The Carrot-Zhang lab develops computational methods to link the germline genome to the somatic phenotypes. We are interested in understanding how genetic determinants shape the tumor genomes, and how the complex interactions between genetic ancestry, environmental exposure and somatic alteration contribute to tumor aggressiveness, progression, and response to treatment. Our goal is to find germline predictors for cancer drivers that will have broad applications in cancer prevention, early detection, and precision medicine. To achieve the goal, we use cutting-edge statistical and machine learning approaches to leverage large-scale, real-world genomic data with linked electronic health records. Another focus of the lab is using whole-genome sequencing to identify novel drivers and biomarkers, with a focus on cancer patients with non-European ancestries to bridge one of the biggest gaps in cancer genomics.
View available career opportunities in the lab here.
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Tumor sequencing of African ancestry reveals differences in clinically relevant alterations across common cancers. Jiagge E, Jin DX, Newberg JY, Perea-Chamblee T, Pekala KR, Fong C, Waters M, Ma D, Dei-Adomakoh Y, Erb G, Arora KS, Maund SL, Njiraini N, Ntekim A, Kim S, Bai X, Thomas M, van Eeden R, Hegde P, Jee J, Chakravarty D, Schultz N, Berger MF, Frampton GM, Sokol ES, Carrot-Zhang J. Cancer Cell. 2023 Nov 13;41(11):1963-1971.e3. Epub 2023 Oct 26. PMID: 37890492.
Ancestry-driven recalibration of tumor mutational burden and disparate clinical outcomes in response to immune checkpoint inhibitors. AH, Adib E, Abou Alaiwi S, El Zarif T, Groha S, Akl EW, Nuzzo PV, Mouhieddine TH, Perea-Chamblee T, Taraszka K, El-Khoury H, Labban M, Fong C, Arora KS, Labaki C, Xu W, Sonpavde G, Haddad RI, Mouw KW, Giannakis M, Hodi FS, Zaitlen N, Schoenfeld AJ, Schultz N, Berger MF, MacConaill LE, Ananda G, Kwiatkowski DJ, Choueiri TK, Schrag D, Carrot-Zhang J, Gusev A. Cancer Cell. 2022 Oct 10;40(10):1161-1172.e5. Epub 2022 Sep 29. PMID: 36179682; PMCID: PMC9559771.
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;11(3):591-598. Epub 2020 Dec 2. PMID: 33268447; PMCID: PMC7933062.
Comprehensive Analysis of Genetic Ancestry and Its Molecular Correlates in Cancer. Carrot-Zhang J, Chambwe N, Damrauer JS, Knijnenburg TA, Robertson AG, Yau C, Zhou W, Berger AC, Huang KL, Newberg JY, Mashl RJ, Romanel A, Sayaman RW, Demichelis F, Felau I, Frampton GM, Han S, Hoadley KA, Kemal A, Laird PW, Lazar AJ, Le X, Oak N, Shen H, Wong CK, Zenklusen JC, Ziv E; Cancer Genome Atlas Analysis Network; Cherniack AD, Beroukhim R. Cancer Cell. 2020 May 11;37(5):639-654.e6.PMID: 32396860; PMCID: PMC7328015.
Germline and somatic SMARCA4 mutations characterize small cell carcinoma of the ovary, hypercalcemic type. Witkowski L, Carrot-Zhang J, Albrecht S, Fahiminiya S, Hamel N, Tomiak E, Grynspan D, Saloustros E, Nadaf J, Rivera B, Gilpin C, Castellsagué E, Silva-Smith R, Plourde F, Wu M, Saskin A, Arseneault M, Karabakhtsian RG, Reilly EA, Ueland FR, Margiolaki A, Pavlakis K, Castellino SM, Lamovec J, Mackay HJ, Roth LM, Ulbright TM, Bender TA, Georgoulias V, Longy M, Berchuck A, Tischkowitz M, Nagel I, Siebert R, Stewart CJ, Arseneau J, McCluggage WG, Clarke BA, Riazalhosseini Y, Hasselblatt M, Majewski J, Foulkes WD.Nat Genet. 2014 May;46(5):438-43. Epub 2014 Mar 23. PMID: 24658002.
Uncover ancestry-associated somatic biomarkers through existing data and new WGS data
Understanding germline influence on immunotherapy outcomes
Develop germline predictors for somatic drivers
Please visit Dr. Carrot- Zhang’s faculty page or Google Scholar for more publications.
