32012a; @schmitzBurkittLymphomaPathogenesis2012]| |
|
| 224 | +|[IER2](IER2)|2|[@morinMutationalStructuralAnalysis2013]| |
|
| 225 | +|[IFNGR1](IFNGR1)|2|[@morinMutationalStructuralAnalysis2013]| |
|
| 226 | +|[IGLL5](IGLL5)|2, aSHM|[@deschGenotypingCirculatingTumor2020; @russler-germainMutationsAssociatedProgression2023b; @paneaWholeGenomeLandscape2019]| |
|
| 227 | +|[IKBKB](IKBKB)|2|[@reddyGeneticFunctionalDrivers2017; @rossiAlterationBIRC3Multiple2011a; @wienandGenomicAnalysesFlowsorted2019b]| |
|
| 228 | +|[IKBKE](IKBKE)|2|[@hubschmannMutationalMechanismsShaping2021b]| |
|
| 229 | +|[IL16](IL16)|2|| |
|
| 230 | +|[IL6](IL6)|2|[@chapuyMolecularSubtypesDiffuse2018b]| |
|
| 231 | +|[INO80](INO80)|2|[@zhangGeneticHeterogeneityDiffuse2013]| |
|
| 232 | +|[IRAG2](IRAG2)|2, aSHM|| |
|
| 233 | +|[IRF1](IRF1)|2, aSHM|[@hubschmannMutationalMechanismsShaping2021b]| |
|
| 234 | +|[JAK1](JAK1)|2|[@mottokIntegrativeGenomicAnalysis2019b; @zhangGeneticHeterogeneityDiffuse2013]| |
|
| 235 | +|[JAK3](JAK3)|2|[@zhangGeneticHeterogeneityDiffuse2013]| |
|
| 236 | +|[JUNB](JUNB)|2|[@reddyGeneticFunctionalDrivers2017; @mottokIntegrativeGenomicAnalysis2019b]| |
|
| 237 | +|[KCMF1](KCMF1)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 238 | +|[KLHL21](KLHL21)|2|[@schmitzGeneticsPathogenesisDiffuse2018a]| |
|
| 239 | +|[LAMA5](LAMA5)|2|[@schmitzGeneticsPathogenesisDiffuse2018a]| |
|
| 240 | +|[LAPTM5](LAPTM5)|2, aSHM|[@hubschmannMutationalMechanismsShaping2021b]| |
|
| 241 | +|[LIN54](LIN54)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 242 | +|[LPP](LPP)|2, aSHM|[@arthurGenomewideDiscoverySomatic2018]| |
|
| 243 | +|[LRP12](LRP12)|2|[@hubschmannMutationalMechanismsShaping2021b]| |
|
| 244 | +|[LRRN3](LRRN3)|2|[@sarkozyMutationalLandscapeGray2021a; @morinMutationalStructuralAnalysis2013]| |
|
| 245 | +|[LYN](LYN)|2|[@chapuyMolecularSubtypesDiffuse2018b]| |
|
| 246 | +|[MAGT1](MAGT1)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 247 | +|[MALAT1](MALAT1)|2, aSHM|[@arthurGenomewideDiscoverySomatic2018]| |
|
| 248 | +|[MAP2K1](MAP2K1)|2|[@louissaintPediatrictypeNodalFollicular2016a; @shinBRAFV600EMAP2K12015]| |
|
| 249 | +|[MAP4K4](MAP4K4)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 250 | +|[MARK1](MARK1)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 251 | +|[MCL1](MCL1)|2|[@paneaWholeGenomeLandscape2019; @dunsCharacterizationDLBCLPMBL2021b; @reddyGeneticFunctionalDrivers2017]| |
|
| 252 | +|[MECOM](MECOM)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 253 | +|[MET](MET)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 254 | +|[MIR142](MIR142)|2, aSHM|[@grandeGenomewideDiscoverySomatic2019; @kwanhianMicroRNA142Mutated202012b]| |
|
| 255 | +|[MIR155HG](MIR155HG)|2, aSHM|| |
|
| 256 | +|[MPDZ](MPDZ)|2|[@morinMutationalStructuralAnalysis2013; @reichelFlowSortingExome2015a]| |
|
| 257 | +|[MSH2](MSH2)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 258 | +|[MSH6](MSH6)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 259 | +|[MYB](MYB)|2|[@reddyGeneticFunctionalDrivers2017; @deschGenotypingCirculatingTumor2020]| |
|
| 260 | +|[MYBPC2](MYBPC2)|2|[@schmitzGeneticsPathogenesisDiffuse2018a]| |
|
| 261 | +|[MYO1E](MYO1E)|2, aSHM|| |
|
| 262 | +|[MYOM2](MYOM2)|2|[@pasqualucciAnalysisCodingGenome2011]| |
|
| 263 | +|[N2RF2](N2RF2)|2|[@hubschmannMutationalMechanismsShaping2021b]| |
|
| 264 | +|[NANOG](NANOG)|2|[@chapuyMolecularSubtypesDiffuse2018b]| |
|
| 265 | +|[NAV1](NAV1)|2|[@chapuyMolecularSubtypesDiffuse2018b]| |
|
| 266 | +|[NCOA3](NCOA3)|2, aSHM|| |
|
| 267 | +|[NCOR1](NCOR1)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 268 | +|[NCOR2](NCOR2)|2|[@schmitzBurkittLymphomaPathogenesis2012; @spinaGeneticsNodalMarginal2016b; @sarkozyMutationalLandscapeGray2021a]| |
|
| 269 | +|[NEAT1](NEAT1)|2, aSHM|[@arthurGenomewideDiscoverySomatic2018]| |
|
| 270 | +|[NF1](NF1)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 271 | +|[NFKB1](NFKB1)|2|| |
|
| 272 | +|[NFKB2](NFKB2)|2|[@mottokIntegrativeGenomicAnalysis2019b; @reddyGeneticFunctionalDrivers2017]| |
|
| 273 | +|[NLRC5](NLRC5)|2|| |
|
| 274 | +|[NLRP5](NLRP5)|2|[@morinMutationalStructuralAnalysis2013]| |
|
| 275 | +|[NLRP8](NLRP8)|2|[@chapuyMolecularSubtypesDiffuse2018b]| |
|
| 276 | +|[ODZ3](ODZ3)|2|[@morinMutationalStructuralAnalysis2013]| |
|
| 277 | +|[P2RX5](P2RX5)|2, aSHM|[@morinMutationalStructuralAnalysis2013]| |
|
| 278 | +|[PAPOLG](PAPOLG)|2|[@schmitzGeneticsPathogenesisDiffuse2018a]| |
|
| 279 | +|[PASK](PASK)|2|[@morinMutationalStructuralAnalysis2013]| |
|
| 280 | +|[PAX5](PAX5)|2, aSHM|[@pasqualucciHypermutationMultipleProtooncogenes2001a]| |
|
| 281 | +|[PCBP1](PCBP1)|2|[@schmitzBurkittLymphomaPathogenesis2012]| |
|
| 282 | +|[PCDHB11](PCDHB11)|2|[@morinMutationalStructuralAnalysis2013]| |
|
| 283 | +|[PCLO](PCLO)|2|[@lohrDiscoveryPrioritizationSomatic2012a]| |
|
| 284 | +|[PDE4DIP](PDE4DIP)|2|[@chapuyMolecularSubtypesDiffuse2018b]| |
|
| 285 | +|[PDS5B](PDS5B)|2|[@hubschmannMutationalMechanismsShaping2021b; @morinMutationalStructuralAnalysis2013]| |
|
| 286 | +|[PHF6](PHF6)|2|[@reddyGeneticFunctionalDrivers2017; @thomasGeneticSubgroupsInform2023]| |
|
| 287 | +|[PIK3CD](PIK3CD)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 288 | +|[PIK3R1](PIK3R1)|2|[@zhangGeneticHeterogeneityDiffuse2013; @paneaWholeGenomeLandscape2019]| |
|
| 289 | +|[PKD1](PKD1)|2|[@morinMutationalStructuralAnalysis2013]| |
|
| 290 | +|[PNPO](PNPO)|2|[@hubschmannMutationalMechanismsShaping2021b]| |
|
| 291 | +|[POGZ](POGZ)|2|[@morinMutationalStructuralAnalysis2013]| |
|
| 292 | +|[PPP1R9B](PPP1R9B)|2|| |
|
| 293 | +|[PRKCB](PRKCB)|2|[@morinMutationalStructuralAnalysis2013]| |
|
| 294 | +|[PRKDC](PRKDC)|2|[@schmitzGeneticsPathogenesisDiffuse2018a; @hubschmannMutationalMechanismsShaping2021b]| |
|
| 295 | +|[PRPS1](PRPS1)|2|[@chapuyMolecularSubtypesDiffuse2018b]| |
|
| 296 | +|[PTMA](PTMA)|2, aSHM|| |
|
| 297 | +|[PTPN1](PTPN1)|2, aSHM|[@gunawardanaRecurrentSomaticMutations2014c]| |
|
| 298 | +|[PTPN23](PTPN23)|2|[@morinMutationalStructuralAnalysis2013]| |
|
| 299 | +|[PTPN6](PTPN6)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 300 | +|[PTPRK](PTPRK)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 301 | +|[RAC2](RAC2)|2|[@paneaWholeGenomeLandscape2019; @hubschmannMutationalMechanismsShaping2021b]| |
|
| 302 | +|[RAD9A](RAD9A)|2|[@chapuyMolecularSubtypesDiffuse2018b]| |
|
| 303 | +|[RARA](RARA)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 304 | +|[RCC](RCC)|2, aSHM|| |
|
| 305 | +|[RFTN1](RFTN1)|2, aSHM|[@dunsCharacterizationDLBCLPMBL2021b; @arthurGenomewideDiscoverySomatic2018]| |
|
| 306 | +|[RFXAP](RFXAP)|2|| |
|
| 307 | +|[RHEX](RHEX)|2, aSHM|| |
|
| 308 | +|[RHOH](RHOH)|2, aSHM|[@pasqualucciHypermutationMultipleProtooncogenes2001a]| |
|
| 309 | +|[RUBCNL](RUBCNL)|2, aSHM|| |
|
| 310 | +|[RUNX1](RUNX1)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 311 | +|[SAMD9L](SAMD9L)|2|[@morinMutationalStructuralAnalysis2013]| |
|
| 312 | +|[SARM1](SARM1)|2|[@morinMutationalStructuralAnalysis2013]| |
|
| 313 | +|[SEL1L3](SEL1L3)|2, aSHM|| |
|
| 314 | +|[SEPTIN9](SEPTIN9)|2, aSHM|| |
|
| 315 | +|[SERPINA9](SERPINA9)|2, aSHM|[@arthurGenomewideDiscoverySomatic2018]| |
|
| 316 | +|[SETD2](SETD2)|2|[@zhangGeneticHeterogeneityDiffuse2013]| |
|
| 317 | +|[SETD5](SETD5)|2|[@reddyGeneticFunctionalDrivers2017; @tiacciPervasiveMutationsJAKSTAT2018b]| |
|
| 318 | +|[SIAH2](SIAH2)|2|[@hubschmannMutationalMechanismsShaping2021b; @reichelFlowSortingExome2015a]| |
|
| 319 | +|[SLC34A2](SLC34A2)|2|[@hubschmannMutationalMechanismsShaping2021b]| |
|
| 320 | +|[SMEK1](SMEK1)|2|[@chapuyMolecularSubtypesDiffuse2018b]| |
|
| 321 | +|[SRRM2](SRRM2)|2|[@morinMutationalStructuralAnalysis2013; @russler-germainMutationsAssociatedProgression2023b]| |
|
| 322 | +|[ST6GAL1](ST6GAL1)|2, aSHM|[@arthurGenomewideDiscoverySomatic2018]| |
|
| 323 | +|[STAT5B](STAT5B)|2|[@zhangGeneticHeterogeneityDiffuse2013; @tiacciPervasiveMutationsJAKSTAT2018b]| |
|
| 324 | +|[SYK](SYK)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 325 | +|[SYPL1](SYPL1)|2|[@morinMutationalStructuralAnalysis2013]| |
|
| 326 | +|[TAP1](TAP1)|2|[@schmitzGeneticsPathogenesisDiffuse2018a]| |
|
| 327 | +|[TBC1D4](TBC1D4)|2, aSHM|[@arthurGenomewideDiscoverySomatic2018]| |
|
| 328 | +|[TCL1A](TCL1A)|2, aSHM|[@grandeGenomewideDiscoverySomatic2019]| |
|
| 329 | +|[TGFBR2](TGFBR2)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 330 | +|[TIPARP](TIPARP)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 331 | +|[TLR2](TLR2)|2|[@beaLandscapeSomaticMutations2013; @chapuyMolecularSubtypesDiffuse2018b]| |
|
| 332 | +|[TRAF3](TRAF3)|2|[@pasqualucciAnalysisCodingGenome2011; @rossiAlterationBIRC3Multiple2011a; @ottoGeneticLesionsTRAF32012a]| |
|
| 333 | +|[TRAF6](TRAF6)|2|[@hubschmannMutationalMechanismsShaping2021b]| |
|
| 334 | +|[TRIP12](TRIP12)|2|| |
|
| 335 | +|[UBE2J1](UBE2J1)|2, aSHM|| |
|
