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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+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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## Procedure for gene retirement (Tier 3)
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*See also:* [IGV reports](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Love/)
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-### CARD4 - pass
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+![CARD4 (**pass**) - Average rating: ★ ★ ★ ★ ☆](primary/Love_CARD4.svg)
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-![CARD4](primary/Love_CARD4.svg)
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+![ACAD9 (**fail**) - Average rating: ★ ☆ ☆ ☆ ☆](primary/Love_ACAD9.svg)
97 97
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-Average rating: ★ ★ ★ ★ ☆
99 98
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-### ACAD9 - fail (insufficient support)
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+![ACE (**fail**) - Average rating: ★ ☆ ☆ ☆ ☆](primary/Love_ACE.svg)
101 100
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-![ACAD9](primary/Love_ACAD9.svg)
103 101
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-Average rating: ★ ☆ ☆ ☆ ☆
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+![ATP2C2 (**fail**) - Average rating: ★ ★ ☆ ☆ ☆](primary/Love_ATP2C2.svg)
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-<div style="page-break-after: always;"></div>
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-
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-
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-### ACE - fail (insufficient support)
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-
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-![ACE](primary/Love_ACE.svg)
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-
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-Average rating: &starf; &star; &star; &star; &star;
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-
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-### ATP2C2 - fail (insufficient support)
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-
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-![ATP2C2](primary/Love_ATP2C2.svg)
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-
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-Average rating: &starf; &starf; &star; &star; &star;
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-
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-<div style="page-break-after: always;"></div>
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-
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-
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-### BRAF - fail (insufficient support)
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-
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-![BRAF](primary/Love_BRAF.svg)
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-
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-Average rating: &starf; &star; &star; &star; &star;
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-
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-### c6orf27 - fail (germline)
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-
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-![c6orf27](primary/Love_C6orf27_germline.svg)
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-
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-Average rating: Germline
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-
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-<div style="page-break-after: always;"></div>
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-
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-### BRD4 - fail (insufficient support)
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-
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-![BRD4](primary/Love_BRD4.svg)
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-
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-Average rating: &starf; &star; &star; &star; &star;
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-
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-### CYB5D1 - fail (insufficient support)
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-
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-![CYB5D1](primary/Love_CYB5D1.svg)
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-
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-Average rating: &starf; &star; &star; &star; &star;
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-
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-<div style="page-break-after: always;"></div>
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-
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-### BTG2 - fail (insufficient support)
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-
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-![BTG2](primary/Love_BTG2.svg)
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-
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-Average rating: &starf; &star; &star; &star; &star;
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-
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-
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-
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-### CAD - fail (insufficient support)
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-
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-![CAD](primary/Love_CAD.svg)
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-
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-Average rating: &starf; &star; &star; &star; &star;
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-
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-<div style="page-break-after: always;"></div>
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-
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-### CCT6B - fail (germline)
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-
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-![CCT6B](primary/Love_CCT6B.svg)
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-
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-Average rating: Gremline
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-
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-### CDH17 - fail (insufficient support)
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-
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-![CDH17](primary/Love_CDH17.svg)
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-
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-Average rating: &starf; &star; &star; &star; &star;
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-
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-<div style="page-break-after: always;"></div>
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-
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-### COL4A2 - fail (insufficient support)
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-
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-![COL4A2](primary/Love_COL4A2.svg)
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-
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-Average rating: &starf; &star; &star; &star; &star;
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-
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-
