diff --git a/resources/curated/bl_genes.tsv b/resources/curated/bl_genes.tsv index dbb0f3c8..3209b2b6 100644 --- a/resources/curated/bl_genes.tsv +++ b/resources/curated/bl_genes.tsv @@ -1,175 +1,175 @@ -Gene Tier aSHM QC Mean Variant Quality citekey PMID -ACAD9 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 -ACE 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 -ADAMTS5 2 burkhardtClinicalRelevanceMolecular2022b 35794096 -ADNP 2 burkhardtClinicalRelevanceMolecular2022b 35794096 -AGO4 2 burkhardtClinicalRelevanceMolecular2022b 35794096 -ALPK2 3 FAIL 1 paneaWholeGenomeLandscape2019 31558468 -ARHGEF1 2 muppidiLossSignalingGa132014b 25274307 -ARID1A 1 loveGeneticLandscapeMutations2012 23143597 -ATP2C2 3 FAIL 2 loveGeneticLandscapeMutations2012 23143597 -BACH2 1 TRUE grandeGenomewideDiscoverySomatic2019 30617194 -BCL2 2 TRUE burkhardtClinicalRelevanceMolecular2022b 35794096 -BCL6 1 TRUE PASS 4 loveGeneticLandscapeMutations2012 30617194 -BCL7A 1 TRUE grandeGenomewideDiscoverySomatic2019 30617194 -BMP7 1 paneaWholeGenomeLandscape2019 31558468 -BRAF 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 -BRD4 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 -BTG1 2 TRUE burkhardtClinicalRelevanceMolecular2022b 35794096 -BTG2 3 TRUE FAIL 1 loveGeneticLandscapeMutations2012 31558468 -C16orf48 2 schmitzBurkittLymphomaPathogenesis2012 22885699 -C6orf27 3 FAIL Germline loveGeneticLandscapeMutations2012 23143597 -CAD 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 -CARD4 2 PASS 4 loveGeneticLandscapeMutations2012 23143597 -CCND3 1 richterRecurrentMutationID32012a 23143595 -CCNF 2 abateDistinctViralMutational2015a 26468873 -CCT6B 3 FAIL Germline loveGeneticLandscapeMutations2012 23143597 -CD79A 2 burkhardtClinicalRelevanceMolecular2022b 35794096 -CD79B 3 FAIL 2 paneaWholeGenomeLandscape2019 31558468 -CD83 2 TRUE PASS 3 paneaWholeGenomeLandscape2019 31558468 -CDC73 2 PASS 3 loveGeneticLandscapeMutations2012 23143597 -CDH17 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 -CDKN2A 2 grandeGenomewideDiscoverySomatic2019 30617194 -CDKN2C 2 thomasGeneticSubgroupsInform2023 36201743 -CHD4 2 burkhardtClinicalRelevanceMolecular2022b 35794096 -CHD8 1 grandeGenomewideDiscoverySomatic2019 36201743 -COL4A2 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 -CPXM2 2 burkhardtClinicalRelevanceMolecular2022b 35794096 -CREBBP 1 PASS 4 loveGeneticLandscapeMutations2012 23143597 -CTCF 3 FAIL 1 paneaWholeGenomeLandscape2019 31558468 -CXCR4 2 TRUE PASS 4 paneaWholeGenomeLandscape2019 31558468 -CYB5D1 3 FAIL 2 loveGeneticLandscapeMutations2012 23143597 -CYP4F22 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 -DDX3X 1 schmitzBurkittLymphomaPathogenesis2012 22885699 -DHCR7 2 schmitzBurkittLymphomaPathogenesis2012 22885699 -DLGAP1 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 -DNMT1 3 FAIL 1 paneaWholeGenomeLandscape2019 31558468 -DTX1 3 TRUE FAIL 1 loveGeneticLandscapeMutations2012 31558468 -E2F2 2 burkhardtClinicalRelevanceMolecular2022b 