| 336 | +|[UBR5](UBR5)|2|[@pararajalingamCodingNoncodingDrivers2020; @zhangGeneticHeterogeneityDiffuse2013]| |
|
| 337 | +|[UNC5B](UNC5B)|2|[@hubschmannMutationalMechanismsShaping2021b]| |
|
| 338 | +|[UNC5D](UNC5D)|2|| |
|
| 339 | +|[WAC](WAC)|2|[@reddyGeneticFunctionalDrivers2017; @rossiCodingGenomeSplenic2012c]| |
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| 340 | +|[WDFY3](WDFY3)|2|[@morinMutationalStructuralAnalysis2013]| |
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| 341 | +|[WNK1](WNK1)|2|[@thomasGeneticSubgroupsInform2023; @jalladesExomeSequencingIdentifies2017; @hubschmannMutationalMechanismsShaping2021b]| |
|
| 342 | +|[XBP1](XBP1)|2, aSHM|| |
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| 343 | +|[YY1](YY1)|2|[@reddyGeneticFunctionalDrivers2017]| |
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| 344 | +|[ZBTB7A](ZBTB7A)|2|[@reddyGeneticFunctionalDrivers2017; @burkhardtClinicalRelevanceMolecular2022b]| |
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| 345 | +|[ZCCHC7](ZCCHC7)|2, aSHM|[@arthurGenomewideDiscoverySomatic2018]| |
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| 346 | +|[ZEB2](ZEB2)|2|[@zhangGeneticHeterogeneityDiffuse2013]| |
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| 347 | +|[ZFAT](ZFAT)|2|[@reddyGeneticFunctionalDrivers2017]| |
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| 348 | +|[ZFX](ZFX)|2|[@reddyGeneticFunctionalDrivers2017]| |
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| 349 | +|[ZNF217](ZNF217)|2|[@reichelFlowSortingExome2015a; @hubschmannMutationalMechanismsShaping2021b]| |
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| 350 | +|[ZNF423](ZNF423)|2|[@chapuyMolecularSubtypesDiffuse2018b]| |
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| 1121 | -<div id="ref-viganoSomaticIL4RMutations2018b" class="csl-entry"> |
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| 1122 | - |
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| 1123 | -Viganò, Elena, Jay Gunawardana, Anja Mottok, Tessa Van Tol, Katina Mak, |
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| 1124 | -Fong Chun Chan, Lauren Chong, et al. 2018. “Somatic IL4R Mutations in |
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| 1125 | -Primary Mediastinal Large <span class="nocase">B-cell</span> Lymphoma |
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| 1126 | -Lead to Constitutive JAK-STAT Signaling Activation.” *Blood* 131 18: |
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| 1127 | -2036–46. <https://doi.org/10.1182/blood-2017-09-808907>. |
|
| 1128 | - |
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| 1129 | -</div> |
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| 1130 | - |
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| 1131 | -<div id="ref-wenigerMutationsTumorSuppressor2006a" class="csl-entry"> |
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| 1132 | - |
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| 1133 | -Weniger, M. A., I. Melzner, C. K. Menz, S. Wegener, A. J. Bucur, K. |
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| 1134 | -Dorsch, T. Mattfeldt, T. F. E. Barth, and P. Möller. 2006. “Mutations of |
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| 1135 | -the Tumor Suppressor Gene SOCS-1 in Classical Hodgkin Lymphoma Are |
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| 1136 | -Frequent and Associated with Nuclear Phospho-STAT5 Accumulation.” |
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| 1137 | -*Oncogene* 25 18: 2679–84. <https://doi.org/10.1038/sj.onc.1209151>. |
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| 1138 | - |
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| 1139 | -</div> |
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| 1140 | - |
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|
| 1142 | - |
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| 1143 | -Wienand, Kirsty, Bjoern Chapuy, Chip Stewart, Andrew J. Dunford, David |
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| 1144 | -Wu, Jaegil Kim, Atanas Kamburov, et al. 2019. “Genomic Analyses of |
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| 1145 | -Flow-Sorted Hodgkin Reed-Sternberg Cells Reveal Complementary Mechanisms |
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| 1146 | -of Immune Evasion.” *Blood Advances* 3 23: 4065–80. |
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| 1147 | -<https://doi.org/10.1182/bloodadvances.2019001012>. |
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| 1148 | - |
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| 1149 | -</div> |
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| 1151 | -<div id="ref-wildaInactivationARFMDM2p53Pathway2004" class="csl-entry"> |
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| 1152 | - |
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| 1154 | -W. Woessmann. 2004. “Inactivation of the <span |
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| 1155 | -class="nocase">ARF-MDM-2-p53</span> Pathway in Sporadic Burkitt’s |
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| 1156 | -Lymphoma in Children.” *Leukemia* 18 3: 584–88. |
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| 1157 | -<https://doi.org/10.1038/sj.leu.2403254>. |
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| 1158 | - |
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| 1159 | -</div> |
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| 1160 | - |
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| 1161 | -<div id="ref-wuGeneticHeterogeneityPrimary2016" class="csl-entry"> |
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| 1162 | - |
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| 1163 | -Wu, Chenglin, Noel Fcc de Miranda, Longyun Chen, Agata M. Wasik, Larry |
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| 1164 | -Mansouri, Wojciech Jurczak, Krystyna Galazka, et al. 2016. “Genetic |
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| 1165 | -Heterogeneity in Primary and Relapsed Mantle Cell Lymphomas: Impact of |
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| 1166 | -Recurrent CARD11 Mutations.” *Oncotarget* 7 25: 38180–90. |
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| 1167 | -<https://doi.org/10.18632/oncotarget.9500>. |
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| 1168 | - |
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| 1179 | - |
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| 1188 | - |
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| 1219 | - |
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| 1220 | -</div> |
|
| 353 | +# References |
MCL_genes.md
| ... | ... | @@ -1,467 +1,96 @@ |
| 1 | -# MCL genes |
|
| 2 | - |
|
| 3 | -## Origins of MCL genes |
|
| 4 | -```mermaid |
|
| 5 | 1 | --- |
| 6 | -config: |
|
| 7 | - sankey: |
|
| 8 | - showValues: false |
|
| 9 | - linkColor: target |
|
| 10 | - width: 800 |
|
| 11 | - height: 1000 |
|
| 12 | - nodeAlignment: right |
|
| 2 | +title: 'MCL genes' |
|
| 3 | +bibliography: 'morinlab.bib' |
|
| 4 | +csl: 'NLM.csl' |
|
| 5 | +link-citations: true |
|
| 13 | 6 | --- |
| 14 | -sankey-beta |
|
| 15 | -Zhang 2014, MCL Tier 1, 2 |
|
| 16 | -Zhang 2014, MCL Tier 2, 26 |
|
| 17 | -Nadeu 2020, MCL Tier 1, 3 |
|
| 18 | -Nadeu 2020, MCL Tier 2, 2 |
|
| 19 | -Pararajalingam 2020, MCL Tier 1, 6 |
|
| 20 | -Pararajalingam 2020, MCL Tier 2, 1 |
|
| 21 | -Bea 2013, MCL Tier 1, 11 |
|
| 22 | -Bea 2013, MCL Tier 2, 16 |
|
| 23 | -MCL, exome, 28 |
|
| 24 | -exome, Zhang 2014, 28 |
|
| 25 | -MCL, WGS/exome, 7 |
|
| 26 | -WGS/exome, Pararajalingam 2020, 7 |
|
| 27 | -MCL, WGS, 5 |
|
| 28 | -WGS, Nadeu 2020, 5 |
|
| 29 | -MCL, WGS/exome, 27 |
|
| 30 | -WGS/exome, Bea 2013, 27 |
|
| 31 | -``` |
|
| 7 | + |
|
| 8 | +## Origins of MCL genes |
|
| 9 | + |
|
| 10 | + |
|
| 32 | 11 | |
| 33 | 12 | ## Tier 1 MCL genes |
| 34 | 13 | |
| 35 | 14 | ### *23 total* |
| 36 | 15 | |
| 37 | -| Gene | Tier | Relevant references | |
|
| 38 | -|:------------------:|:------------:|:-----------------------------------------------------------------------------------------------| |
|
| 39 | -| [ATM](ATM) | 1 | Beà et al. 2013; Braggio et al. 2012; Reddy et al. 2017 | |
|
| 40 | -| [BIRC3](BIRC3) | 1 | Duns et al. 2021; Rossi et al. 2011; Arthur et al. 2018; Beà et al. 2013 | |
|
| 41 | -| [CARD11](CARD11) | 1 | Wu et al. 2016; Panea et al. 2019; Morin et al. 2011; Yan et al. 2012; Lenz et al. 2008 | |
|
| 42 | -| [CCND1](CCND1) | 1, aSHM | Beà et al. 2013 | |
|
| 43 | -| [DAZAP1](DAZAP1) | 1 | Pararajalingam et al. 2020 | |
|
| 44 | -| [EWSR1](EWSR1) | 1 | Pararajalingam et al. 2020 | |
|
| 45 | -| [HNRNPH1](HNRNPH1) | 1, noncoding | Pararajalingam et al. 2020 | |
|
| 46 | -| [KMT2D](KMT2D) | 1 | Grande et al. 2019; Beà et al. 2013; Morin et al. 2011; Desch et al. 2020; Rossi et al. 2012 | |
