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Page 1
A community approach to the cancer-variant-interpretation bottleneck.
Krysiak K, Danos AM, Kiwala S, McMichael JF, Coffman AC, Barnell EK, Sheta L, Saliba J, Grisdale CJ, Kujan L, Pema S, Lever J, Spies NC, Chiorean A, Rieke DT, Clark KA, Jani P, Takahashi H, Horak P, Ritter DI, Zhou X, Ainscough BJ, Delong S, Lamping M, Marr AR, Li BV, Lin WH, Terraf P, Salama Y, Campbell KM, Farncombe KM, Ji J, Zhao X, Xu X, Kanagal-Shamanna R, Cotto KC, Skidmore ZL, Walker JR, Zhang J, Milosavljevic A, Patel RY, Giles RH, Kim RH, Schriml LM, Mardis ER, Jones SJM, Raca G, Rao S, Madhavan S, Wagner AH, Griffith OL, Griffith M. Krysiak K, et al. Among authors: xu x. Nat Cancer. 2022 May;3(5):522-525. doi: 10.1038/s43018-022-00379-w. Nat Cancer. 2022. PMID: 35624339 Free PMC article.
Assessing copy number abnormalities and copy-neutral loss-of-heterozygosity across the genome as best practice in diagnostic evaluation of acute myeloid leukemia: An evidence-based review from the cancer genomics consortium (CGC) myeloid neoplasms working group.
Xu X, Bryke C, Sukhanova M, Huxley E, Dash DP, Dixon-Mciver A, Fang M, Griepp PT, Hodge JC, Iqbal A, Jeffries S, Kanagal-Shamanna R, Quintero-Rivera F, Shetty S, Slovak ML, Yenamandra A, Lennon PA, Raca G. Xu X, et al. Cancer Genet. 2018 Dec;228-229:218-235. doi: 10.1016/j.cancergen.2018.07.005. Epub 2018 Oct 6. Cancer Genet. 2018. PMID: 30344013 Free article. Review.
Assessing copy number aberrations and copy neutral loss of heterozygosity across the genome as best practice: An evidence based review of clinical utility from the cancer genomics consortium (CGC) working group for myelodysplastic syndrome, myelodysplastic/myeloproliferative and myeloproliferative neoplasms.
Kanagal-Shamanna R, Hodge JC, Tucker T, Shetty S, Yenamandra A, Dixon-McIver A, Bryke C, Huxley E, Lennon PA, Raca G, Xu X, Jeffries S, Quintero-Rivera F, Greipp PT, Slovak ML, Iqbal MA, Fang M. Kanagal-Shamanna R, et al. Among authors: xu x. Cancer Genet. 2018 Dec;228-229:197-217. doi: 10.1016/j.cancergen.2018.07.003. Epub 2018 Oct 10. Cancer Genet. 2018. PMID: 30377088 Free article. Review.
Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity): Joint recommendations of Clinical Genome Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant Interpretation for Cancer Consortium (VICC).
Horak P, Griffith M, Danos AM, Pitel BA, Madhavan S, Liu X, Chow C, Williams H, Carmody L, Barrow-Laing L, Rieke D, Kreutzfeldt S, Stenzinger A, Tamborero D, Benary M, Rajagopal PS, Ida CM, Lesmana H, Satgunaseelan L, Merker JD, Tolstorukov MY, Campregher PV, Warner JL, Rao S, Natesan M, Shen H, Venstrom J, Roy S, Tao K, Kanagal-Shamanna R, Xu X, Ritter DI, Pagel K, Krysiak K, Dubuc A, Akkari YM, Li XS, Lee J, King I, Raca G, Wagner AH, Li MM, Plon SE, Kulkarni S, Griffith OL, Chakravarty D, Sonkin D. Horak P, et al. Among authors: xu x. Genet Med. 2022 May;24(5):986-998. doi: 10.1016/j.gim.2022.01.001. Epub 2022 Jan 29. Genet Med. 2022. PMID: 35101336 Free PMC article.
Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity): Joint recommendations of Clinical Genome Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant Interpretation for Cancer Consortium (VICC).
