University of California San Francisco
Helen Diller Family Comprehensive Cancer Center
David A. Quigley, PhD

David A. Quigley, PhD

Assistant Adjunct Professor, Dept. of Epidemiology and Biostatistics, UCSF

Cancer Center Program Memberships

Cancer Genetics

Research Summary

I am a translational geneticist focused on improving outcomes for patients whose tumors bear DNA repair defects, in particular patients with metastatic prostate cancer. I have wide experience in germline genetics, somatic genetics, and wet lab techinques to engineer novel cell lines. During my graduate training I identified candidate mechanisms of germline cancer susceptibility variants in mouse models of skin cancer and human breast cancer by combining bioinformatic and genetic approaches. To this end, I developed methods for expression Quantitative Trait Loci (eQTL) network analysis to identify germline variants that influence genes with a common functional role. My current research explores how defects in homologous recombination repair (HRR) affect tumor genomes, and how to detect and overcome resistance to targeted PARP inhibitor therapy in patients with HRR-deficient tumors. This includes analysis of PARPi resistance mechanisms in patients using liquid biopsy techniques, whole genome analysis of prostate tumors, and developing new models of PARPi-resistant prostate tumors.

Education

Carleton College, BA, 1998, Computer Science
Columbia University, MA, 2006, Biomedical Informatics
University of Oslo, PhD, 2014, Genetics


Professional Experience

  • 1998-1999
    Consultant, Software Architects, Inc., Minneapolis MN
  • 1999-2002
    Software Developer, CBS Marketwatch.com Inc., Minneapolis MN
  • 2002-2004
    Software Developer, Orrick, Herrington, & Sutcliffe L.L.P., San Francisco CA
  • 2004-2006
    Graduate Research Assistant, Columbia University, New York NY
  • 2006-2006
    Analyst II, Proctor Institute, UCSF Proctor Institute, San Francisco CA
  • 2006-present
    Bioinformatics Programmer III, UCSF Helen Diller Family Comprehensive Cancer Center
  • 2015-present
    Assistant Adjunct Professor, Department of Epidemiology and Biostatistics, UCSF

Honors & Awards

  • 1998
    National Merit Scholar. B.A. degree awarded Magna Cum Laude
  • 2006
    M.A. degree awarded with honors
  • 2014
    AACR Scholar in Training award
  • 2017-2020
    Prostate Cancer Foundation Young Investigator Award

