Publications on Google Scholar and Pubmed Bibliography
2025
Feng EM, Vo-Phamhi J, Subramanian AN, Dias M, Foye A, Vinson J, Hong JC, Freedland SJ, Alumkal JJ, Beltran H, Morrissey C, Nelson PS, Chinnaiyan AM, Aggarwal R, Small EJ, Quigley DA, Sjöström M, Zhao SG, Chen WS. Prostate Cancer Prostatic Dis. 2025 Mar 31. doi: 10.1038/s41391-025-00949-w. Online ahead of print.
Aggarwal RR, Vuky J, VanderWeele D, Rettig M, Heath EI, Quigley D, Huang J, Chumber A, Cheung A, Foye A, Leung S, Abbey J, Dorr A, Nasoff M, Hunter J, Wang S, Flavell RR, Fong L, Liu B, Small EJ. J Clin Oncol. 2025 Mar 26:JCO2401989. doi: 10.1200/JCO-24-01989. Online ahead of print. PMID: 40138611
Chesner LN, Polesso F, Graff JN, Hawley JE, Smith AK, Lundberg A, Das R, Shenoy T, Sjöström M, Zhao F, Hu YM, Linder S, Chen WS, Hawkins RM, Shrestha R, Zhu X, Foye A, Li H, Kim LM, Bhalla M, O'loughlin T, Kuzuoglu-Ozturk D, Hua JT, Badura ML, Wilkinson S, Trostel SY, Bergman AM, Ruggero D, Drake CG, Sowalsky AG, Fong L, Cooperberg MR, Zwart W, Guan X, Ashworth A, Xia Z, Quigley DA, Gilbert LA, Feng FY, Moran AE. Cancer Discovery. 2025 Mar 26:JCO2401989. doi: 10.1200/JCO-24-01989. PMID: 39652470
Sharifi MN, Feng E, Rydzewski NR, Taylor AK, Sperger JM, Shi Y, Helzer KT, Bootsma ML, Carreno V, Chang AH, Nunamaker LA, Blitzer GC, Shang TA, Subramanian A, Bjartell A, Josefsson A, Wikström P, Feng E, Kohli M, Yang R, Dehm SM, Small EJ, Aggarwal R, Quigley DA, Lang JM, Zhao SG, Sjöström M. Mol Oncol. 2025 Feb 22. doi: 10.1002/1878-0261.70001. PMID: 39985777
2024
Seed G, Beije N, Yuan W, Bertan C, Goodall J, Lundberg A, Tyler M, Figueiredo I, Pereira R, Baker C, Bogdan D, Gallagher L, Cieslik JP, Greening S, Lambros M, Neves R, Magraner-Pardo L, Fowler G, Ebbs B, Miranda S, Flohr P, Bianchini D, Rescigno P, Porta N, Hall E, Gurel B, Tunariu N, Sharp A, Pettit S, Stoecklein NH, Sandhu S, Quigley D, Lord CJ, Mateo J, Carreira S, de Bono J. Cancer Cell. 2024 Dec 9;42(12):2113-2123.e4. doi: 10.1016/j.ccell.2024.10.015. PMID: 39577422
Chou J, Robinson TM, Egusa EA, Lodha R, Zhang M, Badura M, Mikayelyan M, Delavan H, Swinderman J, Wilson C, Zhu J, Das R, Nguyen M, Loehr A, Golsorkhi T, Simmons A, Abida W, Chinnaiyan AM, Arkin MR, Small EJ, Quigley DA, Yang L, Kim M, Ashworth A, Feng FY. Clin Cancer Res. 2024 Sep 25. doi: 10.1158/1078-0432.CCR-23-3785. PMID: 39321214
Zhu X, Farsh T, Vis D, Yu I, Li H, Liu T, Sjöström M, Shrestha R, Kneppers J, Severson T, Zhang M, Lundberg A, Moreno Rodriguez T, Weinstein AS, Foye A, Mehra N, Aggarwal RR, Bergman AM, Small EJ, Lack NA, Zwart W, Quigley DA, van der Heijden MS, Feng FY. Journal of Clinical Investigation. 2024 Aug 13;134(19):e178604. doi: 10.1172/JCI178604. PMID: 39352383
Zhu X, Chan E, Turski ML, Mendez CE, Hsu SC, Kumar V, Shipp C, Jindal T, Chang K, Onodera C, Devine WP, Grenert JP, Stohr BA, Ding CC, Stachler MD, Quigley DA, Feng FY, Chu CE, Porten SP, Chou J, Friedlander TW, Koshkin VS. The Oncologist, 2024 Aug 5;29(8):e1094-e1097. doi: 10.1093/oncolo/oyae127.
