Changes in 504ee69: add refs

				Supplemental_Methods_and_Results.md
			
          @@ -6,6 +6,10 @@ csl: NLM.csl

           # Supplemental Methods and Results

          +## Studies

          +

          +Any study that described at least one gene as recurrently mutated in DLBCL, FL or BL was eligible to contribute to the gene lists. This included 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

          +

           ## Procedure for gene retirement (Tier 3) 

           The pattern of mutations in Tier 2 genes has, by definition, not been independently reproduced. To counteract the continued growth of Tier 2 over time, genes can be retired to Tier 3 in certain scenarios. Specifically, when a new analysis or scrutiny of the original data draws the validity of a gene  or study into question, Tier 2 genes from a study may be retired idividually or *en masse*, depending on the situation. Ideally, the entire set of mutations that led to the original nomination of each gene will be reviewed individually to reduce the likelihood that a gene is retired unnecessarily. However, when systematic manual review is impossible, genes may be retired when the originating study is deemd to have low reproducibility. In these rare situations, all Tier 2 genes from that study can be moved to Tier 3.

...	...	@@ -6,6 +6,10 @@ csl: NLM.csl
6	6
7	7	# Supplemental Methods and Results
8	8
	9	+## Studies
	10	+
	11	+Any study that described at least one gene as recurrently mutated in DLBCL, FL or BL was eligible to contribute to the gene lists. This included 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
	12	+
9	13	## Procedure for gene retirement (Tier 3)
10	14
11	15	The pattern of mutations in Tier 2 genes has, by definition, not been independently reproduced. To counteract the continued growth of Tier 2 over time, genes can be retired to Tier 3 in certain scenarios. Specifically, when a new analysis or scrutiny of the original data draws the validity of a gene or study into question, Tier 2 genes from a study may be retired idividually or en masse, depending on the situation. Ideally, the entire set of mutations that led to the original nomination of each gene will be reviewed individually to reduce the likelihood that a gene is retired unnecessarily. However, when systematic manual review is impossible, genes may be retired when the originating study is deemd to have low reproducibility. In these rare situations, all Tier 2 genes from that study can be moved to Tier 3.