|
| 47 | -| [MEF2B](MEF2B) | 1 | Beà et al. 2013; Morin et al. 2011 | |
|
| 48 | -| [NFKBIE](NFKBIE) | 1 | Mansouri et al. 2016; Pararajalingam et al. 2020; Morin et al. 2016 | |
|
| 49 | -| [NOTCH1](NOTCH1) | 1 | Rossi et al. 2012; Love et al. 2012; Pasqualucci et al. 2011; Beà et al. 2013 | |
|
| 50 | -| [NOTCH2](NOTCH2) | 1 | Trøen et al. 2008; Beà et al. 2013; Rossi et al. 2012; Panea et al. 2019 | |
|
| 51 | -| [NSD2](NSD2) | 1 | Beà et al. 2013 | |
|
| 52 | -| [POT1](POT1) | 1 | Zhang et al. 2014 | |
|
| 53 | -| [RB1](RB1) | 1 | Zhang et al. 2014; Morin et al. 2013 | |
|
| 54 | -| [S1PR1](S1PR1) | 1 | Pararajalingam et al. 2020 | |
|
| 55 | -| [SMARCA4](SMARCA4) | 1 | Nadeu et al. 2020; Zhang et al. 2013; Krysiak et al. 2017; Richter et al. 2012 | |
|
| 56 | -| [SP140](SP140) | 1 | Beà et al. 2013 | |
|
| 57 | -| [SYNE1](SYNE1) | 1 | Nadeu et al. 2020 | |
|
| 58 | -| [TERT](TERT) | 1, noncoding | Nadeu et al. 2020 | |
|
| 59 | -| [TLR2](TLR2) | 1 | Chapuy et al. 2018; Beà et al. 2013 | |
|
| 60 | -| [TP53](TP53) | 1 | Rossi et al. 2012; Wilda et al. 2004; Morin et al. 2011; Tiacci et al. 2018; Beà et al. 2013 | |
|
| 61 | -| [UBR5](UBR5) | 1 | Pararajalingam et al. 2020; Zhang et al. 2013 | |
|
| 16 | +|Gene|Tier| Relevant references| |
|
| 17 | +|:-:|:-:|:-| |
|
| 18 | +|[ATM](ATM)|1|[@reddyGeneticFunctionalDrivers2017; @braggioGenomicAnalysisMarginal2012; @beaLandscapeSomaticMutations2013]| |
|
| 19 | +|[BIRC3](BIRC3)|1|[@rossiAlterationBIRC3Multiple2011a; @beaLandscapeSomaticMutations2013; @arthurGenomewideDiscoverySomatic2018; @dunsCharacterizationDLBCLPMBL2021b]| |
|
| 20 | +|[CARD11](CARD11)|1|[@yanBCRTLRSignaling2012a; @lenzOncogenicCARD11Mutations2008; @morinFrequentMutationHistonemodifying2011; @wuGeneticHeterogeneityPrimary2016; @paneaWholeGenomeLandscape2019]| |
|
| 21 | +|[CCND1](CCND1)|1, aSHM|[@beaLandscapeSomaticMutations2013]| |
|
| 22 | +|[DAZAP1](DAZAP1)|1|[@pararajalingamCodingNoncodingDrivers2020]| |
|
| 23 | +|[EWSR1](EWSR1)|1|[@pararajalingamCodingNoncodingDrivers2020]| |
|
| 24 | +|[HNRNPH1](HNRNPH1)|1, noncoding|[@pararajalingamCodingNoncodingDrivers2020]| |
|
| 25 | +|[KMT2D](KMT2D)|1|[@rossiCodingGenomeSplenic2012c; @morinFrequentMutationHistonemodifying2011; @beaLandscapeSomaticMutations2013; @grandeGenomewideDiscoverySomatic2019; @deschGenotypingCirculatingTumor2020]| |
|
| 26 | +|[MEF2B](MEF2B)|1|[@beaLandscapeSomaticMutations2013; @morinFrequentMutationHistonemodifying2011]| |
|
| 27 | +|[NFKBIE](NFKBIE)|1|[@pararajalingamCodingNoncodingDrivers2020; @mansouriFrequentNFKBIEDeletions2016; @morinGeneticLandscapesRelapsed2016]| |
|
| 28 | +|[NOTCH1](NOTCH1)|1|[@rossiCodingGenomeSplenic2012c; @loveGeneticLandscapeMutations2012; @beaLandscapeSomaticMutations2013; @pasqualucciAnalysisCodingGenome2011]| |
|
| 29 | +|[NOTCH2](NOTCH2)|1|[@troenNOTCH2MutationsMarginal2008; @paneaWholeGenomeLandscape2019; @rossiCodingGenomeSplenic2012c; @beaLandscapeSomaticMutations2013]| |
|
| 30 | +|[NSD2](NSD2)|1|[@beaLandscapeSomaticMutations2013]| |
|
| 31 | +|[POT1](POT1)|1|[@zhangGenomicLandscapeMantle2014]| |
|
| 32 | +|[RB1](RB1)|1|[@morinMutationalStructuralAnalysis2013; @zhangGenomicLandscapeMantle2014]| |
|
| 33 | +|[S1PR1](S1PR1)|1|[@pararajalingamCodingNoncodingDrivers2020]| |
|
| 34 | +|[SMARCA4](SMARCA4)|1|[@richterRecurrentMutationID32012a; @nadeuGenomicEpigenomicInsights2020b; @zhangGeneticHeterogeneityDiffuse2013; @krysiakRecurrentSomaticMutations2017b]| |
|
| 35 | +|[SP140](SP140)|1|[@beaLandscapeSomaticMutations2013]| |
|
| 36 | +|[SYNE1](SYNE1)|1|[@nadeuGenomicEpigenomicInsights2020b]| |
|
| 37 | +|[TERT](TERT)|1, noncoding|[@nadeuGenomicEpigenomicInsights2020b]| |
|
| 38 | +|[TLR2](TLR2)|1|[@chapuyMolecularSubtypesDiffuse2018b; @beaLandscapeSomaticMutations2013]| |
|
| 39 | +|[TP53](TP53)|1|[@beaLandscapeSomaticMutations2013; @wildaInactivationARFMDM2p53Pathway2004; @tiacciPervasiveMutationsJAKSTAT2018b; @morinFrequentMutationHistonemodifying2011; @rossiCodingGenomeSplenic2012c]| |
|
| 40 | +|[UBR5](UBR5)|1|[@zhangGeneticHeterogeneityDiffuse2013; @pararajalingamCodingNoncodingDrivers2020]| |
|
| 62 | 41 | |
| 63 | 42 | ## Tier 2 MCL genes |
| 64 | 43 | |
| 65 | 44 | ### *46 total* |
| 66 | 45 | |
| 67 | -| Gene | Tier | Relevant references | |
|
| 68 | -|:--------------------:|:----:|:------------------------------------------------------------------------------| |
|
| 69 | -| [ABCA3](ABCA3) | 2 | Beà et al. 2013 | |
|
| 70 | -| [ABCC9](ABCC9) | 2 | Beà et al. 2013 | |
|
| 71 | -| [ANK2](ANK2) | 2 | Zhang et al. 2014 | |
|
| 72 | -| [ARID1B](ARID1B) | 2 | Reddy et al. 2017 | |
|
| 73 | -| [ATP11C](ATP11C) | 2 | Zhang et al. 2014 | |
|
| 74 | -| [B2M](B2M) | 2 | Pararajalingam et al. 2020; Reichel et al. 2015; Morin et al. 2011 | |
|
| 75 | -| [BCOR](BCOR) | 2 | Nadeu et al. 2020; Jallades et al. 2017 | |
|
| 76 | -| [CDH8](CDH8) | 2 | Zhang et al. 2014 | |
|
| 77 | -| [CHMP4C](CHMP4C) | 2 | Beà et al. 2013 | |
|
| 78 | -| [COL11A1](COL11A1) | 2 | Zhang et al. 2014 | |
|
| 79 | -| [COL16A1](COL16A1) | 2 | Zhang et al. 2014 | |
|
| 80 | -| [CRYBG3](CRYBG3) | 2 | Beà et al. 2013 | |
|
| 81 | -| [CTNNA2](CTNNA2) | 2 | Zhang et al. 2014 | |
|
| 82 | -| [DCP1B](DCP1B) | 2 | Beà et al. 2013 | |
|
| 83 | -| [DHDH](DHDH) | 2 | Zhang et al. 2014 | |
|
| 84 | -| [DLC1](DLC1) | 2 | Zhang et al. 2014 | |
|
| 85 | -| [DLGAP2](DLGAP2) | 2 | Beà et al. 2013 | |
|
| 86 | -| [DNAJC6](DNAJC6) | 2 | Beà et al. 2013 | |
|
| 87 | -| [EIF2AK4](EIF2AK4) | 2 | Zhang et al. 2014 | |
|
| 88 | -| [ESX1](ESX1) | 2 | Zhang et al. 2014 | |
|
| 89 | -| [FAT4](FAT4) | 2 | Parry et al. 2013; Zhang et al. 2014; Morin et al. 2013 | |
|
| 90 | -| [GRIN2A](GRIN2A) | 2 | Zhang et al. 2014 | |
|
| 91 | -| [HEPH](HEPH) | 2 | Zhang et al. 2014 | |
|
| 92 | -| [KCNC2](KCNC2) | 2 | Beà et al. 2013 | |
|
| 93 | -| [KIAA1671](KIAA1671) | 2 | Beà et al. 2013 | |
|
| 94 | -| [KMT2C](KMT2C) | 2 | Sarkozy et al. 2021; Zhang et al. 2014; Zhang et al. 2013; Zhou et al. 2019 | |
|
| 95 | -| [LUZP4](LUZP4) | 2 | Beà et al. 2013 | |
|
| 96 | -| [MRGPRF](MRGPRF) | 2 | Zhang et al. 2014 | |
|
| 97 | -| [NIN](NIN) | 2 | Zhang et al. 2014 | |
|
| 98 | -| [OGDHL](OGDHL) | 2 | Zhang et al. 2014 | |
|
| 99 | -| [PCDHB2](PCDHB2) | 2 | Zhang et al. 2014 | |
|
| 100 | -| [PCSK2](PCSK2) | 2 | Beà et al. 2013 | |
|
| 101 | -| [PDLIM3](PDLIM3) | 2 | Beà et al. 2013 | |
|
| 102 | -| [PLXNB3](PLXNB3) | 2 | Spina et al. 2016; Zhang et al. 2014 | |
|
| 103 | -| [RGS4](RGS4) | 2 | Beà et al. 2013 | |
|
| 104 | -| [ROBO2](ROBO2) | 2 | Zhang et al. 2014 | |
|
| 105 | -| [SALL3](SALL3) | 2 | Love et al. 2012; Zhang et al. 2014 | |
|
| 106 | -| [SI](SI) | 2 | Zhang et al. 2014 | |
|
| 107 | -| [SLC17A6](SLC17A6) | 2 | Beà et al. 2013 | |
|
| 108 | -| [SMARCB1](SMARCB1) | 2 | Nadeu et al. 2020 | |
|
| 109 | -| [SMC1A](SMC1A) | 2 | Zhang et al. 2014 | |
|
| 110 | -| [TBC1D26](TBC1D26) | 2 | Zhang et al. 2014 | |
|
| 111 | -| [TNRC6B](TNRC6B) | 2 | Beà et al. 2013 | |
|
| 112 | -| [TRPM6](TRPM6) | 2 | Beà et al. 2013 | |
|
| 113 | -| [ZNF117](ZNF117) | 2 | Zhang et al. 2014 | |
|
| 114 | -| [ZNF296](ZNF296) | 2 | Zhang et al. 2014 | |
|
| 115 | - |
|
| 116 | -# References |
|
| 117 | - |
|
| 118 | -<div id="refs" class="references csl-bib-body hanging-indent"> |
|
| 119 | - |
|
| 120 | -<div id="ref-arthurGenomewideDiscoverySomatic2018" class="csl-entry"> |
|
| 121 | - |
|
| 122 | -Arthur, Sarah E., Aixiang Jiang, Bruno M. Grande, Miguel Alcaide, Razvan |
|
| 123 | -Cojocaru, Christopher K. Rushton, Anja Mottok, et al. 2018. “Genome-Wide |
|
| 124 | -Discovery of Somatic Regulatory Variants in Diffuse Large <span |
|
| 125 | -class="nocase">B-cell</span> Lymphoma.” *Nature Communications* 9 1: |
|
| 126 | -4001. <https://doi.org/10.1038/s41467-018-06354-3>. |
|
| 127 | - |
|
| 128 | -</div> |
|
| 129 | - |
|
| 130 | -<div id="ref-beaLandscapeSomaticMutations2013" class="csl-entry"> |
|
| 131 | - |
|
| 132 | -Beà, Sílvia, Rafael Valdés-Mas, Alba Navarro, Itziar Salaverria, David |
|
| 133 | -Martín-Garcia, Pedro Jares, Eva Giné, et al. 2013. “Landscape of Somatic |
|
| 134 | -Mutations and Clonal Evolution in Mantle Cell Lymphoma.” *Proceedings of |
|
| 135 | -the National Academy of Sciences* 110 45: 18250–55. |
|
| 136 | -<https://doi.org/10.1073/pnas.1314608110>. |
|
| 137 | - |
|
| 138 | -</div> |
|
| 139 | - |
|
| 140 | -<div id="ref-braggioGenomicAnalysisMarginal2012" class="csl-entry"> |
|
| 141 | - |
|
| 142 | -Braggio, Esteban, Ahmet Dogan, Jonathan J. Keats, Wee J. Chng, Gaofeng |
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| 143 | -Huang, Julie M. Matthews, Matthew J. Maurer, et al. 2012. “Genomic |
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| 144 | -Analysis of Marginal Zone and Lymphoplasmacytic Lymphomas Identified |
