The Quigley Lab at UCSF
Publications on Google Scholar and Pubmed Bibliography

The DNA methylation landscape of advanced prostate cancer
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 E, Perry M, Dang HX, Yang R, Moussavi-Baygi R, Zhang L, Alshalalfa M,, Chang SL, Houlahan KE, Shiah Y, Beer TM, Thomas G, Chi KN, Gleave M, Zoubeidi A, Reiter RE, Rettig MB,, Witte O, Kim MY, 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 N, Lara PN, Evans CP, Febbo P, Batzoglou S, Knudsen KE, He HH,, Huang J, Zwart W, Costello JF, Luo J, Tomlins SW, Wyatt AW, Dehm SM, Ashworth A, Gilbert LA, Boutros PC, Farh K, Chinnaiyan AM#, Maher CA#, Small EJ#, Quigley DA#, Feng FY#
Nature Genetics in press, online July 13 2020
We performed whole genome methylation analysis of 100 metastatic prostate tumors, extending our investigation of the cohort wepublished in (Quigley et al Cell 2018).We identify a hypermethylation phenotype associated with mutations in affects the Androgen Receptor in approximately 80% of mCRPC and demonstrated how DNA repair defects associated with loss of BRCA2, CDK12, and TP53 are associated with genomic scars of deletions, tandem duplication, and chromothripsis. We have published the processed genomic data and the raw data (at GDC).
Pierson WE, Peters PN, Chang MT, Chen L, Quigley DA, Ashworth A,, Chapman JS
Gynecologic Oncology 2020 Apr;157(1):55-61. doi: 10.1016/j.ygyno.2020.02.011
Chou J, Quigley DA, Robinson TM, Feng FY,, Ashworth A
Cancer Discovery 2020 Feb 18. doi: 10.1158/2159-8290.CD-19-0528.
Reviews the roles of CDKs in cancer, with a focus on CDK12.
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
Clinical Cancer Research 2020 Jan 13. doi: 10.1158/1078-0432.CCR-19-3023
Work led by Scott Dehm's lab that investigated how AR gene rearrangements contribute to endocrine therapy resistance in castration-resistant prostate cancer.
Miyahira AK, Sharp A, Ellis L, Jones J, Kaochar S, Larman HB, Quigley DA, Ye H, Simons JW, Pienta KJ, Soule HR
The Prostate 2019 Dec 11. doi: 10.1002/pros.23934
Summarizes research presented at the 2019 PCF Coffey-Holden meeting.
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
Developmental Cell 2019 Nov 4;51(3):326-340.e4. doi: 10.1016/j.devcel.2019.08.015.
Kothari V, Goodwin J, Zhao S, Drake J, Yin Y, Chang L, Evans J, Wilder-Romans K, Gabbara K, Dylgjeri E, Chou J, Sun G, Tomlins S,, Hege R, Kristen , Filvaroff E, Schaeffer EM, Karnes RJ, Quigley DA, Rathkopf D, Hansen H ,, Speers C, Spratt D, Gilbert L, Ashworth A, Chinnaiyan A, Raj G, Knudsen K, Feng FY
Clinical Cancer Research 2019 Sep 15;25(18):5608-5622. doi: 10.1158/1078-0432.CCR-18-2387.
Chen WS*, Alshalalfa M*, Zhao SG, Liu Y, Mahal B, Quigley DA, Wei T, Davicioni E, Rebbeck TR, Kantoff PW, Maher CA, Knudsen KE, Small EJ, Nguyen PL#, Feng FY#
Clinical Cancer Research 2019 Apr 22. pii: clincanres.0404.2019. doi: 10.1158/1078-0432.CCR-19-0404.
We developed a transcriptomic signature of biallelic RB1 loss and demonstrate RB1 loss is associated with shorter survival in Pan-cancer and in mCRPC.
