faculty

Gavin Ha

gha@fredhutch.org

Assistant Member

Fred Hutch

Public Health Sciences

Cancer Biology

Computational Biology

Genetics, Genomics & Evolution

1100 Fairview Ave N

Faculty Contact Information

Building: Arnold Building Room: M1-B869 Box: M1-B514 Phone: 206-667-2802 https://GavinHaLab.org/

Research Summary

My laboratory is interested in studying the role of genomic alterations in cancer and expanding applications for precision medicine. We develop novel algorithms to identify genomic structural alterations in tumor and circulating cell-free DNA from patients with cancer. Our goals are to uncover the genetic and epigenetic mechanisms of treatment resistance, to identify blood-based genomic biomarkers, and to translate these findings and innovations to advance clinical research and precision medicine.

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Publications

The following publications were retrieved from PubMed:

The Immune Landscape of Cancer.

Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang TH, Porta-Pardo E, Gao GF, Plaisier CL, Eddy JA, Ziv E, Culhane AC, Paull EO, Sivakumar IKA, Gentles AJ, Malhotra R, Farshidfar F, Colaprico A, Parker JS, Mose LE, Vo NS, Liu J, Liu Y, Rader J, Dhankani V, Reynolds SM, Bowlby R, Califano A, Cherniack AD, Anastassiou D, Bedognetti D, Mokrab Y, Newman AM, Rao A, Chen K, Krasnitz A, Hu H, Malta TM, Noushmehr H, Pedamallu CS, Bullman S, Ojesina AI, Lamb A, Zhou W, Shen H, Choueiri TK, Weinstein JN, Guinney J, Saltz J, Holt RA, Rabkin CS, Cancer Genome Atlas Research Network., Lazar AJ, Serody JS, Demicco EG, Disis ML, Vincent BG, Shmulevich I.

Immunity. 2019 Aug 20; 2(51)411-412

Genomic distinctions between metastatic lower and upper tract urothelial carcinoma revealed through rapid autopsy.

Winters BR, De Sarkar N, Arora S, Bolouri H, Jana S, Vakar-Lopez F, Cheng HH, Schweizer MT, Yu EY, Grivas P, Lee JK, Kollath L, Holt SK, McFerrin L, Ha G, Nelson PS, Montgomery RB, Wright JL, Lam HM, Hsieh AC.

JCI Insight. 2019 May 30; (5)

Correction: Detection of circulating tumour DNA is associated with inferior outcomes in Ewing sarcoma and osteosarcoma: a report from the Children's Oncology Group.

Shulman DS, Klega K, Imamovic-Tuco A, Clapp A, Nag A, Thorner AR, Van Allen E, Ha G, Lessnick SL, Gorlick R, Janeway KA, Leavey PJ, Mascarenhas L, London WB, Vo KT, Stegmaier K, Hall D, Krailo MD, Barkauskas DA, DuBois SG, Crompton BD.

Br J Cancer. 2019 Apr; 8(120)869

Detection of Circulating Tumor DNA in Patients With Leiomyosarcoma With Progressive Disease.

Hemming ML, Klega KS, Rhoades J, Ha G, Acker KE, Andersen JL, Thai E, Nag A, Thorner AR, Raut CP, George S, Crompton BD.

JCO Precis Oncol. 2019; (2019)

Tumor fraction in cell-free DNA as a biomarker in prostate cancer.

Choudhury AD, Werner L, Francini E, Wei XX, Ha G, Freeman SS, Rhoades J, Reed SC, Gydush G, Rotem D, Lo C, Taplin ME, Harshman LC, Zhang Z, O'Connor EP, Stover DG, Parsons HA, Getz G, Meyerson M, Love JC, Hahn WC, Adalsteinsson VA.

JCI Insight. 2018 Nov 2; 21(3)

Comprehensive Molecular Characterization of the Hippo Signaling Pathway in Cancer.

Wang Y, Xu X, Maglic D, Dill MT, Mojumdar K, Ng PK, Jeong KJ, Tsang YH, Moreno D, Bhavana VH, Peng X, Ge Z, Chen H, Li J, Chen Z, Zhang H, Han L, Du D, Creighton CJ, Mills GB, Cancer Genome Atlas Research Network., Camargo F, Liang H.

Cell Rep. 2018 Oct 30; 5(25)1304-1317.e5

Neutral tumor evolution?

Tarabichi M, Martincorena I, Gerstung M, Leroi AM, Markowetz F, PCAWG Evolution and Heterogeneity Working Group., Spellman PT, Morris QD, Lingjærde OC, Wedge DC, Van Loo P.

Nat Genet. 2018 Dec; 12(50)1630-1633

A Pan-Cancer Analysis Reveals High-Frequency Genetic Alterations in Mediators of Signaling by the TGF-β Superfamily.

