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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: kujan l. Nat Cancer. 2022 May;3(5):522-525. doi: 10.1038/s43018-022-00379-w. Nat Cancer. 2022. PMID: 35624339 Free PMC article.
Standard operating procedure for curation and clinical interpretation of variants in cancer.
Danos AM, Krysiak K, Barnell EK, Coffman AC, McMichael JF, Kiwala S, Spies NC, Sheta LM, Pema SP, Kujan L, Clark KA, Wollam AZ, Rao S, Ritter DI, Sonkin D, Raca G, Lin WH, Grisdale CJ, Kim RH, Wagner AH, Madhavan S, Griffith M, Griffith OL. Danos AM, et al. Among authors: kujan l. Genome Med. 2019 Nov 29;11(1):76. doi: 10.1186/s13073-019-0687-x. Genome Med. 2019. PMID: 31779674 Free PMC article. Review.
Large scale genotype- and phenotype-driven machine learning in Von Hippel-Lindau disease.
Chiorean A, Farncombe KM, Delong S, Andric V, Ansar S, Chan C, Clark K, Danos AM, Gao Y, Giles RH, Goldenberg A, Jani P, Krysiak K, Kujan L, Macpherson S, Maher ER, McCoy LG, Salama Y, Saliba J, Sheta L, Griffith M, Griffith OL, Erdman L, Ramani A, Kim RH. Chiorean A, et al. Among authors: kujan l. Hum Mutat. 2022 Sep;43(9):1268-1285. doi: 10.1002/humu.24392. Epub 2022 May 10. Hum Mutat. 2022. PMID: 35475554 Free PMC article.
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: kujan l. Nucleic Acids Res. 2023 Jan 6;51(D1):D1230-D1241. doi: 10.1093/nar/gkac979. Nucleic Acids Res. 2023. PMID: 36373660 Free PMC article.
CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer.
Griffith M, Spies NC, Krysiak K, McMichael JF, Coffman AC, Danos AM, Ainscough BJ, Ramirez CA, Rieke DT, Kujan L, Barnell EK, Wagner AH, Skidmore ZL, Wollam A, Liu CJ, Jones MR, Bilski RL, Lesurf R, Feng YY, Shah NM, Bonakdar M, Trani L, Matlock M, Ramu A, Campbell KM, Spies GC, Graubert AP, Gangavarapu K, Eldred JM, Larson DE, Walker JR, Good BM, Wu C, Su AI, Dienstmann R, Margolin AA, Tamborero D, Lopez-Bigas N, Jones SJ, Bose R, Spencer DH, Wartman LD, Wilson RK, Mardis ER, Griffith OL. Griffith M, et al. Among authors: kujan l. Nat Genet. 2017 Jan 31;49(2):170-174. doi: 10.1038/ng.3774. Nat Genet. 2017. PMID: 28138153 Free PMC article.
Adapting crowdsourced clinical cancer curation in CIViC to the ClinGen minimum variant level data community-driven standards.
Danos AM, Ritter DI, Wagner AH, Krysiak K, Sonkin D, Micheel C, McCoy M, Rao S, Raca G, Boca SM, Roy A, Barnell EK, McMichael JF, Kiwala S, Coffman AC, Kujan L, Kulkarni S, Griffith M, Madhavan S, Griffith OL; Clinical Genome Resource Somatic Working Group and Clinical Interpretation of Variants in Cancer team members. Danos AM, et al. Among authors: kujan l. Hum Mutat. 2018 Nov;39(11):1721-1732. doi: 10.1002/humu.23651. Hum Mutat. 2018. PMID: 30311370 Free PMC article.