Zhao SG*, Bootsma M*, Zhou S*, Shrestha S, Moreno-Rodriguez T, Lundberg A, Pan C, Arlidge C, Hawley JR, Adam Foye, Weinstein AS, Sjöström M, Zhang M, Li H, Chesner LN, Rydzewski NR, Helzer KT, Shi Y, The West Coast Dream Team Consortium, Lynch M, Dehm SM, Lang JM, Alumkal JJ, He HH, Wyatt AW, Aggarwal R, Zwart W, Small EJ, Quigley DA*, Lupien M* & Feng FY*. Nature Genetics. 2024 Online ahead of Print, https://doi.org/10.1038/s41588-024-01826-3
Shrestha R, Chesner LN, Zhang M, Zhou S, Foye A, Lundberg A, Weinstein AS, Sjöström M, Zhu X, Moreno-Rodriguez T, Li H, SU2C/PCF West Coast Prostate Cancer Dream Team, Alumkal JJ, Aggarwal R, Small EJ, Lupien M*, Quigley DA*, Feng FY* Cancer Research. 2024 Jul 11. doi.org/10.1158/0008-5472.CAN-24-0890
Subramanian A, Zhang M, Sharifi M, Moreno-Rodriguez T, Feng E, Rydzewski NR, Shrestha R, Zhu X, Zhao SG, Aggarwal A, Small EJ, Ding CC, Quigley DA, Sjöström M. bioRxiv 2024 Jun 3:2024.06.02.595931. doi: 10.1101/2024.06.02.595931.
Zhang M, Sjöström M, Cui X, Foye A, Farh K, Shrestha R, Lundberg A, Dang HX, Li H, Febbo PG, Aggarwal R, Alumkal J, Small EJ, The SU2C/PCF West Coast Prostate Cancer Dream Team, Maher CA *, Feng FY *, & Quigley DA *. Nature Cell Biology. 2024 doi 10.1038/s41556-024-01438-3
This study was highlighted in Nature Reviews: Urology.
Taylor MA, Kandyba E, Halliwill K, Delrosario R, Khoroshkin M, Goodarzi H, David Quigley Li YR, Wu D, Bollam SR, Mirzoeva OK, Akhurst RJ, Balmain A. Science. 2024 May 31;384(6699):eadi7453 doi: 10.1126/science.adi7453.
Saha D, Dang HX, Zhang M, Quigley DA, Feng FY, Maher CA. NPJ Genomic Medicine. 2024 Feb 23;9(1):14. doi: 10.1038/s41525-024-00401-3.
Chappidi MR, Sjöström M, Greenland NY, Cowan JE, Baskin AS, Shee K, Simko JP, Chan E, Stohr BA, Washington SL 3rd, Nguyen HG, Quigley DA, Davicioni E, Feng FY, Carroll PR, Cooperberg MR. Eur Urol Oncol.. 2024 Mar 19:S2588-9311(23)00120-7. doi: 10.1016/j.euo.2023.06.007
2023
Helzer KT, Sharifi MN, Sperger JM, Shi Y, Annala M, Bootsma ML, Reese SR, Taylor A, Kaufmann KR, Krause HK, Schehr JL, Sethakorn N, Kosoff D, Kyriakopoulos C, Burkard ME, Rydzewski NR, Yu M, Harari PM, Bassetti M, Blitzer G, Floberg J, Sjöström M, Quigley DA, Dehm SM, Armstrong AJ, Beltran H, McKay RR, Feng FY, O'Regan R, Wisinski KB, Emamekhoo H, Wyatt AW, Lang JM, Zhao SG. Ann Oncol.. 2023 Sep;34(9):813-825. doi: 10.1016/j.annonc.2023.06.001. Epub 2023 Jun 16.