Korkut A, Zaidi S, Kanchi RS, Rao S, Gough NR, Schultz A, Li X, Lorenzi PL, Berger AC, Robertson G, Kwong LN, Datto M, Roszik J, Ling S, Ravikumar V, Manyam G, Rao A, Shelley S, Liu Y, Ju Z, Hansel D, de Velasco G, Pennathur A, Andersen JB, O'Rourke CJ, Ohshiro K, Jogunoori W, Nguyen BN, Li S, Osmanbeyoglu HU, Ajani JA, Mani SA, Houseman A, Wiznerowicz M, Chen J, Gu S, Ma W, Zhang J, Tong P, Cherniack AD, Deng C, Resar L, Cancer Genome Atlas Research Network., Weinstein JN, Mishra L, Akbani R.

Cell Syst. 2018 Oct 24; 4(7)422-437.e7

Detection of circulating tumour DNA is associated with inferior outcomes in Ewing sarcoma and osteosarcoma: a report from the Children's Oncology Group.

Br J Cancer. 2018 Aug; 5(119)615-621

Comprehensive Characterization of Cancer Driver Genes and Mutations.

Bailey MH, Tokheim C, Porta-Pardo E, Sengupta S, Bertrand D, Weerasinghe A, Colaprico A, Wendl MC, Kim J, Reardon B, Kwok-Shing Ng P, Jeong KJ, Cao S, Wang Z, Gao J, Gao Q, Wang F, Liu EM, Mularoni L, Rubio-Perez C, Nagarajan N, Cortés-Ciriano I, Zhou DC, Liang WW, Hess JM, Yellapantula VD, Tamborero D, Gonzalez-Perez A, Suphavilai C, Ko JY, Khurana E, Park PJ, Van Allen EM, Liang H, MC3 Working Group., Cancer Genome Atlas Research Network., Lawrence MS, Godzik A, Lopez-Bigas N, Stuart J, Wheeler D, Getz G, Chen K, Lazar AJ, Mills GB, Karchin R, Ding L.

Cell. 2018 Aug 9; 4(174)1034-1035

Genetic and transcriptional evolution alters cancer cell line drug response.

Ben-David U, Siranosian B, Ha G, Tang H, Oren Y, Hinohara K, Strathdee CA, Dempster J, Lyons NJ, Burns R, Nag A, Kugener G, Cimini B, Tsvetkov P, Maruvka YE, O'Rourke R, Garrity A, Tubelli AA, Bandopadhayay P, Tsherniak A, Vazquez F, Wong B, Birger C, Ghandi M, Thorner AR, Bittker JA, Meyerson M, Getz G, Beroukhim R, Golub TR.

Nature. 2018 Aug; 7718(560)325-330

Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients.

Kahles A, Lehmann KV, Toussaint NC, Hüser M, Stark SG, Sachsenberg T, Stegle O, Kohlbacher O, Sander C, Cancer Genome Atlas Research Network., Rätsch G.

Cancer Cell. 2018 Aug 13; 2(34)211-224.e6

Detection of Somatic Structural Variants Enables Quantification and Characterization of Circulating Tumor DNA in Children With Solid Tumors.

Klega K, Imamovic-Tuco A, Ha G, Clapp AN, Meyer S, Ward A, Clinton C, Nag A, Van Allen E, Mullen E, DuBois SG, Janeway K, Meyerson M, Thorner AR, Crompton BD.

JCO Precis Oncol. 2018; (2018)

The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma.

Ricketts CJ, De Cubas AA, Fan H, Smith CC, Lang M, Reznik E, Bowlby R, Gibb EA, Akbani R, Beroukhim R, Bottaro DP, Choueiri TK, Gibbs RA, Godwin AK, Haake S, Hakimi AA, Henske EP, Hsieh JJ, Ho TH, Kanchi RS, Krishnan B, Kwiatkowski DJ, Lui W, Merino MJ, Mills GB, Myers J, Nickerson ML, Reuter VE, Schmidt LS, Shelley CS, Shen H, Shuch B, Signoretti S, Srinivasan R, Tamboli P, Thomas G, Vincent BG, Vocke CD, Wheeler DA, Yang L, Kim WY, Robertson AG, Cancer Genome Atlas Research Network., Spellman PT, Rathmell WK, Linehan WM.

Cell Rep. 2018 Jun 19; 12(23)3698

Structural Alterations Driving Castration-Resistant Prostate Cancer Revealed by Linked-Read Genome Sequencing.

Viswanathan SR, Ha G, Hoff AM, Wala JA, Carrot-Zhang J, Whelan CW, Haradhvala NJ, Freeman SS, Reed SC, Rhoades J, Polak P, Cipicchio M, Wankowicz SA, Wong A, Kamath T, Zhang Z, Gydush GJ, Rotem D, PCF/SU2C International Prostate Cancer Dream Team., Love JC, Getz G, Gabriel S, Zhang CZ, Dehm SM, Nelson PS, Van Allen EM, Choudhury AD, Adalsteinsson VA, Beroukhim R, Taplin ME, Meyerson M.

