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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: yang m. 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.
Liquid biopsy and its role in an advanced clinical trial for lung cancer.
Johann DJ Jr, Steliga M, Shin IJ, Yoon D, Arnaoutakis K, Hutchins L, Liu M, Liem J, Walker K, Pereira A, Yang M, Jeffus SK, Peterson E, Xu J. Johann DJ Jr, et al. Among authors: yang m. Exp Biol Med (Maywood). 2018 Feb;243(3):262-271. doi: 10.1177/1535370217750087. Exp Biol Med (Maywood). 2018. PMID: 29405770 Free PMC article. Review.
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, Thierry-Mi… See abstract for full author list ➔ Gong B, et al. Among authors: yang m. Genome Biol. 2021 Apr 16;22(1):109. doi: 10.1186/s13059-021-02315-0. Genome Biol. 2021. PMID: 33863344 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: yang m. Genome Biol. 2022 Jun 29;23(1):141. doi: 10.1186/s13059-022-02709-8. Genome Biol. 2022. PMID: 35768876 Free PMC article.
DNAp: A Pipeline for DNA-seq Data Analysis.
Causey JL, Ashby C, Walker K, Wang ZP, Yang M, Guan Y, Moore JH, Huang X. Causey JL, et al. Among authors: yang m. Sci Rep. 2018 May 1;8(1):6793. doi: 10.1038/s41598-018-25022-6. Sci Rep. 2018. PMID: 29717215 Free PMC article.
Artificial Intelligence and Cancer Drug Development.
Yang F, Darsey JA, Ghosh A, Li HY, Yang MQ, Wang S. Yang F, et al. Recent Pat Anticancer Drug Discov. 2022;17(1):2-8. doi: 10.2174/1574892816666210728123758. Recent Pat Anticancer Drug Discov. 2022. PMID: 34323201 Review.
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