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, on behalf of the West Coast Prostate Cancer Dream Team
European Urology 2019 Mar 27. pii: S0302-2838(19)30206-4. doi: 10.1016/j.eururo.2019.03.020
We used whole genome and transcriptome analysis of men with advanced prostate cancer to demonstrate that biallelic loss of RB1 is independently associated with poor overall survival among men with mCRPC. WNT pathway deregulation is assocaited with enzalutamide resistance in these patients.
Aggarwal R*, Quigley DA*, Huang J, Zhang L, Beer T, Rettig M, Reiter R, Gleave M, Thomas G, Foye A, Denis Playdle, Lloyd P, Chi K, Evans C, Lara P, Feng FY#, Alumkal J#, Small EJ#
Molecular Cancer Research 2019 Mar 27. pii: molcanres.1101.2018. doi: 10.1158/1541-7786.MCR-18-1101.
Using an expression-based definition of t-SCNC, we found t-SCNC tumors were significantly less likely to have amplification of AR or an intergenic AR-enhancer locus. These t-SCNC tumors demonstrated both inter- and intra-individual heterogeneity, in particular with respect to neuroendocrine markers.
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
Experimental Cell Research 2019 Mar 5. pii: S0014-4827(19)30091-6. doi: 10.1016/j.yexcr.2019.03.003
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 SB, Ruggero D
eLife 2019 Sep 3;8. pii: e48847. doi: 10.7554/eLife.48847.
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
J Natl Compr Canc Network 2018 Aug;16(8):933-937. doi: 10.6004/jnccn.2018.7020
Quigley DA*, Dang H*, Zhao SG*, Lloyd P, Aggarwal R, Alumkal JJ, Foye A, Kothari V,, Perry M, Bailey A, Playdle D, Barnard T, Zhang L, Zhang J, Youngren J, Cieslik M, Parolia A,, Beer T, Thomas G, Chi K, Gleave M, Lack A, Zoubeidi A, Reiter R, Rettig M, Witte O, Ryan C,, Fong L, Kim W, Friedlander T, Chou J, Li H, Das R, Li H, Moussavi-Baygi R, Goodarzi H,, Gilbert L, Lara P, Evans C, Goldstein T, Stuart J, Tomlins S, Spratt D, Cheetham RK, Cheng D,, Farh K, Gehring J, Hakenberg J, Liao A, Febbo P, Shon J, Sickler B, Batzoglou S, Knudsen KE,, He H, Huang J, Wyatt A, Dehm S, Ashworth A, Chinnaiyan A#, Maher CA#, Small EJ#, Feng FY#
Cell 2018 Jul 26;174(3):758-769.e9. doi: 10.1016/j.cell.2018.06.039
We performed integrated analysis of DNA and RNA from 101 metastatic prostate cancer whole genomes. We show an enhancer region affects the Androgen Receptor in approximately 80% of mCRPC and demonstrated how DNA repair defects associated with loss of BRCA2, CDK12, and TP53 are associated with genomic scars of deletions, tandem duplication, and chromothripsis.
summary genomic data, raw genomic data.
Nature News and Views
Gonzalez V, Samusik N, Chen T, Savig E, Aghaeepour A, Quigley DA, Huang Y, Giangarra V, Borowsky A, Hubbard N, Chen S, Han G,, Ashworth A, Kipps T, Berek J, Nolan G, Fantl W
Cell Reports 2018 Feb 13;22(7):1875-1888. doi: 10.1016/j.celrep.2018.01.053
Ilkhanizadeh S, Sabelström H, Miroshnikova Y, Frantz A, Zhu W, Idilli A, Lakins J, Schmidt C, Quigley D, Fenster T, Yuan E, Trzeciak J, Saxena S, Lindberg O , Mouw J, Burdick J, Magnitsky S, Berger M, Philips J, Arosio D, Sun S, Weaver V, Weiss WA, Persson A
Molecular Cancer Research 2018 Feb 5. pii: molcanres.0413.2017. doi: 10.1158/1541-7786.MCR-17-0413
Quigley DA*, Alumkal JJ*, Wyatt A, 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 C, Ryan C, Youngren J, Beer T, Ashworth A#, Small E#, Feng FY#
Cancer Discovery 2017 Sep;7(9):999-1005. doi: 10.1158/2159-8290.CD-17-0146.
