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. 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]
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-15 studies for FL.[@barariaCathepsinAlterationsInduce2020; @cheungAcquiredTNFRSF14Mutations2010; @drevalGeneticSubdivisionsFollicular2023; @hubschmannMutationalMechanismsShaping2021; @krysiakRecurrentSomaticMutations2017; @laurentFollicularLymphomaComprises2024; @louissaintPediatrictypeNodalFollicular2016; @maSubtypespecificCooccurringGenetic2022; @morinFrequentMutationHistonemodifying2011; @morinSomaticMutationsAltering2010; @okosunRecurrentMTORC1activatingRRAGC2016; @pasqualucciInactivatingMutationsAcetyltransferase2011; @rossiAberrantSomaticHypermutation2006; @russler-germainMutationsAssociatedProgression2023; @yildizActivatingSTAT6Mutations2015]
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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. 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]
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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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## Procedure for gene retirement (Tier 3)
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morinlab.bib
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+@article{rossiAberrantSomaticHypermutation2006,
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+ title = {Aberrant somatic hypermutation in transformation of follicular lymphoma and chronic lymphocytic leukemia to diffuse large {B}-cell lymphoma},
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+ volume = {91},
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+ issn = {1592-8721},
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+ abstract = {The molecular mechanisms involved in histologic transformation of follicular lymphoma (FL) and B-chronic lymphocytic leukemia (B-CLL) to diffuse large B-cell lymphoma (DLBCL) are heterogeneous and largely unknown. Here we explored whether aberrant somatic hypermutation, leading to the acquisition of new mutations in PIM-1, PAX-5, RhoH/TTF and c-MYC genes, is involved in transformation from FL or B-CLL to DLBCL. Eighteen sequential pairs of FL/DLBCL (n=9) and B-CLL/DLBCL (n=9) were investigated. Our findings demonstrate that acquisition of novel mutations due to aberrant somatic hypermutation was associated with DLBCL transformation in 5/9 (55.5\%) cases of FL and 2/9 (22.2\%) cases of B-CLL.},
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+ language = {eng},
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+ number = {10},
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+ journal = {Haematologica},
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+ author = {Rossi, Davide and Berra, Eva and Cerri, Michaela and Deambrogi, Clara and Barbieri, Caterina and Franceschetti, Silvia and Lunghi, Monia and Conconi, Annarita and Paulli, Marco and Matolcsy, Andràs and Pasqualucci, Laura and Capello, Daniela and Gaidano, Gianluca},
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+ month = oct,
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+ year = {2006},
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+ pmid = {17018394},
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+ keywords = {Humans, Gene Frequency, Lymphoma, B-Cell, Cell Transformation, Neoplastic, Leukemia, Lymphocytic, Chronic, B-Cell, Lymphoma, Follicular, Somatic Hypermutation, Immunoglobulin, Gene Rearrangement, B-Lymphocyte},
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+ pages = {1405--1409},
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+}
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+
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@article{barariaCathepsinAlterationsInduce2020,
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title = {Cathepsin {S} {Alterations} {Induce} a {Tumor}-{Promoting} {Immune} {Microenvironment} in {Follicular} {Lymphoma}},
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volume = {31},