35794096 -EBF1 2 TRUE thomasGeneticSubgroupsInform2023 NA -EDNRB 2 burkhardtClinicalRelevanceMolecular2022b 35794096 -EHD1 2 thomasGeneticSubgroupsInform2023 NA -EIF2C4 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 -EIF4A1 2 paneaWholeGenomeLandscape2019 31558468 -ELP2 2 schmitzBurkittLymphomaPathogenesis2012 22885699 -EML2 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 -ENTPD3 3 FAIL 2 loveGeneticLandscapeMutations2012 23143597 -EPHB2 3 FAIL 2 loveGeneticLandscapeMutations2012 23143597 -EPPK1 2 paneaWholeGenomeLandscape2019 31558468 -ERAP1 2 burkhardtClinicalRelevanceMolecular2022b 35794096 -ETS1 3 TRUE FAIL 1 paneaWholeGenomeLandscape2019 31558468 -EXOSC6 2 schmitzBurkittLymphomaPathogenesis2012 22885699 -EZH2 2 PASS 5 loveGeneticLandscapeMutations2012 23143597 -FAM129B 3 FAIL 2 loveGeneticLandscapeMutations2012 23143597 -FBXO11 1 richterRecurrentMutationID32012a 23143595 -FGFR3 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 -FLYWCH1 2 schmitzBurkittLymphomaPathogenesis2012 22885699 -FOXO1 1 schmitzBurkittLymphomaPathogenesis2012 22885699 -FTCD 3 FAIL Germline loveGeneticLandscapeMutations2012 23143597 -FZD3 3 FAIL 1 paneaWholeGenomeLandscape2019 31558468 -GGTLA4 2 PASS 4 loveGeneticLandscapeMutations2012 23143597 -GNA13 1 loveGeneticLandscapeMutations2012 23143597 -GNAI2 1 grandeGenomewideDiscoverySomatic2019 30617194 -GRIK5 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 -GTSE1 2 schmitzBurkittLymphomaPathogenesis2012 22885699 -HIST1H1C 3 TRUE FAIL 2 paneaWholeGenomeLandscape2019 31558468 -HIST1H1E 1 TRUE grandeGenomewideDiscoverySomatic2019 31558468 -HIST1H2AG 3 TRUE FAIL 2 paneaWholeGenomeLandscape2019 31558468 -HIST1H2AM 3 TRUE FAIL 0 paneaWholeGenomeLandscape2019 31558468 -HIST1H2BK 3 TRUE FAIL 1 paneaWholeGenomeLandscape2019 31558468 -HIST1H3D 2 TRUE PASS 3 paneaWholeGenomeLandscape2019 31558468 -HIST1H3H 3 TRUE FAIL 0 paneaWholeGenomeLandscape2019 31558468 -HIST1H3I 2 TRUE PASS 4 paneaWholeGenomeLandscape2019 31558468 -HIST1H3J 3 TRUE FAIL 0 paneaWholeGenomeLandscape2019 31558468 -HIST1H4J 2 TRUE PASS 3 paneaWholeGenomeLandscape2019 31558468 -HLA-DQB1 2 burkhardtClinicalRelevanceMolecular2022b 35794096 -HNRNPU 1 TRUE paneaWholeGenomeLandscape2019 31558468 -ICK 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 -ID3 1 richterRecurrentMutationID32012a 23143595 -IGLL5 2 TRUE PASS 4 paneaWholeGenomeLandscape2019 31558468 -IKZF3 2 TRUE PASS 3 paneaWholeGenomeLandscape2019 31558468 -IRF8 2 TRUE PASS 4 paneaWholeGenomeLandscape2019 31558468 -ITPR3 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 -KANK2 2 schmitzBurkittLymphomaPathogenesis2012 22885699 -KCNK10 3 FAIL 2 paneaWholeGenomeLandscape2019 31558468 -KIFC3 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 -KLHL26 2 burkhardtClinicalRelevanceMolecular2022b 35794096 -KMT2C 2 zhouSporadicEndemicBurkitt2019 31300419 -KMT2D 1 grandeGenomewideDiscoverySomatic2019 30617194 -MAP3K6 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 -MCL1 2 PASS 4 paneaWholeGenomeLandscape2019 31558468 -MIR142 2 TRUE grandeGenomewideDiscoverySomatic2019 30617194 -MKI67 2 schmitzBurkittLymphomaPathogenesis2012 22885699 -MME 3 FAIL 1 paneaWholeGenomeLandscape2019 31558468 -MTOR 3 FAIL 1 paneaWholeGenomeLandscape2019 31558468 -MYC 1 TRUE johnstonCmycHypermutationBurkitt1992 1297477 -MYH10 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 -MYO18A 2 schmitzBurkittLymphomaPathogenesis2012 22885699 -NBEAL1 2 PASS 4 loveGeneticLandscapeMutations2012 23143597 -NCOR2 2 schmitzBurkittLymphomaPathogenesis2012 22885699 -NOA1 2 burkhardtClinicalRelevanceMolecular2022b 35794096 -NOTCH1 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 -NRXN2 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 -P2RY2 2 PASS 4 loveGeneticLandscapeMutations2012 23143597 -P2RY8 1 muppidiLossSignalingGa132014b 25274307 -PABPC4L 3 FAIL 2 paneaWholeGenomeLandscape2019 31558468 -PC 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 -PCBP1 1 schmitzBurkittLymphomaPathogenesis2012 22885699 -PCDHA11 3 FAIL 1 paneaWholeGenomeLandscape2019 31558468 -PDCD11 2 schmitzBurkittLymphomaPathogenesis2012 22885699 -PDZRN3 3 FAIL 1 paneaWholeGenomeLandscape2019 31558468 -PHF6 1 thomasGeneticSubgroupsInform2023 36201743 -PIK3R1 3 FAIL 1 paneaWholeGenomeLandscape2019 31558468 -PIM1 2 TRUE burkhardtClinicalRelevanceMolecular2022b 35794096 -PLCG2 2 PASS 3 paneaWholeGenomeLandscape2019 31558468 -POLRMT 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 -POR 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 -PPP6R2 2 burkhardtClinicalRelevanceMolecular2022b 35794096 -PREX1 2 burkhardtClinicalRelevanceMolecular2022b 35794096 -PRSS22 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 -PTEN 1 loveGeneticLandscapeMutations2012 23143597 -PTPRN 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 -PXDNL 3 FAIL 1 paneaWholeGenomeLandscape2019 31558468 -RANBP6 2 PASS 5 loveGeneticLandscapeMutations2012 23143597 -RBP3 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 -RET 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 -REV3L 2 burkhardtClinicalRelevanceMolecular2022b 35794096 -RFX7 1 grandeGenomewideDiscoverySomatic2019 30617194 -RHOA 1 richterRecurrentMutationID32012a 23143595 -RNF144B 2 PASS 3 paneaWholeGenomeLandscape2019 31558468 -RPL10 2 burkhardtClinicalRelevanceMolecular2022b 35794096 -S1PR2 2 TRUE muppidiLossSignalingGa132014b 25274307 -SAL3 2 burkhardtClinicalRelevanceMolecular2022b 35794096 -SALL3 3 FAIL 2 loveGeneticLandscapeMutations2012 23143597 -SAPS2 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 -SBF1 3 FAIL 2 loveGeneticLandscapeMutations2012 23143597 -SF3B1 3 FAIL 4 loveGeneticLandscapeMutations2012 23143597 -SHANK1 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 -SIN3A 1 grandeGenomewideDiscoverySomatic2019 30617194 -SLC29A2 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 -SMARCA4 1 richterRecurrentMutationID32012a 23143595 -SNTB2 3 FAIL 2 paneaWholeGenomeLandscape2019 31558468 -SYNGAP1 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 -TBC1D9B 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 -TCF3 1 schmitzBurkittLymphomaPathogenesis2012 22885699 -TCL1A 1 TRUE grandeGenomewideDiscoverySomatic2019 30617194 -TET2 2 thomasGeneticSubgroupsInform2023 36201743 -TFAP4 1 grandeGenomewideDiscoverySomatic2019 30617194 -TIGD6 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 -TOP2A 2 schmitzBurkittLymphomaPathogenesis2012 22885699 -TP53 1 wildaInactivationARFMDM2p53Pathway2004 14712292 -TPST2 3 FAIL 0 loveGeneticLandscapeMutations2012 23143597 -TTN 2 burkhardtClinicalRelevanceMolecular2022b 35794096 -USP7 1 grandeGenomewideDiscoverySomatic2019 30617194 -VWA7 2 burkhardtClinicalRelevanceMolecular2022b 35794096 -WDR7 3 FAIL 2 paneaWholeGenomeLandscape2019 31558468 -WDR90 2 schmitzBurkittLymphomaPathogenesis2012 22885699 -WHAMM 2 schmitzBurkittLymphomaPathogenesis2012 22885699 -WNK1 1 thomasGeneticSubgroupsInform2023 36201743 -WNK2 2 PASS 4 paneaWholeGenomeLandscape2019 31558468 -YY1AP1 2 schmitzBurkittLymphomaPathogenesis2012 22885699 -ZAN 2 burkhardtClinicalRelevanceMolecular2022b 35794096 -ZBTB7A 2 burkhardtClinicalRelevanceMolecular2022b 35794096 -ZFP36L1 2 TRUE PASS 4 paneaWholeGenomeLandscape2019 31558468 -ZNF229 3 FAIL Germline loveGeneticLandscapeMutations2012 23143597 -ZNF85 2 burkhardtClinicalRelevanceMolecular2022b 35794096 +Gene Tier aSHM QC Mean Variant Quality citekey PMID MutationEffect Mutation-PMID +ARID1A 1 loveGeneticLandscapeMutations2012 23143597 LOF 38458187 +BACH2 1 TRUE grandeGenomewideDiscoverySomatic2019 30617194 +BCL6 1 TRUE PASS 4 loveGeneticLandscapeMutations2012 30617194 LOF 12504096 +BCL7A 1 TRUE grandeGenomewideDiscoverySomatic2019 30617194 LOF 32576963 +BMP7 1 paneaWholeGenomeLandscape2019 31558468 +CCND3 1 richterRecurrentMutationID32012a 23143595 GOF 22885699 +CHD8 1 grandeGenomewideDiscoverySomatic2019 36201743 +CREBBP 1 PASS 4 loveGeneticLandscapeMutations2012 23143597 LOF 33431788 +DDX3X 1 schmitzBurkittLymphomaPathogenesis2012 22885699 LOF 34437837 +FBXO11 1 richterRecurrentMutationID32012a 23143595 LOF 22113614 +FOXO1 1 schmitzBurkittLymphomaPathogenesis2012 22885699 GOF 23460611 +GNA13 1 loveGeneticLandscapeMutations2012 23143597 LOF 26616858 +GNAI2 1 grandeGenomewideDiscoverySomatic2019 30617194 GOF 23699601 +HIST1H1E 1 TRUE grandeGenomewideDiscoverySomatic2019 31558468 +HNRNPU 1 TRUE paneaWholeGenomeLandscape2019 31558468 LOF 36201743 +ID3 1 richterRecurrentMutationID32012a 23143595 LOF 23143595 +KMT2D 1 grandeGenomewideDiscoverySomatic2019 30617194 LOF 26366712 +MYC 1 TRUE johnstonCmycHypermutationBurkitt1992 1297477 GOF 38565249 +P2RY8 1 muppidiLossSignalingGa132014b 25274307 LOF 25274307 +PCBP1 1 schmitzBurkittLymphomaPathogenesis2012 22885699 +PHF6 1 thomasGeneticSubgroupsInform2023 36201743 +PTEN 1 loveGeneticLandscapeMutations2012 23143597 LOF 23840064 +RFX7 1 grandeGenomewideDiscoverySomatic2019 30617194 LOF 30926791 +RHOA 1 richterRecurrentMutationID32012a 