faculty

Gavin Ha

gha@fredhutch.org

Assistant Professor

Fred Hutch

Public Health Sciences

Cancer Biology

Computational Biology

Genetics, Genomics & Evolution

Cancer genomics and liquid biopsies for precision medicine

Faculty Contact Information

Building: Steam Plant Room: S2-111 Box: S2-140 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:

Liquid biopsy detection of genomic alterations in pediatric brain tumors from cell-free DNA in peripheral blood, CSF, and urine.

Pagès M, Rotem D, Gydush G, Reed S, Rhoades J, Ha G, Lo C, Fleharty M, Duran M, Jones R, Becker S, Haller M, Sinai CE, Goumnerova L, Golub TR, Love JC, Ligon KL, Wright K, Adalsteinsson VA, Beroukhim R, Bandopadhayay P.

Neuro Oncol. 2022 Jan 4;

Genomic attributes of homology-directed DNA repair deficiency in metastatic prostate cancer.

De Sarkar N, Dasgupta S, Chatterjee P, Coleman I, Ha G, Ang LS, Kohlbrenner EA, Frank SB, Nunez TA, Salipante SJ, Corey E, Morrissey C, Van Allen E, Schweizer MT, Haffner MC, Patel R, Hanratty B, Lucas JM, Dumpit RF, Pritchard CC, Montgomery RB, Nelson PS.

JCI Insight. 2021 Dec 8; 23(6)

Association of 17q22 Amplicon Via Cell-Free DNA With Platinum Chemotherapy Response in Metastatic Triple-Negative Breast Cancer.

Collier KA, Asad S, Tallman D, Jenison J, Rajkovic A, Mardis ER, Parsons HA, Tolaney SM, Winer EP, Lin NU, Ha G, Adalsteinsson VA, Stover DG.

JCO Precis Oncol. 2021; (5)

Circulating tumor DNA is readily detectable among Ghanaian breast cancer patients supporting non-invasive cancer genomic studies in Africa.

Ahuno ST, Doebley AL, Ahearn TU, Yarney J, Titiloye N, Hamel N, Adjei E, Clegg-Lamptey JN, Edusei L, Awuah B, Song X, Vanderpuye V, Abubakar M, Duggan M, Stover DG, Nyarko K, Bartlett JMS, Aitpillah F, Ansong D, Gardner KL, Boateng FA, Bowcock AM, Caldas C, Foulkes WD, Wiafe S, Wiafe-Addai B, Garcia-Closas M, Kwarteng A, Ha G, Figueroa JD, Polak P, Ghana Breast Health Study Team..

NPJ Precis Oncol. 2021 Sep 17; 1(5)83

Circulating Cell-Free DNA as Biomarker of Taxane Resistance in Metastatic Castration-Resistant Prostate Cancer.

Francini E, Ou FS, Rhoades J, Wolfe EG, O'Connor EP, Ha G, Gydush G, Kelleher KM, Bhatt RS, Balk SP, Sweeney CJ, Adalsteinsson VA, Taplin ME, Choudhury AD.

Cancers (Basel). 2021 Aug 12; 16(13)

Haplotype-resolved germline and somatic alterations in renal medullary carcinomas.

Tan KT, Kim H, Carrot-Zhang J, Zhang Y, Kim WJ, Kugener G, Wala JA, Howard TP, Chi YY, Beroukhim R, Li H, Ha G, Alper SL, Perlman EJ, Mullen EA, Hahn WC, Meyerson M, Hong AL.

Genome Med. 2021 Jul 14; 1(13)114

Multiplexed functional genomic analysis of 5' untranslated region mutations across the spectrum of prostate cancer.

Lim Y, Arora S, Schuster SL, Corey L, Fitzgibbon M, Wladyka CL, Wu X, Coleman IM, Delrow JJ, Corey E, True LD, Nelson PS, Ha G, Hsieh AC.

Nat Commun. 2021 Jul 9; 1(12)4217

Modeling clonal structure over narrow time frames via circulating tumor DNA in metastatic breast cancer.

Weber ZT, Collier KA, Tallman D, Forman J, Shukla S, Asad S, Rhoades J, Freeman S, Parsons HA, Williams NO, Barroso-Sousa R, Stover EH, Mahdi H, Cibulskis C, Lennon NJ, Ha G, Adalsteinsson VA, Tolaney SM, Stover DG.

