John S. Witte, PhD

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
John S. Witte, PhD

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

wittej@humgen.ucsf.edu

Phone: (415) 502-6882 (voice)
Box 0794, UCSF, San Francisco, CA 94143-0794

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Cancer Center Membership

Program Member » Prostate Cancer» 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. A Cross-Cancer Genetic Association Analysis of the DNA Repair and DNA Damage Signaling Pathways for Lung, Ovary, Prostate, Breast, and Colorectal Cancer. Cancer Epidemiol Biomarkers Prev. 2016 Jan; 25(1):193-200.
    View on PubMed
  2. Semiparametric Allelic Tests for Mapping Multiple Phenotypes: Binomial Regression and Mahalanobis Distance. Genet Epidemiol. 2015 Dec; 39(8):635-50.
    View on PubMed
  3. Strategies for Imputing and Analyzing Rare Variants in Association Studies. Trends Genet. 2015 Oct; 31(10):556-63.
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  4. MDS-associated somatic mutations and clonal hematopoiesis are common in idiopathic cytopenias of undetermined significance. Blood. 2015 Nov 19; 126(21):2355-61.
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  5. Cross Cancer Genomic Investigation of Inflammation Pathway for Five Common Cancers: Lung, Ovary, Prostate, Breast, and Colorectal Cancer. J Natl Cancer Inst. 2015 Nov; 107(11).
    View on PubMed
  6. Integration of multiethnic fine-mapping and genomic annotation to prioritize candidate functional SNPs at prostate cancer susceptibility regions. Hum Mol Genet. 2015 Oct 1; 24(19):5603-18.
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  7. Methodological Considerations in Estimation of Phenotype Heritability Using Genome-Wide SNP Data, Illustrated by an Analysis of the Heritability of Height in a Large Sample of African Ancestry Adults. PLoS One. 2015; 10(6):e0131106.
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  8. A Large Multiethnic Genome-Wide Association Study of Prostate Cancer Identifies Novel Risk Variants and Substantial Ethnic Differences. Cancer Discov. 2015 Aug; 5(8):878-91.
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  9. Developments in our understanding of the genetic basis of birth defects. Birth Defects Res A Clin Mol Teratol. 2015 Aug; 103(8):680-91.
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  10. Detecting gene-environment interactions in human birth defects: Study designs and statistical methods. Birth Defects Res A Clin Mol Teratol. 2015 Aug; 103(8):692-702.
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  11. Replication and heritability of prostate cancer risk variants: impact of population-specific factors. Cancer Epidemiol Biomarkers Prev. 2015 Jun; 24(6):938-43.
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  12. Associations of prostate cancer risk variants with disease aggressiveness: results of the NCI-SPORE Genetics Working Group analysis of 18,343 cases. Hum Genet. 2015 Apr; 134(4):439-50.
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  13. Imputation of the Rare HOXB13 G84E Mutation and Cancer Risk in a Large Population-Based Cohort. PLoS Genet. 2015 Jan; 11(1):e1004930.
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  14. Population genetic simulations of complex phenotypes with implications for rare variant association tests. Genet Epidemiol. 2015 Jan; 39(1):35-44.
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  15. Genetic Polymorphisms in ESR1 and ESR2 Genes, and Risk of Hypospadias in a Multiethnic Study Population. J Urol. 2015 May; 193(5):1625-31.
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  16. Leveraging population admixture to characterize the heritability of complex traits. Nat Genet. 2014 Dec; 46(12):1356-62.
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  17. Genetic simulation tools for post-genome wide association studies of complex diseases. Genet Epidemiol. 2015 Jan; 39(1):11-9.
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  18. Polymorphisms of an innate immune gene, toll-like receptor 4, and aggressive prostate cancer risk: a systematic review and meta-analysis. PLoS One. 2014; 9(10):e110569.
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  19. Selenoprotein and antioxidant genes and the risk of high-grade prostate cancer and prostate cancer recurrence. Prostate. 2015 Jan; 75(1):60-9.
    View on PubMed
  20. Genome-wide scan of 29,141 African Americans finds no evidence of directional selection since admixture. Am J Hum Genet. 2014 Oct 2; 95(4):437-44.
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