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| 145 | -Common and Disease-Specific Abnormalities.” *Modern Pathology: An |
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| 146 | -Official Journal of the United States and Canadian Academy of Pathology, |
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| 147 | -Inc* 25 5: 651–60. <https://doi.org/10.1038/modpathol.2011.213>. |
|
| 148 | - |
|
| 149 | -</div> |
|
| 150 | - |
|
| 151 | -<div id="ref-chapuyMolecularSubtypesDiffuse2018b" class="csl-entry"> |
|
| 152 | - |
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| 153 | -Chapuy, Bjoern, Chip Stewart, Andrew J. Dunford, Jaegil Kim, Atanas |
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| 154 | -Kamburov, Robert A. Redd, Mike S. Lawrence, et al. 2018. “Molecular |
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| 155 | -Subtypes of Diffuse Large B Cell Lymphoma Are Associated with Distinct |
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| 156 | -Pathogenic Mechanisms and Outcomes.” *Nature Medicine* 24 5: 679–90. |
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| 157 | -<https://doi.org/10.1038/s41591-018-0016-8>. |
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| 158 | - |
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| 159 | -</div> |
|
| 160 | - |
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| 161 | -<div id="ref-deschGenotypingCirculatingTumor2020" class="csl-entry"> |
|
| 162 | - |
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| 163 | -Desch, Ann-Kathrin, Kristin Hartung, Ante Botzen, Alexander Brobeil, |
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| 164 | -Mathias Rummel, Lars Kurch, Thomas Georgi, et al. 2020. “Genotyping |
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| 193 | -Sequencing Identifies Recurrent BCOR Alterations and the Absence of |
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| 223 | -Miles, Kristy L. Richards, et al. 2012. “The Genetic Landscape of |
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| 268 | -</div> |
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| 270 | -<div id="ref-nadeuGenomicEpigenomicInsights2020b" class="csl-entry"> |
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| 271 | - |
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| 272 | -Nadeu, F., D. Martín-García, G. Clot, A. Díaz-Navarro, M. Duran-Ferrer, |
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|
| 46 | +|Gene|Tier| Relevant references| |
|
| 47 | +|:-:|:-:|:-| |
|
| 48 | +|[ABCA3](ABCA3)|2|[@beaLandscapeSomaticMutations2013]| |
|
| 49 | +|[ABCC9](ABCC9)|2|[@beaLandscapeSomaticMutations2013]| |
|
| 50 | +|[ANK2](ANK2)|2|[@zhangGenomicLandscapeMantle2014]| |
|
| 51 | +|[ARID1B](ARID1B)|2|[@reddyGeneticFunctionalDrivers2017]| |
|
| 52 | +|[ATP11C](ATP11C)|2|[@zhangGenomicLandscapeMantle2014]| |
|
| 53 | +|[B2M](B2M)|2|[@pararajalingamCodingNoncodingDrivers2020; @reichelFlowSortingExome2015a; @morinFrequentMutationHistonemodifying2011]| |
|
| 54 | +|[BCOR](BCOR)|2|[@jalladesExomeSequencingIdentifies2017; @nadeuGenomicEpigenomicInsights2020b]| |
|
| 55 | +|[CDH8](CDH8)|2|[@zhangGenomicLandscapeMantle2014]| |
|
| 56 | +|[CHMP4C](CHMP4C)|2|[@beaLandscapeSomaticMutations2013]| |
|
| 57 | +|[COL11A1](COL11A1)|2|[@zhangGenomicLandscapeMantle2014]| |
|
| 58 | +|[COL16A1](COL16A1)|2|[@zhangGenomicLandscapeMantle2014]| |
|
| 59 | +|[CRYBG3](CRYBG3)|2|[@beaLandscapeSomaticMutations2013]| |
|
| 60 | +|[CTNNA2](CTNNA2)|2|[@zhangGenomicLandscapeMantle2014]| |
|
| 61 | +|[DCP1B](DCP1B)|2|[@beaLandscapeSomaticMutations2013]| |
|
| 62 | +|[DHDH](DHDH)|2|[@zhangGenomicLandscapeMantle2014]| |
|
| 63 | +|[DLC1](DLC1)|2|[@zhangGenomicLandscapeMantle2014]| |
|
| 64 | +|[DLGAP2](DLGAP2)|2|[@beaLandscapeSomaticMutations2013]| |
|
| 65 | +|[DNAJC6](DNAJC6)|2|[@beaLandscapeSomaticMutations2013]| |
|
| 66 | +|[EIF2AK4](EIF2AK4)|2|[@zhangGenomicLandscapeMantle2014]| |
|
| 67 | +|[ESX1](ESX1)|2|[@zhangGenomicLandscapeMantle2014]| |
|
| 68 | +|[FAT4](FAT4)|2|[@parryWholeExomeSequencing2013; @zhangGenomicLandscapeMantle2014; @morinMutationalStructuralAnalysis2013]| |
|
| 69 | +|[GRIN2A](GRIN2A)|2|[@zhangGenomicLandscapeMantle2014]| |
|
| 70 | +|[HEPH](HEPH)|2|[@zhangGenomicLandscapeMantle2014]| |
|
| 71 | +|[KCNC2](KCNC2)|2|[@beaLandscapeSomaticMutations2013]| |
|
| 72 | +|[KIAA1671](KIAA1671)|2|[@beaLandscapeSomaticMutations2013]| |
|
| 73 | +|[KMT2C](KMT2C)|2|[@sarkozyMutationalLandscapeGray2021a; @zhangGeneticHeterogeneityDiffuse2013; @zhangGenomicLandscapeMantle2014; @zhouSporadicEndemicBurkitt2019]| |
|
| 74 | +|[LUZP4](LUZP4)|2|[@beaLandscapeSomaticMutations2013]| |
|
| 75 | +|[MRGPRF](MRGPRF)|2|[@zhangGenomicLandscapeMantle2014]| |
|
| 76 | +|[NIN](NIN)|2|[@zhangGenomicLandscapeMantle2014]| |
|
| 77 | +|[OGDHL](OGDHL)|2|[@zhangGenomicLandscapeMantle2014]| |
|
| 78 | +|[PCDHB2](PCDHB2)|2|[@zhangGenomicLandscapeMantle2014]| |
|
| 79 | +|[PCSK2](PCSK2)|2|[@beaLandscapeSomaticMutations2013]| |
|
| 80 | +|[PDLIM3](PDLIM3)|2|[@beaLandscapeSomaticMutations2013]| |
|
| 81 | +|[PLXNB3](PLXNB3)|2|[@zhangGenomicLandscapeMantle2014; @spinaGeneticsNodalMarginal2016b]| |
|
| 82 | +|[RGS4](RGS4)|2|[@beaLandscapeSomaticMutations2013]| |
|
| 83 | +|[ROBO2](ROBO2)|2|[@zhangGenomicLandscapeMantle2014]| |
|
| 84 | +|[SALL3](SALL3)|2|[@loveGeneticLandscapeMutations2012; @zhangGenomicLandscapeMantle2014]| |
|
| 85 | +|[SI](SI)|2|[@zhangGenomicLandscapeMantle2014]| |
|
| 86 | +|[SLC17A6](SLC17A6)|2|[@beaLandscapeSomaticMutations2013]| |
|
| 87 | +|[SMARCB1](SMARCB1)|2|[@nadeuGenomicEpigenomicInsights2020b]| |
|
| 88 | +|[SMC1A](SMC1A)|2|[@zhangGenomicLandscapeMantle2014]| |
|
| 89 | +|[TBC1D26](TBC1D26)|2|[@zhangGenomicLandscapeMantle2014]| |
|
| 90 | +|[TNRC6B](TNRC6B)|2|[@beaLandscapeSomaticMutations2013]| |
|
| 91 | +|[TRPM6](TRPM6)|2|[@beaLandscapeSomaticMutations2013]| |
|
| 92 | +|[ZNF117](ZNF117)|2|[@zhangGenomicLandscapeMantle2014]| |
|
| 93 | +|[ZNF296](ZNF296)|2|[@zhangGenomicLandscapeMantle2014]| |
|
| 281 | 94 | |
| 282 | -Panea, R., C. Love, Jennifer R. Shingleton, Anupama Reddy, J. Bailey, A. |
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| 283 | -Moormann, J. Otieno, et al. 2019. “The Whole Genome Landscape of Burkitt |
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| 284 | -Lymphoma Subtypes.” *Blood*. <https://doi.org/10.1182/blood.2019001880>. |
|
| 285 | 95 | |
| 286 | -</div> |
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| 287 | - |
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| 288 | -<div id="ref-pararajalingamCodingNoncodingDrivers2020" |
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| 289 | -class="csl-entry"> |
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| 290 | - |
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| 291 | -Pararajalingam, Prasath, Krysta M. Coyle, Sarah E. Arthur, Nicole |
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| 292 | -Thomas, Miguel Alcaide, Barbara Meissner, Merrill Boyle, et al. 2020. |
|
| 293 | -“Coding and Noncoding Drivers of Mantle Cell Lymphoma Identified Through |
|
| 294 | -Exome and Genome Sequencing.” *Blood* 136 5: 572–84. |
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| 295 | -<https://doi.org/10.1182/blood.2019002385>. |
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| 296 | - |
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| 297 | -</div> |
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| 298 | - |
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| 299 | -<div id="ref-parryWholeExomeSequencing2013" class="csl-entry"> |
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| 300 | - |
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| 301 | -Parry, Marina, Matthew J. J. Rose-Zerilli, Jane Gibson, Sarah Ennis, |
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| 302 | -Renata Walewska, Jade Forster, Helen Parker, et al. 2013. “Whole Exome |
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| 303 | -Sequencing Identifies Novel Recurrently Mutated Genes in Patients with |
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| 304 | -Splenic Marginal Zone Lymphoma.” *PloS One* 8 12: e83244. |
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| 305 | -<https://doi.org/10.1371/journal.pone.0083244>. |
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| 306 | - |
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| 307 | -</div> |
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| 308 | - |
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| 309 | -<div id="ref-pasqualucciAnalysisCodingGenome2011" class="csl-entry"> |
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| 310 | - |
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| 311 | -Pasqualucci, Laura, Vladimir Trifonov, Giulia Fabbri, Jing Ma, Davide |
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| 312 | -Rossi, Annalisa Chiarenza, Victoria A. Wells, et al. 2011. “Analysis of |