Genome Med. 2021 May 20; 1(13)89

Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes.

Dentro SC, Leshchiner I, Haase K, Tarabichi M, Wintersinger J, Deshwar AG, Yu K, Rubanova Y, Macintyre G, Demeulemeester J, Vázquez-García I, Kleinheinz K, Livitz DG, Malikic S, Donmez N, Sengupta S, Anur P, Jolly C, Cmero M, Rosebrock D, Schumacher SE, Fan Y, Fittall M, Drews RM, Yao X, Watkins TBK, Lee J, Schlesner M, Zhu H, Adams DJ, McGranahan N, Swanton C, Getz G, Boutros PC, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Martincorena I, Markowetz F, Mustonen V, Yuan K, Gerstung M, Spellman PT, Wang W, Morris QD, Wedge DC, Van Loo P, PCAWG Evolution and Heterogeneity Working Group and the PCAWG Consortium..

Cell. 2021 Apr 15; 8(184)2239-2254.e39

Genetic Ancestry Contributes to Somatic Mutations in Lung Cancers from Admixed Latin American Populations.

Carrot-Zhang J, Soca-Chafre G, Patterson N, Thorner AR, Nag A, Watson J, Genovese G, Rodriguez J, Gelbard MK, Corrales-Rodriguez L, Mitsuishi Y, Ha G, Campbell JD, Oxnard GR, Arrieta O, Cardona AF, Gusev A, Meyerson M.

Cancer Discov. 2021 Mar; 3(11)591-598

Author Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.

Bailey MH, Meyerson WU, Dursi LJ, Wang LB, Dong G, Liang WW, Weerasinghe A, Li S, Li Y, Kelso S, MC3 Working Group., PCAWG novel somatic mutation calling methods working group., Saksena G, Ellrott K, Wendl MC, Wheeler DA, Getz G, Simpson JT, Gerstein MB, Ding L, PCAWG Consortium..

Nat Commun. 2020 Nov 30; 1(11)6232

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.

Nat Commun. 2020 Sep 21; 1(11)4748

Sex differences in oncogenic mutational processes.

Li CH, Prokopec SD, Sun RX, Yousif F, Schmitz N, PCAWG Tumour Subtypes and Clinical Translation., Boutros PC, PCAWG Consortium..

Nat Commun. 2020 Aug 28; 1(11)4330

Prostate cancer reactivates developmental epigenomic programs during metastatic progression.

Pomerantz MM, Qiu X, Zhu Y, Takeda DY, Pan W, Baca SC, Gusev A, Korthauer KD, Severson TM, Ha G, Viswanathan SR, Seo JH, Nguyen HM, Zhang B, Pasaniuc B, Giambartolomei C, Alaiwi SA, Bell CA, O'Connor EP, Chabot MS, Stillman DR, Lis R, Font-Tello A, Li L, Cejas P, Bergman AM, Sanders J, van der Poel HG, Gayther SA, Lawrenson K, Fonseca MAS, Reddy J, Corona RI, Martovetsky G, Egan B, Choueiri T, Ellis L, Garraway IP, Lee GM, Corey E, Long HW, Zwart W, Freedman ML.

Nat Genet. 2020 Aug; 8(52)790-799

CDK12-Mutated Prostate Cancer: Clinical Outcomes With Standard Therapies and Immune Checkpoint Blockade.

Schweizer MT, Ha G, Gulati R, Brown LC, McKay RR, Dorff T, Hoge ACH, Reichel J, Vats P, Kilari D, Patel V, Oh WK, Chinnaiyan A, Pritchard CC, Armstrong AJ, Montgomery RB, Alva A.

JCO Precis Oncol. 2020; (4)382-392

Genome-wide cell-free DNA mutational integration enables ultra-sensitive cancer monitoring.

Zviran A, Schulman RC, Shah M, Hill STK, Deochand S, Khamnei CC, Maloney D, Patel K, Liao W, Widman AJ, Wong P, Callahan MK, Ha G, Reed S, Rotem D, Frederick D, Sharova T, Miao B, Kim T, Gydush G, Rhoades J, Huang KY, Omans ND, Bolan PO, Lipsky AH, Ang C, Malbari M, Spinelli CF, Kazancioglu S, Runnels AM, Fennessey S, Stolte C, Gaiti F, Inghirami GG, Adalsteinsson V, Houck-Loomis B, Ishii J, Wolchok JD, Boland G, Robine N, Altorki NK, Landau DA.

