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Ennishi D, Jiang A, Boyle M, Collinge B, Grande BM, Ben-Neriah S, Rushton C, Tang J, Thomas N, Slack GW, Farinha P, Takata K, Miyata-Takata T, Craig J, Mottok A, Meissner B, Saberi S, Bashashati A, Villa D, Savage KJ, Sehn LH, Kridel R, Mungall AJ, Marra MA, Shah SP, Steidl C, Connors JM, Gascoyne RD, Morin RD, Scott DW. Double-Hit Gene Expression Signature Defines a Distinct Subgroup of Germinal Center B-Cell-Like Diffuse Large B-Cell Lymphoma. J Clin Oncol. 2019 Jan 20;37(3):190-201. doi: 10.1200/JCO.18.01583. Epub 2018 Dec 3. PubMed PMID: 30523716; PubMed Central PMCID: PMC6804880.
Arthur SE, Jiang A, Grande BM, Alcaide M, Cojocaru R, Rushton CK, Mottok A, Hilton LK, Lat PK, Zhao EY, Culibrk L, Ennishi D, Jessa S, Chong L, Thomas N, Pararajalingam P, Meissner B, Boyle M, Davidson J, Bushell KR, Lai D, Farinha P, Slack GW, Morin GB, Shah S, Sen D, Jones SJM, Mungall AJ, Gascoyne RD, Audas TE, Unrau P, Marra MA, Connors JM, Steidl C, Scott DW, Morin RD. Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma. Nat Commun. 2018 Oct 1;9(1):4001. doi: 10.1038/s41467-018-06354-3. PubMed PMID: 30275490; PubMed Central PMCID: PMC6167379.
Shah SP. Copy number signatures in ovarian cancer. Nat Genet. 2018 Sep;50(9):1208-1209. doi: 10.1038/s41588-018-0212-y. PubMed PMID: 30158680.
Pilsworth JA, Cochrane DR, Xia Z, Aubert G, Färkkilä AEM, Horlings HM, Yanagida S, Yang W, Lim JLP, Wang YK, Bashashati A, Keul J, Wong A, Norris K, Brucker SY, Taran FA, Krämer B, Staebler A, van Meurs H, Oliva E, Shah SP, Kommoss S, Kommoss F, Gilks CB, Baird DM, Huntsman DG. TERT promoter mutation in adult granulosa cell tumor of the ovary. Mod Pathol. 2018 Jul;31(7):1107-1115. doi: 10.1038/s41379-018-0007-9. Epub 2018 Feb 15. PubMed PMID: 29449679.
Zhang AW, McPherson A, Milne K, Kroeger DR, Hamilton PT, Miranda A, Funnell T, Little N, de Souza CPE, Laan S, LeDoux S, Cochrane DR, Lim JLP, Yang W, Roth A, Smith MA, Ho J, Tse K, Zeng T, Shlafman I, Mayo MR, Moore R, Failmezger H, Heindl A, Wang YK, Bashashati A, Grewal DS, Brown SD, Lai D, Wan ANC, Nielsen CB, Huebner C, Tessier-Cloutier B, Anglesio MS, Bouchard-Côté A, Yuan Y, Wasserman WW, Gilks CB, Karnezis AN, Aparicio S, McAlpine JN, Huntsman DG, Holt RA, Nelson BH, Shah SP. Interfaces of Malignant and Immunologic Clonal Dynamics in Ovarian Cancer. Cell. 2018 Jun 14;173(7):1755-1769.e22. doi: 10.1016/j.cell.2018.03.073. Epub 2018 May 10. PubMed PMID: 29754820.
Ding J, Condon A, Shah SP. Interpretable dimensionality reduction of single cell transcriptome data with deep generative models. Nat Commun. 2018 May 21;9(1):2002. doi: 10.1038/s41467-018-04368-5. PubMed PMID: 29784946; PubMed Central PMCID: PMC5962608.
McPherson AW, Chan FC, Shah SP. Observing Clonal Dynamics across Spatiotemporal Axes: A Prelude to Quantitative Fitness Models for Cancer. Cold Spring Harb Perspect Med. 2018 Feb 1;8(2). doi: 10.1101/cshperspect.a029603. Review. PubMed PMID: 28630229; PubMed Central PMCID: PMC5793737.