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-
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-### CYP4F22 - fail (insufficient support)
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-![CYP4F22](primary/Love_CYP4F22_15523136.png)
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-
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-Average rating: &starf; &star; &star; &star; &star;
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-
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-
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-### DLGAP1 - fail (insufficient support)
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-
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-![DLGAP1](primary/Love_DLGAP_chr18_3869854.png)
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-Average rating: &starf; &star; &star; &star; &star;
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-
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-<div style="page-break-after: always;"></div>
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-
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-### DTX1 - fail (insufficient support)
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-
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-![DTX1](primary/Love_DTX1_chr12_112017255.png)
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-Average rating: &starf; &star; &star; &star; &star;
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-
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-
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-### EIF2C4 - fail (insufficient support)
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-
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-![EIF2C4](primary/Love_EIF2C4.svg)
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-Average rating: &starf; &star; &star; &star; &star;
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-
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-<div style="page-break-after: always;"></div>
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-
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-### EML2 - fail (insufficient support)
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-
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-![EML2](primary/Love_EML2_50816396.png)
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-
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-Average rating: &starf; &star; &star; &star; &star;
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-
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-### ENTPD3 - fail (insufficient support)
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-
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-![ENTPD3](primary/Love_ENTPD3.svg)
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-Average rating: &starf; &starf; &star; &star; &star;
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-<div style="page-break-after: always;"></div>
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-### EPHB2 - fail (insufficient support)
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-![EPHB2](primary/Love_EPHB2.svg)
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-Average rating: &starf; &starf; &star; &star; &star;
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-
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-### FAM129B - fail (insufficient support)
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-
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-![FAM129B](primary/Love_FAM129B.svg)
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-Average rating: &starf; &starf; &star; &star; &star;
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-<div style="page-break-after: always;"></div>
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-
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-### FGFR3 - fail (insufficient support)
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-
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-![FGFR3](primary/Love_FGFR3.svg)
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-Average rating: &starf; &star; &star; &star; &star;
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-
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-### FTCD - fail (germline)
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+![BRAF (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Love_BRAF.svg)
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-![FTCD](primary/Love_FTCD.svg)
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+![c6orf27 (**fail**) - Average rating: Germline](primary/Love_C6orf27_germline.svg)
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-Average rating: Germline
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+![BRD4 (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Love_BRD4.svg)
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-<div style="page-break-after: always;"></div>
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-
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-### GRIK5 - fail (insufficient support)
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-
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-![GRIK5](primary/Love_GRIK5.svg)
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-Average rating: &starf; &star; &star; &star; &star;
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-
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-### ICK - fail (insufficient support)
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-
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-![ICK](primary/Love_ICK.svg)
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+![CYB5D1 (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Love_CYB5D1.svg)
272 111
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-Average rating: &starf; &star; &star; &star; &star;
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+![BTG2 (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Love_BTG2.svg)
274 113
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+![CAD (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Love_CAD.svg)
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-<div style="page-break-after: always;"></div>
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-
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-### ITPR3 - fail (insufficient support)
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+![CCT6B (**fail**) - Average rating: Germline](primary/Love_CCT6B.svg)
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-![ITPR3](primary/Love_ITPR3.svg)
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+![CDH17 (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Love_CDH17.svg)
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-Average rating: &starf; &star; &star; &star; &star;
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+![COL4A2 (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Love_COL4A2.svg)
283 121
284 122
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-### KIFC3 - fail (insufficient support)
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+![CYP4F22 (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Love_CYP4F22_15523136.png)
286 124
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-![KIFC3](primary/Love_KIFC3_2_56362071.png)
125
+![DLGAP1 (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Love_DLGAP_chr18_3869854.png)
288 126
289