Cell. 2018 Jul 12; 2(174)433-447.e19

Genomic discovery and clonal tracking in multiple myeloma by cell-free DNA sequencing.

Guo G, Raje NS, Seifer C, Kloeber J, Isenhart R, Ha G, Yee AJ, O'Donnell EK, Tai YT, Richardson PG, Bianchi G, Laubach JP, Warren D, Gemme E, Voisine J, Frede J, Kokkalis A, Yun H, Dimitrova V, Vijaykumar T, Meyerson M, Munshi NC, Anderson KC, Knoechel B, Lohr JG.

Leukemia. 2018 Aug; 8(32)1838-1841

The Immune Landscape of Cancer.

Immunity. 2018 Apr 17; 4(48)812-830.e14

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics.

Liu J, Lichtenberg T, Hoadley KA, Poisson LM, Lazar AJ, Cherniack AD, Kovatich AJ, Benz CC, Levine DA, Lee AV, Omberg L, Wolf DM, Shriver CD, Thorsson V, Cancer Genome Atlas Research Network., Hu H.

Cell. 2018 Apr 5; 2(173)400-416.e11

A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples.

Chen H, Li C, Peng X, Zhou Z, Weinstein JN, Cancer Genome Atlas Research Network., Liang H.

Cell. 2018 Apr 5; 2(173)386-399.e12

Comprehensive Characterization of Cancer Driver Genes and Mutations.

Bailey MH, Tokheim C, Porta-Pardo E, Sengupta S, Bertrand D, Weerasinghe A, Colaprico A, Wendl MC, Kim J, Reardon B, Ng PK, Jeong KJ, Cao S, Wang Z, Gao J, Gao Q, Wang F, Liu EM, Mularoni L, Rubio-Perez C, Nagarajan N, Cortés-Ciriano I, Zhou DC, Liang WW, Hess JM, Yellapantula VD, Tamborero D, Gonzalez-Perez A, Suphavilai C, Ko JY, Khurana E, Park PJ, Van Allen EM, Liang H, MC3 Working Group., Cancer Genome Atlas Research Network., Lawrence MS, Godzik A, Lopez-Bigas N, Stuart J, Wheeler D, Getz G, Chen K, Lazar AJ, Mills GB, Karchin R, Ding L.

Cell. 2018 Apr 5; 2(173)371-385.e18

Pathogenic Germline Variants in 10,389 Adult Cancers.

Huang KL, Mashl RJ, Wu Y, Ritter DI, Wang J, Oh C, Paczkowska M, Reynolds S, Wyczalkowski MA, Oak N, Scott AD, Krassowski M, Cherniack AD, Houlahan KE, Jayasinghe R, Wang LB, Zhou DC, Liu D, Cao S, Kim YW, Koire A, McMichael JF, Hucthagowder V, Kim TB, Hahn A, Wang C, McLellan MD, Al-Mulla F, Johnson KJ, Cancer Genome Atlas Research Network., Lichtarge O, Boutros PC, Raphael B, Lazar AJ, Zhang W, Wendl MC, Govindan R, Jain S, Wheeler D, Kulkarni S, Dipersio JF, Reimand J, Meric-Bernstam F, Chen K, Shmulevich I, Plon SE, Chen F, Ding L.

Cell. 2018 Apr 5; 2(173)355-370.e14

Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation.

Malta TM, Sokolov A, Gentles AJ, Burzykowski T, Poisson L, Weinstein JN, Kamińska B, Huelsken J, Omberg L, Gevaert O, Colaprico A, Czerwińska P, Mazurek S, Mishra L, Heyn H, Krasnitz A, Godwin AK, Lazar AJ, Cancer Genome Atlas Research Network., Stuart JM, Hoadley KA, Laird PW, Noushmehr H, Wiznerowicz M.

Cell. 2018 Apr 5; 2(173)338-354.e15

Oncogenic Signaling Pathways in The Cancer Genome Atlas.

Sanchez-Vega F, Mina M, Armenia J, Chatila WK, Luna A, La KC, Dimitriadoy S, Liu DL, Kantheti HS, Saghafinia S, Chakravarty D, Daian F, Gao Q, Bailey MH, Liang WW, Foltz SM, Shmulevich I, Ding L, Heins Z, Ochoa A, Gross B, Gao J, Zhang H, Kundra R, Kandoth C, Bahceci I, Dervishi L, Dogrusoz U, Zhou W, Shen H, Laird PW, Way GP, Greene CS, Liang H, Xiao Y, Wang C, Iavarone A, Berger AH, Bivona TG, Lazar AJ, Hammer GD, Giordano T, Kwong LN, McArthur G, Huang C, Tward AD, Frederick MJ, McCormick F, Meyerson M, Cancer Genome Atlas Research Network., Van Allen EM, Cherniack AD, Ciriello G, Sander C, Schultz N.

