The Molecular Taxonomy of Primary Prostate Cancer

Cell

Volumn 163, Issue 4, 2015, Pages 1011-1025

  Abeshouse, Adam ^a   Ahn, Jaeil ^a   Akbani, Rehan ^a   Ally, Adrian ^a   Amin, Samirkumar ^a   Andry, Christopher D ^a   Annala, Matti ^a   Aprikian, Armen ^a   Armenia, Joshua ^a   Arora, Arshi ^a   Auman, J Todd ^a   Balasundaram, Miruna ^a   Balu, Saianand ^a   Barbieri, Christopher E ^a   Bauer, Thomas ^a   Benz, Christopher C ^a   Bergeron, Alain ^a   Beroukhim, Rameen ^a   Berrios, Mario ^a   Bivol, Adrian ^a   Bodenheimer, Tom ^a   Boice, Lori ^a   Bootwalla, Moiz S ^a   Borges Dos Reis, Rodolfo ^a   Boutros, Paul C ^a   Bowen, Jay ^a   Bowlby, Reanne ^a   Boyd, Jeffrey ^a   Bradley, Robert K ^a   Breggia, Anne ^a   Brimo, Fadi ^a   Bristow, Christopher A ^a   Brooks, Denise ^a   Broom, Bradley M ^a   Bryce, Alan H ^a   Bubley, Glenn ^a   Burks, Eric ^a   Butterfield, Yaron S N ^a   Button, Michael ^a   Canes, David ^a   Carlotti, Carlos G ^a   Carlsen, Rebecca ^a   Carmel, Michel ^a   Carroll, Peter R ^a   Carter, Scott L ^a   Cartun, Richard ^a   Carver, Brett S ^a   Chan, June M ^a   Chang, Matthew T ^a   Chen, Yu ^a   Cherniack, Andrew D ^a   Chevalier, Simone ^a   Chin, Lynda ^a   Cho, Juok ^a   Chu, Andy ^a   Chuah, Eric ^a   Chudamani, Sudha ^a   Cibulskis, Kristian ^a   Ciriello, Giovanni ^a   Clarke, Amanda ^a   Cooperberg, Matthew R ^a   Corcoran, Niall M ^a   Costello, Anthony J ^a   Cowan, Janet ^a   Crain, Daniel ^a   Curley, Erin ^a   David, Kerstin ^a   Demchok, John A ^a   Demichelis, Francesca ^a   Dhalla, Noreen ^a   Dhir, Rajiv ^a   Doueik, Alexandre ^a   Drake, Bettina ^a   Dvinge, Heidi ^a   Dyakova, Natalya ^a   Felau, Ina ^a   Ferguson, Martin L ^a   Frazer, Scott ^a   Freedland, Stephen ^a   Fu, Yao ^a   Gabriel, Stacey B ^a   Gao, Jianjiong ^a   Gardner, Johanna ^a   Gastier Foster, Julie M ^a   Gehlenborg, Nils ^a   Gerken, Mark ^a   Gerstein, Mark B ^a   Getz, Gad ^a   Godwin, Andrew K ^a   Gopalan, Anuradha ^a   Graefen, Markus ^a   Graim, Kiley ^a   Gribbin, Thomas ^a   Guin, Ranabir ^a   Gupta, Manaswi ^a   Hadjipanayis, Angela ^a   Haider, Syed ^a   Hamel, Lucie ^a   Hayes, D Neil ^a   Heiman, David I ^a   Hess, Julian ^a   Hoadley, Katherine A ^a   Holbrook, Andrea H ^a   Holt, Robert A ^a   Holway, Antonia ^a   Hovens, Christopher M ^a   Hoyle, Alan P ^a   Huang, Mei ^a   Hutter, Carolyn M ^a   Ittmann, Michael ^a   Iype, Lisa ^a   Jefferys, Stuart R ^a   Jones, Corbin D ^a   Jones, Steven J M ^a   Juhl, Hartmut ^a   Kahles, Andre ^a   Kane, Christopher J ^a   Kasaian, Katayoon ^a   Kerger, Michael ^a   Khurana, Ekta ^a   Kim, Jaegil ^a   Klein, Robert J ^a   Kucherlapati, Raju ^a   Lacombe, Louis ^a   Ladanyi, Marc ^a   Lai, Phillip H ^a   Laird, Peter W ^a   Lander, Eric S ^a   Latour, Mathieu ^a   Lawrence, Michael S ^a   Lau, Kevin ^a   Lebien, Tucker ^a   Lee, Darlene ^a   Lee, Semin ^a   Lehmann, Kjong Van ^a   Leraas, Kristen M ^a   Leshchiner, Ignaty ^a   Leung, Robert ^a   Libertino, John A ^a   Lichtenberg, Tara M ^a   Lin, Pei ^a   Linehan, W Marston ^a   Ling, Shiyun ^a   Lippman, Scott M ^a   Liu, Jia ^a   Liu, Wenbin ^a   Lochovsky, Lucas ^a   Loda, Massimo ^a   Logothetis, Christopher ^a   Lolla, Laxmi ^a   Longacre, Teri ^a   Lu, Yiling ^a   Luo, Jianhua ^a   Ma, Yussanne ^a   