Xia Z, Cochrane DR, Anglesio MS, Wang YK, Nazeran T, Tessier-Cloutier B, McConechy MK, Senz J, Lum A, Bashashati A, Shah SP, Huntsman DG. LINE-1 retrotransposon-mediated DNA transductions in endometriosis associated ovarian cancers. Gynecol Oncol. 2017 Dec;147(3):642-647. doi: 10.1016/j.ygyno.2017.09.032. Epub 2017 Oct 9. PubMed PMID: 29032825.
Chan FC, Mottok A, Gerrie AS, Power M, Nijland M, Diepstra A, van den Berg A, Kamper P, d'Amore F, d'Amore AL, Hamilton-Dutoit S, Savage KJ, Shah SP, Connors JM, Gascoyne RD, Scott DW, Steidl C. Prognostic Model to Predict Post-Autologous Stem-Cell Transplantation Outcomes in Classical Hodgkin Lymphoma. J Clin Oncol. 2017 Nov 10;35(32):3722-3733. doi: 10.1200/JCO.2017.72.7925. Epub 2017 Sep 12. PubMed PMID: 28898161.
Farahani H, de Souza CPE, Billings R, Yap D, Shumansky K, Wan A, Lai D, Mes-Masson AM, Aparicio S, P Shah S. Engineered in-vitro cell line mixtures and robust evaluation of computational methods for clonal decomposition and longitudinal dynamics in cancer. Sci Rep. 2017 Oct 18;7(1):13467. doi: 10.1038/s41598-017-13338-8. PubMed PMID: 29044127; PubMed Central PMCID: PMC5647443.
Tarpey PS, Behjati S, Young MD, Martincorena I, Alexandrov LB, Farndon SJ, Guzzo C, Hardy C, Latimer C, Butler AP, Teague JW, Shlien A, Futreal PA, Shah S, Bashashati A, Jamshidi F, Nielsen TO, Huntsman D, Baumhoer D, Brandner S, Wunder J, Dickson B, Cogswell P, Sommer J, Phillips JJ, Amary MF, Tirabosco R, Pillay N, Yip S, Stratton MR, Flanagan AM, Campbell PJ. The driver landscape of sporadic chordoma. Nat Commun. 2017 Oct 12;8(1):890. doi: 10.1038/s41467-017-01026-0. PubMed PMID: 29026114; PubMed Central PMCID: PMC5638846.
McPherson AW, Roth A, Ha G, Chauve C, Steif A, de Souza CPE, Eirew P, Bouchard-Côté A, Aparicio S, Sahinalp SC, Shah SP. ReMixT: clone-specific genomic structure estimation in cancer. Genome Biol. 2017 Jul 27;18(1):140. doi: 10.1186/s13059-017-1267-2. PubMed PMID: 28750660; PubMed Central PMCID: PMC5530528.
Taghiyar MJ, Rosner J, Grewal D, Grande BM, Aniba R, Grewal J, Boutros PC, Morin RD, Bashashati A, Shah SP. Kronos: a workflow assembler for genome analytics and informatics. Gigascience. 2017 Jul 1;6(7):1-10. doi: 10.1093/gigascience/gix042. PubMed PMID: 28655203; PubMed Central PMCID: PMC5569921.
Oricchio E, Katanayeva N, Donaldson MC, Sungalee S, Pasion JP, Béguelin W, Battistello E, Sanghvi VR, Jiang M, Jiang Y, Teater M, Parmigiani A, Budanov AV, Chan FC, Shah SP, Kridel R, Melnick AM, Ciriello G, Wendel HG. Genetic and epigenetic inactivation of SESTRIN1 controls mTORC1 and response to EZH2 inhibition in follicular lymphoma. Sci Transl Med. 2017 Jun 28;9(396). doi: 10.1126/scitranslmed.aak9969. PubMed PMID: 28659443; PubMed Central PMCID: PMC5559734.
Tien JF, Mazloomian A, Cheng SG, Hughes CS, Chow CCT, Canapi LT, Oloumi A, Trigo-Gonzalez G, Bashashati A, Xu J, Chang VC, Shah SP, Aparicio S, Morin GB. CDK12 regulates alternative last exon mRNA splicing and promotes breast cancer cell invasion. Nucleic Acids Res. 2017 Jun 20;45(11):6698-6716. doi: 10.1093/nar/gkx187. PubMed PMID: 28334900; PubMed Central PMCID: PMC5499812.