23143595 LOF 26616858 +SIN3A 1 grandeGenomewideDiscoverySomatic2019 30617194 +SMARCA4 1 richterRecurrentMutationID32012a 23143595 LOF 33144586 +TCF3 1 schmitzBurkittLymphomaPathogenesis2012 22885699 GOF 22885699 +TCL1A 1 TRUE grandeGenomewideDiscoverySomatic2019 30617194 +TFAP4 1 grandeGenomewideDiscoverySomatic2019 30617194 LOF 34283887 +TP53 1 wildaInactivationARFMDM2p53Pathway2004 14712292 LOF 12826609 +USP7 1 grandeGenomewideDiscoverySomatic2019 30617194 +WNK1 1 thomasGeneticSubgroupsInform2023 36201743 +ADAMTS5 2 burkhardtClinicalRelevanceMolecular2022b 35794096 +ADNP 2 burkhardtClinicalRelevanceMolecular2022b 35794096 +AGO4 2 burkhardtClinicalRelevanceMolecular2022b 35794096 +ARHGEF1 2 muppidiLossSignalingGa132014b 25274307 +BCL2 2 TRUE burkhardtClinicalRelevanceMolecular2022b 35794096 +BTG1 2 TRUE burkhardtClinicalRelevanceMolecular2022b 35794096 +C16orf48 2 schmitzBurkittLymphomaPathogenesis2012 22885699 +CARD4 2 PASS 4 loveGeneticLandscapeMutations2012 23143597 +CCNF 2 abateDistinctViralMutational2015a 26468873 +CD79A 2 burkhardtClinicalRelevanceMolecular2022b 35794096 +CD83 2 TRUE PASS 3 paneaWholeGenomeLandscape2019 31558468 +CDC73 2 PASS 3 loveGeneticLandscapeMutations2012 23143597 +CDKN2A 2 grandeGenomewideDiscoverySomatic2019 30617194 +CDKN2C 2 thomasGeneticSubgroupsInform2023 36201743 +CHD4 2 burkhardtClinicalRelevanceMolecular2022b 35794096 +CPXM2 2 burkhardtClinicalRelevanceMolecular2022b 35794096 +CXCR4 2 TRUE PASS 4 paneaWholeGenomeLandscape2019 31558468 +DHCR7 2 schmitzBurkittLymphomaPathogenesis2012 22885699 +E2F2 2 burkhardtClinicalRelevanceMolecular2022b 35794096 +EBF1 2 TRUE thomasGeneticSubgroupsInform2023 NA +EDNRB 2 burkhardtClinicalRelevanceMolecular2022b 35794096 +EHD1 2 thomasGeneticSubgroupsInform2023 NA +EIF4A1 2 paneaWholeGenomeLandscape2019 31558468 +ELP2 2 schmitzBurkittLymphomaPathogenesis2012 22885699 +EPPK1 2 paneaWholeGenomeLandscape2019 31558468 +ERAP1 2 burkhardtClinicalRelevanceMolecular2022b 35794096 +EXOSC6 2 schmitzBurkittLymphomaPathogenesis2012 22885699 +EZH2 2 PASS 5 loveGeneticLandscapeMutations2012 23143597 +FLYWCH1 2 schmitzBurkittLymphomaPathogenesis2012 22885699 +GGTLA4 2 PASS 4 loveGeneticLandscapeMutations2012 23143597 +GTSE1 2 schmitzBurkittLymphomaPathogenesis2012 22885699 +HIST1H3D 2 TRUE PASS 3 paneaWholeGenomeLandscape2019 31558468 +HIST1H3I 2 TRUE PASS 4 paneaWholeGenomeLandscape2019 31558468 +HIST1H4J 2 TRUE PASS 3 paneaWholeGenomeLandscape2019 31558468 +HLA-DQB1 2 burkhardtClinicalRelevanceMolecular2022b 35794096 +IGLL5 2 TRUE PASS 4 paneaWholeGenomeLandscape2019 31558468 +IKZF3 2 TRUE PASS 3 paneaWholeGenomeLandscape2019 31558468 +IRF8 2 TRUE PASS 4 paneaWholeGenomeLandscape2019 31558468 +KANK2 2 schmitzBurkittLymphomaPathogenesis2012 22885699 +KLHL26 2 burkhardtClinicalRelevanceMolecular2022b 35794096 +KMT2C 2 zhouSporadicEndemicBurkitt2019 31300419 +MCL1 2 PASS 4 paneaWholeGenomeLandscape2019 31558468 +MIR142 2 TRUE grandeGenomewideDiscoverySomatic2019 30617194 +MKI67 2 