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2021 3
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Page 1
Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology.
Deveson IW, Gong B, Lai K, LoCoco JS, Richmond TA, Schageman J, Zhang Z, Novoradovskaya N, Willey JC, Jones W, Kusko R, Chen G, Madala BS, Blackburn J, Stevanovski I, Bhandari A, Close D, Conroy J, Hubank M, Marella N, Mieczkowski PA, Qiu F, Sebra R, Stetson D, Sun L, Szankasi P, Tan H, Tang LY, Arib H, Best H, Burgher B, Bushel PR, Casey F, Cawley S, Chang CJ, Choi J, Dinis J, Duncan D, Eterovic AK, Feng L, Ghosal A, Giorda K, Glenn S, Happe S, Haseley N, Horvath K, Hung LY, Jarosz M, Kushwaha G, Li D, Li QZ, Li Z, Liu LC, Liu Z, Ma C, Mason CE, Megherbi DB, Morrison T, Pabón-Peña C, Pirooznia M, Proszek PZ, Raymond A, Rindler P, Ringler R, Scherer A, Shaknovich R, Shi T, Smith M, Song P, Strahl M, Thodima VJ, Tom N, Verma S, Wang J, Wu L, Xiao W, Xu C, Yang M, Zhang G, Zhang S, Zhang Y, Shi L, Tong W, Johann DJ Jr, Mercer TR, Xu J; SEQC2 Oncopanel Sequencing Working Group. Deveson IW, et al. Among authors: lococo js. Nat Biotechnol. 2021 Sep;39(9):1115-1128. doi: 10.1038/s41587-021-00857-z. Epub 2021 Apr 12. Nat Biotechnol. 2021. PMID: 33846644 Free PMC article.
Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples.
Zhang Y, Blomquist TM, Kusko R, Stetson D, Zhang Z, Yin L, Sebra R, Gong B, Lococo JS, Mittal VK, Novoradovskaya N, Yeo JY, Dominiak N, Hipp J, Raymond A, Qiu F, Arib H, Smith ML, Brock JE, Farkas DH, Craig DJ, Crawford EL, Li D, Morrison T, Tom N, Xiao W, Yang M, Mason CE, Richmond TA, Jones W, Johann DJ Jr, Shi L, Tong W, Willey JC, Xu J. Zhang Y, et al. Among authors: lococo js. Genome Biol. 2022 Jun 29;23(1):141. doi: 10.1186/s13059-022-02709-8. Genome Biol. 2022. PMID: 35768876 Free PMC article.
Advancing NGS quality control to enable measurement of actionable mutations in circulating tumor DNA.
Willey JC, Morrison TB, Austermiller B, Crawford EL, Craig DJ, Blomquist TM, Jones WD, Wali A, Lococo JS, Haseley N, Richmond TA, Novoradovskaya N, Kusko R, Chen G, Li QZ, Johann DJ Jr, Deveson IW, Mercer TR, Wu L, Xu J. Willey JC, et al. Among authors: lococo js. Cell Rep Methods. 2021 Nov 3;1(7):100106. doi: 10.1016/j.crmeth.2021.100106. eCollection 2021 Nov 22. Cell Rep Methods. 2021. PMID: 35475002 Free PMC article.
Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions.
Gong B, Li D, Kusko R, Novoradovskaya N, Zhang Y, Wang S, Pabón-Peña C, Zhang Z, Lai K, Cai W, LoCoco JS, Lader E, Richmond TA, Mittal VK, Liu LC, Johann DJ Jr, Willey JC, Bushel PR, Yu Y, Xu C, Chen G, Burgess D, Cawley S, Giorda K, Haseley N, Qiu F, Wilkins K, Arib H, Attwooll C, Babson K, Bao L, Bao W, Lucas AB, Best H, Bhandari A, Bisgin H, Blackburn J, Blomquist TM, Boardman L, Burgher B, Butler DJ, Chang CJ, Chaubey A, Chen T, Chierici M, Chin CR, Close D, Conroy J, Cooley Coleman J, Craig DJ, Crawford E, Del Pozo A, Deveson IW, Duncan D, Eterovic AK, Fan X, Foox J, Furlanello C, Ghosal A, Glenn S, Guan M, Haag C, Hang X, Happe S, Hennigan B, Hipp J, Hong H, Horvath K, Hu J, Hung LY, Jarosz M, Kerkhof J, Kipp B, Kreil DP, Łabaj P, Lapunzina P, Li P, Li QZ, Li W, Li Z, Liang Y, Liu S, Liu Z, Ma C, Marella N, Martín-Arenas R, Megherbi DB, Meng Q, Mieczkowski PA, Morrison T, Muzny D, Ning B, Parsons BL, Paweletz CP, Pirooznia M, Qu W, Raymond A, Rindler P, Ringler R, Sadikovic B, Scherer A, Schulze E, Sebra R, Shaknovich R, Shi Q, Shi T, Silla-Castro JC, Smith M, López MS, Song P, Stetson D, Strahl M, Stuart A, Supplee J, Szankasi P, Tan H, Tang LY, Tao Y, Thakkar S, Thi… See abstract for full author list ➔ Gong B, et al. Among authors: lococo js. Genome Biol. 2021 Apr 16;22(1):109. doi: 10.1186/s13059-021-02315-0. Genome Biol. 2021. PMID: 33863344 Free PMC article.