Wang YK, Bashashati A, Anglesio MS, Cochrane DR, Grewal DS, Ha G, McPherson A, Horlings HM, Senz J, Prentice LM, Karnezis AN, 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 AM, McAlpine JN, Aparicio S, Huntsman DG, Shah SP. Genomic consequences of aberrant DNA repair mechanisms stratify ovarian cancer histotypes. Nat Genet. 2017 Jun;49(6):856-865. doi: 10.1038/ng.3849. Epub 2017 Apr 24. PubMed PMID: 28436987.
Smith MA, Nielsen CB, Chan FC, McPherson A, Roth A, Farahani H, Machev D, Steif A, Shah SP. E-scape: interactive visualization of single-cell phylogenetics and cancer evolution. Nat Methods. 2017 May 30;14(6):549-550. doi: 10.1038/nmeth.4303. PubMed PMID: 28557980.
Ennishi D, Mottok A, Ben-Neriah S, Shulha HP, Farinha P, Chan FC, Meissner B, Boyle M, Hother C, Kridel R, Lai D, Saberi S, Bashashati A, Shah SP, Morin RD, Marra MA, Savage KJ, Sehn LH, Steidl C, Connors JM, Gascoyne RD, Scott DW. Genetic profiling of MYC and BCL2 in diffuse large B-cell lymphoma determines cell-of-origin-specific clinical impact. Blood. 2017 May 18;129(20):2760-2770. doi: 10.1182/blood-2016-11-747022. Epub 2017 Mar 28. PubMed PMID: 28351934.
Albuquerque MA, Grande BM, Ritch EJ, Pararajalingam P, Jessa S, Krzywinski M, Grewal JK, Shah SP, Boutros PC, Morin RD. Enhancing knowledge discovery from cancer genomics data with Galaxy. Gigascience. 2017 May 1;6(5):1-13. doi: 10.1093/gigascience/gix015. PubMed PMID: 28327945; PubMed Central PMCID: PMC5437943.
Salehi S, Steif A, Roth A, Aparicio S, Bouchard-Côté A, Shah SP. ddClone: joint statistical inference of clonal populations from single cell and bulk tumour sequencing data. Genome Biol. 2017 Mar 1;18(1):44. doi: 10.1186/s13059-017-1169-3. PubMed PMID: 28249593; PubMed Central PMCID: PMC5333399.
Funnell T, Tasaki S, Oloumi A, Araki S, Kong E, Yap D, Nakayama Y, Hughes CS, Cheng SG, Tozaki H, Iwatani M, Sasaki S, Ohashi T, Miyazaki T, Morishita N, Morishita D, Ogasawara-Shimizu M, Ohori M, Nakao S, Karashima M, Sano M, Murai A, Nomura T, Uchiyama N, Kawamoto T, Hara R, Nakanishi O, Shumansky K, Rosner J, Wan A, McKinney S, Morin GB, Nakanishi A, Shah S, Toyoshiba H, Aparicio S. CLK-dependent exon recognition and conjoined gene formation revealed with a novel small molecule inhibitor. Nat Commun. 2017 Feb 23;8(1):7. doi: 10.1038/s41467-016-0008-7. PubMed PMID: 28232751; PubMed Central PMCID: PMC5431906.
Xu H, Di Antonio M, McKinney S, Mathew V, Ho B, O'Neil NJ, Santos ND, Silvester J, Wei V, Garcia J, Kabeer F, Lai D, Soriano P, Banáth J, Chiu DS, Yap D, Le DD, Ye FB, Zhang A, Thu K, Soong J, Lin SC, Tsai AH, Osako T, Algara T, Saunders DN, Wong J, Xian J, Bally MB, Brenton JD, Brown GW, Shah SP, Cescon D, Mak TW, Caldas C, Stirling PC, Hieter P, Balasubramanian S, Aparicio S. CX-5461 is a DNA G-quadruplex stabilizer with selective lethality in BRCA1/2 deficient tumours. Nat Commun. 2017 Feb 17;8:14432. doi: 10.1038/ncomms14432. PubMed PMID: 28211448; PubMed Central PMCID: PMC5321743.
Zahn H, Steif A, Laks E, Eirew P, VanInsberghe M, Shah SP, Aparicio S, Hansen CL. Scalable whole-genome single-cell library preparation without preamplification. Nat Methods. 2017 Feb;14(2):167-173. doi: 10.1038/nmeth.4140. Epub 2017 Jan 9. PubMed PMID: 28068316.