Mahadeshwar, Harshad S ^a   Mallery, David ^a   Mariamidze, Armaz ^a   Marra, Marco A ^a   Mayo, Michael ^a   McCall, Shannon ^a   McKercher, Ginette ^a   Meng, Shaowu ^a   Mes Masson, Anne Marie ^a   Merino, Maria J ^a   Meyerson, Matthew ^a   Mieczkowski, Piotr A ^a   Mills, Gordon B ^a   Shaw, Kenna R Mills ^a   Minner, Sarah ^a   Moinzadeh, Alireza ^a   Moore, Richard A ^a   Morris, Scott ^a   Morrison, Carl ^a   Mose, Lisle E ^a   Mungall, Andrew J ^a   Murray, Bradley A ^a   Myers, Jerome B ^a   Naresh, Rashi ^a   Nelson, Joel ^a   Nelson, Mark A ^a   Nelson, Peter S ^a   Newton, Yulia ^a   Noble, Michael S ^a   Noushmehr, Houtan ^a   Nykter, Matti ^a   Pantazi, Angeliki ^a   Parfenov, Michael ^a   Park, Peter J ^a   Parker, Joel S ^a   Paulauskis, Joseph ^a   Penny, Robert ^a   Perou, Charles M ^a   Piché, Alain ^a   Pihl, Todd ^a   Pinto, Peter A ^a   Prandi, Davide ^a   Protopopov, Alexei ^a   Ramirez, Nilsa C ^a   Rao, Arvind ^a   Rathmell, W Kimryn ^a   Rätsch, Gunnar ^a   Ren, Xiaojia ^a   Reuter, Victor E ^a   Reynolds, Sheila M ^a   Rhie, Suhn K ^a   Rieger Christ, Kimberly ^a   Roach, Jeffrey ^a   Robertson, A Gordon ^a   Robinson, Brian ^a   Rubin, Mark A ^a   Saad, Fred ^a   Sadeghi, Sara ^a   Saksena, Gordon ^a   Saller, Charles ^a   Salner, Andrew ^a   Sanchez Vega, Francisco ^a   Sander, Chris ^a   Sandusky, George ^a   Sauter, Guido ^a   Sboner, Andrea ^a   Scardino, Peter T ^a   Scarlata, Eleonora ^a   Schein, Jacqueline E ^a   Schlomm, Thorsten ^a   Schmidt, Laura S ^a   Schultz, Nikolaus ^a   Schumacher, Steven E ^a   Seidman, Jonathan ^a   Neder, Luciano ^a   Seth, Sahil ^a   Sharp, Alexis ^a   Shelton, Candace ^a   Shelton, Troy ^a   Shen, Hui ^a   Shen, Ronglai ^a   Sherman, Mark ^a   Sheth, Margi ^a   Shi, Yan ^a   Shih, Juliann ^a   Shmulevich, Ilya ^a   Simko, Jeffry ^a   Simon, Ronald ^a   Simons, Janae V ^a   Sipahimalani, Payal ^a   Skelly, Tara ^a   Sofia, Heidi J ^a   Soloway, Matthew G ^a   Song, Xingzhi ^a   Sorcini, Andrea ^a   Sougnez, Carrie ^a   Stepa, Serghei ^a   Stewart, Chip ^a   Stewart, John ^a   Stuart, Joshua M ^a   Sullivan, Travis B ^a   Sun, Charlie ^a   Sun, Huandong ^a   Tam, Angela ^a   Tan, Donghui ^a   Tang, Jiabin ^a   Tarnuzzer, Roy ^a   Tarvin, Katherine ^a   Taylor, Barry S ^a   Teebagy, Patrick ^a   Tenggara, Imelda ^a   Têtu, Bernard ^a   Tewari, Ashutosh ^a   Thiessen, Nina ^a   Thompson, Timothy ^a   Thorne, Leigh B ^a   Tirapelli, Daniela P ^a   Tomlins, Scott A ^a   Trevisan, Felipe Amstalden ^a   Troncoso, Patricia ^a   True, Lawrence D ^a   Tsourlakis, Maria Christina ^a   Tyekucheva, Svitlana ^a   Van Allen, Eliezer ^a   Van Den Berg, David J ^a   Veluvolu, Umadevi ^a   Verhaak, Roel ^a   Vocke, Cathy D ^a   Voet, Doug ^a   Wan, Yunhu ^a   Wang, Qingguo ^a   Wang, Wenyi ^a   Wang, Zhining ^a   Weinhold, Nils ^a   Weinstein, John N ^a   Weisenberger, Daniel J ^a   Wilkerson, Matthew D ^a   Wise, Lisa ^a   Witte, John ^a   Wu, Chia Chin ^a   Wu, Junyuan ^a   Wu, Ye ^a   Xu, Andrew W ^a   Yadav, Shalini S ^a   Yang, Liming ^a   Yang, Lixing ^a   Yau, Christina ^a   Ye, Huihui ^a   Yena, Peggy ^a   Zeng, Thomas ^a   Zenklusen, Jean C ^a   Zhang, Hailei ^a   Zhang, Jianhua ^a   Zhang, Jiashan ^a   Zhang, Wei ^a   Zhong, Yi ^a   Zhu, Kelsey ^a   Zmuda, Erik ^a   more..