Cell. 2018 Apr 5; 2(173)321-337.e10

Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics.

Ding L, Bailey MH, Porta-Pardo E, Thorsson V, Colaprico A, Bertrand D, Gibbs DL, Weerasinghe A, Huang KL, Tokheim C, Cortés-Ciriano I, Jayasinghe R, Chen F, Yu L, Sun S, Olsen C, Kim J, Taylor AM, Cherniack AD, Akbani R, Suphavilai C, Nagarajan N, Stuart JM, Mills GB, Wyczalkowski MA, Vincent BG, Hutter CM, Zenklusen JC, Hoadley KA, Wendl MC, Shmulevich L, Lazar AJ, Wheeler DA, Getz G, Cancer Genome Atlas Research Network..

Cell. 2018 Apr 5; 2(173)305-320.e10

Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer.

Hoadley KA, Yau C, Hinoue T, Wolf DM, Lazar AJ, Drill E, Shen R, Taylor AM, Cherniack AD, Thorsson V, Akbani R, Bowlby R, Wong CK, Wiznerowicz M, Sanchez-Vega F, Robertson AG, Schneider BG, Lawrence MS, Noushmehr H, Malta TM, Cancer Genome Atlas Network., Stuart JM, Benz CC, Laird PW.

Cell. 2018 Apr 5; 2(173)291-304.e6

Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas.

Liu Y, Sethi NS, Hinoue T, Schneider BG, Cherniack AD, Sanchez-Vega F, Seoane JA, Farshidfar F, Bowlby R, Islam M, Kim J, Chatila W, Akbani R, Kanchi RS, Rabkin CS, Willis JE, Wang KK, McCall SJ, Mishra L, Ojesina AI, Bullman S, Pedamallu CS, Lazar AJ, Sakai R, Cancer Genome Atlas Research Network., Thorsson V, Bass AJ, Laird PW.

Cancer Cell. 2018 Apr 9; 4(33)721-735.e8

lncRNA Epigenetic Landscape Analysis Identifies EPIC1 as an Oncogenic lncRNA that Interacts with MYC and Promotes Cell-Cycle Progression in Cancer.

Wang Z, Yang B, Zhang M, Guo W, Wu Z, Wang Y, Jia L, Li S, Cancer Genome Atlas Research Network., Xie W, Yang D.

Cancer Cell. 2018 Apr 9; 4(33)706-720.e9

A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers.

Berger AC, Korkut A, Kanchi RS, Hegde AM, Lenoir W, Liu W, Liu Y, Fan H, Shen H, Ravikumar V, Rao A, Schultz A, Li X, Sumazin P, Williams C, Mestdagh P, Gunaratne PH, Yau C, Bowlby R, Robertson AG, Tiezzi DG, Wang C, Cherniack AD, Godwin AK, Kuderer NM, Rader JS, Zuna RE, Sood AK, Lazar AJ, Ojesina AI, Adebamowo C, Adebamowo SN, Baggerly KA, Chen TW, Chiu HS, Lefever S, Liu L, MacKenzie K, Orsulic S, Roszik J, Shelley CS, Song Q, Vellano CP, Wentzensen N, Cancer Genome Atlas Research Network., Weinstein JN, Mills GB, Levine DA, Akbani R.

Cancer Cell. 2018 Apr 9; 4(33)690-705.e9

Genomic and Functional Approaches to Understanding Cancer Aneuploidy.

Taylor AM, Shih J, Ha G, Gao GF, Zhang X, Berger AC, Schumacher SE, Wang C, Hu H, Liu J, Lazar AJ, Cancer Genome Atlas Research Network., Cherniack AD, Beroukhim R, Meyerson M.

Cancer Cell. 2018 Apr 9; 4(33)676-689.e3

The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma.

Cell Rep. 2018 Apr 3; 1(23)313-326.e5

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context.

Chiu HS, Somvanshi S, Patel E, Chen TW, Singh VP, Zorman B, Patil SL, Pan Y, Chatterjee SS, Cancer Genome Atlas Research Network., Sood AK, Gunaratne PH, Sumazin P.

Cell Rep. 2018 Apr 3; 1(23)297-312.e12

Somatic Mutational Landscape of Splicing Factor Genes and Their Functional Consequences across 33 Cancer Types.

Seiler M, Peng S, Agrawal AA, Palacino J, Teng T, Zhu P, Smith PG, Cancer Genome Atlas Research Network., Buonamici S, Yu L.

Cell Rep. 2018 Apr 3; 1(23)282-296.e4

Systematic Analysis of Splice-Site-Creating Mutations in Cancer.

Jayasinghe RG, Cao S, Gao Q, Wendl MC, Vo NS, Reynolds SM, Zhao Y, Climente-González H, Chai S, Wang F, Varghese R, Huang M, Liang WW, Wyczalkowski MA, Sengupta S, Li Z, Payne SH, Fenyö D, Miner JH, Walter MJ, Cancer Genome Atlas Research Network., Vincent B, Eyras E, Chen K, Shmulevich I, Chen F, Ding L.

