Shah SP*, Roth A, Goya R, Oloumi A, Ha G, Zhao Y, Turashvili G, Ding J, Tse K, Haffari G, Bashashati A, Prentice LM, Khattra J, Burleigh A, Yap D, Bernard V, McPherson A, Shumansky K, Crisan A, Giuliany R, Heravi-Moussavi A, Rosner J, Lai D, Birol I, Varhol R, Tam A, Dhalla N, Zeng T, Ma K, Chan SK, Griffith M, Moradian A, Cheng SW, Morin GB, Watson P, Gelmon K, Chia S, Chin SF, Curtis C, Rueda OM, Pharoah PD, Damaraju S, Mackey J, Hoon K, Harkins T, Tadigotla V, Sigaroudinia M, Gascard P, Tlsty T, Costello JF, Meyer IM, Eaves CJ, Wasserman WW, Jones S, Huntsman D, Hirst M, Caldas C*, Marra MA*, Aparicio S*. The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature 2012 Apr 4;486(7403):395-9.
Roth A, Khattra J, Yap D, Wan A, Laks E, Biele J, Ha G, Aparicio S, Bouchard-Cote A, Shah SP. PyClone: statistical inference of clonal population structure in cancer. Nature Methods. 2014 Apr;11(4):396-8. doi: 10.1038/nmeth.2883.
McPherson A, Roth A, Laks E, Masud T, Bashashati A, Zhang AW, Ha G, Biele J, Yap D, Wan A, Prentice L, Khattra J, Mullaly SC, Kalloger S, Karnezis A, Shumansky K, Siu C, Rosner J, Chan HL, Ho J, Melnyk N, Senz J, Yang W, Moore R, Mungall A, Marra MA, Bouchard-Cote A, Gilks CB, Huntsman DG, McAlpine J, Aparicio S, Shah SP. Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer. Nat Genetics. 2016; 48(7):758-67. doi:10.1038/ ng.3573.
Wang YK, Bashashati A, Anglesio MS, Cochrane DR, Grewal D, Ha G, McPherson A, Horlings HM, Senz J, Prentice LM, Karnezis, Anthony N, Lai D, Aniba MR, Zhang AW, Shumansky K, Siu C, Wan A, McConechy MK, Li-Chang H, Tone A, Provencher D, de Ladurantaye M, Fleury H, Okamoto A, Yanagida S, Yanaihara N, Saito M, Mungall AJ, Moore R, Marra MA, Gilks CB, Mes-Masson A, McAlpine JN, Aparicio S, Huntsman DG and Shah SP. Genomic consequences of aberrant DNA repair mechanisms stratify ovarian cancer histotypes. Nature Genetics. 2017 Jun;49(6):856-865. doi: 10.1038/ng.3849.
Zhang A, McPherson A, Milne K, Kroeger DR, Hamilton PT, Miranda A, Funnell T, Litlle N, De Souza CPE, Laan S, LeDoux S, Cochrane DR, Lim J, Yang W, Roth A, Smith MA, Ho J, Tse K, Zeng T, Shlafman I, Mayo MR, Moore R, Failmezger H, Heindl A, Wang Y, Bashashati A, Grewal D, Brown SD, Lai D, Wan A, Nielsen C, Anglesio M, Bouchard-Cote A, Yuan Y, Wasserman W, Gilks B, Karnezis AN, Aparicio S, McAlpine J, Huntsman DG, Holt RA, Nelson BH, Shah SP. Interfaces of malignant and immunologic clonal dynamics in ovarian cancer. Cell. 2018 May 7. Pii: S0092-8674(18)30445-8.doi:10.1016/j.cell.2018.03.073.[Epub ahead of print]
Vázquez-García I, Uhlitz F, Ceglia N, Lim JLP, Wu M, Mohibullah N, Niyazov J, Ruiz AEB, Boehm KM, Bojilova V, Fong CJ, Funnell T, Grewal D, Havasov E, Leung S, Pasha A, Patel DM, Pourmaleki M, Rusk N, Shi H, Vanguri R, Williams MJ, Zhang AW, Broach V, Chi DS, Da Cruz Paula A, Gardner GJ, Kim SH, Lennon M, Long Roche K, Sonoda Y, Zivanovic O, Kundra R, Viale A, Derakhshan FN, Geneslaw L, Issa Bhaloo S, Maroldi A, Nunez R, Pareja F, Stylianou A, Vahdatinia M, Bykov Y, Grisham RN, Liu YL, Lakhman Y, Nikolovski I, Kelly D, Gao J, Schietinger A, Hollmann TJ, Bakhoum SF, Soslow RA, Ellenson LH, Abu-Rustum NR, Aghajanian C, Friedman CF, McPherson A, Weigelt B, Zamarin D, Shah SP. Ovarian cancer mutational processes drive site-specific immune evasion Nature. 2022 612(7941):778-786. PMID: 36517593; PMCID: PMC9771812.
Funnell T, O’Flanagan CH, Williams MJ, McPherson A, McKinney S, Kabeer F, Lee H, Salehi S, Vázquez-García I, Shi H, Leventhal E, Masud T, Eirew P, Yap D, Zhang AW, Lim JLP, Wang B, Brimhall J, Biele J, Ting J, Au V, Van Vliet M, Liu YF, Beatty S, Lai D, Pham J, Grewal D, Abrams D, Havasov E, Leung S, Bojilova V, Moore RA, Rusk N, Uhlitz F, Ceglia N, Weiner AC, Zaikova E, Douglas JM, Zamarin D, Weigelt B, Kim SH, Da Cruz Paula A, Reis-Filho JS, Martin SD, Li Y, Xu H, de Algara TR, Lee SR, Llanos VC, Huntsman DG, McAlpine JN; IMAXT Consortium; Shah SP, Aparicio S. Single-cell genomic variation induced by mutational processes in cancer. Nature. 2022 612(7938):106-115. PMID: 36289342; PMCID: PMC9712114.