Research Summary

I study how genomic and epigenomic alterations affect tumor biology and patient outcomes. I have a particular interest in understanding how urological tumors develop resistance to targeted therapy. Recent projects have used large-scale genome sequencing to identify non-coding DNA structural variants associated with therapy resistance in advanced prostate cancer (Quigley Cell 2018) and a novel prostate cancer epigenomic disease subtype (Zhao Nature Genetics 2020). To achieve our goals, the laboratory works in close collaboration with physicians and laboratory investigators, and uses a wide variety of genome sequencing methods to study patient biopsy samples and preclinical models. This includes analysis of therapy resistance mechanisms in patients using liquid biopsy techniques and whole genome analysis of tumors. The lab has a long-term interest in understanding how inherited or somatic 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.


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

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
    Prostate Cancer Foundation Young Investigator Award
  • 2018
    BRCA Foundation Young Investigator Award

Selected Publications

  1. Ahmed M, Soares F, Xia JH, Yang Y, Li J, Guo H, Su P, Tian Y, Lee HJ, Wang M, Akhtar N, Houlahan KE, Bosch A, Zhou S, Mazrooei P, Hua JT, Chen S, Petricca J, Zeng Y, Davies A, Fraser M, Quigley DA, Feng FY, Boutros PC, Lupien M, Zoubeidi A, Wang L, Walsh MJ, Wang T, Ren S, Wei GH, He HH CRISPRi screens reveal a DNA methylation-mediated 3D genome dependent causal mechanism in prostate cancer.  View on PubMed
  2. Martin Sjöström, Shuang Zhao, Eric Jay Small, Yuhong Ning, Corinne Maurice-Dror, Adam Foye, Jun Jie T. Hua, Haolong Li, Tomasz M. Beer, Christopher P. Evans, Matthew Rettig, Kim N. Chi, Joshi J. Alumkal, Rahul Raj Aggarwal, Alan Ashworth, Samuel Levy, Housheng H. He, Alexander W. Wyatt, David A. Quigley, Felix Y Feng 5-hydroxymethylcytosine as a liquid biopsy biomarker in mCRPC.  View on PubMed
  3. Quigley DA One of These Things is Not Like the Others: Targeting ATM-mutant Prostate Cancer.  View on PubMed
  4. Eteleeb AM, Quigley DA, Zhao SG, Pham D, Yang R, Dehm SM, Luo J, Feng FY, Dang HX, Maher CA SV-HotSpot: detection and visualization of hotspots targeted by structural variants associated with gene expression.  View on PubMed
  5. Chen WS, Haynes WA, Waitz R, Kamath K, Vega-Crespo A, Shrestha R, Zhang M, Foye A, Baselga Carretero I, Perez Garcilazo I, Zhang M, Zhao SG, Sjöström M, Quigley DA, Chou J, Beer TM, Rettig M, Gleave M, Evans CP, Lara P, Chi KN, Reiter RE, Alumkal JJ, Ashworth A, Aggarwal R, Small EJ, Daugherty PS, Ribas A, Oh DY, Shon JC, Feng FY Autoantibody Landscape in Patients with Advanced Prostate Cancer.  View on PubMed
  6. Guan X, Sun D, Lu E, Urrutia JA, Reiter RE, Rettig M, Evans CP, Lara P, Gleave M, Beer TM, Thomas GV, Huang J, Aggarwal RR, Quigley DA, Foye A, Chen WS, Youngren J, Weinstein AS, Stuart JM, Feng FY, Small EJ, Xia Z, Alumkal JJ Copy Number Loss of 17q22 Is Associated with Enzalutamide Resistance and Poor Prognosis in Metastatic Castration-Resistant Prostate Cancer.  View on PubMed