Selected Publications

  1. Veniaminova NA, Grachtchouk M, Doane OJ, Peterson JK, Quigley DA, Lull MV, Pyrozhenko DV, Nair RR, Patrick MT, Balmain A, Dlugosz AA, Tsoi LC, Wong SY. Niche-Specific Factors Dynamically Regulate Sebaceous Gland Stem Cells in the Skin. Dev Cell. 2019 Sep 25.
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  2. McMahon M, Contreras A, Holm M, Uechi T, Forester CM, Pang X, Jackson C, Calvert ME, Chen B, Quigley DA, Luk JM, Kelley RK, Gordan JD, Gill RM, Blanchard SC, Ruggero D. A single H/ACA small nucleolar RNA mediates tumor suppression downstream of oncogenic RAS. Elife. 2019 09 03; 8.
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  3. Kothari V, Goodwin JF, Zhao SG, Drake JM, Yin Y, Chang SL, Evans JR, Wilder-Romans K, Gabbara K, Dylgjeri E, Chou J, Sun G, Tomlins SA, Mehra R, Hege K, Filvaroff EH, Schaeffer EM, Karnes RJ, Quigley DA, Rathkopf DE, He HH, Speers C, Spratt DE, Gilbert LA, Ashworth A, Chinnaiyan AM, Raj GV, Knudsen KE, Feng FY. DNA-Dependent Protein Kinase Drives Prostate Cancer Progression through Transcriptional Regulation of the Wnt Signaling Pathway. Clin Cancer Res. 2019 Sep 15; 25(18):5608-5622.
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  4. A. Freeman, S. Bakker, A. Weeks, M.E. Diolaiti, D. Quigley, J.S. Chapman, L.M. Chen, A. Ashworth. Differential cell surface protein expression in response to PARP inhibition in BRCA1 mutant isogenic ovarian and breast cancer cells using a novel proteomic technique. Gynecologic Oncology. 2019 Jun 1; 154:50.
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  5. Chen WS, Alshalalfa M, Zhao SG, Liu Y, Mahal BA, Quigley DA, Wei T, Davicioni E, Rebbeck TR, Kantoff PW, Maher CA, Knudsen KE, Small EJ, Nguyen PL, Feng FY. Novel RB1-Loss Transcriptomic Signature Is Associated with Poor Clinical Outcomes across Cancer Types. Clin Cancer Res. 2019 Jul 15; 25(14):4290-4299.
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  6. Chen WS, Aggarwal R, Zhang L, Zhao SG, Thomas GV, Beer TM, Quigley DA, Foye A, Playdle D, Huang J, Lloyd P, Lu E, Sun D, Guan X, Rettig M, Gleave M, Evans CP, Youngren J, True L, Lara P, Kothari V, Xia Z, Chi KN, Reiter RE, Maher CA, Feng FY, Small EJ, Alumkal JJ. Genomic Drivers of Poor Prognosis and Enzalutamide Resistance in Metastatic Castration-resistant Prostate Cancer. Eur Urol. 2019 Nov; 76(5):562-571.
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  7. Aggarwal RR, Quigley DA, Huang J, Zhang L, Beer TM, Rettig MB, Reiter RE, Gleave ME, Thomas GV, Foye A, Playdle D, Lloyd P, Chi KN, Evans CP, Lara PN, Feng FY, Alumkal JJ, Small EJ. Whole-Genome and Transcriptional Analysis of Treatment-Emergent Small-Cell Neuroendocrine Prostate Cancer Demonstrates Intraclass Heterogeneity. Mol Cancer Res. 2019 Jun; 17(6):1235-1240.
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  8. Sabelström H, Quigley DA, Fenster T, Foster DJ, Fuchshuber CAM, Saxena S, Yuan E, Li N, Paterno F, Phillips JJ, James CD, Norling B, Berger MS, Persson AI. High density is a property of slow-cycling and treatment-resistant human glioblastoma cells. Exp Cell Res. 2019 May 01; 378(1):76-86.
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  9. William S. Chen, Rahul Raj Aggarwal, Li Zhang, Shuang Zhao, Tomasz M. Beer, David A Quigley, Adam Foye, Denise Playdle, Paul Lloyd, Matthew Rettig, Martin Gleave, Christopher P. Evans, Primo Lara, Vishal Kothari, Kim N. Chi, Robert Evan Reiter, Christopher Maher, Felix Y Feng, Eric Jay Small, Joshi J. Alumkal. Genomic drivers of poor prognosis and enzalutamide resistance in metastatic castration-resistant prostate cancer. Journal of Clinical Oncology. 2019 Mar 1; 37(7_suppl):146-146.
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  10. Zhao SG, Chen WS, Das R, Chang SL, Tomlins SA, Chou J, Quigley DA, Dang HX, Barnard TJ, Mahal BA, Gibb EA, Liu Y, Davicioni E, Duska LR, Posadas EM, Jolly S, Spratt DE, Nguyen PL, Maher CA, Small EJ, Feng FY. Clinical and Genomic Implications of Luminal and Basal Subtypes Across Carcinomas. Clin Cancer Res. 2019 Apr 15; 25(8):2450-2457.