We demonstrated that a common form of PARP inhibitor resistance, called reversion mutations, can be detected in advanced prostate cancer by liquid biopsy. We employed deep sequencing of pre- and post-resistance DNA from patients with advanced prostate cancer who progressed on two different PARP inhibitors. We showed that resistance arises many times independently in different cells.
Quigley DA, Tahiri A, Lüders T, Riis M, Balmain A, Børresen-Dale A, Bukholm I, Kristensen V
OncoImmunology 2017 Aug 10;6(11):e1356142. doi: 10.1080/2162402X.2017.1356142
We performed gene expression analysis of 200 breast adenocarcinomas with matched adjacent normal tissue.
Raw microarray data can be downloaded from GEO GSE70947, GEO GSE70947, GEO GSE70951
Code and data to reproduce this analysis
Halliwill K, Quigley DA, Kang HC, Rosario R, Ginzinger D, Balmain A
Genome Medicine 2016 Aug 9;8(1):83.
Campbell J, Ryan C, Brough R, Bajrami I, Pemberton H, Chong I, Costa-Cabral S, Frankum J,, Gulati A, Holme H, Miller R, Postel-Vinay S, Rafiq R, Wei W, Williamson C, Quigley DA,, Tym J, Al-Lazikani B, Fenton T, Natrajan R, Strauss S, Ashworth A, Lord C
Cell Reports 2016 Mar 15;14(10):2490-501
Quigley DA, Kandyba E, Huang P, Halliwill K, Sjölund J, Pelorosso F, Wong C, Hirst G, Wu D, Delrosario R, Kumar A, Balmain A
Cell Reports 2016 Jul 26;16(4):1153-65.
Here we mapped the genetic architecture of skin perturbed by genetics, inflammation, and tumorigenesis.
Code and data to reproduce these analyses.
Quigley DA, Kristensen V
Molecular Oncology 2015 Dec;9(10):2054-62.
Quigley DA
BMC Bioinformatics 2015, 16:238 (30 July 2015)
The software package equalizer allows you to remove probes from Affymetrix microarrays using VCF files that describe the location of germline SNPs. See the equalizer project page for more information.
Hackett C, Quigley DA, Wong R, Chen J, Cheng C, Song Y, Wei J, Pawlikowska L, Bao Y,, Goldenberg D, Nguyen K, Gustafson W, Rallapalli S, Cho Y, Cook J, Kozlov S, Mao J, Van Dyke T,, Kwok P, Kahn J, Balmain A, Fan Q, Weiss W
Cell Reports 2014 Nov 6;9(3):1034-46
Westcott PM, Halliwill KD, To M, Mamunar R, Rust A, Keane T, Delrosario R, Jen K, Fredlund E, Quigley DA, Gurley K, Kemp C, Adams D, Balmain A
Nature 2014 Nov 2. doi: 10.1038/nature13898.
Silwal-Pandit L, Vollan HK, Chin SF, Rueda OM, McKinney S, Osako T, Quigley DA,, Kristensen VN, Aparicio S, Børresen-Dale AL, Caldas C, Langerød A
Clinical Cancer Research 2014 Jul 1;20(13):3569-80.
Yang YL, Hung MS, Wang Y, Ni J, Mao JH, Hsieh D, Au A, Kumar A, Quigley D, Fang LT, Yeh CC, Xu Z, Jablons DM, You#, L#
Journal of Pathology 2014 Mar 19.