Cell Rep. 2018 Apr 3; 1(23)270-281.e3

Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers.

Peng X, Chen Z, Farshidfar F, Xu X, Lorenzi PL, Wang Y, Cheng F, Tan L, Mojumdar K, Du D, Ge Z, Li J, Thomas GV, Birsoy K, Liu L, Zhang H, Zhao Z, Marchand C, Weinstein JN, Cancer Genome Atlas Research Network., Bathe OF, Liang H.

Cell Rep. 2018 Apr 3; 1(23)255-269.e4

Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas.

Knijnenburg TA, Wang L, Zimmermann MT, Chambwe N, Gao GF, Cherniack AD, Fan H, Shen H, Way GP, Greene CS, Liu Y, Akbani R, Feng B, Donehower LA, Miller C, Shen Y, Karimi M, Chen H, Kim P, Jia P, Shinbrot E, Zhang S, Liu J, Hu H, Bailey MH, Yau C, Wolf D, Zhao Z, Weinstein JN, Li L, Ding L, Mills GB, Laird PW, Wheeler DA, Shmulevich I, Cancer Genome Atlas Research Network., Monnat RJ Jr, Xiao Y, Wang C.

Cell Rep. 2018 Apr 3; 1(23)239-254.e6

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.

Gao Q, Liang WW, Foltz SM, Mutharasu G, Jayasinghe RG, Cao S, Liao WW, Reynolds SM, Wyczalkowski MA, Yao L, Yu L, Sun SQ, Fusion Analysis Working Group., Cancer Genome Atlas Research Network., Chen K, Lazar AJ, Fields RC, Wendl MC, Van Tine BA, Vij R, Chen F, Nykter M, Shmulevich I, Ding L.

Cell Rep. 2018 Apr 3; 1(23)227-238.e3

Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types.

Ge Z, Leighton JS, Wang Y, Peng X, Chen Z, Chen H, Sun Y, Yao F, Li J, Zhang H, Liu J, Shriver CD, Hu H, Cancer Genome Atlas Research Network., Piwnica-Worms H, Ma L, Liang H.

Cell Rep. 2018 Apr 3; 1(23)213-226.e3

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas.

Campbell JD, Yau C, Bowlby R, Liu Y, Brennan K, Fan H, Taylor AM, Wang C, Walter V, Akbani R, Byers LA, Creighton CJ, Coarfa C, Shih J, Cherniack AD, Gevaert O, Prunello M, Shen H, Anur P, Chen J, Cheng H, Hayes DN, Bullman S, Pedamallu CS, Ojesina AI, Sadeghi S, Mungall KL, Robertson AG, Benz C, Schultz A, Kanchi RS, Gay CM, Hegde A, Diao L, Wang J, Ma W, Sumazin P, Chiu HS, Chen TW, Gunaratne P, Donehower L, Rader JS, Zuna R, Al-Ahmadie H, Lazar AJ, Flores ER, Tsai KY, Zhou JH, Rustgi AK, Drill E, Shen R, Wong CK, Cancer Genome Atlas Research Network., Stuart JM, Laird PW, Hoadley KA, Weinstein JN, Peto M, Pickering CR, Chen Z, Van Waes C.

Cell Rep. 2018 Apr 3; 1(23)194-212.e6

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images.

Saltz J, Gupta R, Hou L, Kurc T, Singh P, Nguyen V, Samaras D, Shroyer KR, Zhao T, Batiste R, Van Arnam J, Cancer Genome Atlas Research Network., Shmulevich I, Rao AUK, Lazar AJ, Sharma A, Thorsson V.

Cell Rep. 2018 Apr 3; 1(23)181-193.e7

Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas.

Way GP, Sanchez-Vega F, La K, Armenia J, Chatila WK, Luna A, Sander C, Cherniack AD, Mina M, Ciriello G, Schultz N, Cancer Genome Atlas Research Network., Sanchez Y, Greene CS.

Cell Rep. 2018 Apr 3; 1(23)172-180.e3

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas.

Schaub FX, Dhankani V, Berger AC, Trivedi M, Richardson AB, Shaw R, Zhao W, Zhang X, Ventura A, Liu Y, Ayer DE, Hurlin PJ, Cherniack AD, Eisenman RN, Bernard B, Grandori C, Cancer Genome Atlas Network..

Cell Syst. 2018 Mar 28; 3(6)282-300.e2

Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines.

Ellrott K, Bailey MH, Saksena G, Covington KR, Kandoth C, Stewart C, Hess J, Ma S, Chiotti KE, McLellan M, Sofia HJ, Hutter C, Getz G, Wheeler D, Ding L, MC3 Working Group., Cancer Genome Atlas Research Network..