-Average rating: &starf; &star; &star; &star; &star;
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+![DTX1 (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Love_DTX1_chr12_112017255.png)
290 128
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+![EIF2C4 (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Love_EIF2C4.svg)
291 130
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-<div style="page-break-after: always;"></div>
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+![EML2 (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Love_EML2_50816396.png)
293 132
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-### MAP3K6 - fail (insufficient support)
133
+![ENTPD3 (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Love_ENTPD3.svg)
295 134
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-![MAP3K6](primary/Love_MAP3K6.svg)
135
+![EPHB2 (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Love_EPHB2.svg)
297 136
298
-Average rating: &starf; &star; &star; &star; &star;
137
+![FAM129B (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Love_FAM129B.svg)
299 138
139
+![FGFR3 (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Love_FGFR3.svg)
300 140
141
+![FTCD (**fail**) - Average rating: Germline](primary/Love_FTCD.svg)
301 142
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-### MYH10 - fail (insufficient support)
143
+![GRIK5 (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Love_GRIK5.svg)
303 144
304
-![MYH10](primary/Love_MYH10.svg)
145
+![ICK (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Love_ICK.svg)
305 146
306
-Average rating: &starf; &star; &star; &star; &star;
147
+![ITPR3 (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Love_ITPR3.svg)
307 148
308
-<div style="page-break-after: always;"></div>
149
+![KIFC3 (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Love_KIFC3_2_56362071.png)
309 150
310
-### NOTCH1 - fail (insufficient support)
151
+![MAP3K6 (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Love_MAP3K6.svg)
311 152
312
-![NOTCH1](primary/Love_NOTCH1.svg)
153
+![MYH10 (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Love_MYH10.svg)
313 154
314
-Average rating: &starf; &star; &star; &star; &star;
155
+![NOTCH1 (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Love_NOTCH1.svg)
315 156
316
-### NRXN2 - fail (insufficient support)
157
+![NRXN2 (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Love_NRXN2.svg)
317 158
318
-![NRXN2](primary/Love_NRXN2.svg)
159
+![PC (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Love_PC_chr11_66374870.png)
319 160
320
-Average rating: &starf; &star; &star; &star; &star;
161
+![POLRMT (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Love_POLRMT.svg)
321 162
322
-<div style="page-break-after: always;"></div>
163
+![POR (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Love_POR.svg)
323 164
324
-### PC - fail (insufficient support)
165
+![PRSS22 (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Love_PRSS22.svg)
325 166
326
-![PC](primary/Love_PC_chr11_66374870.png)
167
+![PTPRN (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Love_PTPRN.svg)
327 168
328
-Average rating: &starf; &star; &star; &star; &star;
169
+![RBP3 (**fail**)](primary/Love_RBP3.svg)
329 170
330
-### POLRMT - fail (insufficient support)
171
+![RET (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Love_RET_42930092.png)
331 172
332
-![POLRMT](primary/Love_POLRMT.svg)
173
+![SALL3 (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Love_SALL3.svg)
333 174
334
-Average rating: &starf; &star; &star; &star; &star;
335 175
336
-<div style="page-break-after: always;"></div>
337 176
338
-### POR - fail (insufficient support)
177
+![SAPS2 (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Love_SAPS2.svg)
339 178
340
-![POR](primary/Love_POR.svg)
341 179
342
-Average rating: &starf; &star; &star; &star; &star;
180
+![SBF1 (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Love_SBF1.svg)
343 181
182
+![SLC29A2 (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Love_SLC29A2.svg)
344 183
345
-### PRSS22 - fail (insufficient support)
184
+![SHANK1 (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Love_SHANK1.svg)
346 185
347
-![PRSS22](primary/Love_PRSS22.svg)
186
+![SYNGAP1 (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Love_SYNGAP1_33518868.png)
348 187
349
-Average rating: &starf; &star; &star; &star; &star;
350 188
351
-<div style="page-break-after: always;"></div>
189
+![TBC1D9B (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Love_TBC1D9B.svg)
352 190
353
-### PTPRN - fail (insufficient support)
191
+![TIGD6 (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Love_TIGD6.svg)
354 192
355
-![PTPRN](primary/Love_PTPRN.svg)
193
+![TPST2 (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Love_TPST2.svg)
356 194
357
-Average rating: &starf; &star; &star; &star; &star;
358 195
359
-### RBP3 - fail (insufficient support)
196
+![ZNF229 (**fail**) - Average rating: Germline](primary/Love_ZNF229_chr19_49624750_also_in_germline.png)
360 197
361
-![RBP3](primary/Love_RBP3.svg)
362 198
363
-Average rating: &starf; &star; &star; &star; &star;
364
-
365
-<div style="page-break-after: always;"></div>
366
-
367
-### RET - fail (insufficient support)
368
-
369
-![RET](primary/Love_RET_42930092.png)
370
-
371
-Average rating: &starf; &star; &star; &star; &star;
372
-
373
-### SALL3 - fail (insufficient support)
374
-
375
-![SALL3](primary/Love_SALL3.svg)
376
-
377
-Average rating: &starf; &starf; &star; &star; &star;
378
-
379
-<div style="page-break-after: always;"></div>
380
-
381
-### SAPS2 - fail (insufficient support)
382
-
383
-![SAPS2](primary/Love_SAPS2.svg)
384
-
385
-Average rating: &starf; &star; &star; &star; &star;
386
-
387
-
388
-
389
-### SBF1 - fail (insufficient support)
390
-
391
-![SBF1](primary/Love_SBF1.svg)
392
-
393
-Average rating: &starf; &starf; &star; &star; &star;
394
-
395
-<div style="page-break-after: always;"></div>
396
-
397
-### SF3B1 - fail (insufficient support)
398
-
399
-![SF3B1](primary/Love_SF3B1.svg)
400
-
401
-Average rating: &starf; &starf; &starf; &starf; &star;
402
-
403
-### SLC29A2 - fail (insufficient support)
404
-
405
-![SLC29A2](primary/Love_SLC29A2.svg)
406
-
407
-Average rating: &starf; &star; &star; &star; &star;
408
-
409
-<div style="page-break-after: always;"></div>
410
-
411
-
412
-### SHANK1 - fail (insufficient support)
413
-
414
-![SHANK1](primary/Love_SHANK1.svg)
415
-
416
-Average rating: &starf; &star; &star; &star; &star;
417
-
418
-
419
-### SYNGAP1 - fail (insufficient support)
420
-
421
-![SYNGAP1](primary/Love_SYNGAP1_33518868.png)
422
-
423
-Average rating: &starf; &star; &star; &star; &star;
424
-
425
-<div style="page-break-after: always;"></div>
426
-
427
-### TBC1D9B - fail (insufficient support)
428
-
429
-![TBC1D9B](primary/Love_TBC1D9B.svg)
430
-
431
-Average rating: &starf; &star; &star; &star; &star;
432
-
433
-
434
-
435
-### TIGD6 - fail (insufficient support)
436
-
437
-![TIGD6](primary/Love_TIGD6.svg)
438
-
439
-Average rating: &starf; &star; &star; &star; &star;
440
-
441
-<div style="page-break-after: always;"></div>
442
-
443
-### TPST2 - fail (insufficient support)
444
-
445
-![TPST2](primary/Love_TPST2.svg)
446
-
447
-Average rating: &starf; &star; &star; &star; &star;
448
-
449
-### ZNF229 - fail (germline)
450
-
451
-![ZNF229](primary/Love_ZNF229_chr19_49624750_also_in_germline.png)
452
-
453
-Average rating: Germline
454 199
455 200
<div style="page-break-after: always;"></div>
456 201
... ...