Quigley DA, Fiorito E, Nord S, Van Loo P, Alnaes G, Fleischer T, Tost J,, Vollan HK, Tramm T, Overgaard J, Bukholm IR, Hurtado A, Balmain A, Börresen-Dale A,, Kristensen V
Molecular Oncology 2014 Mar;8(2):273-84
Here we used eQTL mapping and functional analysis in normal breast tissue and breast tumors to propose a mechanism for the breast cancer susceptibility locus on 5p12, previously identified by GWAS.
Sjölund J, Pelorosso F, Quigley DA, DelRosario R, Balmain A
Proceedings of the National Academy of Sciences 2014 May 20;111(20):7373-8
Kim IJ, Quigley D, To M, Jen, Pham P, Lin K, Jo B, Jen K, Raz D, Kim J, Mao JH, Jablons D, Balmain A
Nature Communications 2013 Apr 16.
Wong C, Yu J, Quigley DA, To M, Jen Kuang-Yu, Huang P, Del Rosario R, Balmain A
Genes and Development 2013 Mar 15;27(6):670-82
Kang HC, Quigley D, Kim IJ, Wakabayashi Y, Ferguson-Smith MA, D'Alessandro M, Lane EB, Akhurst RJ, Goudie DR, Balmain A
Journal of Investigative Dermatology 2013 January 28.
Benzinou M, Clermont FF, Letteboer TG, Kim JH, Espejel S, Harradine KA, Arbelaez J, Luu MT, Roy R, Quigley D, Higgins MN, Zaid M,, Aouizerat BE, van Amstel JK, Giraud S, Dupuis-Girod S, Lesca G, Plauchu H, Hughes CC, Westermann CJ, Akhurst RJ
Nature Communications 2012 January 10.
To MD, Quigley D, Mao J, Rosario R, Hsu J, Hodgson G, Jacks T, Balmain A
Molecular Cancer Research 2011 August 1
Quigley DA, To MD, Kim IJ, Lin KK, Albertson DG, Sjolund J, Perez-Losada J, Balmain A
Genome Biology 2011 Jan 18;12(1):R5.
Here we show how the genetic architecture of skin cancer is affected by somatic alterations during progression from normal tissue through benign and malignant tumors. Raw expression and array-CGH data are available in GEO in SuperSeries GSE21264.
Chan MF, Sack R, Quigley DA, Sathe S, Vijmasi T, Li S, Holsclaw D, Strauss EC,, McNamara NA
Optometry & Visual Science 2011 May 5
Lalitha P, Shapiro BL, Loh AR, Fothergill AW, Prajna NV, Srinivasan M, Oldenburg CE, Quigley DA, Chidambaram JD, McLeod SD, Acharya NR, Lietman TM
British Journal 2011 May;95(5):744-5
Connolly EC, Saunier EF, Quigley D, Luu MT, De Sapio A, Hann B, Yingling JM, Akhurst RJ
Cancer Research 2011 Mar 15;71(6):2339-49
Climent J, Perez-Losada J, Quigley DA, Kim IJ, Delrosario R, Jen KY, Bosch A, Lluch A, Mao JH, Balmain A
Journal 2010. Aug 10;28(23):3770-8
Quigley DA, Balmain A
Nature Reviews: Genetics 2009. Sep;10(9) 651-7.
This Perspective reviewed the state of systems genetics analysis of cancer.
Quigley DA, To MD, Perez-Losada J, Pelorosso F, Mao J, Nagase H, Ginzinger D, Balmain A
Nature 2009. Mar 26;458(7237):505-8.
Here we used eQTL mapping in normal skin of mice who had developed tumors to define the genetic architecture of normal tissue and identify loci associated with hematopoietic traits and tumor development
Li S, Sack R, Vijmasi T, Sathe S, Beaton A, Quigley D, Gallup M, McNamara N
Optometry & Vision Science 2008. Aug;85(8):653-60
Kundaje A, Lianoglou S, Li X, Quigley D, Arias M, Wiggins CH, Zhang L,, Leslie C
Ann N Y Acad Sci. 2007 Dec;1115:178-202