Cell Syst. 2018 Mar 28; 3(6)271-281.e7

The Integrated Genomic Landscape of Thymic Epithelial Tumors.

Radovich M, Pickering CR, Felau I, Ha G, Zhang H, Jo H, Hoadley KA, Anur P, Zhang J, McLellan M, Bowlby R, Matthew T, Danilova L, Hegde AM, Kim J, Leiserson MDM, Sethi G, Lu C, Ryan M, Su X, Cherniack AD, Robertson G, Akbani R, Spellman P, Weinstein JN, Hayes DN, Raphael B, Lichtenberg T, Leraas K, Zenklusen JC, Cancer Genome Atlas Network., Fujimoto J, Scapulatempo-Neto C, Moreira AL, Hwang D, Huang J, Marino M, Korst R, Giaccone G, Gokmen-Polar Y, Badve S, Rajan A, Ströbel P, Girard N, Tsao MS, Marx A, Tsao AS, Loehrer PJ.

Cancer Cell. 2018 Feb 12; 2(33)244-258.e10

Association of Cell-Free DNA Tumor Fraction and Somatic Copy Number Alterations With Survival in Metastatic Triple-Negative Breast Cancer.

Stover DG, Parsons HA, Ha G, Freeman SS, Barry WT, Guo H, Choudhury AD, Gydush G, Reed SC, Rhoades J, Rotem D, Hughes ME, Dillon DA, Partridge AH, Wagle N, Krop IE, Getz G, Golub TR, Love JC, Winer EP, Tolaney SM, Lin NU, Adalsteinsson VA.

J Clin Oncol. 2018 Feb 20; 6(36)543-553

Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors.

Adalsteinsson VA, Ha G, Freeman SS, Choudhury AD, Stover DG, Parsons HA, Gydush G, Reed SC, Rotem D, Rhoades J, Loginov D, Livitz D, Rosebrock D, Leshchiner I, Kim J, Stewart C, Rosenberg M, Francis JM, Zhang CZ, Cohen O, Oh C, Ding H, Polak P, Lloyd M, Mahmud S, Helvie K, Merrill MS, Santiago RA, O'Connor EP, Jeong SH, Leeson R, Barry RM, Kramkowski JF, Zhang Z, Polacek L, Lohr JG, Schleicher M, Lipscomb E, Saltzman A, Oliver NM, Marini L, Waks AG, Harshman LC, Tolaney SM, Van Allen EM, Winer EP, Lin NU, Nakabayashi M, Taplin ME, Johannessen CM, Garraway LA, Golub TR, Boehm JS, Wagle N, Getz G, Love JC, Meyerson M.

Nat Commun. 2017 Nov 6; 1(8)1324

Patient-derived xenografts undergo mouse-specific tumor evolution.

Ben-David U, Ha G, Tseng YY, Greenwald NF, Oh C, Shih J, McFarland JM, Wong B, Boehm JS, Beroukhim R, Golub TR.

Nat Genet. 2017 Nov; 11(49)1567-1575

Correction to: ReMixT: clone-specific genomic structure estimation in cancer.

McPherson AW, Roth A, Ha G, Chauve C, Steif A, de Souza CPE, Eirew P, Bouchard-Côté A, Aparicio S, Sahinalp SC, Shah SP.

Genome Biol. 2017 Oct 6; 1(18)188

Genomic Heterogeneity as a Barrier to Precision Medicine in Gastroesophageal Adenocarcinoma.

Pectasides E, Stachler MD, Derks S, Liu Y, Maron S, Islam M, Alpert L, Kwak H, Kindler H, Polite B, Sharma MR, Allen K, O'Day E, Lomnicki S, Maranto M, Kanteti R, Fitzpatrick C, Weber C, Setia N, Xiao SY, Hart J, Nagy RJ, Kim KM, Choi MG, Min BH, Nason KS, O'Keefe L, Watanabe M, Baba H, Lanman R, Agoston AT, Oh DJ, Dunford A, Thorner AR, Ducar MD, Wollison BM, Coleman HA, Ji Y, Posner MC, Roggin K, Turaga K, Chang P, Hogarth K, Siddiqui U, Gelrud A, Ha G, Freeman SS, Rhoades J, Reed S, Gydush G, Rotem D, Davison J, Imamura Y, Adalsteinsson V, Lee J, Bass AJ, Catenacci DV.

Cancer Discov. 2018 Jan; 1(8)37-48

Somatic Superenhancer Duplications and Hotspot Mutations Lead to Oncogenic Activation of the KLF5 Transcription Factor.

Zhang X, Choi PS, Francis JM, Gao GF, Campbell JD, Ramachandran A, Mitsuishi Y, Ha G, Shih J, Vazquez F, Tsherniak A, Taylor AM, Zhou J, Wu Z, Berger AC, Giannakis M, Hahn WC, Cherniack AD, Meyerson M.