@@ -463,218 +208,63 @@ Average rating: Germline
463 208
|Exome|400|601|0|13|28|26 (39%)|
464 209
465 210
466
-### ARID5B - pass
467
-
468
-![ARID5B](primary/Reddy_ARID5B_1.svg)
469
-
470
-Average rating: &starf; &starf; &starf; &starf; &star;
471
-
472
-### ARID1B - fail (insufficient support)
473
-
474
-![ARID1B](primary/Reddy_ARID1B_1.svg)
475
-
476
-Average rating: &starf; &starf; &star; &star; &star;
477
-
478
-<div style="page-break-after: always;"></div>
479
-
480
-### CBLB - fail (insufficient support)
481
-
482
-![CBLB](primary/Reddy_CBLB_1.svg)
483
-
484
-Average rating: &starf; &starf; &star; &star; &star;
485
-
486
-<div style="page-break-after: always;"></div>
487
-
488
-### CDC73 - fail (insufficient support)
489
-
490
-![CDC73](primary/Reddy_CDC73.svg)
491
-
492
-Average rating: &starf; &starf; &star; &star; &star;
493
-
494
-### CHD8 - fail (insufficient support)
495
-
496
-![CHD8](primary/Reddy_CHD8.svg)
497
-
498
-Average rating: &starf; &starf; &star; &star; &star;
499
-
500
-<div style="page-break-after: always;"></div>
501
-
502
-### CHD1 - fail (insufficient support)
503
-
504
-![CHD1](primary/Reddy_CHD1.svg)
505
-
506
-Average rating: &starf; &starf; &star; &star; &star;
507 211
508
-<div style="page-break-after: always;"></div>
509
-
510
-### CHST2 - fail (insufficient support)
511
-
512
-![CHST2](primary/Reddy_CHST2.svg)
212
+![ARID5B (**pass**) - Average rating: &starf; &starf; &starf; &starf; &star;](primary/Reddy_ARID5B_1.svg)
513 213
514
-Average rating: &starf; &starf; &star; &star; &star;
515
-
516
-
517
-<div style="page-break-after: always;"></div>
214
+![ARID1B (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Reddy_ARID1B_1.svg)
518 215
519
-### DCAF6 - fail (insufficient support)
216
+![CBLB (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Reddy_CBLB_1.svg)
520 217
521
-![DCAF6](primary/Reddy_DCAF6.svg)
218
+![CDC73 (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Reddy_CDC73.svg)
522 219
523
-Average rating: &starf; &starf; &star; &star; &star;
220
+![CHD8 (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Reddy_CHD8.svg)
524 221
525
-<div style="page-break-after: always;"></div>
222
+![CHD1 (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Reddy_CHD1.svg)
526 223
527
-### DICER1 - fail (insufficient support)
224
+![CHST2 (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Reddy_CHST2.svg)
528 225
529
-![DICER1](primary/Reddy_DICER1.svg)
226
+![DCAF6 (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Reddy_DCAF6.svg)
530 227
531
-Average rating: &starf; &starf; &star; &star; &star;
532 228
229
+![DICER1 (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Reddy_DICER1.svg)
533 230
534
-<div style="page-break-after: always;"></div>
535 231
536
-### DNMT3A - fail (insufficient support)
232
+![DNMT3A (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Reddy_DNMT3A.svg)
537 233
538
-![DNMT3A](primary/Reddy_DNMT3A.svg)
234
+![GNAS (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Reddy_GNAS.svg)
539 235
540
-Average rating: &starf; &star; &star; &star; &star;
236
+![HRAS (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Reddy_HRAS.svg)
541 237
542
-<div style="page-break-after: always;"></div>
238
+![LIN54 (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Reddy_LIN54.svg)
543 239
544
-### GNAS - fail (insufficient support)
240
+![MAP4K4 (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Reddy_MAP4K4.svg)
545 241
