University of California San Francisco
Helen Diller Family Comprehensive Cancer Center
John S. Witte, PhD

John S. Witte, PhD

Professor, Department of Epidemiology/Biostatistics and Urology, UCSF; Leader, Cancer Genetics Program, UCSF Helen Diller Family Comprehensive Cancer Center

Cancer Center Program Memberships

Cancer Genetics

Research Summary

The Witte Lab is a computational and epidemiological research group investigating the genetic and environmental contributions to disease risk and progression. We develop and apply novel genetic epidemiological methods to decipher the mechanisms underlying complex diseases. In particular, we focus on: 1) Pleiotropy: assessing the shared genetic basis across cancers and other diseases; 2) Risk Modeling: evaluating disease risk with polygenic risk scores (PRS) and hierarchical models; 3) Prostate Cancer: finding genetic risk factors, improving screening, and reducing disparities; and 4) Liquid Biopsy: detecting tumor mutations and determining response to immunotherapy.

Education

University of California, Santa Barbara, CA, BS, 1986, Mathematical Sciences
University of California, Berkeley, CA, MS, 1988, Industrial Engineering and Operations Research
University of California, Los Angeles, CA, PhD, 1994, Epidemiology

Honors & Awards

  • 1986
    Undergraduate Honors, University of California, Santa Barbara
  • 1989-1994
    National Research Service Award, NIH
  • 1994
    Ruth F. Richards Outstanding Student Award, UCLA School of Public Health Alumni Association
  • 1999-2000
    Glennan Fellow, Case Western Reserve University
  • 2002-2003
    Visiting Scientist Award, International Agency for Research on Cancer
  • 2010
    Directors Invited Lecture, NHGRI / NIH
  • 2011
    Stephen B. Hulley Award for Excellence In Teaching, UCSF Training in Clinical Research
  • 2016
    Up for a Challenge Grand Prize, National Cancer Institute
  • 2017
    Robert Millikan Symposium Memorial Lecture, Univ North Carolina Lineberger Comprehensive Cancer Center
  • 2018
    Leadership Award, International Genetic Epidemiology Society