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| 313 | -the Coding Genome of Diffuse Large <span class="nocase">B-cell</span> |
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| 314 | -Lymphoma.” *Nature Genetics* 43 9: 830–37. |
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| 315 | -<https://doi.org/10.1038/ng.892>. |
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| 316 | - |
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| 317 | -</div> |
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| 318 | - |
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| 319 | -<div id="ref-reddyGeneticFunctionalDrivers2017" class="csl-entry"> |
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| 320 | - |
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| 321 | -Reddy, Anupama, Jenny Zhang, Nicholas S Davis, Andrea B Moffitt, |
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| 322 | -Cassandra L Love, Alexander Waldrop, Sirpa Leppa, et al. 2017. “Genetic |
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| 323 | -and Functional Drivers of Diffuse Large B Cell Lymphoma.” *Cell* 171 |
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| 324 | -2: 481–494.e15. |
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| 325 | - |
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| 326 | -</div> |
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| 327 | - |
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| 328 | -<div id="ref-reichelFlowSortingExome2015a" class="csl-entry"> |
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| 329 | - |
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| 330 | -Reichel, Jonathan, Amy Chadburn, Paul G. Rubinstein, Lisa Giulino-Roth, |
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| 331 | -Wayne Tam, Yifang Liu, Rafael Gaiolla, et al. 2015. “Flow Sorting and |
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| 332 | -Exome Sequencing Reveal the Oncogenome of Primary Hodgkin and |
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| 333 | -Reed-Sternberg Cells.” *Blood* 125 7: 1061–72. |
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| 334 | -<https://doi.org/10.1182/blood-2014-11-610436>. |
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| 335 | - |
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| 338 | -<div id="ref-richterRecurrentMutationID32012a" class="csl-entry"> |
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| 339 | - |
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| 340 | -Richter, Julia, Matthias Schlesner, Steve Hoffmann, Markus Kreuz, Ellen |
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| 341 | -Leich, Birgit Burkhardt, Maciej Rosolowski, et al. 2012. “Recurrent |
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| 342 | -Mutation of the ID3 Gene in Burkitt Lymphoma Identified by Integrated |
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| 343 | -Genome, Exome and Transcriptome Sequencing.” *Nature Genetics* 44 12: |
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| 344 | -1316–20. <https://doi.org/10.1038/ng.2469>. |
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| 345 | - |
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| 349 | - |
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| 350 | -Rossi, Davide, Silvia Deaglio, David Dominguez-Sola, Silvia Rasi, |
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| 351 | -Tiziana Vaisitti, Claudio Agostinelli, Valeria Spina, et al. 2011. |
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| 352 | -“Alteration of BIRC3 and Multiple Other <span |
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| 353 | -class="nocase">NF-κB</span> Pathway Genes in Splenic Marginal Zone |
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| 360 | - |
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| 361 | -Rossi, Davide, Vladimir Trifonov, Marco Fangazio, Alessio Bruscaggin, |
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| 362 | -Silvia Rasi, Valeria Spina, Sara Monti, et al. 2012. “The Coding Genome |
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| 363 | -of Splenic Marginal Zone Lymphoma: Activation of NOTCH2 and Other |
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| 382 | -Cascione, Alessio Bruscaggin, Elisa Spaccarotella, et al. 2016. “The |
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| 383 | -Genetics of Nodal Marginal Zone Lymphoma.” *Blood* 128 10: 1362–73. |
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| 440 | -Zhang, Jenny, Vladimir Grubor, Cassandra L Love, Anjishnu Banerjee, |
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| 441 | -Kristy L Richards, Piotr A Mieczkowski, Cherie Dunphy, et al. 2013. |
|
| 442 | -“Genetic Heterogeneity of Diffuse Large <span |
|
| 443 | -class="nocase">B-cell</span> Lymphoma.” January. |
|
| 444 | - |
|
| 445 | -</div> |
|
| 446 | - |
|
| 447 | -<div id="ref-zhangGenomicLandscapeMantle2014" class="csl-entry"> |
|
| 448 | - |
|
| 449 | -Zhang, Jenny, Dereje Jima, Andrea B. Moffitt, Qingquan Liu, Magdalena |
|
| 450 | -Czader, Eric D. Hsi, Yuri Fedoriw, et al. 2014. “The Genomic Landscape |
|
| 451 | -of Mantle Cell Lymphoma Is Related to the Epigenetically Determined |
|
| 452 | -Chromatin State of Normal B Cells.” *Blood* 123 19: 2988–96. |
|
| 453 | -<https://doi.org/10.1182/blood-2013-07-517177>. |
|
| 454 | - |
|
| 455 | -</div> |
|
| 456 | - |
|
| 457 | -<div id="ref-zhouSporadicEndemicBurkitt2019" class="csl-entry"> |
|
| 458 | - |
|
| 459 | -Zhou, Peixun, Alex E. Blain, Alexander M. Newman, Masood Zaka, George |
|
| 460 | -Chagaluka, Filbert R. Adlar, Ugonna T. Offor, et al. 2019. “Sporadic and |
|
| 461 | -Endemic Burkitt Lymphoma Have Frequent FOXO1 Mutations but Distinct |
|
| 462 | -Hotspots in the AKT Recognition Motif.” *Blood Advances* 3 14: |
|
| 463 | -2118–27. <https://doi.org/10.1182/bloodadvances.2018029546>. |
|
| 464 | - |
|
| 465 | -</div> |
|
| 466 | - |
|
| 467 | -</div> |
|
| 96 | +# References |
MZL_genes.md
| ... | ... | @@ -0,0 +1,143 @@ |
| 1 | +--- |
|
| 2 | +title: 'MZL genes' |
|
| 3 | +bibliography: 'morinlab.bib' |
|
| 4 | +csl: 'NLM.csl' |
|
| 5 | +link-citations: true |
|
| 6 | +--- |
|
| 7 | + |
|
| 8 | +## Origins of MZL genes |
|
| 9 | + |
|
| 10 | + |
|
| 11 | + |
|
| 12 | +## Tier 1 MZL genes |
|
| 13 | + |
|
| 14 | +### *42 total* |
|
| 15 | + |
|
| 16 | +|Gene|Tier| Relevant references| |
|
| 17 | +|:-:|:-:|:-| |
|
| 18 | +|[ACTB](ACTB)|1|[@lohrDiscoveryPrioritizationSomatic2012a; @wienandGenomicAnalysesFlowsorted2019b]| |
|
| 19 | +|[ARID1A](ARID1A)|1|[@krysiakRecurrentSomaticMutations2017b; @rossiCodingGenomeSplenic2012c; @zhangGeneticHeterogeneityDiffuse2013; @wienandGenomicAnalysesFlowsorted2019b; @loveGeneticLandscapeMutations2012]| |
|
| 20 | +|[ATM](ATM)|1|[@beaLandscapeSomaticMutations2013; @reddyGeneticFunctionalDrivers2017; @braggioGenomicAnalysisMarginal2012]| |
|
| 21 | +|[BCL10](BCL10)|1|[@spinaGeneticsNodalMarginal2016b; @russler-germainMutationsAssociatedProgression2023b; @morinFrequentMutationHistonemodifying2011]| |
|
| 22 | +|[BCL7A](BCL7A)|1|[@reichelFlowSortingExome2015a; @grandeGenomewideDiscoverySomatic2019; @arthurGenomewideDiscoverySomatic2018; @krysiakRecurrentSomaticMutations2017b]| |
|
| 23 | +|[BIRC3](BIRC3)|1|[@rossiAlterationBIRC3Multiple2011a; @beaLandscapeSomaticMutations2013; @arthurGenomewideDiscoverySomatic2018; @dunsCharacterizationDLBCLPMBL2021b]| |
|
| 24 | +|[BRAF](BRAF)|1|[@loveGeneticLandscapeMutations2012; @tiacciBRAFMutationsHairycell2011a]| |
|
| 25 | +|[BTG1](BTG1)|1|[@burkhardtClinicalRelevanceMolecular2022b; @sarkozyMutationalLandscapeGray2021a; @morinFrequentMutationHistonemodifying2011]| |
|
| 26 | +|[CARD11](CARD11)|1|[@lenzOncogenicCARD11Mutations2008; @wuGeneticHeterogeneityPrimary2016; @morinFrequentMutationHistonemodifying2011; @paneaWholeGenomeLandscape2019; @yanBCRTLRSignaling2012a]| |
|
| 27 | +|[CCND3](CCND3)|1|[@jalladesExomeSequencingIdentifies2017; @morinFrequentMutationHistonemodifying2011; @deschGenotypingCirculatingTumor2020; @richterRecurrentMutationID32012a]| |
|
| 28 | +|[CXCR4](CXCR4)|1|[@krysiakRecurrentSomaticMutations2017b; @paneaWholeGenomeLandscape2019; @khodabakhshiRecurrentTargetsAberrant2012]| |
|
| 29 | +|[DTX1](DTX1)|1|[@gomezUltraDeepSequencingReveals2023; @schmitzGeneticsPathogenesisDiffuse2018a; @paneaWholeGenomeLandscape2019; @rossiCodingGenomeSplenic2012c]| |
|
| 30 | +|[EP300](EP300)|1|[@pasqualucciInactivatingMutationsAcetyltransferase2011a; @rossiCodingGenomeSplenic2012c; @paneaWholeGenomeLandscape2019]| |
|
| 31 | +|[EZH2](EZH2)|1|[@loveGeneticLandscapeMutations2012; @mottokIntegrativeGenomicAnalysis2019b; @morinSomaticMutationsAltering2010a]| |
|
| 32 | +|[FAS](FAS)|1|[@spinaGeneticsNodalMarginal2016b; @schollMutationsRegionFAS2007]| |
|