546
-![GNAS](primary/Reddy_GNAS.svg)
242
+![MARK1 (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Reddy_MARK1.svg)
547 243
548
-Average rating: &starf; &starf; &star; &star; &star;
244
+![MSH2 (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Reddy_MSH2.svg)
549 245
550
-<div style="page-break-after: always;"></div>
246
+![MYB (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Reddy_MYB.svg)
551 247
552
-### HRAS - fail (insufficient support)
248
+![NCOR1 (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Reddy_NCOR1.svg)
553 249
554
-![HRAS](primary/Reddy_HRAS.svg)
250
+![NFKB2 (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Reddy_NFKB2.svg)
555 251
556
-Average rating: &starf; &starf; &star; &star; &star;
252
+![PHF6 (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Reddy_PHF6.svg)
557 253
558
-<div style="page-break-after: always;"></div>
254
+![PTPRK (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Reddy_PTPRK.svg)
559 255
560
-### LIN54 - fail (insufficient support)
256
+![RARA (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Reddy_RARA.svg)
561 257
562
-![LIN54](primary/Reddy_LIN54.svg)
258
+![RUNX1 (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Reddy_RUNX1.svg)
563 259
564
-Average rating: &starf; &starf; &star; &star; &star;
260
+![SYK (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Reddy_SYK.svg)
565 261
566
-<div style="page-break-after: always;"></div>
262
+![WAC (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Reddy_WAC.svg)
567 263
568
-### MAP4K4 - fail (insufficient support)
264
+![ZBTB7A (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Reddy_ZBTB7A.svg)
569 265
570
-![MAP4K4](primary/Reddy_MAP4K4.svg)
266
+![ZFAT (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Reddy_ZFAT.svg)
571 267
572
-Average rating: &starf; &starf; &star; &star; &star;
573
-
574
-<div style="page-break-after: always;"></div>
575
-
576
-### MARK1 - fail (insufficient support)
577
-
578
-![MARK1](primary/Reddy_MARK1.svg)
579
-
580
-Average rating: &starf; &star; &star; &star; &star;
581
-
582
-<div style="page-break-after: always;"></div>
583
-
584
-### MSH2 - fail (insufficient support)
585
-
586
-![MSH2](primary/Reddy_MSH2.svg)
587
-
588
-Average rating: &starf; &starf; &star; &star; &star;
589
-
590
-<div style="page-break-after: always;"></div>
591
-
592
-### MYB - fail (insufficient support)
593
-
594
-![MYB](primary/Reddy_MYB.svg)
595
-
596
-Average rating: &starf; &starf; &star; &star; &star;
597
-
598
-<div style="page-break-after: always;"></div>
599
-
600
-### NCOR1 - fail (insufficient support)
601
-
602
-![NCOR1](primary/Reddy_NCOR1.svg)
603
-
604
-Average rating: &starf; &starf; &star; &star; &star;
605
-
606
-<div style="page-break-after: always;"></div>
607
-
608
-### NFKB2 - fail (insufficient support)
609
-
610
-![NFKB2](primary/Reddy_NFKB2.svg)
611
-
612
-Average rating: &starf; &starf; &star; &star; &star;
613
-
614
-<div style="page-break-after: always;"></div>
615
-
616
-### PHF6 - fail (insufficient support)
617
-
618
-![PHF6](primary/Reddy_PHF6.svg)
619
-
620
-Average rating: &starf; &starf; &star; &star; &star;
621
-
622
-<div style="page-break-after: always;"></div>
623
-
624
-### PTPRK - fail (insufficient support)
625
-
626
-![PTPRK](primary/Reddy_PTPRK.svg)
627
-
628
-Average rating: &starf; &starf; &star; &star; &star;
629
-
630
-
631
-<div style="page-break-after: always;"></div>
632
-
633
-### RARA - fail (insufficient support)