schmitzBurkittLymphomaPathogenesis2012 22885699 +MYO18A 2 schmitzBurkittLymphomaPathogenesis2012 22885699 +NBEAL1 2 PASS 4 loveGeneticLandscapeMutations2012 23143597 +NCOR2 2 schmitzBurkittLymphomaPathogenesis2012 22885699 +NOA1 2 burkhardtClinicalRelevanceMolecular2022b 35794096 +P2RY2 2 PASS 4 loveGeneticLandscapeMutations2012 23143597 +PDCD11 2 schmitzBurkittLymphomaPathogenesis2012 22885699 +PIM1 2 TRUE burkhardtClinicalRelevanceMolecular2022b 35794096 +PLCG2 2 PASS 3 paneaWholeGenomeLandscape2019 31558468 +PPP6R2 2 burkhardtClinicalRelevanceMolecular2022b 35794096 +PREX1 2 burkhardtClinicalRelevanceMolecular2022b 35794096 +RANBP6 2 PASS 5 loveGeneticLandscapeMutations2012 23143597 +REV3L 2 burkhardtClinicalRelevanceMolecular2022b 35794096 +RNF144B 2 PASS 3 paneaWholeGenomeLandscape2019 31558468 +RPL10 2 burkhardtClinicalRelevanceMolecular2022b 35794096 +S1PR2 2 TRUE muppidiLossSignalingGa132014b 25274307 +SAL3 2 burkhardtClinicalRelevanceMolecular2022b 35794096 +TET2 2 thomasGeneticSubgroupsInform2023 36201743 +TOP2A 2 schmitzBurkittLymphomaPathogenesis2012 22885699 +TTN 2 burkhardtClinicalRelevanceMolecular2022b 35794096 +VWA7 2 burkhardtClinicalRelevanceMolecular2022b 35794096 +WDR90 2 schmitzBurkittLymphomaPathogenesis2012 22885699 +WHAMM 2 schmitzBurkittLymphomaPathogenesis2012 22885699 +WNK2 2 PASS 4 paneaWholeGenomeLandscape2019 31558468 +YY1AP1 2 schmitzBurkittLymphomaPathogenesis2012 22885699 +ZAN 2 burkhardtClinicalRelevanceMolecular2022b 35794096 +ZBTB7A 2 burkhardtClinicalRelevanceMolecular2022b 35794096 +ZFP36L1 2 TRUE PASS 4 paneaWholeGenomeLandscape2019 31558468 +ZNF85 2 burkhardtClinicalRelevanceMolecular2022b 35794096 +ACAD9 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 +ACE 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 +ALPK2 3 FAIL 1 paneaWholeGenomeLandscape2019 31558468 +ATP2C2 3 FAIL 2 loveGeneticLandscapeMutations2012 23143597 +BRAF 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 +BRD4 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 +BTG2 3 TRUE FAIL 1 loveGeneticLandscapeMutations2012 31558468 +C6orf27 3 FAIL Germline loveGeneticLandscapeMutations2012 23143597 +CAD 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 +CCT6B 3 FAIL Germline loveGeneticLandscapeMutations2012 23143597 +CD79B 3 FAIL 2 paneaWholeGenomeLandscape2019 31558468 +CDH17 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 +COL4A2 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 +CTCF 3 FAIL 1 paneaWholeGenomeLandscape2019 31558468 +CYB5D1 3 FAIL 2 loveGeneticLandscapeMutations2012 23143597 +CYP4F22 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 +DLGAP1 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 +DNMT1 3 FAIL 1 paneaWholeGenomeLandscape2019 31558468 +DTX1 3 TRUE FAIL 1 loveGeneticLandscapeMutations2012 31558468 +EIF2C4 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 +EML2 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 +ENTPD3 3 FAIL 2 loveGeneticLandscapeMutations2012 