Moreno T, Magana J, Quigley DA
Bioinformatics. 2023 Aug 1;39(8):btad509. doi: 10.1093/bioinformatics/btad509
Bioinformatics. 2023 Aug 1;39(8):btad509. doi: 10.1093/bioinformatics/btad509
Lundberg A, Zhang M, Aggarwal R, Li H, Zhang L, Foye A, Sjöström M, Chou J, Chang K, Moreno-Rodriguez T, Shrestha R, Baskin A, Zhu X, Weinstein AS, Younger N, Alumkal JJ, Beer TM, Chi KN, Evans CP, Gleave M, Lara PN, Reiter RE, Rettig MB, Witte ON, Wyatt AW, Feng FY*, Small EJ*, Quigley DA*
Cancer Research. 2023 Jun 8;CAN-23-0593. doi: 10.1158/0008-5472.CAN-23-0593
Cancer Research. 2023 Jun 8;CAN-23-0593. doi: 10.1158/0008-5472.CAN-23-0593
Taylor MA, Kandyba E, Halliwill K, Delrosario R, Koroshkin M, Goodarzi H, Quigley D, Li YR, Wu D, Bollam S, Mirzoeva O, Akhurst RJ, Balmain A.
bioRxiv. 2023 May 10:2023.05.08.539863. doi: 10.1101/2023.05.08.539863. Preprint
bioRxiv. 2023 May 10:2023.05.08.539863. doi: 10.1101/2023.05.08.539863. Preprint
Sayar E, Patel RA, Coleman IM, Roudier MP, Zhang A, Mustafi P, Low JY, Hanratty B, Ang LS, Bhatia V, Adil M, Bakbak H, Quigley DA, Schweizer MT, Hawley JE, Kollath L, True LD, Feng FY, Bander NH, Corey E, Lee JK, Morrissey C, Gulati R, Nelson PS, Haffner MC.
JCI Insight. 2023 Feb 23:e162907. doi: 10.1172/jci.insight.162907.
JCI Insight. 2023 Feb 23:e162907. doi: 10.1172/jci.insight.162907.
2022
Westbrook TC, Guan X, Rodansky E, Flores D, Liu CJ, Udager AM, Patel RA, Haffner MC, Hu YM, Sun D, Beer TM, Foye A, Aggarwal R, Quigley DA, Youngren JF, Ryan CJ, Gleave M, Wang Y, Huang J, Coleman I, Morrissey C, Nelson PS, Evans CP, Lara P, Reiter RE, Witte O, Rettig M, Wong CK, Weinstein AS, Uzunangelov V, Stuart JM, Thomas GV, Feng FY, Small EJ, Yates JA, Xia Z, Alumkal JJ.
Nat Commun. 2022 Sep 15;13(1):5345. doi: 10.1038/s41467-022-32701-6.
Nat Commun. 2022 Sep 15;13(1):5345. doi: 10.1038/s41467-022-32701-6.
O'Leary PC, Chen H, Doruk YU, Williamson T, Polacco B, McNeal AS, Shenoy T, Kale N, Carnevale J, Stevenson E, Quigley DA, Chou J, Feng FY, Swaney DL, Krogan NJ, Kim M, Diolaiti ME, Ashworth A.
Cancer Res. 2022 Oct 23:OF1-OF12. doi: 10.1158/0008-5472.CAN-21-4335.
Cancer Res. 2022 Oct 23:OF1-OF12. doi: 10.1158/0008-5472.CAN-21-4335.
Feng E, Rydzewski NR, Zhang M, Lundberg A, Bootsma M, Helzer KT, Lang JM, Aggarwal R, Small EJ, Quigley DA, Sjöström M, Zhao SG.
Clin Cancer Res. 2022 Oct 19:CCR-22-2567. doi: 10.1158/1078-0432.CCR-22-2567.
Clin Cancer Res. 2022 Oct 19:CCR-22-2567. doi: 10.1158/1078-0432.CCR-22-2567.