| 33 | +|[FAT1](FAT1)|1|[@spinaGeneticsNodalMarginal2016b]| |
|
| 34 | +|[FOXO1](FOXO1)|1|[@schmitzBurkittLymphomaPathogenesis2012; @morinFrequentMutationHistonemodifying2011; @dunsCharacterizationDLBCLPMBL2021b]| |
|
| 35 | +|[H1-4](H1-4)|1|| |
|
| 36 | +|[H1-5](H1-5)|1|| |
|
| 37 | +|[ID3](ID3)|1|[@richterRecurrentMutationID32012a; @spinaGeneticsNodalMarginal2016b; @schmitzBurkittLymphomaPathogenesis2012]| |
|
| 38 | +|[KLF2](KLF2)|1|[@jalladesExomeSequencingIdentifies2017; @pasqualucciAnalysisCodingGenome2011; @deschGenotypingCirculatingTumor2020]| |
|
| 39 | +|[KLHL6](KLHL6)|1|[@paneaWholeGenomeLandscape2019; @morinFrequentMutationHistonemodifying2011; @ganapathiGeneticLandscapeDural2016]| |
|
| 40 | +|[KMT2D](KMT2D)|1|[@beaLandscapeSomaticMutations2013; @grandeGenomewideDiscoverySomatic2019; @deschGenotypingCirculatingTumor2020; @rossiCodingGenomeSplenic2012c; @morinFrequentMutationHistonemodifying2011]| |
|
| 41 | +|[MAP3K14](MAP3K14)|1|[@rossiAlterationBIRC3Multiple2011a; @ottoGeneticLesionsTRAF32012a]| |
|
| 42 | +|[MPEG1](MPEG1)|1|[@morinMutationalStructuralAnalysis2013]| |
|
| 43 | +|[MYD88](MYD88)|1|[@ngoOncogenicallyActiveMYD882011a; @yanBCRTLRSignaling2012a]| |
|
| 44 | +|[NCOR2](NCOR2)|1|[@sarkozyMutationalLandscapeGray2021a; @schmitzBurkittLymphomaPathogenesis2012; @spinaGeneticsNodalMarginal2016b]| |
|
| 45 | +|[NOL9](NOL9)|1|[@spinaGeneticsNodalMarginal2016b; @schmitzGeneticsPathogenesisDiffuse2018a]| |
|
| 46 | +|[NOTCH1](NOTCH1)|1|[@rossiCodingGenomeSplenic2012c; @loveGeneticLandscapeMutations2012; @beaLandscapeSomaticMutations2013; @pasqualucciAnalysisCodingGenome2011]| |
|
| 47 | +|[NOTCH2](NOTCH2)|1|[@troenNOTCH2MutationsMarginal2008; @paneaWholeGenomeLandscape2019; @rossiCodingGenomeSplenic2012c; @beaLandscapeSomaticMutations2013]| |
|
| 48 | +|[PCLO](PCLO)|1|[@lohrDiscoveryPrioritizationSomatic2012a]| |
|
| 49 | +|[POU2AF1](POU2AF1)|1|[@krysiakRecurrentSomaticMutations2017b]| |
|
| 50 | +|[PTPRD](PTPRD)|1|[@spinaGeneticsNodalMarginal2016b]| |
|
| 51 | +|[SIN3A](SIN3A)|1|[@rossiCodingGenomeSplenic2012c; @grandeGenomewideDiscoverySomatic2019]| |
|
| 52 | +|[SOCS1](SOCS1)|1|[@morinFrequentMutationHistonemodifying2011; @wenigerMutationsTumorSuppressor2006a]| |
|
| 53 | +|[SPEN](SPEN)|1|[@rossiCodingGenomeSplenic2012c; @sarkozyMutationalLandscapeGray2021a]| |
|
| 54 | +|[STAT6](STAT6)|1|[@ritzRecurrentMutationsSTAT62009a; @yildizActivatingSTAT6Mutations2015c]| |
|
| 55 | +|[TBL1XR1](TBL1XR1)|1|[@mareschalWholeExomeSequencing2016; @rossiCodingGenomeSplenic2012c]| |
|
| 56 | +|[TNFAIP3](TNFAIP3)|1|[@compagnoMutationsMultipleGenes2009a; @rossiAlterationBIRC3Multiple2011a; @schmitzTNFAIP3A20Tumor2009a]| |
|
| 57 | +|[TNFRSF14](TNFRSF14)|1|[@spinaGeneticsNodalMarginal2016b; @cheungAcquiredTNFRSF14Mutations2010a]| |
|
| 58 | +|[TP53](TP53)|1|[@tiacciPervasiveMutationsJAKSTAT2018b; @morinFrequentMutationHistonemodifying2011; @rossiCodingGenomeSplenic2012c; @beaLandscapeSomaticMutations2013; @wildaInactivationARFMDM2p53Pathway2004]| |
|
| 59 | +|[TRAF3](TRAF3)|1|[@ottoGeneticLesionsTRAF32012a; @rossiAlterationBIRC3Multiple2011a; @pasqualucciAnalysisCodingGenome2011]| |
|
| 60 | + |
|
| 61 | +## Tier 2 MZL genes |
|
| 62 | + |
|
| 63 | +### *74 total* |
|
| 64 | + |
|
| 65 | +|Gene|Tier| Relevant references| |
|
| 66 | +|:-:|:-:|:-| |
|
| 67 | +|[ABCA13](ABCA13)|2|[@spinaGeneticsNodalMarginal2016b; @sarkozyMutationalLandscapeGray2021a]| |
|
| 68 | +|[ACTG1](ACTG1)|2|[@hubschmannMutationalMechanismsShaping2021b; @spinaGeneticsNodalMarginal2016b; @deschGenotypingCirculatingTumor2020]| |
|
| 69 | +|[ADD2](ADD2)|2|[@spinaGeneticsNodalMarginal2016b]| |
|
| 70 | +|[AMN](AMN)|2|[@spinaGeneticsNodalMarginal2016b]| |
|
| 71 | +|[AMOTL1](AMOTL1)|2|[@parryWholeExomeSequencing2013]| |
|
| 72 | +|[AOC2](AOC2)|2|[@spinaGeneticsNodalMarginal2016b]| |
|
| 73 | +|[ARHGAP20](ARHGAP20)|2|[@jalladesExomeSequencingIdentifies2017]| |
|
| 74 | +|[ARHGEF15](ARHGEF15)|2|[@jalladesExomeSequencingIdentifies2017]| |
|
| 75 | +|[ARHGEF17](ARHGEF17)|2|[@jalladesExomeSequencingIdentifies2017]| |
|
| 76 | +|[BCOR](BCOR)|2|[@jalladesExomeSequencingIdentifies2017; @nadeuGenomicEpigenomicInsights2020b]| |
|
| 77 | +|[C6orf103](C6orf103)|2|[@spinaGeneticsNodalMarginal2016b]| |
|
| 78 | +|[CBFA2T3](CBFA2T3)|2|[@parryWholeExomeSequencing2013]| |
|
| 79 | +|[CD79A](CD79A)|2|[@rossiCodingGenomeSplenic2012c; @burkhardtClinicalRelevanceMolecular2022b]| |
|
| 80 | +|[CD9B](CD9B)|2|[@vandenbrandRecurrentMutationsGenes2017]| |
|
| 81 | +|[CDC42BPB](CDC42BPB)|2|[@spinaGeneticsNodalMarginal2016b]| |
|
| 82 | +|[CDKN2A](CDKN2A)|2|[@grandeGenomewideDiscoverySomatic2019; @spinaGeneticsNodalMarginal2016b; @morinMutationalStructuralAnalysis2013]| |
|
| 83 | +|[CLGN](CLGN)|2|[@spinaGeneticsNodalMarginal2016b]| |
|
| 84 | +|[CNKSR2](CNKSR2)|2|[@spinaGeneticsNodalMarginal2016b]| |
|
| 85 | +|[CREBBP](CREBBP)|2|[@dunsCharacterizationDLBCLPMBL2021b; @parryWholeExomeSequencing2013; @loveGeneticLandscapeMutations2012; @pasqualucciInactivatingMutationsAcetyltransferase2011a]| |
|
| 86 | +|[DNAH5](DNAH5)|2|[@jalladesExomeSequencingIdentifies2017; @morinMutationalStructuralAnalysis2013]| |
|
| 87 | +|[DNAH7](DNAH7)|2|[@jalladesExomeSequencingIdentifies2017]| |
|
| 88 | +|[DNAI1](DNAI1)|2|[@jalladesExomeSequencingIdentifies2017]| |
|
| 89 | +|[DOCK6](DOCK6)|2|[@jalladesExomeSequencingIdentifies2017]| |
|
| 90 | +|[DSP](DSP)|2|| |
|
| 91 | +|[DTNB](DTNB)|2|| |
|
| 92 | +|[DTX3L](DTX3L)|2|[@jalladesExomeSequencingIdentifies2017]| |
|
| 93 | +|[EGR1](EGR1)|2|[@reichelFlowSortingExome2015a; @rossiCodingGenomeSplenic2012c; @krysiakRecurrentSomaticMutations2017b]| |
|
| 94 | +|[EGR2](EGR2)|2|[@rossiCodingGenomeSplenic2012c]| |
|
| 95 | +|[EZH1](EZH1)|2|[@jalladesExomeSequencingIdentifies2017]| |
|
| 96 | +|[FAT4](FAT4)|2|[@zhangGenomicLandscapeMantle2014; @morinMutationalStructuralAnalysis2013; @parryWholeExomeSequencing2013]| |
|
| 97 | +|[FBXO11](FBXO11)|2|[@hubschmannMutationalMechanismsShaping2021b; @richterRecurrentMutationID32012a; @parryWholeExomeSequencing2013]| |
|
| 98 | +|[GPR98](GPR98)|2|[@spinaGeneticsNodalMarginal2016b]| |
|
| 99 | +|[GPS2](GPS2)|2|[@rossiCodingGenomeSplenic2012c]| |
|
| 100 | +|[HIST1H1D](HIST1H1D)|2|[@morinMutationalStructuralAnalysis2013; @krysiakRecurrentSomaticMutations2017b; @jalladesExomeSequencingIdentifies2017]| |
|
| 101 | +|[HIST1H2AD](HIST1H2AD)|2|[@jalladesExomeSequencingIdentifies2017]| |
|
| 102 | +|[HIST1H2AG](HIST1H2AG)|2|[@morinMutationalStructuralAnalysis2013; @paneaWholeGenomeLandscape2019; @krysiakRecurrentSomaticMutations2017b; @rossiCodingGenomeSplenic2012c]| |
|
| 103 | +|[HIST1H2BK](HIST1H2BK)|2|[@paneaWholeGenomeLandscape2019; @rossiCodingGenomeSplenic2012c]| |
|
| 104 | +|[HIST4H4](HIST4H4)|2|[@jalladesExomeSequencingIdentifies2017]| |
|
| 105 | +|[HRAS](HRAS)|2|[@jalladesExomeSequencingIdentifies2017; @reddyGeneticFunctionalDrivers2017]| |
|
| 106 | +|[IKBKB](IKBKB)|2|[@rossiAlterationBIRC3Multiple2011a; @wienandGenomicAnalysesFlowsorted2019b; @reddyGeneticFunctionalDrivers2017]| |
|
| 107 | +|[KAT6A](KAT6A)|2|[@jalladesExomeSequencingIdentifies2017]| |
|
| 108 | +|[KDM6A](KDM6A)|2|[@jalladesExomeSequencingIdentifies2017]| |
|
| 109 | +|[KIF26A](KIF26A)|2|[@jalladesExomeSequencingIdentifies2017]| |
|
| 110 | +|[LRP1B](LRP1B)|2|[@spinaGeneticsNodalMarginal2016b]| |
|
| 111 | +|[MCRS1](MCRS1)|2|[@rossiCodingGenomeSplenic2012c]| |
|
| 112 | +|[MGA](MGA)|2|[@zhangGeneticHeterogeneityDiffuse2013; @jalladesExomeSequencingIdentifies2017]| |
|
| 113 | +|[MSL2](MSL2)|2|[@rossiCodingGenomeSplenic2012c]| |
|
| 114 | +|[MYC](MYC)|2|[@jalladesExomeSequencingIdentifies2017; @dunsCharacterizationDLBCLPMBL2021b; @johnstonCmycHypermutationBurkitt1992; @pasqualucciHypermutationMultipleProtooncogenes2001a]| |
|
| 115 | +|[MYLK](MYLK)|2|[@jalladesExomeSequencingIdentifies2017]| |
|
| 116 | +|[NCOA6](NCOA6)|2|[@jalladesExomeSequencingIdentifies2017]| |
|
| 117 | +|[NRAS](NRAS)|2|[@jalladesExomeSequencingIdentifies2017]| |
|
| 118 | +|[PACRG](PACRG)|2|[@spinaGeneticsNodalMarginal2016b]| |
|
| 119 | +|[PARK2](PARK2)|2|[@spinaGeneticsNodalMarginal2016b]| |
|
| 120 | +|[PLA2G4D](PLA2G4D)|2|[@parryWholeExomeSequencing2013]| |
|
| 121 | +|[PLXNB3](PLXNB3)|2|[@spinaGeneticsNodalMarginal2016b; @zhangGenomicLandscapeMantle2014]| |
|
| 122 | +|[RAF1](RAF1)|2|[@jalladesExomeSequencingIdentifies2017]| |
|
| 123 | +|[RAPGEF2](RAPGEF2)|2|| |
|
| 124 | +|[RCOR1](RCOR1)|2|[@spinaGeneticsNodalMarginal2016b]| |
|
| 125 | +|[RFTN1](RFTN1)|2|[@arthurGenomewideDiscoverySomatic2018; @dunsCharacterizationDLBCLPMBL2021b]| |
|
| 126 | +|[ROCK1](ROCK1)|2|[@jalladesExomeSequencingIdentifies2017]| |
|
| 127 | +|[RPL1L](RPL1L)|2|[@spinaGeneticsNodalMarginal2016b]| |
|
| 128 | +|[SAMD5](SAMD5)|2|[@spinaGeneticsNodalMarginal2016b]| |
|
| 129 | +|[SCG3](SCG3)|2|[@spinaGeneticsNodalMarginal2016b]| |
|
| 130 | +|[STXBP5](STXBP5)|2|[@spinaGeneticsNodalMarginal2016b]| |
|
