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 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 cancer, birth defects, and pharmacogenomics. Current projects in my lab include developing methods for effectively evaluating pleiotropy, determining the germline and somatic basis of prostate cancer risk and aggressiveness, and detecting genes that impact drug / treatment response. We have also recently been evaluating the use of cell free DNA (liquid biopsies) for prediction of prostate cancer risk and progression. In addition, I direct an NIH-Funded post-Doctoral training grant in Genetic Cancer Epidemiology, and have mentored over 40 pre- and post-doctoral fellows.

Research Funding

  • June 16, 2021 - May 31, 2026 - Leveraging Diversity in Cancer Epidemiology Cohorts and Novel Methods to Improve Polygenic Risk Scores , Co-Principal Investigator . Sponsor: NIH, Sponsor Award ID: U01CA261339
  • December 1, 2004 - June 30, 2025 - Training in the Molecular & Genetic Epidemiology of Cancer , Principal Investigator . Sponsor: NIH, Sponsor Award ID: T32CA112355
  • April 1, 2020 - March 31, 2024 - Precision Prostate Cancer Screening with Genetically Adjusted Prostate-Specific Antigen Levels , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01CA241410
  • August 5, 1999 - May 31, 2023 - Cancer Center Support Grant , Co-Investigator . Sponsor: NIH, Sponsor Award ID: P30CA082103

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. Lyu C, Huang M, Liu N, Chen Z, Lupo PJ, Tycko B, Witte JS, Hobbs CA, Li M. Random field modeling of multi-trait multi-locus association for detecting methylation quantitative trait loci. Bioinformatics. 2022 08 10; 38(16):3853-3862.  View on PubMed
  2. Gabriel AAG, Atkins JR, Penha RCC, Smith-Byrne K, Gaborieau V, Voegele C, Abedi-Ardekani B, Milojevic M, Olaso R, Meyer V, Boland A, Deleuze JF, Zaridze D, Mukeriya A, Swiatkowska B, Janout V, Schejbalová M, Mates D, Stojšic J, Ognjanovic M, ILCCO consortium, Witte JS, Rashkin SR, Kachuri L, Hung RJ, Kar S, Brennan P, Sertier AS, Ferrari A, Viari A, Johansson M, Amos CI, Foll M, McKay JD. Genetic Analysis of Lung Cancer and the Germline Impact on Somatic Mutation Burden. J Natl Cancer Inst. 2022 08 08; 114(8):1159-1166.  View on PubMed
  3. Mabry PL, Pronk NP, Amos CI, Witte JS, Wedlock PT, Bartsch SM, Lee BY. Cancer systems epidemiology: Overcoming misconceptions and integrating systems approaches into cancer research. PLoS Med. 2022 06; 19(6):e1004027.  View on PubMed
  4. Hayes-Larson E, Shaw C, Ackley SF, Zimmerman SC, Glymour MM, Graff RE, Witte JS, Kobayashi LC, Mayeda ER. The Role of Dementia Diagnostic Delay in the Inverse Cancer-Dementia Association. J Gerontol A Biol Sci Med Sci. 2022 06 01; 77(6):1254-1260.  View on PubMed
  5. Rashkin SR, Cleves M, Shaw GM, Nembhard WN, Nestoridi E, Jenkins MM, Romitti PA, Lou XY, Browne ML, Mitchell LE, Olshan AF, Lomangino K, Bhattacharyya S, Witte JS, Hobbs CA, National Birth Defects Prevention Study. A genome-wide association study of obstructive heart defects among participants in the National Birth Defects Prevention Study. Am J Med Genet A. 2022 08; 188(8):2303-2314.  View on PubMed