Zhang M, Moreno-Rodriguez T and Quigley D
Cancer Discovery 2022 Sep 2;12(9):2017-2019. doi: 10.1158/2159-8290.CD-22-0702.
Cancer Discovery 2022 Sep 2;12(9):2017-2019. doi: 10.1158/2159-8290.CD-22-0702.
Commentary on Linder et al. Cancer Discovery 2022
Sjöström M*, Zhao SG*, Levy S*, Zhang M, Ning Y, Shrestha R, Lundberg A, Herberts C, Foye A, Aggarwal R, Hua JT, Li H, Bergamaschi A, Maurice-Dror C, Maheshwari A, Chen S, Ng SWS, Ye W, Petricca J, Fraser M, Chesner L, Perry MD, Moreno-Rodriguez T, Chen WS, Alumkal JJ, Chou J, Morgans AK, Beer TM, Thomas GV, Gleave M, Lloyd P, Phillips T, McCarthy E, Haffner MC, Zoubeidi A, Annala M, Reiter RE, Rettig MB, Witte ON, Fong L, Bose R, Huang FW, Luo J, Bjartell A, Lang JM, Mahajan NP, Lara PN, Evans CP, Tran PT, Posadas EM, He C, Cui XL, Huang J, Zwart W, Gilbert LA, Maher CA, Boutros PC, Chi KN, Ashworth A, Small EJ, He HH, Wyatt A#, Quigley D#, and Feng FY#.
Cancer Research 2022 Oct 17:OF1-OF15. doi: 10.1158/0008-5472.CAN-22-1123
Cancer Research 2022 Oct 17:OF1-OF15. doi: 10.1158/0008-5472.CAN-22-1123
Herberts C, Annala M, Sipola J, Ng SWS, Chen XE, Nurminen A, Korhonen OV, Munzur AD, Beja K, Schönlau E, Bernales CQ, Ritch E, Bacon JVW, Lack NA, Nykter M, Aggarwal R, Small EJ, Gleave ME; SU2C/PCF West Coast Prostate Cancer Dream Team, Quigley DA, Feng FY#, Chi KN#, Wyatt AW#.
Nature 2022 Jul 20. doi: 10.1038/s41586-022-04975-9
Nature 2022 Jul 20. doi: 10.1038/s41586-022-04975-9
Severson T, Qiu X, Alshalalfa M, Sjöström M, Quigley D, Bergman A, Long H, Feng F, Freedman ML, Zwart W, Pomerantz MM.
Clin Epigenetics 2022 May 4;14(1):60. doi: 10.1186/s13148-022-01278-8.
Clin Epigenetics 2022 May 4;14(1):60. doi: 10.1186/s13148-022-01278-8.
2021
Aggarwal R, Rydzewski NR, Zhang L, Foye A, Kim W, Helzer KT, Bakhtiar H, Chang SL, Perry MD, Gleave M, Reiter RE, Huang J, Evans CP, Alumkal JJ, Lang JM, Yu M, Quigley DA, Sjöström M, Small EJ, Feng FY, Zhao SG
JAMA Oncology 10.1001/jamaoncol.2021.3987
JAMA Oncology 10.1001/jamaoncol.2021.3987
The largest integrated clinical, transcriptomic, and genomic analysis of mCRPC samples to date suggests that mCRPC can be classified as luminal and basal tumors.