Kridel R, Chan FC, Mottok A, Boyle M, Farinha P, Tan K, Meissner B, Bashashati A, McPherson A, Roth A, Shumansky K, Yap D, Ben-Neriah S, Rosner J, Smith MA, Nielsen C, Giné E, Telenius A, Ennishi D, Mungall A, Moore R, Morin RD, Johnson NA, Sehn LH, Tousseyn T, Dogan A, Connors JM, Scott DW, Steidl C, Marra MA, Gascoyne RD, Shah SP. Histological Transformation and Progression in Follicular Lymphoma: A Clonal Evolution Study. PLoS Med. 2016 Dec;13(12):e1002197. doi: 10.1371/journal.pmed.1002197. eCollection 2016 Dec. PubMed PMID: 27959929; PubMed Central PMCID: PMC5154502.
Duffy S, Fam HK, Wang YK, Styles EB, Kim JH, Ang JS, Singh T, Larionov V, Shah SP, Andrews B, Boerkoel CF, Hieter P. Overexpression screens identify conserved dosage chromosome instability genes in yeast and human cancer. Proc Natl Acad Sci U S A. 2016 Sep 6;113(36):9967-76. doi: 10.1073/pnas.1611839113. Epub 2016 Aug 22. PubMed PMID: 27551064; PubMed Central PMCID: PMC5018746.
Ding J, Shah S, Condon A. densityCut: an efficient and versatile topological approach for automatic clustering of biological data. Bioinformatics. 2016 Sep 1;32(17):2567-76. doi: 10.1093/bioinformatics/btw227. Epub 2016 Apr 23. PubMed PMID: 27153661; PubMed Central PMCID: PMC5013902.
Leung K, Klaus A, Lin BK, Laks E, Biele J, Lai D, Bashashati A, Huang YF, Aniba R, Moksa M, Steif A, Mes-Masson AM, Hirst M, Shah SP, Aparicio S, Hansen CL. Robust high-performance nanoliter-volume single-cell multiple displacement amplification on planar substrates. Proc Natl Acad Sci U S A. 2016 Jul 26;113(30):8484-9. doi: 10.1073/pnas.1520964113. Epub 2016 Jul 13. PubMed PMID: 27412862; PubMed Central PMCID: PMC4968760.
Roth A, McPherson A, Laks E, Biele J, Yap D, Wan A, Smith MA, Nielsen CB, McAlpine JN, Aparicio S, Bouchard-Côté A, Shah SP. Clonal genotype and population structure inference from single-cell tumor sequencing. Nat Methods. 2016 Jul;13(7):573-6. doi: 10.1038/nmeth.3867. Epub 2016 May 16. PubMed PMID: 27183439.
McPherson A, Roth A, Laks E, Masud T, Bashashati A, Zhang AW, Ha G, Biele J, Yap D, Wan A, Prentice LM, Khattra J, Smith MA, Nielsen CB, 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 AJ, Marra MA, Bouchard-Côté A, Gilks CB, Huntsman DG, McAlpine JN, Aparicio S, Shah SP. Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer. Nat Genet. 2016 Jul;48(7):758-67. doi: 10.1038/ng.3573. Epub 2016 May 16. PubMed PMID: 27182968.
Anglesio MS, Wang YK, Maassen M, Horlings HM, Bashashati A, Senz J, Mackenzie R, Grewal DS, Li-Chang H, Karnezis AN, Sheffield BS, McConechy MK, Kommoss F, Taran FA, Staebler A, Shah SP, Wallwiener D, Brucker S, Gilks CB, Kommoss S, Huntsman DG. Synchronous Endometrial and Ovarian Carcinomas: Evidence of Clonality. J Natl Cancer Inst. 2016 Jun;108(6):djv428. doi: 10.1093/jnci/djv428. Print 2016 Jun. PubMed PMID: 26832771.
Pereira B, Chin SF, Rueda OM, Vollan HK, Provenzano E, Bardwell HA, Pugh M, Jones L, Russell R, Sammut SJ, Tsui DW, Liu B, Dawson SJ, Abraham J, Northen H, Peden JF, Mukherjee A, Turashvili G, Green AR, McKinney S, Oloumi A, Shah S, Rosenfeld N, Murphy L, Bentley DR, Ellis IO, Purushotham A, Pinder SE, Børresen-Dale AL, Earl HM, Pharoah PD, Ross MT, Aparicio S, Caldas C. The somatic mutation profiles of 2,433 breast cancers refines their genomic and transcriptomic landscapes. Nat Commun. 2016 May 10;7:11479. doi: 10.1038/ncomms11479. PubMed PMID: 27161491; PubMed Central PMCID: PMC4866047.