^a NATIONAL CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANDROGEN RECEPTOR; PHOSPHATIDYLINOSITOL 3 KINASE; RAS PROTEIN;

ADULT; AGED; ARTICLE; DISEASE COURSE; DNA REPAIR; EPIGENETICS; GENE; GENE FUSION; GENE MUTATION; GENETIC HETEROGENEITY; HUMAN; MUTANT; PHENOTYPE; PRIMARY PROSTATE CANCER; PRIMARY TUMOR; PRIORITY JOURNAL; PROSTATE CANCER; TAXONOMY; GENE EXPRESSION REGULATION; GENETIC EPIGENESIS; GENETICS; MALE; METABOLISM; METASTASIS; MUTATION; PATHOLOGY; PROSTATE TUMOR; SIGNAL TRANSDUCTION;

DNA REPAIR; EPIGENESIS, GENETIC; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE FUSION; HUMANS; MALE; MUTATION; NEOPLASM METASTASIS; PHOSPHATIDYLINOSITOL 3-KINASES; PROSTATIC NEOPLASMS; RAS PROTEINS; RECEPTORS, ANDROGEN; SIGNAL TRANSDUCTION;

EID: 84946195510     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2015.10.025     Document Type: Article

References (92)

1. J. Ahn, Y. Yuan, G. Parmigiani, M.B. Suraokar, L. Diao, I.I. Wistuba, and W. Wang DeMix: deconvolution for mixed cancer transcriptomes using raw measured data Bioinformatics 29 2013 1865 1871
2. A.A. Al Olama, Z. Kote-Jarai, S.I. Berndt, D.V. Conti, F. Schumacher, Y. Han, S. Benlloch, D.J. Hazelett, Z. Wang, E. Saunders, et al. Breast and Prostate Cancer Cohort Consortium (BPC3) PRACTICAL (Prostate Cancer Association Group to Investigate Cancer-Associated Alterations in the Genome) Consortium COGS (Collaborative Oncological Gene-environment Study) Consortium GAME-ON/ELLIPSE Consortium A meta-analysis of 87,040 individuals identifies 23 new susceptibility loci for prostate cancer Nat. Genet. 46 2014 1103 1109
3. L.B. Alexandrov, S. Nik-Zainal, D.C. Wedge, S.A. Aparicio, S. Behjati, A.V. Biankin, G.R. Bignell, N. Bolli, A. Borg, A.L. Børresen-Dale, et al. Australian Pancreatic Cancer Genome Initiative ICGC Breast Cancer Consortium ICGC MMML-Seq Consortium ICGC PedBrain Signatures of mutational processes in human cancer Nature 500 2013 415 421
4. J. An, C. Wang, Y. Deng, L. Yu, and H. Huang Destruction of full-length androgen receptor by wild-type SPOP, but not prostate-cancer-associated mutants Cell Rep. 6 2014 657 669
5. E.S. Antonarakis, C. Lu, H. Wang, B. Luber, M. Nakazawa, J.C. Roeser, Y. Chen, T.A. Mohammad, Y. Chen, H.L. Fedor, and et al. AR-V7 and resistance to enzalutamide and abiraterone in prostate cancer N. Engl. J. Med. 371 2014 1028 1038
6. S.C. Baca, D. Prandi, M.S. Lawrence, J.M. Mosquera, A. Romanel, Y. Drier, K. Park, N. Kitabayashi, T.Y. MacDonald, M. Ghandi, and et al. Punctuated evolution of prostate cancer genomes Cell 153 2013 666 677
7. E. Baena, Z. Shao, D.E. Linn, K. Glass, M.J. Hamblen, Y. Fujiwara, J. Kim, M. Nguyen, X. Zhang, F.J. Godinho, and et al. ETV1 directs androgen metabolism and confers aggressive prostate cancer in targeted mice and patients Genes Dev. 27 2013 683 698
8. C.E. Barbieri, S.C. Baca, M.S. Lawrence, F. Demichelis, M. Blattner, J.P. Theurillat, T.A. White, P. Stojanov, E. Van Allen, N. Stransky, and et al. Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer Nat. Genet. 44 2012 685 689
9. M.F. Berger, M.S. Lawrence, F. Demichelis, Y. Drier, K. Cibulskis, A.Y. Sivachenko, A. Sboner, R. Esgueva, D. Pflueger, C. Sougnez, and et al. The genomic complexity of primary human prostate cancer Nature 470 2011 214 220
10. M. Blattner, D.J. Lee, C. O'Reilly, K. Park, T.Y. MacDonald, F. Khani, K.R. Turner, Y.L. Chiu, P.J. Wild, I. Dolgalev, and et al. SPOP mutations in prostate cancer across demographically diverse patient cohorts Neoplasia 16 2014 14 20
11. D. Blazek, J. Kohoutek, K. Bartholomeeusen, E. Johansen, P. Hulinkova, Z. Luo, P. Cimermancic, J. Ule, and B.M. Peterlin The Cyclin K/Cdk12 complex maintains genomic stability via regulation of expression of DNA damage response genes Genes Dev. 25 2011 2158 2172
12. S.T. Börno, A. Fischer, M. Kerick, M. Fälth, M. Laible, J.C. Brase, R. Kuner, A. Dahl, C. Grimm, B. Sayanjali, and et al. Genome-wide DNA methylation events in TMPRSS2-ERG fusion-negative prostate cancers implicate an EZH2-dependent mechanism with miR-26a hypermethylation Cancer Discov. 2 2012 1024 1035
