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

I have extensive experience in the design and statistical analysis of genetic epidemiologic projects. My research program encompasses a synthesis of methodological and applied genetic epidemiology, with the overall aim of deciphering the mechanisms underlying complex diseases and traits. I have developed extensive, widely used methods and software for studying rare genetic variants, pathways, interactions, and genome-wide association studies. I am applying these methods to studies of prostate cancer, birth defects, and pharmacogenomics. My lab has developed extensive methods and software for studying rare genetic variants, pathways, interactions, and genome-wide association studies. For analyzing rare variants, my lab has recently developed novel Bayesian and ‘Step-up’ empirical methods. My work includes showing how hierarchical modeling—a potentially valuable analytic approach—can be used to incorporate existing information to improve estimation. In more applied work, I am presently undertaking studies of the germline and somatic genomic basis of prostate cancer, with a particular focus on disease aggressiveness among understudied populations. Most recently, I am evaluating the use of cell-free DNA (liquid biopsies) for prediction of disease risk and progression. In addition, I direct an NIH-Funded post-Doctoral training grant in Genetic Epidemiology, and have mentored over 40 pre- and post-doctoral fellows.

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


Professional Experience

  • 1994-1995
    Research Assistant Professor, Department of Preventive Medicine, University of Southern California
  • 1995-1999
    Assistant Professor, Department of Epidemiology and Biostatistics, Case Western Reserve University
  • 1999-2003
    Associate Professor, Department of Epidemiology and Biostatistics, Case Western Reserve University
  • 2003-present
    Professor, Department of Epidemiology and Biostatistics, University of California, San Francisco
  • 2005-present
    Leader, Program in Cancer Genetics and Epidemiology, UC San Francisco
  • 2005-present
    Associate Director, Institute for Human Genetics, UC, San Francisco
  • 2008-present
    Head, Division of Cancer Epidemiology, UC, San Francisco

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

Selected Publications

  1. 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 Jun 30; 16(6):e1008725.
    View on PubMed
  2. 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. Genome-Wide Meta-Analysis Validates a Role for S1PR1 in Microtubule Targeting Agent-Induced Sensory Peripheral Neuropathy. Clin Pharmacol Ther. 2020 Jun 20.
    View on PubMed
  3. 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.
    View on PubMed
  4. 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.
    View on PubMed
  5. 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 May 13.
    View on PubMed
  6. 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.
    View on PubMed
  7. 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.
    View on PubMed
  8. 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.
    View on PubMed
  9. 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.
    View on PubMed
  10. 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.
    View on PubMed
  11. 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.
    View on PubMed
  12. 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.
    View on PubMed
  13. 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.
    View on PubMed
  14. 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.
    View on PubMed
  15. 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.
    View on PubMed
  16. Cario CL, Witte JS. Samasy: an automated system for sample selection and robotic transfer. Biotechniques. 2018 12; 65(6):357-360.
    View on PubMed
  17. Rashkin SR, Chua KC, Ho C, Mulkey F, Jiang C, Mushiroda T, Kubo M, Friedman PN, Rugo HS, McLeod HL, Ratain MJ, Castillos F, Naughton M, Overmoyer B, Toppmeyer D, Witte JS, Owzar K, Kroetz DL. A Pharmacogenetic Prediction Model of Progression-Free Survival in Breast Cancer using Genome-Wide Genotyping Data from CALGB 40502 (Alliance). Clin Pharmacol Ther. 2019 03; 105(3):738-745.
    View on PubMed
  18. McCarthy ME, Oltman SP, Baer RJ, Ryckman KK, Rogers EE, Steurer-Muller MA, Witte JS, Jelliffe-Pawlowski LL. Newborn Metabolic Profile Associated with Hyperbilirubinemia With and Without Kernicterus. Clin Transl Sci. 2019 01; 12(1):28-38.
    View on PubMed
  19. Graff RE, Kachuri L, Witte JS. Personalized Prostate Cancer Screening Based on a Single Midlife Prostate-specific Antigen Measurement. Eur Urol. 2019 03; 75(3):408-409.
    View on PubMed
  20. Li M, He Z, Tong X, Witte JS, Lu Q. Detecting Rare Mutations with Heterogeneous Effects Using a Family-Based Genetic Random Field Method. Genetics. 2018 10; 210(2):463-476.
    View on PubMed

Go to UCSF Profiles, powered by CTSI