Clermont PL, Crea F, Chiang YT, Lin D, Zhang A, Wang JZ, Parolia A, Wu R, Xue H, Wang Y, Ding J, Thu KL, Lam WL, Shah SP, Collins CC, Wang Y, Helgason CD. Identification of the epigenetic reader CBX2 as a potential drug target in advanced prostate cancer. Clin Epigenetics. 2016;8:16. doi: 10.1186/s13148-016-0182-9. eCollection 2016. PubMed PMID: 26877821; PubMed Central PMCID: PMC4751702.
Morrissy AS, Garzia L, Shih DJ, Zuyderduyn S, Huang X, Skowron P, Remke M, Cavalli FM, Ramaswamy V, Lindsay PE, Jelveh S, Donovan LK, Wang X, Luu B, Zayne K, Li Y, Mayoh C, Thiessen N, Mercier E, Mungall KL, Ma Y, Tse K, Zeng T, Shumansky K, Roth AJ, Shah S, Farooq H, Kijima N, Holgado BL, Lee JJ, Matan-Lithwick S, Liu J, Mack SC, Manno A, Michealraj KA, Nor C, Peacock J, Qin L, Reimand J, Rolider A, Thompson YY, Wu X, Pugh T, Ally A, Bilenky M, Butterfield YS, Carlsen R, Cheng Y, Chuah E, Corbett RD, Dhalla N, He A, Lee D, Li HI, Long W, Mayo M, Plettner P, Qian JQ, Schein JE, Tam A, Wong T, Birol I, Zhao Y, Faria CC, Pimentel J, Nunes S, Shalaby T, Grotzer M, Pollack IF, Hamilton RL, Li XN, Bendel AE, Fults DW, Walter AW, Kumabe T, Tominaga T, Collins VP, Cho YJ, Hoffman C, Lyden D, Wisoff JH, Garvin JH Jr, Stearns DS, Massimi L, Schüller U, Sterba J, Zitterbart K, Puget S, Ayrault O, Dunn SE, Tirapelli DP, Carlotti CG, Wheeler H, Hallahan AR, Ingram W, MacDonald TJ, Olson JJ, Van Meir EG, Lee JY, Wang KC, Kim SK, Cho BK, Pietsch T, Fleischhack G, Tippelt S, Ra YS, Bailey S, Lindsey JC, Clifford SC, Eberhart CG, Cooper MK, Packer RJ, Massimino M, Garre ML, Bartels U, Tabori U, Hawkins CE, Dirks P, Bouffet E, Rutka JT, Wechsler-Reya RJ, Weiss WA, Collier LS, Dupuy AJ, Korshunov A, Jones DT, Kool M, Northcott PA, Pfister SM, Largaespada DA, Mungall AJ, Moore RA, Jabado N, Bader GD, Jones SJ, Malkin D, Marra MA, Taylor MD. Divergent clonal selection dominates medulloblastoma at recurrence. Nature. 2016 Jan 21;529(7586):351-7. doi: 10.1038/nature16478. Epub 2016 Jan 13. PubMed PMID: 26760213; PubMed Central PMCID: PMC4936195.
Jamshidi F, Bashashati A, Shumansky K, Dickson B, Gokgoz N, Wunder JS, Andrulis IL, Lazar AJ, Shah SP, Huntsman DG, Nielsen TO. The genomic landscape of epithelioid sarcoma cell lines and tumours. J Pathol. 2016 Jan;238(1):63-73. doi: 10.1002/path.4636. Epub 2015 Oct 19. PubMed PMID: 26365879.
Murtaza M, Dawson SJ, Pogrebniak K, Rueda OM, Provenzano E, Grant J, Chin SF, Tsui DWY, Marass F, Gale D, Ali HR, Shah P, Contente-Cuomo T, Farahani H, Shumansky K, Kingsbury Z, Humphray S, Bentley D, Shah SP, Wallis M, Rosenfeld N, Caldas C. Multifocal clonal evolution characterized using circulating tumour DNA in a case of metastatic breast cancer. Nat Commun. 2015 Nov 4;6:8760. doi: 10.1038/ncomms9760. PubMed PMID: 26530965; PubMed Central PMCID: PMC4659935.