Cancer Discov. 2018 Jan; 1(8)108-125

ReMixT: clone-specific genomic structure estimation in cancer.

McPherson AW, Roth A, Ha G, Chauve C, Steif A, de Souza CPE, Eirew P, Bouchard-Côté A, Aparicio S, Sahinalp SC, Shah SP.

Genome Biol. 2017 Jul 27; 1(18)140

Genomic consequences of aberrant DNA repair mechanisms stratify ovarian cancer histotypes.

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.

Nat Genet. 2017 Jun; 6(49)856-865

The Mutational Landscape of Circulating Tumor Cells in Multiple Myeloma.

Mishima Y, Paiva B, Shi J, Park J, Manier S, Takagi S, Massoud M, Perilla-Glen A, Aljawai Y, Huynh D, Roccaro AM, Sacco A, Capelletti M, Detappe A, Alignani D, Anderson KC, Munshi NC, Prosper F, Lohr JG, Ha G, Freeman SS, Van Allen EM, Adalsteinsson VA, Michor F, San Miguel JF, Ghobrial IM.

Cell Rep. 2017 Apr 4; 1(19)218-224

Genetic interrogation of circulating multiple myeloma cells at single-cell resolution.

Lohr JG, Kim S, Gould J, Knoechel B, Drier Y, Cotton MJ, Gray D, Birrer N, Wong B, Ha G, Zhang CZ, Guo G, Meyerson M, Yee AJ, Boehm JS, Raje N, Golub TR.

Sci Transl Med. 2016 Nov 2; 363(8)363ra147

The landscape of chromosomal aberrations in breast cancer mouse models reveals driver-specific routes to tumorigenesis.

Ben-David U, Ha G, Khadka P, Jin X, Wong B, Franke L, Golub TR.

Nat Commun. 2016 Jul 4; (7)12160

Genomic Copy Number Dictates a Gene-Independent Cell Response to CRISPR/Cas9 Targeting.

Aguirre AJ, Meyers RM, Weir BA, Vazquez F, Zhang CZ, Ben-David U, Cook A, Ha G, Harrington WF, Doshi MB, Kost-Alimova M, Gill S, Xu H, Ali LD, Jiang G, Pantel S, Lee Y, Goodale A, Cherniack AD, Oh C, Kryukov G, Cowley GS, Garraway LA, Stegmaier K, Roberts CW, Golub TR, Meyerson M, Root DE, Tsherniak A, Hahn WC.

Cancer Discov. 2016 Aug; 8(6)914-29

Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer.

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.

Nat Genet. 2016 Jul; 7(48)758-67

Systematic analysis of somatic mutations impacting gene expression in 12 tumour types.

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.

Nat Commun. 2015 Oct 5; (6)8554

Multifocal endometriotic lesions associated with cancer are clonal and carry a high mutation burden.

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.

J Pathol. 2015 Jun; 2(236)201-9

Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution.

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.

Nature. 2015 Feb 19; 7539(518)422-6

An RCOR1 loss-associated gene expression signature identifies a prognostically significant DLBCL subgroup.

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.

Blood. 2015 Feb 5; 6(125)959-66

A tumor DNA complex aberration index is an independent predictor of survival in breast and ovarian cancer.

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, METABRIC Group., Brenton JD, Pharoah PD, Børresen-Dale AL, Aparicio S, Caldas C.

Mol Oncol. 2015 Jan; 1(9)115-27

TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data.

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.

Genome Res. 2014 Nov; 11(24)1881-93

PyClone: statistical inference of clonal population structure in cancer.

Roth A, Khattra J, Yap D, Wan A, Laks E, Biele J, Ha G, Aparicio S, Bouchard-Côté A, Shah SP.

Nat Methods. 2014 Apr; 4(11)396-8

Distinct evolutionary trajectories of primary high-grade serous ovarian cancers revealed through spatial mutational profiling.

Bashashati A, Ha G, Tone A, Ding J, Prentice LM, Roth A, Rosner J, Shumansky K, Kalloger S, Senz J, Yang W, McConechy M, Melnyk N, Anglesio M, Luk MT, Tse K, Zeng T, Moore R, Zhao Y, Marra MA, Gilks B, Yip S, Huntsman DG, McAlpine JN, Shah SP.

J Pathol. 2013 Sep; 1(231)21-34

Distinguishing somatic and germline copy number events in cancer patient DNA hybridized to whole-genome SNP genotyping arrays.

Ha G, Shah S.

Methods Mol Biol. 2013; (973)355-72

DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer.

Bashashati A, Haffari G, Ding J, Ha G, Lui K, Rosner J, Huntsman DG, Caldas C, Aparicio SA, Shah SP.

Genome Biol. 2012 Dec 22; 12(13)R124

Mutation discovery in regions of segmental cancer genome amplifications with CoNAn-SNV: a mixture model for next generation sequencing of tumors.