Nat Med. 2020 Jul; 7(26)1114-1124

Combined TP53 and RB1 Loss Promotes Prostate Cancer Resistance to a Spectrum of Therapeutics and Confers Vulnerability to Replication Stress.

Nyquist MD, Corella A, Coleman I, De Sarkar N, Kaipainen A, Ha G, Gulati R, Ang L, Chatterjee P, Lucas J, Pritchard C, Risbridger G, Isaacs J, Montgomery B, Morrissey C, Corey E, Nelson PS.

Cell Rep. 2020 May 26; 8(31)107669

Identifying Sources of Stress Across Years of General Surgery Residency.

Ha GQ, Go JT, Murayama KM, Steinemann S.

Hawaii J Health Soc Welf. 2020 Mar 1; 3(79)75-81

Sensitive Detection of Minimal Residual Disease in Patients Treated for Early-Stage Breast Cancer.

Parsons HA, Rhoades J, Reed SC, Gydush G, Ram P, Exman P, Xiong K, Lo CC, Li T, Fleharty M, Kirkner GJ, Rotem D, Cohen O, Yu F, Fitarelli-Kiehl M, Leong KW, Hughes ME, Rosenberg SM, Collins LC, Miller KD, Blumenstiel B, Trippa L, Cibulskis C, Neuberg DS, DeFelice M, Freeman SS, Lennon NJ, Wagle N, Ha G, Stover DG, Choudhury AD, Getz G, Winer EP, Meyerson M, Lin NU, Krop I, Love JC, Makrigiorgos GM, Partridge AH, Mayer EL, Golub TR, Adalsteinsson VA.

Clin Cancer Res. 2020 Jun 1; 11(26)2556-2564

The evolutionary history of 2,658 cancers.

Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez S, Rosebrock D, Mitchell TJ, Rubanova Y, Anur P, Yu K, Tarabichi M, Deshwar A, Wintersinger J, Kleinheinz K, Vázquez-García I, Haase K, Jerman L, Sengupta S, Macintyre G, Malikic S, Donmez N, Livitz DG, Cmero M, Demeulemeester J, Schumacher S, Fan Y, Yao X, Lee J, Schlesner M, Boutros PC, Bowtell DD, Zhu H, Getz G, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Markowetz F, Mustonen V, Yuan K, Wang W, Morris QD, PCAWG Evolution & Heterogeneity Working Group., Spellman PT, Wedge DC, Van Loo P, PCAWG Consortium..

Nature. 2020 Feb; 7793(578)122-128

Pan-cancer analysis of whole genomes.

ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium.

Nature. 2020 Feb; 7793(578)82-93

Inferring structural variant cancer cell fraction.

Cmero M, Yuan K, Ong CS, Schröder J, PCAWG Evolution and Heterogeneity Working Group., Corcoran NM, Papenfuss T, Hovens CM, Markowetz F, Macintyre G, PCAWG Consortium..

Nat Commun. 2020 Feb 5; 1(11)730

Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig.

Rubanova Y, Shi R, Harrigan CF, Li R, Wintersinger J, Sahin N, Deshwar A, PCAWG Evolution and Heterogeneity Working Group., Morris Q, PCAWG Consortium..

Nat Commun. 2020 Feb 5; 1(11)731

Genomic and immune profiling of pre-invasive lung adenocarcinoma.

Chen H, Carrot-Zhang J, Zhao Y, Hu H, Freeman SS, Yu S, Ha G, Taylor AM, Berger AC, Westlake L, Zheng Y, Zhang J, Ramachandran A, Zheng Q, Pan Y, Zheng D, Zheng S, Cheng C, Kuang M, Zhou X, Zhang Y, Li H, Ye T, Ma Y, Gao Z, Tao X, Han H, Shang J, Yu Y, Bao D, Huang Y, Li X, Zhang Y, Xiang J, Sun Y, Li Y, Cherniack AD, Campbell JD, Shi L, Meyerson M.

Nat Commun. 2019 Nov 29; 1(10)5472

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