23143597 +EPHB2 3 FAIL 2 loveGeneticLandscapeMutations2012 23143597 +ETS1 3 TRUE FAIL 1 paneaWholeGenomeLandscape2019 31558468 +FAM129B 3 FAIL 2 loveGeneticLandscapeMutations2012 23143597 +FGFR3 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 +FTCD 3 FAIL Germline loveGeneticLandscapeMutations2012 23143597 +FZD3 3 FAIL 1 paneaWholeGenomeLandscape2019 31558468 +GRIK5 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 +HIST1H1C 3 TRUE FAIL 2 paneaWholeGenomeLandscape2019 31558468 +HIST1H2AG 3 TRUE FAIL 2 paneaWholeGenomeLandscape2019 31558468 +HIST1H2AM 3 TRUE FAIL 0 paneaWholeGenomeLandscape2019 31558468 +HIST1H2BK 3 TRUE FAIL 1 paneaWholeGenomeLandscape2019 31558468 +HIST1H3H 3 TRUE FAIL 0 paneaWholeGenomeLandscape2019 31558468 +HIST1H3J 3 TRUE FAIL 0 paneaWholeGenomeLandscape2019 31558468 +ICK 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 +ITPR3 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 +KCNK10 3 FAIL 2 paneaWholeGenomeLandscape2019 31558468 +KIFC3 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 +MAP3K6 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 +MME 3 FAIL 1 paneaWholeGenomeLandscape2019 31558468 +MTOR 3 FAIL 1 paneaWholeGenomeLandscape2019 31558468 +MYH10 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 +NOTCH1 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 +NRXN2 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 +PABPC4L 3 FAIL 2 paneaWholeGenomeLandscape2019 31558468 +PC 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 +PCDHA11 3 FAIL 1 paneaWholeGenomeLandscape2019 31558468 +PDZRN3 3 FAIL 1 paneaWholeGenomeLandscape2019 31558468 +PIK3R1 3 FAIL 1 paneaWholeGenomeLandscape2019 31558468 +POLRMT 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 +POR 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 +PRSS22 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 +PTPRN 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 +PXDNL 3 FAIL 1 paneaWholeGenomeLandscape2019 31558468 +RBP3 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 +RET 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 +SALL3 3 FAIL 2 loveGeneticLandscapeMutations2012 23143597 +SAPS2 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 +SBF1 3 FAIL 2 loveGeneticLandscapeMutations2012 23143597 +SF3B1 3 FAIL 4 loveGeneticLandscapeMutations2012 23143597 +SHANK1 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 +SLC29A2 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 +SNTB2 3 FAIL 2 paneaWholeGenomeLandscape2019 31558468 +SYNGAP1 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 +TBC1D9B 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 +TIGD6 3 FAIL 1 loveGeneticLandscapeMutations2012 23143597 +TPST2 3 FAIL 0 loveGeneticLandscapeMutations2012 23143597 +WDR7 3 FAIL 2 paneaWholeGenomeLandscape2019 31558468 +ZNF229 3 FAIL Germline loveGeneticLandscapeMutations2012 23143597 \ No newline at end of file diff --git a/resources/curated/fl_genes.tsv b/resources/curated/fl_genes.tsv