13. P.C. Boutros, M. Fraser, N.J. Harding, R. de Borja, D. Trudel, E. Lalonde, A. Meng, P.H. Hennings-Yeomans, A. McPherson, V.Y. Sabelnykova, and et al. Spatial genomic heterogeneity within localized, multifocal prostate cancer Nat. Genet. 47 2015 736 745
14. S.E. Bowyer, A.D. Rao, M. Lyle, S. Sandhu, G.V. Long, G.A. McArthur, J.M. Raleigh, R.J. Hicks, and M. Millward Activity of trametinib in K601E and L597Q BRAF mutation-positive metastatic melanoma Melanoma Res. 24 2014 504 508
15. Cancer Genome Atlas Research Network Comprehensive molecular profiling of lung adenocarcinoma Nature 511 2014 543 550
16. S.L. Carter, K. Cibulskis, E. Helman, A. McKenna, H. Shen, T. Zack, P.W. Laird, R.C. Onofrio, W. Winckler, B.A. Weir, and et al. Absolute quantification of somatic DNA alterations in human cancer Nat. Biotechnol. 30 2012 413 421
17. U.R. Chandran, C. Ma, R. Dhir, M. Bisceglia, M. Lyons-Weiler, W. Liang, G. Michalopoulos, M. Becich, and F.A. Monzon Gene expression profiles of prostate cancer reveal involvement of multiple molecular pathways in the metastatic process BMC Cancer 7 2007 64
18. M.T. Chang, S. Asthana, S.P. Gao, B.H. Lee, J.S. Chapman, C. Kandoth, J. Gao, N.D. Socci, D.B. Solit, A.B. Olshen, and et al. Identifying recurrent mutations in cancer reveals widespread lineage diversity and mutational specificity Nat. Biotechnol. 2015 10.1038/nbt.3391 Published online November 9, 2015
19. C.S. Cooper, R. Eeles, D.C. Wedge, P. Van Loo, G. Gundem, L.B. Alexandrov, B. Kremeyer, A. Butler, A.G. Lynch, N. Camacho, et al. ICGC Prostate Group Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue Nat. Genet. 47 2015 367 372
20. M.R. Cooperberg, J.M. Broering, and P.R. Carroll Risk assessment for prostate cancer metastasis and mortality at the time of diagnosis J. Natl. Cancer Inst. 101 2009 878 887
21. A.V. D'Amico, R. Whittington, S.B. Malkowicz, D. Schultz, K. Blank, G.A. Broderick, J.E. Tomaszewski, A.A. Renshaw, I. Kaplan, C.J. Beard, and A. Wein Biochemical outcome after radical prostatectomy, external beam radiation therapy, or interstitial radiation therapy for clinically localized prostate cancer JAMA 280 1998 969 974
22. K.B. Dahlman, J. Xia, K. Hutchinson, C. Ng, D. Hucks, P. Jia, M. Atefi, Z. Su, S. Branch, P.L. Lyle, and et al. BRAF(L597) mutations in melanoma are associated with sensitivity to MEK inhibitors Cancer Discov. 2 2012 791 797
23. S.M. Dehm, L.J. Schmidt, H.V. Heemers, R.L. Vessella, and D.J. Tindall Splicing of a novel androgen receptor exon generates a constitutively active androgen receptor that mediates prostate cancer therapy resistance Cancer Res. 68 2008 5469 5477
24. M. Delahaye-Sourdeix, D. Anantharaman, M.N. Timofeeva, V. Gaborieau, A. Chabrier, M.P. Vallée, P. Lagiou, I. Holcátová, L. Richiardi, K. Kjaerheim, and et al. A rare truncating BRCA2 variant and genetic susceptibility to upper aerodigestive tract cancer J. Natl. Cancer Inst. 107 2015 djv037
25. F. Demichelis, S.R. Setlur, R. Beroukhim, S. Perner, J.O. Korbel, C.J. Lafargue, D. Pflueger, C. Pina, M.D. Hofer, A. Sboner, and et al. Distinct genomic aberrations associated with ERG rearranged prostate cancer Genes Chromosomes Cancer 48 2009 366 380
26. D.J. Farrugia, M.K. Agarwal, V.S. Pankratz, A.M. Deffenbaugh, D. Pruss, C. Frye, L. Wadum, K. Johnson, J. Mentlick, S.V. Tavtigian, and et al. Functional assays for classification of BRCA2 variants of uncertain significance Cancer Res. 68 2008 3523 3531
27. L.R. Ferguson, H. Chen, A.R. Collins, M. Connell, G. Damia, S. Dasgupta, M. Malhotra, A.K. Meeker, A. Amedei, A. Amin, and et al. Genomic instability in human cancer: Molecular insights and opportunities for therapeutic attack and prevention through diet and nutrition Semin. Cancer Biol. 2015 10.1016/j.semcancer.2015.03.005 Published online April 11, 2015