Selected Publications

  1. Rashkin SR, Graff RE, Kachuri L, Thai KK, Alexeeff SE, Blatchins MA, Cavazos TB, Corley DA, Emami NC, Hoffman JD, Jorgenson E, Kushi LH, Meyers TJ, Van Den Eeden SK, Ziv E, Habel LA, Hoffmann TJ, Sakoda LC, Witte JS. Pan-cancer study detects genetic risk variants and shared genetic basis in two large cohorts. Nat Commun. 2020 Sep 04; 11(1):4423.
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  2. Hayes-Larson E, Ackley SF, Zimmerman SC, Ospina-Romero M, Glymour MM, Graff RE, Witte JS, Kobayashi LC, Mayeda ER. The competing risk of death and selective survival cannot fully explain the inverse cancer-dementia association. Alzheimers Dement. 2020 Sep 03.
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  3. Cario CL, Chen E, Leong L, Emami NC, Lopez K, Tenggara I, Simko JP, Friedlander TW, Li PS, Paris PL, Carroll PR, Witte JS. A machine learning approach to optimizing cell-free DNA sequencing panels: with an application to prostate cancer. BMC Cancer. 2020 Aug 28; 20(1):820.
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  4. Carmichael SL, Ma C, Witte JS, Yang W, Rasmussen SA, Brunelli L, Nestoridi E, Shaw GM, Feldkamp ML. Congenital diaphragmatic hernia and maternal dietary nutrient pathways and diet quality. Birth Defects Res. 2020 Aug 03.
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  5. Ferreira MAR, Vonk JM, Baurecht H, Marenholz I, Tian C, Hoffman JD, Helmer Q, Tillander A, Ullemar V, Lu Y, Grosche S, Rüschendorf F, Granell R, Brumpton BM, Fritsche LG, Bhatta L, Gabrielsen ME, Nielsen JB, Zhou W, Hveem K, Langhammer A, Holmen OL, Løset M, Abecasis GR, Willer CJ, Emami NC, Cavazos TB, Witte JS, Szwajda A, Hinds DA, Hübner N, Weidinger S, Magnusson PK, Jorgenson E, Karlsson R, Paternoster L, Boomsma DI, Almqvist C, Lee YA, Koppelman GH. Age-of-onset information helps identify 76 genetic variants associated with allergic disease. PLoS Genet. 2020 06; 16(6):e1008725.
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  6. Chua KC, Xiong C, Ho C, Mushiroda T, Jiang C, Mulkey F, Lai D, Schneider BP, Rashkin SR, Witte JS, Friedman PN, Ratain MJ, McLeod HL, Rugo HS, Shulman LN, Kubo M, Owzar K, Kroetz DL. Genomewide Meta-Analysis Validates a Role for S1PR1 in Microtubule Targeting Agent-Induced Sensory Peripheral Neuropathy. Clin Pharmacol Ther. 2020 Jun 20.
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  7. Ospina-Romero M, Brenowitz WD, Glymour MM, Mayeda ER, Graff RE, Witte JS, Ackley SF, Lu KP, Kobayashi LC. The Association Between Cancer and Spousal Rate of Memory Decline: A Negative Control Study to Evaluate (Unmeasured) Social Confounding of the Cancer-memory Relationship. Alzheimer Dis Assoc Disord. 2020 Jun 19.
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  8. Kachuri L, Francis SS, Morrison M, Bossé Y, Cavazos TB, Rashkin SR, Ziv E, Witte JS. The landscape of host genetic factors involved in infection to common viruses and SARS-CoV-2. medRxiv. 2020 May 30.
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  9. Meyers TJ, Weiner AB, Graff RE, Desai AS, Cooley LF, Catalona WJ, Hanauer SB, Wu JD, Schaeffer EM, Abdulkadir SA, Kundu SD, Witte JS. Association between inflammatory bowel disease and prostate cancer: A large-scale, prospective, population-based study. Int J Cancer. 2020 Nov 15; 147(10):2735-2742.
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  10. Mefford J, Park D, Zheng Z, Ko A, Ala-Korpela M, Laakso M, Pajukanta P, Yang J, Witte J, Zaitlen N. Efficient Estimation and Applications of Cross-Validated Genetic Predictions to Polygenic Risk Scores and Linear Mixed Models. J Comput Biol. 2020 Apr; 27(4):599-612.
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  11. Du Z, Weinhold N, Song GC, Rand KA, Van Den Berg DJ, Hwang AE, Sheng X, Hom V, Ailawadhi S, Nooka AK, Singhal S, Pawlish K, Peters ES, Bock C, Mohrbacher A, Stram A, Berndt SI, Blot WJ, Casey G, Stevens VL, Kittles R, Goodman PJ, Diver WR, Hennis A, Nemesure B, Klein EA, Rybicki BA, Stanford JL, Witte JS, Signorello L, John EM, Bernstein L, Stroup AM, Stephens OW, Zangari M, Van Rhee F, Olshan A, Zheng W, Hu JJ, Ziegler R, Nyante SJ, Ingles SA, Press MF, Carpten JD, Chanock SJ, Mehta J, Colditz GA, Wolf J, Martin TG, Tomasson M, Fiala MA, Terebelo H, Janakiraman N, Kolonel L, Anderson KC, Le Marchand L, Auclair D, Chiu BC, Ziv E, Stram D, Vij R, Bernal-Mizrachi L, Morgan GJ, Zonder JA, Huff CA, Lonial S, Orlowski RZ, Conti DV, Haiman CA, Cozen W. A meta-analysis of genome-wide association studies of multiple myeloma among men and women of African ancestry. Blood Adv. 2020 Jan 14; 4(1):181-190.
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  12. Kachuri L, Johansson M, Rashkin SR, Graff RE, Bossé Y, Manem V, Caporaso NE, Landi MT, Christiani DC, Vineis P, Liu G, Scelo G, Zaridze D, Shete SS, Albanes D, Aldrich MC, Tardón A, Rennert G, Chen C, Goodman GE, Doherty JA, Bickeböller H, Field JK, Davies MP, Dawn Teare M, Kiemeney LA, Bojesen SE, Haugen A, Zienolddiny S, Lam S, Le Marchand L, Cheng I, Schabath MB, Duell EJ, Andrew AS, Manjer J, Lazarus P, Arnold S, McKay JD, Emami NC, Warkentin MT, Brhane Y, Obeidat M, Martin RM, Relton C, Davey Smith G, Haycock PC, Amos CI, Brennan P, Witte JS, Hung RJ. Immune-mediated genetic pathways resulting in pulmonary function impairment increase lung cancer susceptibility. Nat Commun. 2020 01 07; 11(1):27.
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  13. Belkora J, Chan JM, Cooperberg MR, Neuhaus J, Stupar L, Weinberg T, Broering JM, Tenggara I, Cowan JE, Rosenfeld S, Kenfield SA, Van Blarigan EL, Simko JP, Witte J, Carroll PR. Development and pilot evaluation of a personalized decision support intervention for low risk prostate cancer patients. Cancer Med. 2020 01; 9(1):125-132.
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  14. Carroll PR, Witte JS, Parsons JK. Germline testing in those at risk of prostate cancer. Can J Urol. 2019 Oct; 26(5 Suppl 2):31-33.
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  15. Emami NC, Kachuri L, Meyers TJ, Das R, Hoffman JD, Hoffmann TJ, Hu D, Shan J, Feng FY, Ziv E, Van Den Eeden SK, Witte JS. Author Correction: Association of imputed prostate cancer transcriptome with disease risk reveals novel mechanisms. Nat Commun. 2019 Aug 28; 10(1):3948.
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  16. Emami NC, Kachuri L, Meyers TJ, Das R, Hoffman JD, Hoffmann TJ, Hu D, Shan J, Feng FY, Ziv E, Van Den Eeden SK, Witte JS. Association of imputed prostate cancer transcriptome with disease risk reveals novel mechanisms. Nat Commun. 2019 07 15; 10(1):3107.
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  17. Du Z, Hopp H, Ingles SA, Huff C, Sheng X, Weaver B, Stern M, Hoffmann TJ, John EM, Van Den Eeden SK, Strom S, Leach RJ, Thompson IM, Witte JS, Conti DV, Haiman CA. A genome-wide association study of prostate cancer in Latinos. Int J Cancer. 2020 04 01; 146(7):1819-1826.
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  18. Witte J, Mehlis K, Surmann B, Lingnau R, Damm O, Greiner W, Winkler EC. Methods for measuring financial toxicity after cancer diagnosis and treatment: a systematic review and its implications. Ann Oncol. 2019 07 01; 30(7):1061-1070.
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  19. Wu L, Wang J, Cai Q, Cavazos TB, Emami NC, Long J, Shu XO, Lu Y, Guo X, Bauer JA, Pasaniuc B, Penney KL, Freedman ML, Kote-Jarai Z, Witte JS, Haiman CA, Eeles RA, Zheng W. Identification of Novel Susceptibility Loci and Genes for Prostate Cancer Risk: A Transcriptome-Wide Association Study in Over 140,000 European Descendants. Cancer Res. 2019 07 01; 79(13):3192-3204.
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  20. Cario CL, Witte JS. Samasy: an automated system for sample selection and robotic transfer. Biotechniques. 2018 12; 65(6):357-360.
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