index dfecb246..5aacad94 100644 --- a/resources/curated/fl_genes.tsv +++ b/resources/curated/fl_genes.tsv @@ -1,114 +1,114 @@ -Gene Tier aSHM QC Mean Variant Quality citekey Dreval Hubschmann Crouch Kalmbach Russler-Germain PMID -ABL2 2 russler-germainMutationsAssociatedProgression2023b FALSE FALSE FALSE TRUE FALSE 37563306 -ACTB 1 TRUE drevalGeneticSubdivisionsFollicular2023 TRUE TRUE FALSE FALSE FALSE NA -ACTG1 2 TRUE hubschmannMutationalMechanismsShaping2021b FALSE TRUE FALSE FALSE FALSE 33953289 -ARID1A 1 krysiakRecurrentSomaticMutations2017b FALSE TRUE TRUE FALSE FALSE 28064239 -ATP6AP1 1 okosunRecurrentMTORC1activatingRRAGC2016a TRUE TRUE FALSE FALSE FALSE 26691987 -ATP6V1A 2 PASS 4 hubschmannMutationalMechanismsShaping2021b FALSE TRUE FALSE FALSE FALSE 33953289 -ATP6V1B2 1 okosunRecurrentMTORC1activatingRRAGC2016a TRUE TRUE FALSE FALSE FALSE 26691987 -B2M 1 morinFrequentMutationHistonemodifying2011 TRUE TRUE FALSE FALSE TRUE 21796119 -BCL10 1 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TRUE NA -CD83 1 TRUE russler-germainMutationsAssociatedProgression2023b TRUE NA TRUE FALSE FALSE 37493986 -CDC42BPB 2 PASS 3 hubschmannMutationalMechanismsShaping2021b FALSE TRUE FALSE FALSE FALSE 33953289 -CILP 2 russler-germainMutationsAssociatedProgression2023b FALSE NA FALSE FALSE TRUE 37493986 -CPNE8 2 PASS 4 hubschmannMutationalMechanismsShaping2021b FALSE TRUE FALSE FALSE FALSE 33953289 -CREBBP 1 pasqualucciInactivatingMutationsAcetyltransferase2011a TRUE NA TRUE TRUE TRUE -CTSS 1 barariaCathepsinAlterationsInduce2020c FALSE NA FALSE FALSE FALSE 32330423 -CXCR4 2 TRUE krysiakRecurrentSomaticMutations2017b FALSE TRUE FALSE FALSE FALSE 28064239 -CYP2A6 2 russler-germainMutationsAssociatedProgression2023b FALSE NA FALSE FALSE TRUE 37493986 -DDX3X 2 NA TRUE NA FALSE FALSE FALSE 37084389 -DHX15 2 PASS 4 hubschmannMutationalMechanismsShaping2021b FALSE TRUE FALSE FALSE FALSE 33953289 -DTX1 2 TRUE NA TRUE NA TRUE FALSE FALSE NA -DUSP2 2 TRUE drevalGeneticSubdivisionsFollicular2023 TRUE 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TRUE NA FALSE FALSE FALSE NA +ZNF608 2 krysiakRecurrentSomaticMutations2017b FALSE FALSE FALSE FALSE FALSE 28064239 \ No newline at end of file diff --git a/resources/curated/individual_study_lists/DLBCL/pasqualucciAnalysisCodingGenome2011.tsv b/resources/curated/individual_study_lists/DLBCL/pasqualucciAnalysisCodingGenome2011.tsv new file mode 100644 index 00000000..304f7817 --- /dev/null +++ b/resources/curated/individual_study_lists/DLBCL/pasqualucciAnalysisCodingGenome2011.tsv @@ -0,0 +1,58 @@ +Gene +KMT2D +CREBBP +TP53 +MYOM2 +TNFAIP3 +PIM1 +CD36 +B2M +CD79B +PRDM1 +CARD11 +BCL2 +MEF2B +MYD88 +ANKLE2 +KDM2B +HNF1B +MYC +CD58 +EZH2 +ADAMTSL3 +AKAP8 +C12orf35 +CCND3 +DCHS1 +DUSP27 +MAGEC3 +TLL2 +TMEM30A +EP300 +DPYD +DSC3 +KLF2 +MED12L +MTMR8 +PMS1 +TSC22D1 +OFD1 +TRAF3 +BCL2L10 +BRSK1 +CAMTA1 +CYTSB +DUSP9 +FBXO31 +GRB2 +HMGB1 +MYO1G +PPP2R5A +RASGEF1A +RGAG1 +SERPINA1 +SMARCA1 +ZNF521 +ZWILCH +NOTCH1 +