634
-
635
-![RARA](primary/Reddy_RARA.svg)
636
-
637
-Average rating: &starf; &star; &star; &star; &star;
638
-
639
-<div style="page-break-after: always;"></div>
640
-
641
-### RUNX1 - fail (insufficient support)
642
-
643
-![RUNX1](primary/Reddy_RUNX1.svg)
644
-
645
-Average rating: &starf; &starf; &star; &star; &star;
646
-
647
-<div style="page-break-after: always;"></div>
648
-
649
-### SYK - fail (insufficient support)
650
-
651
-![SYK](primary/Reddy_SYK.svg)
652
-
653
-Average rating: &starf; &starf; &star; &star; &star;
654
-
655
-<div style="page-break-after: always;"></div>
656
-
657
-### WAC - fail (insufficient support)
658
-
659
-![WAC](primary/Reddy_WAC.svg)
660
-
661
-Average rating: &starf; &starf; &star; &star; &star;
662
-
663
-<div style="page-break-after: always;"></div>
664
-
665
-### ZBTB7A - fail (insufficient support)
666
-
667
-![ZBTB7A](primary/Reddy_ZBTB7A.svg)
668
-
669
-Average rating: &starf; &star; &star; &star; &star;
670
-
671
-<div style="page-break-after: always;"></div>
672
-
673
-### ZFAT - fail (insufficient support)
674
-
675
-![ZFAT](primary/Reddy_ZFAT.svg)
676
-
677
-Average rating: &starf; &starf; &star; &star; &star;
678 268
679 269
<div style="page-break-after: always;"></div>
680 270
... ...
@@ -688,53 +278,21 @@ Average rating: &starf; &starf; &star; &star; &star;
688 278
689 279
*See also:* [IGV reports](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Morin_2013/)
690 280
691
-### HDAC7 - pass
692
-
693
-![HDAC7](primary/Morin_HDAC7.svg)
694
-
695
-Average rating: &starf; &starf; &starf; &star; &star;
696
-
697
-<div style="page-break-after: always;"></div>
698
-
699
-### FAM38B - fail (insufficient support)
700
-
701
-![FAM38B](primary/Morin_FAM38B.svg)
702
-
703
-<div style="page-break-after: always;"></div>
704
-
705
-### FNDC1 - fail (insufficient support)
706
-
707
-![FNDC1](primary/Morin_FNDC1.svg)
708
-
709
-<div style="page-break-after: always;"></div>
710
-
711
-### IER2 - fail (insufficient support)
712
-
713
-![IER2](primary/Morin_IER2.svg)
714
-
715
-<div style="page-break-after: always;"></div>
716
-
717
-### PKD1 - fail (insufficient support)
281
+![HDAC7 (**pass**) - Average rating: &starf; &starf; &starf; &star; &star;](primary/Morin_HDAC7.svg)
718 282
719
-![PKD1](primary/Morin_PKD1.svg)
283
+![FAM38B (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Morin_FAM38B.svg)
720 284
721
-<div style="page-break-after: always;"></div>
722
-
723
-### POGZ - fail (insufficient support)
724
-
725
-![POGZ](primary/Morin_POGZ.svg)
285
+![FNDC1 (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Morin_FNDC1.svg)
726 286
727
-<div style="page-break-after: always;"></div>
728
-
729
-### PTPN23 - fail (insufficient support)
287
+![IER2 (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Morin_IER2.svg)
730 288
731
-![PTPN23](primary/Morin_PTPN23.svg)
289
+![PKD1 (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Morin_PKD1.svg)
732 290
733
-<div style="page-break-after: always;"></div>
291
+![POGZ (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Morin_POGZ.svg)
734 292
735
-### SARM1 - fail (insufficient support)
293
+![PTPN23 (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Morin_PTPN23.svg)
736 294
737
-![SARM1](primary/Morin_SARM1.svg)
295
+![SARM1 (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Morin_SARM1.svg)
738 296
739 297
<div style="page-break-after: always;"></div>
740 298
... ...