| 131 | +|[SWAP70](SWAP70)|2|[@rossiCodingGenomeSplenic2012c]| |
|
| 132 | +|[TAF1](TAF1)|2|[@morinMutationalStructuralAnalysis2013; @spinaGeneticsNodalMarginal2016b]| |
|
| 133 | +|[TBK1](TBK1)|2|[@jalladesExomeSequencingIdentifies2017]| |
|
| 134 | +|[TCTN2](TCTN2)|2|[@spinaGeneticsNodalMarginal2016b]| |
|
| 135 | +|[TNIP2](TNIP2)|2|[@vandenbrandRecurrentMutationsGenes2017]| |
|
| 136 | +|[TRRAP](TRRAP)|2|[@rossiCodingGenomeSplenic2012c; @parryWholeExomeSequencing2013]| |
|
| 137 | +|[USH2A](USH2A)|2|[@parryWholeExomeSequencing2013]| |
|
| 138 | +|[WAC](WAC)|2|[@reddyGeneticFunctionalDrivers2017; @rossiCodingGenomeSplenic2012c]| |
|
| 139 | +|[WNK1](WNK1)|2|[@jalladesExomeSequencingIdentifies2017; @thomasGeneticSubgroupsInform2023; @hubschmannMutationalMechanismsShaping2021b]| |
|
| 140 | +|[ZNF9](ZNF9)|2|[@spinaGeneticsNodalMarginal2016b]| |
|
| 141 | + |
|
| 142 | + |
|
| 143 | +# References |
PMBL_genes.md
| ... | ... | @@ -0,0 +1,185 @@ |
| 1 | +--- |
|
| 2 | +title: 'PMBL genes' |
|
| 3 | +bibliography: 'morinlab.bib' |
|
| 4 | +csl: 'NLM.csl' |
|
| 5 | +link-citations: true |
|
| 6 | +--- |
|
| 7 | + |
|
| 8 | +## Origins of PMBL genes |
|
| 9 | + |
|
| 10 | + |
|
| 11 | + |
|
| 12 | +## Tier 1 PMBL genes |
|
| 13 | + |
|
| 14 | +### *76 total* |
|
| 15 | + |
|
| 16 | +|Gene|Tier| Relevant references| |
|
| 17 | +|:-:|:-:|:-| |
|
| 18 | +|[ACTB](ACTB)|1|[@lohrDiscoveryPrioritizationSomatic2012a; @wienandGenomicAnalysesFlowsorted2019b]| |
|
| 19 | +|[ARID1A](ARID1A)|1|[@rossiCodingGenomeSplenic2012c; @krysiakRecurrentSomaticMutations2017b; @zhangGeneticHeterogeneityDiffuse2013; @loveGeneticLandscapeMutations2012; @wienandGenomicAnalysesFlowsorted2019b]| |
|
| 20 | +|[ARID5B](ARID5B)|1|[@gomezUltraDeepSequencingReveals2023; @reddyGeneticFunctionalDrivers2017]| |
|
| 21 | +|[B2M](B2M)|1|[@pararajalingamCodingNoncodingDrivers2020; @reichelFlowSortingExome2015a; @morinFrequentMutationHistonemodifying2011]| |
|
| 22 | +|[BIRC6](BIRC6)|1|[@sarkozyMutationalLandscapeGray2021a; @reddyGeneticFunctionalDrivers2017]| |
|
| 23 | +|[BTG1](BTG1)|1|[@morinFrequentMutationHistonemodifying2011; @sarkozyMutationalLandscapeGray2021a; @burkhardtClinicalRelevanceMolecular2022b]| |
|
| 24 | +|[CD58](CD58)|1|[@morinFrequentMutationHistonemodifying2011; @schneiderAlterationsCD58Gene2015a]| |
|
| 25 | +|[CD83](CD83)|1|[@dunsCharacterizationDLBCLPMBL2021b; @paneaWholeGenomeLandscape2019; @russler-germainMutationsAssociatedProgression2023b; @morinMutationalStructuralAnalysis2013]| |
|
| 26 | +|[CDKN2A](CDKN2A)|1|[@grandeGenomewideDiscoverySomatic2019; @spinaGeneticsNodalMarginal2016b; @morinMutationalStructuralAnalysis2013]| |
|
| 27 | +|[CHD8](CHD8)|1|[@grandeGenomewideDiscoverySomatic2019; @reddyGeneticFunctionalDrivers2017]| |
|
| 28 | +|[CIITA](CIITA)|1|[@mottokGenomicAlterationsCIITA2015b; @morinFrequentMutationHistonemodifying2011]| |
|
| 29 | +|[CISH](CISH)|1|[@mottokIntegrativeGenomicAnalysis2019b]| |
|
| 30 | +|[CREBBP](CREBBP)|1|[@dunsCharacterizationDLBCLPMBL2021b; @parryWholeExomeSequencing2013; @loveGeneticLandscapeMutations2012; @pasqualucciInactivatingMutationsAcetyltransferase2011a]| |
|
| 31 | +|[CSF2RB](CSF2RB)|1|[@reichelFlowSortingExome2015a]| |
|
| 32 | +|[DDX3X](DDX3X)|1|[@schmitzGeneticsPathogenesisDiffuse2018a; @schmitzBurkittLymphomaPathogenesis2012; @mottokIntegrativeGenomicAnalysis2019b]| |
|
| 33 | +|[DTX1](DTX1)|1|[@rossiCodingGenomeSplenic2012c; @paneaWholeGenomeLandscape2019; @schmitzGeneticsPathogenesisDiffuse2018a; @gomezUltraDeepSequencingReveals2023]| |
|
| 34 | +|[DUSP2](DUSP2)|1|[@morinMutationalStructuralAnalysis2013; @dunsCharacterizationDLBCLPMBL2021b]| |
|
| 35 | +|[EBF1](EBF1)|1|[@reichelFlowSortingExome2015a; @thomasGeneticSubgroupsInform2023; @bohleRoleEarlyBcell2013]| |
|
| 36 | +|[EEF1A1](EEF1A1)|1|[@reichelFlowSortingExome2015a; @hubschmannMutationalMechanismsShaping2021b]| |
|
| 37 | +|[ETS1](ETS1)|1|[@paneaWholeGenomeLandscape2019; @morinFrequentMutationHistonemodifying2011]| |
|
| 38 | +|[EWSR1](EWSR1)|1|[@pararajalingamCodingNoncodingDrivers2020]| |
|
| 39 | +|[EZH2](EZH2)|1|[@mottokIntegrativeGenomicAnalysis2019b; @morinSomaticMutationsAltering2010a; @loveGeneticLandscapeMutations2012]| |
|
| 40 | +|[FAS](FAS)|1|[@schollMutationsRegionFAS2007; @spinaGeneticsNodalMarginal2016b]| |
|
| 41 | +|[FAT1](FAT1)|1|[@spinaGeneticsNodalMarginal2016b]| |
|
| 42 | +|[FAT4](FAT4)|1|[@parryWholeExomeSequencing2013; @zhangGenomicLandscapeMantle2014; @morinMutationalStructuralAnalysis2013]| |
|
| 43 | +|[GNA13](GNA13)|1|[@loveGeneticLandscapeMutations2012; @reichelFlowSortingExome2015a; @morinFrequentMutationHistonemodifying2011]| |
|
| 44 | +|[HIST1H1B](HIST1H1B)|1|[@krysiakRecurrentSomaticMutations2017b; @sarkozyMutationalLandscapeGray2021a; @chapuyMolecularSubtypesDiffuse2018b]| |
|
| 45 | +|[HIST1H1C](HIST1H1C)|1|[@morinFrequentMutationHistonemodifying2011; @paneaWholeGenomeLandscape2019]| |
|
| 46 | +|[HIST1H1D](HIST1H1D)|1|[@krysiakRecurrentSomaticMutations2017b; @jalladesExomeSequencingIdentifies2017; @morinMutationalStructuralAnalysis2013]| |
|
| 47 | +|[HIST1H1E](HIST1H1E)|1|[@krysiakRecurrentSomaticMutations2017b; @grandeGenomewideDiscoverySomatic2019; @morinMutationalStructuralAnalysis2013; @reichelFlowSortingExome2015a]| |
|
| 48 | +|[HLA-B](HLA-B)|1|[@wienandGenomicAnalysesFlowsorted2019b]| |
|
| 49 | +|[IL4R](IL4R)|1|[@viganoSomaticIL4RMutations2018b; @dunsCharacterizationDLBCLPMBL2021b]| |
|
| 50 | +|[IRF8](IRF8)|1|[@paneaWholeGenomeLandscape2019; @morinFrequentMutationHistonemodifying2011; @mottokIntegrativeGenomicAnalysis2019b]| |
|
| 51 | +|[ITPKB](ITPKB)|1|[@schmitzGeneticsPathogenesisDiffuse2018a; @reichelFlowSortingExome2015a]| |
|
| 52 | +|[JAK1](JAK1)|1|[@mottokIntegrativeGenomicAnalysis2019b; @zhangGeneticHeterogeneityDiffuse2013]| |
|
| 53 | +|[KMT2C](KMT2C)|1|[@sarkozyMutationalLandscapeGray2021a; @zhangGeneticHeterogeneityDiffuse2013; @zhangGenomicLandscapeMantle2014; @zhouSporadicEndemicBurkitt2019]| |
|
| 54 | +|[LTB](LTB)|1|[@deschGenotypingCirculatingTumor2020; @chapuyMolecularSubtypesDiffuse2018b; @paneaWholeGenomeLandscape2019]| |
|
| 55 | +|[MAP3K14](MAP3K14)|1|[@rossiAlterationBIRC3Multiple2011a; @ottoGeneticLesionsTRAF32012a]| |
|
| 56 | +|[MS4A1](MS4A1)|1|[@mottokIntegrativeGenomicAnalysis2019b; @rushtonGeneticEvolutionaryPatterns2020]| |
|
| 57 | +|[NFKBIA](NFKBIA)|1|[@wienandGenomicAnalysesFlowsorted2019b; @lakeMutationsNFKBIAEncoding2009; @russler-germainMutationsAssociatedProgression2023b]| |
|
| 58 | +|[NFKBIE](NFKBIE)|1|[@mansouriFrequentNFKBIEDeletions2016; @morinGeneticLandscapesRelapsed2016; @pararajalingamCodingNoncodingDrivers2020]| |
|
| 59 | +|[OSBPL10](OSBPL10)|1|[@arthurGenomewideDiscoverySomatic2018]| |
|
| 60 | +|[P2RY8](P2RY8)|1|[@lohrDiscoveryPrioritizationSomatic2012a; @muppidiLossSignalingGa132014b]| |
|
| 61 | +|[PCLO](PCLO)|1|[@lohrDiscoveryPrioritizationSomatic2012a]| |
|
| 62 | +|[PHIP](PHIP)|1|| |
|
| 63 | +|[PIM1](PIM1)|1|[@dunsCharacterizationDLBCLPMBL2021b; @pasqualucciHypermutationMultipleProtooncogenes2001a; @burkhardtClinicalRelevanceMolecular2022b]| |
|
| 64 | +|[PIM2](PIM2)|1|[@arthurGenomewideDiscoverySomatic2018; @reichelFlowSortingExome2015a]| |
|
| 65 | +|[PRKDC](PRKDC)|1|[@schmitzGeneticsPathogenesisDiffuse2018a; @hubschmannMutationalMechanismsShaping2021b]| |
|
| 66 | +|[PTPN1](PTPN1)|1|[@gunawardanaRecurrentSomaticMutations2014c]| |
|
| 67 | +|[PTPRD](PTPRD)|1|[@spinaGeneticsNodalMarginal2016b]| |
|
| 68 | +|[RHOA](RHOA)|1|[@richterRecurrentMutationID32012a]| |
|
| 69 | +|[S1PR2](S1PR2)|1|[@muppidiLossSignalingGa132014b; @morinFrequentMutationHistonemodifying2011]| |
|
| 70 | +|[SGK1](SGK1)|1|[@dunsCharacterizationDLBCLPMBL2021b; @morinFrequentMutationHistonemodifying2011]| |
|
| 71 | +|[SIN3A](SIN3A)|1|[@rossiCodingGenomeSplenic2012c; @grandeGenomewideDiscoverySomatic2019]| |
|
| 72 | +|[SMARCA2](SMARCA2)|1|| |
|
| 73 | +|[SMARCA4](SMARCA4)|1|[@richterRecurrentMutationID32012a; @zhangGeneticHeterogeneityDiffuse2013; @krysiakRecurrentSomaticMutations2017b; @nadeuGenomicEpigenomicInsights2020b]| |
|
| 74 | +|[SOCS1](SOCS1)|1|[@wenigerMutationsTumorSuppressor2006a; @morinFrequentMutationHistonemodifying2011]| |
|
| 75 | +|[SPEN](SPEN)|1|[@rossiCodingGenomeSplenic2012c; @sarkozyMutationalLandscapeGray2021a]| |
|
| 76 | +|[STAT3](STAT3)|1|[@ohgamiSTAT3MutationsAre2014]| |
|
| 77 | +|[STAT6](STAT6)|1|[@ritzRecurrentMutationsSTAT62009a; @yildizActivatingSTAT6Mutations2015c]| |
|
| 78 | +|[TAP1](TAP1)|1|[@schmitzGeneticsPathogenesisDiffuse2018a]| |
|
| 79 | +|[TBL1XR1](TBL1XR1)|1|[@mareschalWholeExomeSequencing2016; @rossiCodingGenomeSplenic2012c]| |
|
| 80 | +|[TCF3](TCF3)|1|[@schmitzBurkittLymphomaPathogenesis2012]| |
|
| 81 | +|[TET3](TET3)|1|| |
|
| 82 | +|[TMSB4X](TMSB4X)|1|[@albuquerqueEnhancingKnowledgeDiscovery2017a]| |
|
| 83 | +|[TNFAIP3](TNFAIP3)|1|[@compagnoMutationsMultipleGenes2009a; @rossiAlterationBIRC3Multiple2011a; @schmitzTNFAIP3A20Tumor2009a]| |