28. J. Ferlay, I. Soerjomataram, M. Ervik, R. Dikshit, S. Eser, C. Mathers, M. Rebelo, D.M. Parkin, D. Forman, and F. Bray GLOBOCAN 2012 v1.0, Cancer Incidence and Mortality Worldwide: IARC CancerBase No. 11 2013 International Agency for Research on Cancer Lyon, France
29. M.E. Figueroa, O. Abdel-Wahab, C. Lu, P.S. Ward, J. Patel, A. Shih, Y. Li, N. Bhagwat, A. Vasanthakumar, H.F. Fernandez, and et al. Leukemic IDH1 and IDH2 mutations result in a hypermethylation phenotype, disrupt TET2 function, and impair hematopoietic differentiation Cancer Cell 18 2010 553 567
30. T.W. Friedlander, R. Roy, S.A. Tomlins, V.T. Ngo, Y. Kobayashi, A. Azameera, M.A. Rubin, K.J. Pienta, A. Chinnaiyan, M.M. Ittmann, and et al. Common structural and epigenetic changes in the genome of castration-resistant prostate cancer Cancer Res. 72 2012 616 625
31. D. Gasi, H.A. van der Korput, H.C. Douben, A. de Klein, C.M. de Ridder, W.M. van Weerden, and J. Trapman Overexpression of full-length ETV1 transcripts in clinical prostate cancer due to gene translocation PLoS ONE 6 2011 e16332
32. C. Geng, B. He, L. Xu, C.E. Barbieri, V.K. Eedunuri, S.A. Chew, M. Zimmermann, R. Bond, J. Shou, C. Li, and et al. Prostate cancer-associated mutations in speckle-type POZ protein (SPOP) regulate steroid receptor coactivator 3 protein turnover Proc. Natl. Acad. Sci. USA 110 2013 6997 7002
33. C. Geng, K. Rajapakshe, S.S. Shah, J. Shou, V.K. Eedunuri, C. Foley, W. Fiskus, M. Rajendran, S.A. Chew, M. Zimmermann, and et al. Androgen receptor is the key transcriptional mediator of the tumor suppressor SPOP in prostate cancer Cancer Res. 74 2014 5631 5643
34. A.F. Ghiam, R.A. Cairns, J. Thoms, A. Dal Pra, O. Ahmed, A. Meng, T.W. Mak, and R.G. Bristow IDH mutation status in prostate cancer Oncogene 31 2012 3826
35. A. Gopalan, M.A. Leversha, J.M. Satagopan, Q. Zhou, H.A. Al-Ahmadie, S.W. Fine, J.A. Eastham, P.T. Scardino, H.I. Scher, S.K. Tickoo, and et al. TMPRSS2-ERG gene fusion is not associated with outcome in patients treated by prostatectomy Cancer Res. 69 2009 1400 1406
36. C.S. Grasso, Y.M. Wu, D.R. Robinson, X. Cao, S.M. Dhanasekaran, A.P. Khan, M.J. Quist, X. Jing, R.J. Lonigro, J.C. Brenner, and et al. The mutational landscape of lethal castration-resistant prostate cancer Nature 487 2012 239 243
37. G. Gundem, P. Van Loo, B. Kremeyer, L.B. Alexandrov, J.M. Tubio, E. Papaemmanuil, D.S. Brewer, H.M. Kallio, G. Högnäs, M. Annala, et al. ICGC Prostate UK Group The evolutionary history of lethal metastatic prostate cancer Nature 520 2015 353 357
38. G. Guo, X. Sun, C. Chen, S. Wu, P. Huang, Z. Li, M. Dean, Y. Huang, W. Jia, Q. Zhou, and et al. Whole-genome and whole-exome sequencing of bladder cancer identifies frequent alterations in genes involved in sister chromatid cohesion and segregation Nat. Genet. 45 2013 1459 1463
39. H.V. Heemers, and D.J. Tindall Androgen receptor (AR) coregulators: a diversity of functions converging on and regulating the AR transcriptional complex Endocr. Rev. 28 2007 778 808
40. H. Hieronymus, J. Lamb, K.N. Ross, X.P. Peng, C. Clement, A. Rodina, M. Nieto, J. Du, K. Stegmaier, S.M. Raj, and et al. Gene expression signature-based chemical genomic prediction identifies a novel class of HSP90 pathway modulators Cancer Cell 10 2006 321 330
41. H. Hieronymus, N. Schultz, A. Gopalan, B.S. Carver, M.T. Chang, Y. Xiao, A. Heguy, K. Huberman, M. Bernstein, M. Assel, and et al. Copy number alteration burden predicts prostate cancer relapse Proc. Natl. Acad. Sci. USA 111 2014 11139 11144
42. D.H. Hovelson, A.S. McDaniel, A.K. Cani, B. Johnson, K. Rhodes, P.D. Williams, S. Bandla, G. Bien, P. Choppa, F. Hyland, and et al. Development and validation of a scalable next-generation sequencing system for assessing relevant somatic variants in solid tumors Neoplasia 17 2015 385 399
43. R. Huether, L. Dong, X. Chen, G. Wu, M. Parker, L. Wei, J. Ma, M.N. Edmonson, E.K. Hedlund, M.C. Rusch, and et al. The landscape of somatic mutations in epigenetic regulators across 1,000 paediatric cancer genomes Nat. Commun. 5 2014 3630