Rydzewski NR, Peterson E, Lang JM, Yu M, Laura Chang S, Sjöström M, Bakhtiar H, Song G, Helzer KT, Bootsma ML, Chen WS, Shrestha RM, Zhang M, Quigley DA, Aggarwal R, Small EJ, Wahl DR, Feng FY, Zhao SG
NPJ Genomic Medicine 10.1038/s41525-021-00239-z
NPJ Genomic Medicine 10.1038/s41525-021-00239-z
Das R, Sjöström M, Shrestha R, Yogodzinski C, Egusa EA, Chesner LN, Chen WS, Chou J, Dang DK, Swinderman JT, Ge A, Hua JT, Kabir S, Quigley DA, Small EJ, Ashworth A, Feng FY, Gilbert LA
Nature Communications 10.1038/s41467-021-24919-7
Nature Communications 10.1038/s41467-021-24919-7
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
Nature Communications 10.1038/s41467-021-21867-0
Nature Communications 10.1038/s41467-021-21867-0
2020
Quigley DA
European Urology 10.1016/j.eururo.2020.11.018
European Urology 10.1016/j.eururo.2020.11.018
Commentary on Neeb et al. European Urology 2020
Eteleeb AM, Quigley DA, Zhao SG, Pham D, Yang R, Dehm SM, Luo J, Feng FY, Dang HX, Maher CA
Scientific Reports 10.1038/s41598-020-71168-7
Scientific Reports 10.1038/s41598-020-71168-7
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
Clinical Cancer Research 10.1158/1078-0432.CCR-20-1966
Clinical Cancer Research 10.1158/1078-0432.CCR-20-1966
Guan X, Sun D, Lu E, Urrutia JA, Reiter RE, Rettig M, Evans CP, Lara P Jr, 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
Clinical Cancer Research 10.1158/1078-0432.CCR-19-2303
Clinical Cancer Research 10.1158/1078-0432.CCR-19-2303
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 10.1038/s41588-020-0648-8. Epub 2020 Jul 13
Nature Genetics 10.1038/s41588-020-0648-8. Epub 2020 Jul 13
We performed whole genome methylation analysis of 100 metastatic prostate tumors, extending our investigation of the cohort we published in (Quigley et al Cell 2018). We observed that 22% of tumors exhibited a novel epigenomic subtype associated with hypermethylation and somatic mutations in TET2, DNMT3B, IDH1 and BRAF. We also identified intergenic regions where methylation is associated with RNA expression of the oncogenic driver genes AR, MYC and ERG. Finally, we showed that differential methylation during progression preferentially occurs at somatic mutational hotspots and putative regulatory regions.
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 Jr, Thomas GV, Li P, Lui A, Small EJ, Aggarwal RR.
Urologic Oncology 10.1016/j.urolonc.2020.06.002
Urologic Oncology 10.1016/j.urolonc.2020.06.002
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
Proc Natl Acad Sci U S A. 10.1073/pnas.1922207117
Proc Natl Acad Sci U S A. 10.1073/pnas.1922207117
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
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.
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
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.
2019
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
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.
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.
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.
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
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.
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
Experimental Cell Research 2019 Mar 5. pii: S0014-4827(19)30091-6. doi: 10.1016/j.yexcr.2019.03.003
2018
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.
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
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
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
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
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
Molecular Cancer Research 2018 Feb 5. pii: molcanres.0413.2017. doi: 10.1158/1541-7786.MCR-17-0413
2017
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.
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
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
Raw microarray data can be downloaded from GEO GSE70947, GEO GSE70947, GEO GSE70951
Code and data to reproduce this analysis
2016
Halliwill K, Quigley DA, Kang HC, Rosario R, Ginzinger D, Balmain A
Genome Medicine 2016 Aug 9;8(1):83.
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
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.
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.
Code and data to reproduce these analyses.
2015
Quigley DA, Kristensen V
Molecular Oncology 2015 Dec;9(10):2054-62.
Molecular Oncology 2015 Dec;9(10):2054-62.
Quigley DA
BMC Bioinformatics 2015, 16:238 (30 July 2015)
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.
2014
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
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.
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.
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.
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
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
Proceedings of the National Academy of Sciences 2014 May 20;111(20):7373-8
2013
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.
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
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.
Journal of Investigative Dermatology 2013 January 28.
2012
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.
Nature Communications 2012 January 10.
2011
To MD, Quigley D, Mao J, Rosario R, Hsu J, Hodgson G, Jacks T, Balmain A
Molecular Cancer Research 2011 August 1
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.
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
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
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
Cancer Research 2011 Mar 15;71(6):2339-49
2010
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
Journal 2010. Aug 10;28(23):3770-8
2009
Quigley DA, Balmain A
Nature Reviews: Genetics 2009. Sep;10(9) 651-7.
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.
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
2008
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
Optometry & Vision Science 2008. Aug;85(8):653-60
2007
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
Ann N Y Acad Sci. 2007 Dec;1115:178-202