|
| 84 | +|[TNFRSF1B](TNFRSF1B)|1|| |
|
| 85 | +|[TP53](TP53)|1|[@wildaInactivationARFMDM2p53Pathway2004; @beaLandscapeSomaticMutations2013; @tiacciPervasiveMutationsJAKSTAT2018b; @morinFrequentMutationHistonemodifying2011; @rossiCodingGenomeSplenic2012c]| |
|
| 86 | +|[TRAF3](TRAF3)|1|[@pasqualucciAnalysisCodingGenome2011; @rossiAlterationBIRC3Multiple2011a; @ottoGeneticLesionsTRAF32012a]| |
|
| 87 | +|[UBE2A](UBE2A)|1|[@reichelFlowSortingExome2015a; @reddyGeneticFunctionalDrivers2017]| |
|
| 88 | +|[UBR5](UBR5)|1|[@pararajalingamCodingNoncodingDrivers2020; @zhangGeneticHeterogeneityDiffuse2013]| |
|
| 89 | +|[UNC5C](UNC5C)|1|| |
|
| 90 | +|[VPS13B](VPS13B)|1|| |
|
| 91 | +|[WEE1](WEE1)|1|[@reichelFlowSortingExome2015a; @schmitzGeneticsPathogenesisDiffuse2018a]| |
|
| 92 | +|[XPO1](XPO1)|1|[@jardinRecurrentMutationsExportin2016a; @mareschalWholeExomeSequencing2016]| |
|
| 93 | +|[ZFP36L1](ZFP36L1)|1|[@morinFrequentMutationHistonemodifying2011; @paneaWholeGenomeLandscape2019; @reichelFlowSortingExome2015a]| |
|
| 94 | + |
|
| 95 | +## Tier 2 PMBL genes |
|
| 96 | + |
|
| 97 | +### *82 total* |
|
| 98 | + |
|
| 99 | +|Gene|Tier| Relevant references| |
|
| 100 | +|:-:|:-:|:-| |
|
| 101 | +|[ABCA13](ABCA13)|2|[@sarkozyMutationalLandscapeGray2021a; @spinaGeneticsNodalMarginal2016b]| |
|
| 102 | +|[ACTG1](ACTG1)|2|[@hubschmannMutationalMechanismsShaping2021b; @spinaGeneticsNodalMarginal2016b; @deschGenotypingCirculatingTumor2020]| |
|
| 103 | +|[AKAP6](AKAP6)|2|[@tiacciPervasiveMutationsJAKSTAT2018b]| |
|
| 104 | +|[ARIH2](ARIH2)|2|[@reichelFlowSortingExome2015a]| |
|
| 105 | +|[AXDND1](AXDND1)|2|[@gomezUltraDeepSequencingReveals2023]| |
|
| 106 | +|[BCL2](BCL2)|2|[@burkhardtClinicalRelevanceMolecular2022b; @tanakaFrequentIncidenceSomatic1992; @morinFrequentMutationHistonemodifying2011; @sarkozyMutationalLandscapeGray2021a]| |
|
| 107 | +|[BCL7A](BCL7A)|2|[@grandeGenomewideDiscoverySomatic2019; @reichelFlowSortingExome2015a; @krysiakRecurrentSomaticMutations2017b; @arthurGenomewideDiscoverySomatic2018]| |
|
| 108 | +|[BIRC3](BIRC3)|2|[@rossiAlterationBIRC3Multiple2011a; @beaLandscapeSomaticMutations2013; @arthurGenomewideDiscoverySomatic2018; @dunsCharacterizationDLBCLPMBL2021b]| |
|
| 109 | +|[CCND3](CCND3)|2|[@jalladesExomeSequencingIdentifies2017; @morinFrequentMutationHistonemodifying2011; @deschGenotypingCirculatingTumor2020; @richterRecurrentMutationID32012a]| |
|
| 110 | +|[CDH2](CDH2)|2|[@deschGenotypingCirculatingTumor2020]| |
|
| 111 | +|[CDH5](CDH5)|2|[@gomezUltraDeepSequencingReveals2023]| |
|
| 112 | +|[CXCR5](CXCR5)|2|[@mottokIntegrativeGenomicAnalysis2019b; @schmitzGeneticsPathogenesisDiffuse2018a]| |
|
| 113 | +|[DGKB](DGKB)|2|[@tiacciPervasiveMutationsJAKSTAT2018b]| |
|
| 114 | +|[DMD](DMD)|2|[@reichelFlowSortingExome2015a]| |
|
| 115 | +|[DNAH12](DNAH12)|2|[@wienandGenomicAnalysesFlowsorted2019b]| |
|
| 116 | +|[EGR1](EGR1)|2|[@reichelFlowSortingExome2015a; @krysiakRecurrentSomaticMutations2017b; @rossiCodingGenomeSplenic2012c]| |
|
| 117 | +|[EPHA7](EPHA7)|2|[@mottokIntegrativeGenomicAnalysis2019b]| |
|
| 118 | +|[EZR](EZR)|2|[@deschGenotypingCirculatingTumor2020]| |
|
| 119 | +|[FOXO1](FOXO1)|2|[@morinFrequentMutationHistonemodifying2011; @dunsCharacterizationDLBCLPMBL2021b; @schmitzBurkittLymphomaPathogenesis2012]| |
|
| 120 | +|[GCSAM](GCSAM)|2|[@mottokIntegrativeGenomicAnalysis2019b]| |
|
| 121 | +|[GPR126](GPR126)|2|[@wenigerMutationsTumorSuppressor2006a]| |
|
| 122 | +|[HECW2](HECW2)|2|[@reichelFlowSortingExome2015a]| |
|
| 123 | +|[HELLS](HELLS)|2|[@reichelFlowSortingExome2015a]| |
|
| 124 | +|[HIST1H2BC](HIST1H2BC)|2|[@reddyGeneticFunctionalDrivers2017; @mottokIntegrativeGenomicAnalysis2019b; @krysiakRecurrentSomaticMutations2017b]| |
|
| 125 | +|[HIST1H3B](HIST1H3B)|2|[@zhangGeneticHeterogeneityDiffuse2013; @reichelFlowSortingExome2015a]| |
|
| 126 | +|[HIST1H4C](HIST1H4C)|2|[@reichelFlowSortingExome2015a]| |
|
| 127 | +|[HIST1H4E](HIST1H4E)|2|[@mottokIntegrativeGenomicAnalysis2019b]| |
|
| 128 | +|[HIST1H4J](HIST1H4J)|2|[@paneaWholeGenomeLandscape2019; @mottokIntegrativeGenomicAnalysis2019b]| |
|
| 129 | +|[HLA-A](HLA-A)|2|[@deschGenotypingCirculatingTumor2020]| |
|
| 130 | +|[HLA-C](HLA-C)|2|[@gomezUltraDeepSequencingReveals2023]| |
|
| 131 | +|[HRNR](HRNR)|2|[@dunsCharacterizationDLBCLPMBL2021b]| |
|
| 132 | +|[IGLL5](IGLL5)|2|[@russler-germainMutationsAssociatedProgression2023b; @paneaWholeGenomeLandscape2019; @deschGenotypingCirculatingTumor2020]| |
|
| 133 | +|[IKBKB](IKBKB)|2|[@rossiAlterationBIRC3Multiple2011a; @wienandGenomicAnalysesFlowsorted2019b; @reddyGeneticFunctionalDrivers2017]| |
|
| 134 | +|[IL13RA1](IL13RA1)|2|[@mottokIntegrativeGenomicAnalysis2019b]| |
|
| 135 | +|[IL1RAPL2](IL1RAPL2)|2|[@mottokIntegrativeGenomicAnalysis2019b]| |
|
| 136 | +|[IRF2BP2](IRF2BP2)|2|[@mottokIntegrativeGenomicAnalysis2019b]| |
|
| 137 | +|[IRF4](IRF4)|2|[@morinFrequentMutationHistonemodifying2011; @mottokIntegrativeGenomicAnalysis2019b]| |
|
| 138 | +|[ITGB2](ITGB2)|2|| |
|
| 139 | +|[ITPR3](ITPR3)|2|[@tiacciPervasiveMutationsJAKSTAT2018b; @loveGeneticLandscapeMutations2012]| |
|
| 140 | +|[JUNB](JUNB)|2|[@reddyGeneticFunctionalDrivers2017; @mottokIntegrativeGenomicAnalysis2019b]| |
|
| 141 | +|[KLF2](KLF2)|2|[@pasqualucciAnalysisCodingGenome2011; @deschGenotypingCirculatingTumor2020; @jalladesExomeSequencingIdentifies2017]| |
|
| 142 | +|[KMT2D](KMT2D)|2|[@rossiCodingGenomeSplenic2012c; @morinFrequentMutationHistonemodifying2011; @beaLandscapeSomaticMutations2013; @grandeGenomewideDiscoverySomatic2019; @deschGenotypingCirculatingTumor2020]| |
|
| 143 | +|[LIMD2](LIMD2)|2|[@gomezUltraDeepSequencingReveals2023]| |
|
| 144 | +|[LPHN3](LPHN3)|2|[@dunsCharacterizationDLBCLPMBL2021b]| |
|
| 145 | +|[LRRN3](LRRN3)|2|[@morinMutationalStructuralAnalysis2013; @sarkozyMutationalLandscapeGray2021a]| |
|
| 146 | +|[MAGEC2](MAGEC2)|2|[@mottokIntegrativeGenomicAnalysis2019b]| |
|
| 147 | +|[MCL1](MCL1)|2|[@reddyGeneticFunctionalDrivers2017; @dunsCharacterizationDLBCLPMBL2021b; @paneaWholeGenomeLandscape2019]| |
|
| 148 | +|[MFHAS1](MFHAS1)|2|[@sarkozyMutationalLandscapeGray2021a]| |
|
| 149 | +|[MPDZ](MPDZ)|2|[@reichelFlowSortingExome2015a; @morinMutationalStructuralAnalysis2013]| |
|
| 150 | +|[MYB](MYB)|2|[@deschGenotypingCirculatingTumor2020; @reddyGeneticFunctionalDrivers2017]| |
|
| 151 | +|[MYC](MYC)|2|[@pasqualucciHypermutationMultipleProtooncogenes2001a; @jalladesExomeSequencingIdentifies2017; @dunsCharacterizationDLBCLPMBL2021b; @johnstonCmycHypermutationBurkitt1992]| |
|
| 152 | +|[NCOR2](NCOR2)|2|[@spinaGeneticsNodalMarginal2016b; @schmitzBurkittLymphomaPathogenesis2012; @sarkozyMutationalLandscapeGray2021a]| |
|
| 153 | +|[NEK1](NEK1)|2|[@reichelFlowSortingExome2015a]| |
|
| 154 | +|[NFKB2](NFKB2)|2|[@mottokIntegrativeGenomicAnalysis2019b; @reddyGeneticFunctionalDrivers2017]| |
|
| 155 | +|[NSD2](NSD2)|2|[@beaLandscapeSomaticMutations2013]| |
|
| 156 | +|[NUP214](NUP214)|2|[@tiacciPervasiveMutationsJAKSTAT2018b]| |
|
| 157 | +|[OR13C2](OR13C2)|2|[@gomezUltraDeepSequencingReveals2023]| |
|
| 158 | +|[PCBP1](PCBP1)|2|[@schmitzBurkittLymphomaPathogenesis2012]| |
|
| 159 | +|[PCDH7](PCDH7)|2|| |
|
| 160 | +|[PRUNE2](PRUNE2)|2|[@tiacciPervasiveMutationsJAKSTAT2018b]| |
|
| 161 | +|[RANBP2](RANBP2)|2|[@reichelFlowSortingExome2015a]| |
|
| 162 | +|[RBM38](RBM38)|2|[@wienandGenomicAnalysesFlowsorted2019b]| |
|
| 163 | +|[RDH12](RDH12)|2|| |
|
| 164 | +|[RELN](RELN)|2|[@sarkozyMutationalLandscapeGray2021a]| |
|
| 165 | +|[RFTN1](RFTN1)|2|[@arthurGenomewideDiscoverySomatic2018; @dunsCharacterizationDLBCLPMBL2021b]| |
|
| 166 | +|[RGS1](RGS1)|2|[@mottokIntegrativeGenomicAnalysis2019b]| |
|
| 167 | +|[SCN9A](SCN9A)|2|| |
|
| 168 | +|[SENP7](SENP7)|2|[@reichelFlowSortingExome2015a]| |
|
| 169 | +|[SETD5](SETD5)|2|[@reddyGeneticFunctionalDrivers2017; @tiacciPervasiveMutationsJAKSTAT2018b]| |
|
| 170 | +|[SETDB1](SETDB1)|2|[@reichelFlowSortingExome2015a]| |
|
| 171 | +|[SIAH2](SIAH2)|2|[@hubschmannMutationalMechanismsShaping2021b; @reichelFlowSortingExome2015a]| |
|
| 172 | +|[SMAD3](SMAD3)|2|| |
|
| 173 | +|[STAT5B](STAT5B)|2|[@zhangGeneticHeterogeneityDiffuse2013; @tiacciPervasiveMutationsJAKSTAT2018b]| |
|
| 174 | +|[STRAP](STRAP)|2|| |
|
| 175 | +|[TBC1D15](TBC1D15)|2|[@reichelFlowSortingExome2015a]| |
|
| 176 | +|[TICRR](TICRR)|2|[@reichelFlowSortingExome2015a]| |
|
| 177 | +|[TNIP1](TNIP1)|2|[@tiacciPervasiveMutationsJAKSTAT2018b]| |
|
| 178 | +|[TRIP11](TRIP11)|2|[@reichelFlowSortingExome2015a]| |
|
| 179 | +|[VMP1](VMP1)|2|[@mottokIntegrativeGenomicAnalysis2019b]| |
|
| 180 | +|[WDR87](WDR87)|2|[@dunsCharacterizationDLBCLPMBL2021b]| |
|
| 181 | +|[ZCCHC11](ZCCHC11)|2|[@tiacciPervasiveMutationsJAKSTAT2018b]| |
|
| 182 | +|[ZNF217](ZNF217)|2|[@reichelFlowSortingExome2015a; @hubschmannMutationalMechanismsShaping2021b]| |
|
| 183 | + |
|
| 184 | + |
|
| 185 | +# References |