Supplemental_Methods_and_Results.md
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## Sources of B-cell lymphoma genes
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Any study that described at least one gene as recurrently mutated in DLBCL, FL or BL was eligible to contribute to the gene lists. The current lists relied on a total of 37 studies for DLBCL,[@albuquerqueEnhancingKnowledgeDiscovery2017; @arthurGenomewideDiscoverySomatic2018; @bohleRoleEarlyBcell2013; @chapuyMolecularSubtypesDiffuse2018; @compagnoMutationsMultipleGenes2009; @davisChronicActiveBcellreceptor2010; @drevalGeneticSubdivisionsFollicular2023; @dunsCharacterizationDLBCLPMBL2021; @fanComprehensiveCharacterizationDriver2020; @hubschmannMutationalMechanismsShaping2021; @khodabakhshiRecurrentTargetsAberrant2012; @kwanhianMicroRNA142Mutated202012; @lenzOncogenicCARD11Mutations2008; @lohrDiscoveryPrioritizationSomatic2012; @mareschalWholeExomeSequencing2016; @morinFrequentMutationHistonemodifying2011; @morinGeneticLandscapesRelapsed2016; @morinMutationalStructuralAnalysis2013; @morinSomaticMutationsAltering2010; @ngoOncogenicallyActiveMYD882011; @novakWholeexomeAnalysisReveals2015; @okosunRecurrentMTORC1activatingRRAGC2016; @pararajalingamCodingNoncodingDrivers2020; @pasqualucciAnalysisCodingGenome2011; @pasqualucciHypermutationMultipleProtooncogenes2001; @pasqualucciInactivatingMutationsAcetyltransferase2011; @pasqualucciInactivationPRDM1BLIMP12006; @reddyGeneticFunctionalDrivers2017; @rushtonGeneticEvolutionaryPatterns2020; @schmitzGeneticsPathogenesisDiffuse2018; @schollMutationsRegionFAS2007; @shinBRAFV600EMAP2K12015; @tanakaFrequentIncidenceSomatic1992; @thomasMutationalAnalysisIkappaBalpha2004; @tiacciBRAFMutationsHairycell2011; @yildizActivatingSTAT6Mutations2015; @zhangGeneticHeterogeneityDiffuse2013]
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-15 studies for FL,[@barariaCathepsinAlterationsInduce2020; @cheungAcquiredTNFRSF14Mutations2010; @drevalGeneticSubdivisionsFollicular2023; @hubschmannMutationalMechanismsShaping2021; @krysiakRecurrentSomaticMutations2017; @laurentFollicularLymphomaComprises2024; @louissaintPediatrictypeNodalFollicular2016; @maSubtypespecificCooccurringGenetic2022; @morinFrequentMutationHistonemodifying2011; @morinSomaticMutationsAltering2010; @okosunRecurrentMTORC1activatingRRAGC2016; @pasqualucciInactivatingMutationsAcetyltransferase2011; @rossiAberrantSomaticHypermutation2006; @russler-germainMutationsAssociatedProgression2023; @yildizActivatingSTAT6Mutations2015] and 13 studies for BL.[@abateDistinctViralMutational2015; @burkhardtClinicalRelevanceMolecular2022; @grandeGenomewideDiscoverySomatic2019; @johnstonCmycHypermutationBurkitt1992; @loveGeneticLandscapeMutations2012; @maSubtypespecificCooccurringGenetic2022; @muppidiLossSignalingGa132014; @paneaWholeGenomeLandscape2019; @richterRecurrentMutationID32012; @schmitzBurkittLymphomaPathogenesis2012; @thomasGeneticSubgroupsInform2023; @wildaInactivationARFMDM2p53Pathway2004; @zhouSporadicEndemicBurkitt2019]
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+15 studies for FL,[@barariaCathepsinAlterationsInduce2020; @cheungAcquiredTNFRSF14Mutations2010; @drevalGeneticSubdivisionsFollicular2023; @hubschmannMutationalMechanismsShaping2021; @krysiakRecurrentSomaticMutations2017; @laurentFollicularLymphomaComprises2024; @louissaintPediatrictypeNodalFollicular2016; @maSubtypespecificCooccurringGenetic2022; @morinFrequentMutationHistonemodifying2011; @morinSomaticMutationsAltering2010; @okosunRecurrentMTORC1activatingRRAGC2016; @pasqualucciInactivatingMutationsAcetyltransferase2011; @rossiAberrantSomaticHypermutation2006; @russler-germainMutationsAssociatedProgression2023; @yildizActivatingSTAT6Mutations2015] and 13 studies for BL.[@abateDistinctViralMutational2015; @burkhardtClinicalRelevanceMolecular2022; @grandeGenomewideDiscoverySomatic2019; @johnstonCmycHypermutationBurkitt1992; @loveGeneticLandscapeMutations2012; @maSubtypespecificCooccurringGenetic2022; @muppidiLossSignalingGa132014; @paneaWholeGenomeLandscape2019; @richterRecurrentMutationID32012; @schmitzBurkittLymphomaPathogenesis2012; @thomasGeneticSubgroupsInform2023; @wildaInactivationARFMDM2p53Pathway2004; @zhouSporadicEndemicBurkitt2019] The number of Tier 1, 2 and 3 genes originating from each of these studies is summarized below.
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+<figure>
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+<img src="" alt="flags1" style="width:500px;"/>
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+<figcaption><strong>Supplemental Figure S1. Comparing FLAGS rank in the DLBCL genes.</strong> <br>
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+The FLAGS rank of DLBCL genes in Tier 1, 2 and 3 is compared. The genes in the COSMIC CGC list are included for comparison. Values closer to 1 indicate the gene has a higher number of rare germline variants.
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+</figcaption>
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+</figure>
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## Procedure for gene retirement (Tier 3)
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<figure>
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<img src="FLAGS_rank_boxplot.png" alt="flags1" style="width:500px;"/>
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-<figcaption><strong>Supplemental Figure S1. Comparing FLAGS rank in the DLBCL genes.</strong> <br>
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+<figcaption><strong>Supplemental Figure S2. Comparing FLAGS rank in the DLBCL genes.</strong> <br>
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The FLAGS rank of DLBCL genes in Tier 1, 2 and 3 is compared. The genes in the COSMIC CGC list are included for comparison. Values closer to 1 indicate the gene has a higher number of rare germline variants.
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</figcaption>
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</figure>