@@ -744,129 +302,53 @@ Average rating: &starf; &starf; &starf; &star; &star;
744 302
745 303
|Methodology|Pairs|Unpaired tumors|Cell lines|Tier 1|Tier 2|Tier 3|
746 304
|:-:|:-:|:-:|:-:|:-:|:-:|:-:|
747
-|WGS|101|0|0|2|15|22 (56%)|
305
+|WGS/exome/RNA-seq|101|0|0|2|15|22 (56%)|
748 306
749
-### CXCR4 - pass
307
+![CXCR4 (**pass**) - Average rating: &starf; &starf; &starf; &star; &star;](primary/Panea_CXCR4_1.svg)
750 308
751
-![CXCR4](primary/Panea_CXCR4_1.svg)
309
+![ALPK2 (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Panea_ALPK2.svg)
752 310
311
+![CD79B (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Panea_CD79B.svg)
753 312
754
-### ALPK2 - fail (insufficient support)
313
+![CTCF (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Panea_CTCF_1.svg)
755 314
756
-![ALPK2](primary/Panea_ALPK2.svg)
757
-
758
-<div style="page-break-after: always;"></div>
315
+![DNMT1 (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Panea_DNMT1_1.svg)
759 316
317
+![ETS1 (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Panea_ETS1_1.svg)
760 318
761
-### CD79B - fail (insufficient support, RNA-only)
319
+![FZD3 (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Panea_FZD3_1.svg)
762 320
763
-![CD79B](primary/Panea_CD79B.svg)
321
+![HIST1H1C (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Panea_HIST1H1C_3.svg)
764 322
323
+![HIST1H2AG (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Panea_HIST1H2AG_3.svg)
765 324
325
+![HIST1H2AM (**fail**) - Average rating: &star; &star; &star; &star; &star;](primary/Panea_HIST1H2AM_1.svg)
766 326
767
-### CTCF - fail (insufficient support)
327
+![HIST1H2BK (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Panea_HIST1H2BK_1.svg)
768 328
769
-![CTCF](primary/Panea_CTCF_1.svg)
329
+![HIST1H3H (**fail**) - Average rating: &star; &star; &star; &star; &star;](primary/Panea_HIST1H3H_1.svg)
770 330
771
-<div style="page-break-after: always;"></div>
331
+![HIST1H3J (**fail**) - Average rating: &star; &star; &star; &star; &star;](primary/Panea_HIST1H3J_1.svg)
772 332
333
+![KCNK10 (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Panea_KCNK10_1.svg)
773 334
774
-### DNMT1 - fail (insufficient support)
335
+![MME (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Panea_MME_1.svg)
775 336
776
-![DNMT1](primary/Panea_DNMT1_1.svg)
337
+![MTOR (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Panea_MTOR_1.svg)
777 338
339
+![PABPC4L (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Panea_PABPC4L_1.svg)
778 340
341
+![PCDHA11 (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Panea_PCDHA11_1.svg)
779 342
780
-### ETS1 - fail (insufficient support, RNA-only)
343
+![PDZRN3 (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Panea_PDZRN3_1.svg)
781 344
782
-![ETS1](primary/Panea_ETS1_1.svg)
345
+![PIK3R1 (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Panea_PIK3R1_1.svg)
783 346
784
-<div style="page-break-after: always;"></div>
347
+![PXDNL (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Panea_PXDNL_1.svg)
785 348
786
-### FZD3 - fail (insufficient support)
349
+![SNTB2 (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Panea_SNTB2_1.svg)
787 350
788
-![FZD3](primary/Panea_FZD3_1.svg)
789
-
790
-<div style="page-break-after: always;"></div>
791
-
792
-### HIST1H1C - fail (insufficient support)
793
-
794
-![HIST1H1C](primary/Panea_HIST1H1C_3.svg)
795
-
796
-<div style="page-break-after: always;"></div>
797
-
798
-
799
-### HIST1H2AG - fail (insufficient support)
800
-
801
-![HIST1H2AG](primary/Panea_HIST1H2AG_3.svg)
802
-
803
-
804
-### HIST1H2AM - fail (insufficient support, RNA-only)
805
-
806
-![HIST1H2AM](primary/Panea_HIST1H2AM_1.svg)
807
-
808
-<div style="page-break-after: always;"></div>
809
-
810
-### HIST1H2BK - fail (insufficient support)
811
-
812
-![HIST1H2BK](primary/Panea_HIST1H2BK_1.svg)
813
-
814
-### HIST1H3H - fail (insufficient support)
815
-
816