Horak P, Griffith M, Danos AM, Pitel BA, Madhavan S, Liu X, Chow C, Williams H, Carmody L, Barrow-Laing L, Rieke D, Kreutzfeldt S, Stenzinger A, Tamborero D, Benary M, Rajagopal PS, Ida CM, Lesmana H, Satgunaseelan L, Merker JD, Tolstorukov MY, Campregher PV, Warner JL, Rao S, Natesan M, Shen H, Venstrom J, Roy S, Tao K, Kanagal-Shamanna R, Xu X, Ritter DI, Pagel K, Krysiak K, Dubuc A, Akkari YM, Li XS, Lee J, King I, Raca G, Wagner AH, Li MM, Plon SE, Kulkarni S, Griffith OL, Chakravarty D, Sonkin D. Horak P, et al. Among authors: xu x. Genet Med. 2022 Sep;24(9):1991. doi: 10.1016/j.gim.2022.07.001. Genet Med. 2022. PMID: 36063163 Free article. No abstract available.
CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase.
Krysiak K, Danos AM, Saliba J, McMichael JF, Coffman AC, Kiwala S, Barnell EK, Sheta L, Grisdale CJ, Kujan L, Pema S, Lever J, Ridd S, Spies NC, Andric V, Chiorean A, Rieke DT, Clark KA, Reisle C, Venigalla AC, Evans M, Jani P, Takahashi H, Suda A, Horak P, Ritter DI, Zhou X, Ainscough BJ, Delong S, Kesserwan C, Lamping M, Shen H, Marr AR, Hoang MH, Singhal K, Khanfar M, Li BV, Lin WH, Terraf P, Corson LB, Salama Y, Campbell KM, Farncombe KM, Ji J, Zhao X, Xu X, Kanagal-Shamanna R, King I, Cotto KC, Skidmore ZL, Walker JR, Zhang J, Milosavljevic A, Patel RY, Giles RH, Kim RH, Schriml LM, Mardis ER, Jones SJM, Raca G, Rao S, Madhavan S, Wagner AH, Griffith M, Griffith OL. Krysiak K, et al. Among authors: xu x. Nucleic Acids Res. 2023 Jan 6;51(D1):D1230-D1241. doi: 10.1093/nar/gkac979. Nucleic Acids Res. 2023. PMID: 36373660 Free PMC article.
OncoKids: A Comprehensive Next-Generation Sequencing Panel for Pediatric Malignancies.
Hiemenz MC, Ostrow DG, Busse TM, Buckley J, Maglinte DT, Bootwalla M, Done J, Ji J, Raca G, Ryutov A, Xu X, Zhen CJ, Conroy JM, Hazard FK, Deignan JL, Rogers BB, Treece AL, Parham DM, Gai X, Judkins AR, Triche TJ, Biegel JA. Hiemenz MC, et al. Among authors: xu x. J Mol Diagn. 2018 Nov;20(6):765-776. doi: 10.1016/j.jmoldx.2018.06.009. Epub 2018 Aug 20. J Mol Diagn. 2018. PMID: 30138724 Free article.
Myeloid malignancies with 5q and 7q deletions are associated with extreme genomic complexity, biallelic TP53 variants, and very poor prognosis.
Pitel BA, Sharma N, Zepeda-Mendoza C, Smadbeck JB, Pearce KE, Cook JM, Vasmatzis G, Sachs Z, Kanagal-Shamanna R, Viswanatha D, Xiao S, Jenkins RB, Xu X, Hoppman NL, Ketterling RP, Peterson JF, Greipp PT, Baughn LB. Pitel BA, et al. Among authors: xu x. Blood Cancer J. 2021 Feb 8;11(2):18. doi: 10.1038/s41408-021-00416-4. Blood Cancer J. 2021. PMID: 33563889 Free PMC article. No abstract available.
Typical, atypical and cryptic t(15;17)(q24;q21) (PML::RARA) observed in acute promyelocytic leukemia: A retrospective review of 831 patients with concurrent chromosome and PML::RARA dual-color dual-fusion FISH studies.
Gagnon MF, Berg HE, Meyer RG, Sukov WR, Van Dyke DL, Jenkins RB, Greipp PT, Thorland EC, Hoppman NL, Xu X, Baughn LB, Reichard KK, Ketterling RP, Peterson JF. Gagnon MF, et al. Among authors: xu x. Genes Chromosomes Cancer. 2022 Oct;61(10):629-634. doi: 10.1002/gcc.23070. Epub 2022 Jun 10. Genes Chromosomes Cancer. 2022. PMID: 35639830
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