44. H.J. Jin, J.C. Zhao, I. Ogden, R.C. Bergan, and J. Yu Androgen receptor-independent function of FoxA1 in prostate cancer metastasis Cancer Res. 73 2013 3725 3736
45. M.R. Kang, M.S. Kim, J.E. Oh, Y.R. Kim, S.Y. Song, S.I. Seo, J.Y. Lee, N.J. Yoo, and S.H. Lee Mutational analysis of IDH1 codon 132 in glioblastomas and other common cancers Int. J. Cancer 125 2009 353 355
46. S. Karanika, T. Karantanos, L. Li, P.G. Corn, and T.C. Thompson DNA damage response and prostate cancer: defects, regulation and therapeutic implications Oncogene 34 2014 2815 2822
47. M.W. Kattan, J.A. Eastham, A.M. Stapleton, T.M. Wheeler, and P.T. Scardino A preoperative nomogram for disease recurrence following radical prostatectomy for prostate cancer J. Natl. Cancer Inst. 90 1998 766 771
48. E. Khurana, Y. Fu, V. Colonna, X.J. Mu, H.M. Kang, T. Lappalainen, A. Sboner, L. Lochovsky, J. Chen, A. Harmanci, et al. 1000 Genomes Project Consortium Integrative annotation of variants from 1092 humans: application to cancer genomics Science 342 2013 1235587
49. J.H. Kim, S.M. Dhanasekaran, J.R. Prensner, X. Cao, D. Robinson, S. Kalyana-Sundaram, C. Huang, S. Shankar, X. Jing, M. Iyer, and et al. Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer Genome Res. 21 2011 1028 1041
50. M. Kluth, J. Hesse, A. Heinl, A. Krohn, S. Steurer, H. Sirma, R. Simon, P.S. Mayer, U. Schumacher, K. Grupp, and et al. Genomic deletion of MAP3K7 at 6q12-22 is associated with early PSA recurrence in prostate cancer and absence of TMPRSS2:ERG fusions Mod. Pathol. 26 2013 975 983
51. Y. Kobayashi, D.M. Absher, Z.G. Gulzar, S.R. Young, J.K. McKenney, D.M. Peehl, J.D. Brooks, R.M. Myers, and G. Sherlock DNA methylation profiling reveals novel biomarkers and important roles for DNA methyltransferases in prostate cancer Genome Res. 21 2011 1017 1027
52. L.P. Kunju, S. Carskadon, J. Siddiqui, S.A. Tomlins, A.M. Chinnaiyan, and N. Palanisamy Novel RNA hybridization method for the in situ detection of ETV1, ETV4, and ETV5 gene fusions in prostate cancer Appl. Immunohistochem. Mol. Morphol. 22 2014 e32 e40
53. E. Lalonde, A.S. Ishkanian, J. Sykes, M. Fraser, H. Ross-Adams, N. Erho, M.J. Dunning, S. Halim, A.D. Lamb, N.C. Moon, and et al. Tumour genomic and microenvironmental heterogeneity for integrated prediction of 5-year biochemical recurrence of prostate cancer: a retrospective cohort study Lancet Oncol. 15 2014 1521 1532
54. J. Lapointe, C. Li, C.P. Giacomini, K. Salari, S. Huang, P. Wang, M. Ferrari, T. Hernandez-Boussard, J.D. Brooks, and J.R. Pollack Genomic profiling reveals alternative genetic pathways of prostate tumorigenesis Cancer Res. 67 2007 8504 8510
55. M.S. Lawrence, P. Stojanov, P. Polak, G.V. Kryukov, K. Cibulskis, A. Sivachenko, S.L. Carter, C. Stewart, C.H. Mermel, S.A. Roberts, and et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes Nature 499 2013 214 218
56. M.S. Lawrence, P. Stojanov, C.H. Mermel, J.T. Robinson, L.A. Garraway, T.R. Golub, M. Meyerson, S.B. Gabriel, E.S. Lander, and G. Getz Discovery and saturation analysis of cancer genes across 21 tumour types Nature 505 2014 495 501
57. C. Lin, L. Yang, B. Tanasa, K. Hutt, B.G. Ju, K. Ohgi, J. Zhang, D.W. Rose, X.D. Fu, C.K. Glass, and M.G. Rosenfeld Nuclear receptor-induced chromosomal proximity and DNA breaks underlie specific translocations in cancer Cell 139 2009 1069 1083
58. J. Lindberg, A. Kristiansen, P. Wiklund, H. Grönberg, and L. Egevad Tracking the origin of metastatic prostate cancer Eur. Urol. 67 2015 819 822
59. S. Mahapatra, E.W. Klee, C.Y. Young, Z. Sun, R.E. Jimenez, G.G. Klee, D.J. Tindall, and K.V. Donkena Global methylation profiling for risk prediction of prostate cancer Clin. Cancer Res. 18 2012 2882 2895
60. R.S. Mani, S.A. Tomlins, K. Callahan, A. Ghosh, M.K. Nyati, S. Varambally, N. Palanisamy, and A.M. Chinnaiyan Induced chromosomal proximity and gene fusions in prostate cancer Science 326 2009 1230