-![HIST1H3H](primary/Panea_HIST1H3H_1.svg)
817
-
818
-<div style="page-break-after: always;"></div>
819
-
820
-### HIST1H3J - fail (insufficient support)
821
-
822
-![HIST1H3J](primary/Panea_HIST1H3J_1.svg)
823
-
824
-### KCNK10 - fail (insufficient support)
825
-
826
-![KCNK10](primary/Panea_KCNK10_1.svg)
827
-
828
-### MME - fail (insufficient support)
829
-
830
-![MME](primary/Panea_MME_1.svg)
831
-
832
-<div style="page-break-after: always;"></div>
833
-
834
-### MTOR - fail (insufficient support)
835
-
836
-![MTOR](primary/Panea_MTOR_1.svg)
837
-
838
-### PABPC4L - fail (insufficient support)
839
-
840
-![PABPC4L](primary/Panea_PABPC4L_1.svg)
841
-
842
-
843
-### PCDHA11 - fail (insufficient support)
844
-
845
-![PCDHA11](primary/Panea_PCDHA11_1.svg)
846
-
847
-### PDZRN3 - fail (insufficient support)
848
-
849
-![PDZRN3](primary/Panea_PDZRN3_1.svg)
850
-
851
-<div style="page-break-after: always;"></div>
852
-
853
-### PIK3R1 - fail (insufficient support)
854
-
855
-![PIK3R1](primary/Panea_PIK3R1_1.svg)
856
-
857
-### PXDNL - fail (insufficient support)
858
-
859
-![PXDNL](primary/Panea_PXDNL_1.svg)
860
-
861
-### SNTB2 - fail (insufficient support)
862
-
863
-![SNTB2](primary/Panea_SNTB2_1.svg)
864
-
865
-<div style="page-break-after: always;"></div>
866
-
867
-### WDR7 - fail (insufficient support)
868
-
869
-![WDR7](primary/Panea_WDR7_3.svg)
351
+![WDR7 (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Panea_WDR7_3.svg)
870 352
871 353
<div style="page-break-after: always;"></div>
872 354
... ...
@@ -879,30 +361,13 @@ Average rating: &starf; &starf; &starf; &star; &star;
879 361
|:-:|:-:|:-:|:-:|:-:|:-:|:-:|
880 362
|Exome|137|167|0|10|13| 6(21%)|
881 363
882
-### DOCK1 - pass
883
-
884
-![DOCK1](primary/Chapuy_DOCK1.svg)
885
-
364
+![DOCK1 (**pass**) - Average rating: &starf; &starf; &starf; &star; &star;](primary/Chapuy_DOCK1.svg)
886 365
887
-<div style="page-break-after: always;"></div>
888
-
889
-### FUT5 - fail (insufficient support)
890
-
891
-![FUT5](primary/Chapuy_FUT5.svg)
892
-
893
-<div style="page-break-after: always;"></div>
894
-
895
-### NLRP8 - fail (insufficient support)
366
+![FUT5 (**fail**) - Average rating: &starf; &star; &star; &star; &star;](primary/Chapuy_FUT5.svg)
896 367
897
-![NLRP8](primary/Chapuy_NLRP8.svg)
368
+![NLRP8 (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Chapuy_NLRP8.svg)
898 369
899
-<div style="page-break-after: always;"></div>
900
-
901
-### PDE4DIP - fail (insufficient support)
902
-
903
-![PDE4DIP](primary/Chapuy_PDE4DIP.svg)
904
-
905
-<div style="page-break-after: always;"></div>
370
+![PDE4DIP (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/Chapuy_PDE4DIP.svg)
906 371
907 372
### Hübschmann *et al*, 2021 <a name="icgc"></a>
908 373
... ...
@@ -913,28 +378,13 @@ Average rating: &starf; &starf; &starf; &star; &star;
913 378
|:-:|:-:|:-:|:-:|:-:|:-:|:-:|
914 379
|WGS|179|2|0|5|31| 3 (7.7%)|
915 380
916
-### IKBKE - pass
381
+![IKBKE (**pass**) - Average rating: &starf; &starf; &starf; &starf; &star;](primary/ICGC_IKBKE.svg)
917 382
918
-![IKBKE](primary/ICGC_IKBKE.svg)
919
-
920
-<div style="page-break-after: always;"></div>
921
-
922
-### GAK - fail (insufficient support)
923
-
924
-![GAK](primary/ICGC_GAK.svg)
925
-
926
-<div style="page-break-after: always;"></div>
927
-
928
-### HLA-DQA1 - fail (insufficient support)
929
-
930
-![HLA-DQA1](primary/ICGC_HLA-DQA1.svg)
931
-
932
-
933
-<div style="page-break-after: always;"></div>
383
+![GAK (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/ICGC_GAK.svg)
934 384
935
-### NR2F2 - fail (insufficient support)
385
+![HLA-DQA1 (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/ICGC_HLA-DQA1.svg)
936 386
937
-![NR2F2](primary/ICGC_NR2F2.svg)
387
+![NR2F2 (**fail**) - Average rating: &starf; &starf; &star; &star; &star;](primary/ICGC_NR2F2.svg)
938 388
939 389
<div style="page-break-after: always;"></div>
940 390