  6. Dawed AY, Yee SW, Zhou K, van Leeuwen N, Zhang Y, Siddiqui MK, Etheridge A, Innocenti F, Xu F, Li JH, Beulens JW, van der Heijden AA, Slieker RC, Chang YC, Mercader JM, Kaur V, Witte JS, Lee MTM, Kamatani Y, Momozawa Y, Kubo M, Palmer CNA, Florez JC, Hedderson MM, 't Hart LM, Giacomini KM, Pearson ER, for MetGen Plus, for the DIRECT Consortium. Response to Comment on Dawed et al. Genome-Wide Meta-analysis Identifies Genetic Variants Associated With Glycemic Response to Sulfonylureas. Diabetes Care 2021;44:2673-2682. Diabetes Care. 2022 04 01; 45(4):e82-e83.  View on PubMed
  7. Gruhn S, Witte J, Greiner W, Damm O, Dietzsch M, Kramer R, Knuf M. Epidemiology and economic burden of meningococcal disease in Germany: A systematic review. Vaccine. 2022 03 18; 40(13):1932-1947.  View on PubMed
  8. Press BH, Jones T, Olawoyin O, Lokeshwar SD, Rahman SN, Khajir G, Lin DW, Cooperberg MR, Loeb S, Darst BF, Zheng Y, Chen RC, Witte JS, Seibert TM, Catalona WJ, Leapman MS, Sprenkle PC. Association Between a 22-feature Genomic Classifier and Biopsy Gleason Upgrade During Active Surveillance for Prostate Cancer. Eur Urol Open Sci. 2022 Mar; 37:113-119.  View on PubMed
  9. Desai AS, Sagar V, Lysy B, Weiner AB, Ko OS, Driscoll C, Rodriguez Y, Vatapalli R, Unno K, Han H, Cohen JE, Vo AX, Pham M, Shin M, Jain-Poster K, Ross J, Morency EG, Meyers TJ, Witte JS, Wu J, Abdulkadir SA, Kundu SD. Correction: Inflammatory bowel disease induces inflammatory and preneoplastic changes in the prostate. Prostate Cancer Prostatic Dis. 2022 Feb; 25(2):375.  View on PubMed
  10. Jiang Y, Meyers TJ, Emeka AA, Cooley LF, Cooper PR, Lancki N, Helenowski I, Kachuri L, Lin DW, Stanford JL, Newcomb LF, Kolb S, Finelli A, Fleshner NE, Komisarenko M, Eastham JA, Ehdaie B, Benfante N, Logothetis CJ, Gregg JR, Perez CA, Garza S, Kim J, Marks LS, Delfin M, Barsa D, Vesprini D, Klotz LH, Loblaw A, Mamedov A, Goldenberg SL, Higano CS, Spillane M, Wu E, Carter HB, Pavlovich CP, Mamawala M, Landis T, Carroll PR, Chan JM, Cooperberg MR, Cowan JE, Morgan TM, Siddiqui J, Martin R, Klein EA, Brittain K, Gotwald P, Barocas DA, Dallmer JR, Gordetsky JB, Steele P, Kundu SD, Stockdale J, Roobol MJ, Venderbos LDF, Sanda MG, Arnold R, Patil D, Evans CP, Dall'Era MA, Vij A, Costello AJ, Chow K, Corcoran NM, Rais-Bahrami S, Phares C, Scherr DS, Flynn T, Karnes RJ, Koch M, Dhondt CR, Nelson JB, McBride D, Cookson MS, Stratton KL, Farriester S, Hemken E, Stadler WM, Pera T, Banionyte D, Bianco FJ, Lopez IH, Loeb S, Taneja SS, Byrne N, Amling CL, Martinez A, Boileau L, Gaylis FD, Petkewicz J, Kirwen N, Helfand BT, Xu J, Scholtens DM, Catalona WJ, Witte JS. Genetic Factors Associated with Prostate Cancer Conversion from Active Surveillance to Treatment. HGG Adv. 2022 Jan 13; 3(1).  View on PubMed
  11. Costello JM, Steurer MA, Baer RJ, Witte JS, Jelliffe-Pawlowski LL. Residential particulate matter, proximity to major roads, traffic density and traffic volume as risk factors for preterm birth in California. Paediatr Perinat Epidemiol. 2022 Jan; 36(1):70-79.  View on PubMed