61. E.R. Mardis, L. Ding, D.J. Dooling, D.E. Larson, M.D. McLellan, K. Chen, D.C. Koboldt, R.S. Fulton, K.D. Delehaunty, S.D. McGrath, and et al. Recurring mutations found by sequencing an acute myeloid leukemia genome N. Engl. J. Med. 361 2009 1058 1066
62. S.T. Martin, H. Matsubayashi, C.D. Rogers, J. Philips, F.J. Couch, K. Brune, C.J. Yeo, S.E. Kern, R.H. Hruban, and M. Goggins Increased prevalence of the BRCA2 polymorphic stop codon K3326X among individuals with familial pancreatic cancer Oncogene 24 2005 3652 3656
63. J. Mateo, E. Hall, S. Sandhu, A.G. Omlin, S. Miranda, S. Carreira, J. Goodall, A. Gillman, H. Mossop, C. Ralph, and et al. LBA20 - Antitumour activity of the PARP inhibitor olaparib in unselected sporadic castration-resistant prostate cancer (CRPC) in the TOPARP trial Ann. Oncol. 25 2014 1 41
64. E.A. Mostaghel, L. Geng, I. Holcomb, I.M. Coleman, J. Lucas, L.D. True, and P.S. Nelson Variability in the androgen response of prostate epithelium to 5alpha-reductase inhibition: implications for prostate cancer chemoprevention Cancer Res. 70 2010 1286 1295
65. H. Noushmehr, D.J. Weisenberger, K. Diefes, H.S. Phillips, K. Pujara, B.P. Berman, F. Pan, C.E. Pelloski, E.P. Sulman, K.P. Bhat, et al. Cancer Genome Atlas Research Network Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma Cancer Cell 17 2010 510 522
66. N. Palanisamy, B. Ateeq, S. Kalyana-Sundaram, D. Pflueger, K. Ramnarayanan, S. Shankar, B. Han, Q. Cao, X. Cao, K. Suleman, and et al. Rearrangements of the RAF kinase pathway in prostate cancer, gastric cancer and melanoma Nat. Med. 16 2010 793 798
67. C. Parikh, V. Janakiraman, W.I. Wu, C.K. Foo, N.M. Kljavin, S. Chaudhuri, E. Stawiski, B. Lee, J. Lin, H. Li, and et al. Disruption of PH-kinase domain interactions leads to oncogenic activation of AKT in human cancers Proc. Natl. Acad. Sci. USA 109 2012 19368 19373
68. P.L. Paris, A. Andaya, J. Fridlyand, A.N. Jain, V. Weinberg, D. Kowbel, J.H. Brebner, J. Simko, J.E. Watson, S. Volik, and et al. Whole genome scanning identifies genotypes associated with recurrence and metastasis in prostate tumors Hum. Mol. Genet. 13 2004 1303 1313
69. K.L. Penney, M.J. Stampfer, J.L. Jahn, J.A. Sinnott, R. Flavin, J.R. Rider, S. Finn, E. Giovannucci, H.D. Sesso, M. Loda, and et al. Gleason grade progression is uncommon Cancer Res. 73 2013 5163 5168
70. A. Pettersson, R.E. Graff, S.R. Bauer, M.J. Pitt, R.T. Lis, E.C. Stack, N.E. Martin, L. Kunz, K.L. Penney, A.H. Ligon, and et al. The TMPRSS2:ERG rearrangement, ERG expression, and prostate cancer outcomes: a cohort study and meta-analysis Cancer Epidemiol. Biomarkers Prev. 21 2012 1497 1509
71. D. Pflueger, S. Terry, A. Sboner, L. Habegger, R. Esgueva, P.C. Lin, M.A. Svensson, N. Kitabayashi, B.J. Moss, T.Y. MacDonald, and et al. Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing Genome Res. 21 2011 56 67
72. D. Prandi, S.C. Baca, A. Romanel, C.E. Barbieri, J.M. Mosquera, J. Fontugne, H. Beltran, A. Sboner, L.A. Garraway, M.A. Rubin, and F. Demichelis Unraveling the clonal hierarchy of somatic genomic aberrations Genome Biol. 15 2014 439
73. C.C. Pritchard, C. Morrissey, A. Kumar, X. Zhang, C. Smith, I. Coleman, S.J. Salipante, J. Milbank, M. Yu, W.M. Grady, and et al. Complex MSH2 and MSH6 mutations in hypermutated microsatellite unstable advanced prostate cancer Nat. Commun. 5 2014 4988
74. G. Quon, S. Haider, A.G. Deshwar, A. Cui, P.C. Boutros, and Q. Morris Computational purification of individual tumor gene expression profiles leads to significant improvements in prognostic prediction Genome Med. 5 2013 29
75. D. Robinson, E.M. Van Allen, Y.M. Wu, N. Schultz, R.J. Lonigro, J.M. Mosquera, B. Montgomery, M.E. Taplin, C.C. Pritchard, G. Attard, and et al. Integrative clinical genomics of advanced prostate cancer Cell 161 2015 1215 1228
76. L.U. Rodrigues, L. Rider, C. Nieto, L. Romero, A. Karimpour-Fard, M. Loda, M.S. Lucia, M. Wu, L. Shi, A. Cimic, and et al. Coordinate loss of MAP3K7 and CHD1 promotes aggressive prostate cancer Cancer Res. 75 2015 1021 1034