Kridel R, Mottok A, Farinha P, Ben-Neriah S, Ennishi D, Zheng Y, Chavez EA, Shulha HP, Tan K, Chan FC, Boyle M, Meissner B, Telenius A, Sehn LH, Marra MA, Shah SP, Steidl C, Connors JM, Scott DW, Gascoyne RD. Cell of origin of transformed follicular lymphoma. Blood. 2015 Oct 29;126(18):2118-27. doi: 10.1182/blood-2015-06-649905. Epub 2015 Aug 25. PubMed PMID: 26307535; PubMed Central PMCID: PMC4626253.
Ding J, McConechy MK, Horlings HM, Ha G, Chun Chan F, Funnell T, Mullaly SC, Reimand J, Bashashati A, Bader GD, Huntsman D, Aparicio S, Condon A, Shah SP. Systematic analysis of somatic mutations impacting gene expression in 12 tumour types. Nat Commun. 2015 Oct 5;6:8554. doi: 10.1038/ncomms9554. PubMed PMID: 26436532; PubMed Central PMCID: PMC4600750.
Boutros PC, Fraser M, Harding NJ, de Borja R, Trudel D, Lalonde E, Meng A, Hennings-Yeomans PH, McPherson A, Sabelnykova VY, Zia A, Fox NS, Livingstone J, Shiah YJ, Wang J, Beck TA, Have CL, Chong T, Sam M, Johns J, Timms L, Buchner N, Wong A, Watson JD, Simmons TT, P'ng C, Zafarana G, Nguyen F, Luo X, Chu KC, Prokopec SD, Sykes J, Dal Pra A, Berlin A, Brown A, Chan-Seng-Yue MA, Yousif F, Denroche RE, Chong LC, Chen GM, Jung E, Fung C, Starmans MH, Chen H, Govind SK, Hawley J, D'Costa A, Pintilie M, Waggott D, Hach F, Lambin P, Muthuswamy LB, Cooper C, Eeles R, Neal D, Tetu B, Sahinalp C, Stein LD, Fleshner N, Shah SP, Collins CC, Hudson TJ, McPherson JD, van der Kwast T, Bristow RG. Spatial genomic heterogeneity within localized, multifocal prostate cancer. Nat Genet. 2015 Jul;47(7):736-45. doi: 10.1038/ng.3315. Epub 2015 May 25. PubMed PMID: 26005866.
Twa DD, Mottok A, Chan FC, Ben-Neriah S, Woolcock BW, Tan KL, Mungall AJ, McDonald H, Zhao Y, Lim RS, Nelson BH, Milne K, Shah SP, Morin RD, Marra MA, Scott DW, Gascoyne RD, Steidl C. Recurrent genomic rearrangements in primary testicular lymphoma. J Pathol. 2015 Jun;236(2):136-41. doi: 10.1002/path.4522. Epub 2015 Mar 26. PubMed PMID: 25712539.
Anglesio MS, Bashashati A, Wang YK, Senz J, Ha G, Yang W, Aniba MR, Prentice LM, Farahani H, Li Chang H, Karnezis AN, Marra MA, Yong PJ, Hirst M, Gilks B, Shah SP, Huntsman DG. Multifocal endometriotic lesions associated with cancer are clonal and carry a high mutation burden. J Pathol. 2015 Jun;236(2):201-9. doi: 10.1002/path.4516. Epub 2015 Mar 23. PubMed PMID: 25692284; PubMed Central PMCID: PMC6680210.
Horlings HM, Shah SP, Huntsman DG. Using Somatic Mutations to Guide Treatment Decisions: Context Matters. JAMA Oncol. 2015 Jun;1(3):275-6. doi: 10.1001/jamaoncol.2015.35. PubMed PMID: 26181166.
Mathelier A, Lefebvre C, Zhang AW, Arenillas DJ, Ding J, Wasserman WW, Shah SP. Cis-regulatory somatic mutations and gene-expression alteration in B-cell lymphomas. Genome Biol. 2015 Apr 23;16:84. doi: 10.1186/s13059-015-0648-7. PubMed PMID: 25903198; PubMed Central PMCID: PMC4467049.