Crisan A, Goya R, Ha G, Ding J, Prentice LM, Oloumi A, Senz J, Zeng T, Tse K, Delaney A, Marra MA, Huntsman DG, Hirst M, Aparicio S, Shah S.

PLoS One. 2012; 8(7)e41551

Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer.

Ha G, Roth A, Lai D, Bashashati A, Ding J, Goya R, Giuliany R, Rosner J, Oloumi A, Shumansky K, Chin SF, Turashvili G, Hirst M, Caldas C, Marra MA, Aparicio S, Shah SP.

Genome Res. 2012 Oct; 10(22)1995-2007

The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups.

Curtis C, Shah SP, Chin SF, Turashvili G, Rueda OM, Dunning MJ, Speed D, Lynch AG, Samarajiwa S, Yuan Y, Gräf S, Ha G, Haffari G, Bashashati A, Russell R, McKinney S, METABRIC Group., Langerød A, Green A, Provenzano E, Wishart G, Pinder S, Watson P, Markowetz F, Murphy L, Ellis I, Purushotham A, Børresen-Dale AL, Brenton JD, Tavaré S, Caldas C, Aparicio S.

Nature. 2012 Apr 18; 7403(486)346-52

The clonal and mutational evolution spectrum of primary triple-negative breast cancers.

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.

Nature. 2012 Apr 4; 7403(486)395-9

JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data.

Roth A, Ding J, Morin R, Crisan A, Ha G, Giuliany R, Bashashati A, Hirst M, Turashvili G, Oloumi A, Marra MA, Aparicio S, Shah SP.

Bioinformatics. 2012 Apr 1; 7(28)907-13

Recurrent somatic DICER1 mutations in nonepithelial ovarian cancers.

Heravi-Moussavi A, Anglesio MS, Cheng SW, Senz J, Yang W, Prentice L, Fejes AP, Chow C, Tone A, Kalloger SE, Hamel N, Roth A, Ha G, Wan AN, Maines-Bandiera S, Salamanca C, Pasini B, Clarke BA, Lee AF, Lee CH, Zhao C, Young RH, Aparicio SA, Sorensen PH, Woo MM, Boyd N, Jones SJ, Hirst M, Marra MA, Gilks B, Shah SP, Foulkes WD, Morin GB, Huntsman DG.

N Engl J Med. 2012 Jan 19; 3(366)234-42

Using next-generation sequencing for the diagnosis of rare disorders: a family with retinitis pigmentosa and skeletal abnormalities.

Schrader KA, Heravi-Moussavi A, Waters PJ, Senz J, Whelan J, Ha G, Eydoux P, Nielsen T, Gallagher B, Oloumi A, Boyd N, Fernandez BA, Young TL, Jones SJ, Hirst M, Shah SP, Marra MA, Green J, Huntsman DG.

J Pathol. 2011 Sep; 1(225)12-8

The variant call format and VCFtools.

Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R, 1000 Genomes Project Analysis Group..

Bioinformatics. 2011 Aug 1; 15(27)2156-8

deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data.

McPherson A, Hormozdiari F, Zayed A, Giuliany R, Ha G, Sun MG, Griffith M, Heravi Moussavi A, Senz J, Melnyk N, Pacheco M, Marra MA, Hirst M, Nielsen TO, Sahinalp SC, Huntsman D, Shah SP.

PLoS Comput Biol. 2011 May; 5(7)e1001138

Tumor growth inhibition by olaparib in BRCA2 germline-mutated patient-derived ovarian cancer tissue xenografts.

Kortmann U, McAlpine JN, Xue H, Guan J, Ha G, Tully S, Shafait S, Lau A, Cranston AN, O'Connor MJ, Huntsman DG, Wang Y, Gilks CB.

Clin Cancer Res. 2011 Feb 15; 4(17)783-91

ARID1A mutations in endometriosis-associated ovarian carcinomas.

Wiegand KC, Shah SP, Al-Agha OM, Zhao Y, Tse K, Zeng T, Senz J, McConechy MK, Anglesio MS, Kalloger SE, Yang W, Heravi-Moussavi A, Giuliany R, Chow C, Fee J, Zayed A, Prentice L, Melnyk N, Turashvili G, Delaney AD, Madore J, Yip S, McPherson AW, Ha G, Bell L, Fereday S, Tam A, Galletta L, Tonin PN, Provencher D, Miller D, Jones SJ, Moore RA, Morin GB, Oloumi A, Boyd N, Aparicio SA, Shih IeM, Mes-Masson AM, Bowtell DD, Hirst M, Gilks B, Marra MA, Huntsman DG.

N Engl J Med. 2010 Oct 14; 16(363)1532-43

SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors.

Goya R, Sun MG, Morin RD, Leung G, Ha G, Wiegand KC, Senz J, Crisan A, Marra MA, Hirst M, Huntsman D, Murphy KP, Aparicio S, Shah SP.

Bioinformatics. 2010 Mar 15; 6(26)730-6

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