77. D. Rohle, J. Popovici-Muller, N. Palaskas, S. Turcan, C. Grommes, C. Campos, J. Tsoi, O. Clark, B. Oldrini, E. Komisopoulou, and et al. An inhibitor of mutant IDH1 delays growth and promotes differentiation of glioma cells Science 340 2013 626 630
78. A. Sboner, L. Habegger, D. Pflueger, S. Terry, D.Z. Chen, J.S. Rozowsky, A.K. Tewari, N. Kitabayashi, B.J. Moss, M.S. Chee, and et al. FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data Genome Biol. 11 2010 R104
79. E.M. Schaeffer, L. Marchionni, Z. Huang, B. Simons, A. Blackman, W. Yu, G. Parmigiani, and D.M. Berman Androgen-induced programs for prostate epithelial growth and invasion arise in embryogenesis and are reactivated in cancer Oncogene 27 2008 7180 7191
80. S. Schwartz, J. Wongvipat, C.B. Trigwell, U. Hancox, B.S. Carver, V. Rodrik-Outmezguine, M. Will, P. Yellen, E. de Stanchina, J. Baselga, and et al. Feedback suppression of PI3Kα signaling in PTEN-mutated tumors is relieved by selective inhibition of PI3Kβ Cancer Cell 27 2015 109 122
81. R. Shen, A.B. Olshen, and M. Ladanyi Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis Bioinformatics 25 2009 2906 2912
82. R.L. Siegel, K.D. Miller, and A. Jemal Cancer statistics, 2015 CA Cancer J. Clin. 65 2015 5 29
83. B.S. Taylor, N. Schultz, H. Hieronymus, A. Gopalan, Y. Xiao, B.S. Carver, V.K. Arora, P. Kaushik, E. Cerami, B. Reva, and et al. Integrative genomic profiling of human prostate cancer Cancer Cell 18 2010 11 22
84. F. Tirode, D. Surdez, X. Ma, M. Parker, M.C. Le Deley, A. Bahrami, Z. Zhang, E. Lapouble, S. Grossetête-Lalami, M. Rusch, et al. St. Jude Children's Research Hospital-Washington University Pediatric Cancer Genome Project and the International Cancer Genome Consortium Genomic landscape of Ewing sarcoma defines an aggressive subtype with co-association of STAG2 and TP53 mutations Cancer Discov. 4 2014 1342 1353
85. S.A. Tomlins, D.R. Rhodes, S. Perner, S.M. Dhanasekaran, R. Mehra, X.W. Sun, S. Varambally, X. Cao, J. Tchinda, R. Kuefer, and et al. Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer Science 310 2005 644 648
86. S.A. Tomlins, B. Laxman, S.M. Dhanasekaran, B.E. Helgeson, X. Cao, D.S. Morris, A. Menon, X. Jing, Q. Cao, B. Han, and et al. Distinct classes of chromosomal rearrangements create oncogenic ETS gene fusions in prostate cancer Nature 448 2007 595 599
87. S.A. Tomlins, A. Bjartell, A.M. Chinnaiyan, G. Jenster, R.K. Nam, M.A. Rubin, and J.A. Schalken ETS gene fusions in prostate cancer: from discovery to daily clinical practice Eur. Urol. 56 2009 275 286
88. S.A. Tomlins, M. Alshalalfa, E. Davicioni, N. Erho, K. Yousefi, S. Zhao, Z. Haddad, R.B. Den, A.P. Dicker, B.J. Trock, and et al. Characterization of 1577 primary prostate cancers reveals novel biological and clinicopathologic insights into molecular subtypes Eur. Urol. 68 2015 555 567
89. H. van Dekken, P.L. Paris, D.G. Albertson, J.C. Alers, A. Andaya, D. Kowbel, T.H. van der Kwast, D. Pinkel, F.H. Schröder, K.J. Vissers, and et al. Evaluation of genetic patterns in different tumor areas of intermediate-grade prostatic adenocarcinomas by high-resolution genomic array analysis Genes Chromosomes Cancer 39 2004 249 256
90. K. Wang, D. Singh, Z. Zeng, S.J. Coleman, Y. Huang, G.L. Savich, X. He, P. Mieczkowski, S.A. Grimm, C.M. Perou, and et al. MapSplice: accurate mapping of RNA-seq reads for splice junction discovery Nucleic Acids Res. 38 2010 e178
91. X.S. Wang, S. Shankar, S.M. Dhanasekaran, B. Ateeq, A.T. Sasaki, X. Jing, D. Robinson, Q. Cao, J.R. Prensner, A.K. Yocum, and et al. Characterization of KRAS rearrangements in metastatic prostate cancer Cancer Discov. 1 2011 35 43
92. P.A. Watson, Y.F. Chen, M.D. Balbas, J. Wongvipat, N.D. Socci, A. Viale, K. Kim, and C.L. Sawyers Constitutively active androgen receptor splice variants expressed in castration-resistant prostate cancer require full-length androgen receptor Proc. Natl. Acad. Sci. USA 107 2010 16759 16765