Hansford S, Kaurah P, Li-Chang H, Woo M, Senz J, Pinheiro H, Schrader KA, Schaeffer DF, Shumansky K, Zogopoulos G, Santos TA, Claro I, Carvalho J, Nielsen C, Padilla S, Lum A, Talhouk A, Baker-Lange K, Richardson S, Lewis I, Lindor NM, Pennell E, MacMillan A, Fernandez B, Keller G, Lynch H, Shah SP, Guilford P, Gallinger S, Corso G, Roviello F, Caldas C, Oliveira C, Pharoah PD, Huntsman DG. Hereditary Diffuse Gastric Cancer Syndrome: CDH1 Mutations and Beyond. JAMA Oncol. 2015 Apr;1(1):23-32. doi: 10.1001/jamaoncol.2014.168. PubMed PMID: 26182300.
Eirew P, Steif A, Khattra J, Ha G, Yap D, Farahani H, Gelmon K, Chia S, Mar C, Wan A, Laks E, Biele J, Shumansky K, Rosner J, McPherson A, Nielsen C, Roth AJ, Lefebvre C, Bashashati A, de Souza C, Siu C, Aniba R, Brimhall J, Oloumi A, Osako T, Bruna A, Sandoval JL, Algara T, Greenwood W, Leung K, Cheng H, Xue H, Wang Y, Lin D, Mungall AJ, Moore R, Zhao Y, Lorette J, Nguyen L, Huntsman D, Eaves CJ, Hansen C, Marra MA, Caldas C, Shah SP, Aparicio S. Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution. Nature. 2015 Feb 19;518(7539):422-6. doi: 10.1038/nature13952. Epub 2014 Nov 26. PubMed PMID: 25470049; PubMed Central PMCID: PMC4864027.
Chan FC, Telenius A, Healy S, Ben-Neriah S, Mottok A, Lim R, Drake M, Hu S, Ding J, Ha G, Scott DW, Kridel R, Bashashati A, Rogic S, Johnson N, Morin RD, Rimsza LM, Sehn L, Connors JM, Marra MA, Gascoyne RD, Shah SP, Steidl C. An RCOR1 loss-associated gene expression signature identifies a prognostically significant DLBCL subgroup. Blood. 2015 Feb 5;125(6):959-66. doi: 10.1182/blood-2013-06-507152. Epub 2014 Nov 13. PubMed PMID: 25395426.
Vollan HK, Rueda OM, Chin SF, Curtis C, Turashvili G, Shah S, Lingjærde OC, Yuan Y, Ng CK, Dunning MJ, Dicks E, Provenzano E, Sammut S, McKinney S, Ellis IO, Pinder S, Purushotham A, Murphy LC, Kristensen VN, Brenton JD, Pharoah PD, Børresen-Dale AL, Aparicio S, Caldas C. A tumor DNA complex aberration index is an independent predictor of survival in breast and ovarian cancer. Mol Oncol. 2015 Jan;9(1):115-27. doi: 10.1016/j.molonc.2014.07.019. Epub 2014 Aug 8. PubMed PMID: 25169931; PubMed Central PMCID: PMC4286124.
Nguyen LV, Cox CL, Eirew P, Knapp DJ, Pellacani D, Kannan N, Carles A, Moksa M, Balani S, Shah S, Hirst M, Aparicio S, Eaves CJ. DNA barcoding reveals diverse growth kinetics of human breast tumour subclones in serially passaged xenografts. Nat Commun. 2014 Dec 23;5:5871. doi: 10.1038/ncomms6871. PubMed PMID: 25532760; PubMed Central PMCID: PMC4284657.
Tone AA, McConechy MK, Yang W, Ding J, Yip S, Kong E, Wong KK, Gershenson DM, Mackay H, Shah S, Gilks B, Tinker AV, Clarke B, McAlpine JN, Huntsman D. Intratumoral heterogeneity in a minority of ovarian low-grade serous carcinomas. BMC Cancer. 2014 Dec 18;14:982. doi: 10.1186/1471-2407-14-982. PubMed PMID: 25523272; PubMed Central PMCID: PMC4320586.
Ha G, Roth A, Khattra J, Ho J, Yap D, Prentice LM, Melnyk N, McPherson A, Bashashati A, Laks E, Biele J, Ding J, Le A, Rosner J, Shumansky K, Marra MA, Gilks CB, Huntsman DG, McAlpine JN, Aparicio S, Shah SP. TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data. Genome Res. 2014 Nov;24(11):1881-93. doi: 10.1101/gr.180281.114. Epub 2014 Jul 24. PubMed PMID: 25060187; PubMed Central PMCID: PMC4216928.
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