  12. Lyu C, Huang M, Liu N, Chen Z, Lupo PJ, Tycko B, Witte JS, Hobbs CA, Li M. Detecting methylation quantitative trait loci using a methylation random field method. Brief Bioinform. 2021 11 05; 22(6).  View on PubMed
  13. Dawed AY, Yee SW, Zhou K, van Leeuwen N, Zhang Y, Siddiqui MK, Etheridge A, Innocenti F, Xu F, Li JH, Beulens JW, van der Heijden AA, Slieker RC, Chang YC, Mercader JM, Kaur V, Witte JS, Lee MTM, Kamatani Y, Momozawa Y, Kubo M, Palmer CNA, Florez JC, Hedderson MM, 't Hart LM, Giacomini KM, Pearson ER, for MetGen Plus, for the DIRECT Consortium, MetGen Plus investigators:. Genome-Wide Meta-analysis Identifies Genetic Variants Associated With Glycemic Response to Sulfonylureas. Diabetes Care. 2021 12; 44(12):2673-2682.  View on PubMed
  14. Cooley LF, Emeka AA, Meyers TJ, Cooper PR, Lin DW, Finelli A, Eastham JA, Logothetis CJ, Marks LS, Vesprini D, Goldenberg SL, Higano CS, Pavlovich CP, Chan JM, Morgan TM, Klein EA, Barocas DA, Loeb S, Helfand BT, Scholtens DM, Witte JS, Catalona WJ, Collaborators. Factors Associated with Time to Conversion from Active Surveillance to Treatment for Prostate Cancer in a Multi-Institutional Cohort. J Urol. 2021 11; 206(5):1147-1156.  View on PubMed
  15. Cooley LF, Emeka AA, Meyers TJ, Cooper PR, Lin DW, Finelli A, Eastham JA, Logothetis CJ, Marks LS, Vesprini D, Goldenberg SL, Higano CS, Pavlovich CP, Chan JM, Morgan TM, Klein EA, Barocas DA, Loeb S, Helfand BT, Scholtens DM, Witte JS, Catalona WJ. Reply by Authors. J Urol. 2021 11; 206(5):1156.  View on PubMed
  16. Kachuri L, Jeon S, DeWan AT, Metayer C, Ma X, Witte JS, Chiang CWK, Wiemels JL, de Smith AJ. Genetic determinants of blood-cell traits influence susceptibility to childhood acute lymphoblastic leukemia. Am J Hum Genet. 2021 10 07; 108(10):1823-1835.  View on PubMed
  17. 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. 2021 Jul-Sep 01; 35(3):271-274.  View on PubMed
  18. Li M, Lyu C, Huang M, Do C, Tycko B, Lupo PJ, MacLeod SL, Randolph CE, Liu N, Witte JS, Hobbs CA. Mapping methylation quantitative trait loci in cardiac tissues nominates risk loci and biological pathways in congenital heart disease. BMC Genom Data. 2021 06 10; 22(1):20.  View on PubMed
  19. Desai AS, Sagar V, Lysy B, Weiner AB, Ko OS, Driscoll C, Rodriguez Y, Vatapalli R, Unno K, Han H, Cohen JE, Vo AX, Pham M, Shin M, Jain-Poster K, Ross J, Morency EG, Meyers TJ, Witte JS, Wu J, Abdulkadir SA, Kundu SD. Inflammatory bowel disease induces inflammatory and pre-neoplastic changes in the prostate. Prostate Cancer Prostatic Dis. 2022 09; 25(3):463-471.  View on PubMed
  20. Chen E, Cario CL, Leong L, Lopez K, Márquez CP, Li PS, Oropeza E, Tenggara I, Cowan J, Simko JP, Kageyama R, Wells DK, Chan JM, Friedlander T, Aggarwal R, Paris PL, Feng F, Carroll PR, Witte JS. Cell-Free DNA Detection of Tumor Mutations in Heterogeneous, Localized Prostate Cancer Via Targeted, Multiregion Sequencing. JCO Precis Oncol. 2021; 5.  View on PubMed

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