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  11. Quigley DA, Dang HX, Zhao SG, Lloyd P, Aggarwal R, Alumkal JJ, Foye A, Kothari V, Perry MD, Bailey AM, Playdle D, Barnard TJ, Zhang L, Zhang J, Youngren JF, Cieslik MP, Parolia A, Beer TM, Thomas G, Chi KN, Gleave M, Lack NA, Zoubeidi A, Reiter RE, Rettig MB, Witte O, Ryan CJ, Fong L, Kim W, Friedlander T, Chou J, Li H, Das R, Li H, Moussavi-Baygi R, Goodarzi H, Gilbert LA, Lara PN, Evans CP, Goldstein TC, Stuart JM, Tomlins SA, Spratt DE, Cheetham RK, Cheng DT, Farh K, Gehring JS, Hakenberg J, Liao A, Febbo PG, Shon J, Sickler B, Batzoglou S, Knudsen KE, He HH, Huang J, Wyatt AW, Dehm SM, Ashworth A, Chinnaiyan AM, Maher CA, Small EJ, Feng FY. Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer. Cell. 2018 10 18; 175(3):889.
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  12. Lu E, Thomas GV, Chen Y, Wyatt AW, Lloyd P, Youngren J, Quigley D, Bergan R, Bailey S, Beer TM, Feng FY, Small EJ, Alumkal JJ. DNA Repair Gene Alterations and PARP Inhibitor Response in Patients With Metastatic Castration-Resistant Prostate Cancer. J Natl Compr Canc Netw. 2018 08; 16(8):933-937.
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  13. Quigley DA, Dang HX, Zhao SG, Lloyd P, Aggarwal R, Alumkal JJ, Foye A, Kothari V, Perry MD, Bailey AM, Playdle D, Barnard TJ, Zhang L, Zhang J, Youngren JF, Cieslik MP, Parolia A, Beer TM, Thomas G, Chi KN, Gleave M, Lack NA, Zoubeidi A, Reiter RE, Rettig MB, Witte O, Ryan CJ, Fong L, Kim W, Friedlander T, Chou J, Li H, Das R, Li H, Moussavi-Baygi R, Goodarzi H, Gilbert LA, Lara PN, Evans CP, Goldstein TC, Stuart JM, Tomlins SA, Spratt DE, Cheetham RK, Cheng DT, Farh K, Gehring JS, Hakenberg J, Liao A, Febbo PG, Shon J, Sickler B, Batzoglou S, Knudsen KE, He HH, Huang J, Wyatt AW, Dehm SM, Ashworth A, Chinnaiyan AM, Maher CA, Small EJ, Feng FY. Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer. Cell. 2018 07 26; 174(3):758-769.e9.
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  14. Gonzalez VD, Samusik N, Chen TJ, Savig ES, Aghaeepour N, Quigley DA, Huang YW, Giangarrà V, Borowsky AD, Hubbard NE, Chen SY, Han G, Ashworth A, Kipps TJ, Berek JS, Nolan GP, Fantl WJ. Commonly Occurring Cell Subsets in High-Grade Serous Ovarian Tumors Identified by Single-Cell Mass Cytometry. Cell Rep. 2018 02 13; 22(7):1875-1888.
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  15. Ilkhanizadeh S, Sabelström H, Miroshnikova YA, Frantz A, Zhu W, Idilli A, Lakins JN, Schmidt C, Quigley DA, Fenster T, Yuan E, Trzeciak JR, Saxena S, Lindberg OR, Mouw JK, Burdick JA, Magnitsky S, Berger MS, Phillips JJ, Arosio D, Sun D, Weaver VM, Weiss WA, Persson AI. Antisecretory Factor-Mediated Inhibition of Cell Volume Dynamics Produces Antitumor Activity in Glioblastoma. Mol Cancer Res. 2018 05; 16(5):777-790.
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  16. Hanna Sabelstrom, Shirin IIkhanizadeh, Yekaterina A Miroshnikova, Aaron Frantz, Wen Zhu, Aurora Idilli, David Quigley, Trenten Fenster, Edith Yuan, Supna Saxena, Janna K Mouw, Jason A Burdick, Sergey Magnitsky, Mitchel S Berger, Daniele Arosio, Dandan Sun, Valerie M Weaver, William A Weiss, Anders I Persson. EXTH-23. ANTISECRETORY FACTOR-MEDIATED LOWERING OF INTERSTITIAL FLUID PRESSURE PRODUCES ANTI-TUMOR ACTIVITY IN GLIOBLASTOMA. Neuro-Oncology. 2017 Nov 6; 19(suppl_6):vi77-vi77.
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  17. Quigley DA, Tahiri A, Lüders T, Riis MH, Balmain A, Børresen-Dale AL, Bukholm I, Kristensen V. Age, estrogen, and immune response in breast adenocarcinoma and adjacent normal tissue. Oncoimmunology. 2017; 6(11):e1356142.
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  18. Quigley D, Alumkal JJ, Wyatt AW, Kothari V, Foye A, Lloyd P, Aggarwal R, Kim W, Lu E, Schwartzman J, Beja K, Annala M, Das R, Diolaiti M, Pritchard C, Thomas G, Tomlins S, Knudsen K, Lord CJ, Ryan C, Youngren J, Beer TM, Ashworth A, Small EJ, Feng FY. Analysis of Circulating Cell-Free DNA Identifies Multiclonal Heterogeneity of BRCA2 Reversion Mutations Associated with Resistance to PARP Inhibitors. Cancer Discov. 2017 09; 7(9):999-1005.
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  19. Halliwill KD, Quigley DA, Kang HC, Del Rosario R, Ginzinger D, Balmain A. Panx3 links body mass index and tumorigenesis in a genetically heterogeneous mouse model of carcinogen-induced cancer. Genome Med. 2016 08 09; 8(1):83.
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  20. Quigley DA, Kandyba E, Huang P, Halliwill KD, Sjölund J, Pelorosso F, Wong CE, Hirst GL, Wu D, Delrosario R, Kumar A, Balmain A. Gene Expression Architecture of Mouse Dorsal and Tail Skin Reveals Functional Differences in Inflammation and Cancer. Cell Rep. 2016 07 26; 16(4):1153-1165.
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