  7. Zhao SG, Chen WS, Li H, Foye A, Zhang M, Sjöström M, Aggarwal R, Playdle D, Liao A, Alumkal JJ, Das R, Chou J, Hua JT, Barnard TJ, Bailey AM, Chow ED, Perry MD, Dang HX, Yang R, Moussavi-Baygi R, Zhang L, Alshalalfa M, Laura Chang S, Houlahan KE, Shiah YJ, Beer TM, Thomas G, Chi KN, Gleave M, Zoubeidi A, Reiter RE, Rettig MB, Witte O, Yvonne Kim M, Fong L, Spratt DE, Morgan TM, Bose R, Huang FW, Li H, Chesner L, Shenoy T, Goodarzi H, Asangani IA, Sandhu S, Lang JM, Mahajan NP, Lara PN, Evans CP, Febbo P, Batzoglou S, Knudsen KE, He HH, Huang J, Zwart W, Costello JF, Luo J, Tomlins SA, Wyatt AW, Dehm SM, Ashworth A, Gilbert LA, Boutros PC, Farh K, Chinnaiyan AM, Maher CA, Small EJ, Quigley DA, Feng FY The DNA methylation landscape of advanced prostate cancer.  View on PubMed
  8. Kwon DH, Zhang L, Quigley DA, Foye A, Chen WS, Wong CK, Feng FY, Bailey A, Huang J, Stuart JM, Friedl V, Weinstein AS, Beer TM, Alumkal JJ, Rettig M, Gleave M, Lara PN, Thomas GV, Li P, Lui A, Small EJ, Aggarwal RR Down-regulation of ADRB2 expression is associated with small cell neuroendocrine prostate cancer and adverse clinical outcomes in castration-resistant prostate cancer.  View on PubMed
  9. Eric Jay Small, Shuang Zhao, William S. Chen, Haolong Li, Adam Foye, Martin Sjöström, Jun Jie Hua, Rahul Raj Aggarwal, Joshi J. Alumkal, Tomasz M. Beer, Martin Gleave, Matthew Rettig, Owen Witte, Primo Lara, Arul Chinnaiyan, Chris Maher, David A. Quigley, Felix Y Feng The comprehensive methylation landscape of metastatic castration-resistant prostate cancer (mCRPC) identifies new phenotypic subtypes: Results from the West Coast Prostate Cancer Dream Team (WCDT).  View on PubMed
  10. Alumkal JJ, Sun D, Lu E, Beer TM, Thomas GV, Latour E, Aggarwal R, Cetnar J, Ryan CJ, Tabatabaei S, Bailey S, Turina CB, Quigley DA, Guan X, Foye A, Youngren JF, Urrutia J, Huang J, Weinstein AS, Friedl V, Rettig M, Reiter RE, Spratt DE, Gleave M, Evans CP, Stuart JM, Chen Y, Feng FY, Small EJ, Witte ON, Xia Z Transcriptional profiling identifies an androgen receptor activity-low, stemness program associated with enzalutamide resistance.  View on PubMed
  11. Pierson WE, Peters PN, Chang MT, Chen LM, Quigley DA, Ashworth A, Chapman JS An integrated molecular profile of endometrioid ovarian cancer.  View on PubMed
  12. Daniel Kwon, Li Zhang, Adam Foye, William S. Chen, Felix Y Feng, Adina Bailey, Jiaoti Huang, David A. Quigley, Josh Stuart, Verena Friedl, Alana Weinstein, Tomasz M. Beer, Joshi J. Alumkal, Matthew Rettig, Martin Gleave, Primo Lara, Patricia Li, Austin Lui, Eric Jay Small, Rahul Raj Aggarwal ADRB2 expression in progressive metastatic castration-resistant prostate cancer.  View on PubMed
  13. Chou J, Quigley DA, Robinson TM, Feng FY, Ashworth A Transcription-Associated Cyclin-Dependent Kinases as Targets and Biomarkers for Cancer Therapy.  View on PubMed
  14. Li Y, Yang R, Henzler CM, Ho Y, Passow C, Auch B, Carreira S, Nava Rodrigues D, Bertan C, Hwang TH, Quigley DA, Dang HX, Morrissey C, Fraser M, Plymate SR, Maher CA, Feng FY, de Bono JS, Dehm SM Diverse AR Gene Rearrangements Mediate Resistance to Androgen Receptor Inhibitors in Metastatic Prostate Cancer.  View on PubMed
  15. Miyahira AK, Sharp A, Ellis L, Jones J, Kaochar S, Larman HB, Quigley DA, Ye H, Simons JW, Pienta KJ, Soule HR Prostate cancer research: The next generation; report from the 2019 Coffey-Holden Prostate Cancer Academy Meeting.  View on PubMed
  16. 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.  View on PubMed
  17. 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.  View on PubMed
  18. 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.  View on PubMed
  19. 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.  View on PubMed
  20. 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.  View on PubMed

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