The genomic landscape of prostate cancer

Frontiers in Endocrinology

Volumn 3, Issue MAY, 2012, Pages

  Baca, Sylvan C ^a,b,c   Garraway, Levi A ^a,b,c  

^a HARVARD MEDICAL SCHOOL   (United States)

^b DANA FARBER CANCER INSTITUTE   (United States)

^c BROAD INSTITUTE OF MIT AND HARVARD   (United States)

Author keywords

Genome sequencing; Genomic; Prostate cancer

Indexed keywords

EID: 84873696198     PISSN: None     EISSN: 16642392     Source Type: Journal    
DOI: 10.3389/fendo.2012.00069     Document Type: Short Survey

References (99)

1. Agell, L., Hernandez, S., Salido, M., De Muga, S., Juanpere, N., Arumi-Uria, M., Menendez, S., Lorenzo, M., Lorente, J. A., Serrano, S., and Lloreta, J. (2011). PI3K signaling pathway is activated by PIK3CA mRNA overex-pression and copy gain in prostate tumors, but PIK3CA, BRAF, KRAS and AKT1 mutations are infrequent events. Mod. Pathol. 24, 443-452.
2. Ahmad, I., Patel, R., Singh, L. B., Nixon, C., Seywright, M., Barnetson, R. J., Brunton, V. G., Muller, W. J., Edwards, J., Sansom, O. J., and Leung, H. Y. (2011). HER2 overcomes PTEN (loss)-induced senescence to cause aggressive prostate cancer. Proc. Natl. Acad. Sci. U.S.A. 108, 16392-16397.
3. Alers, J. C., Rochat, J., Krijtenburg, P. J., Hop, W. C., Kranse, R., Rosenberg, C., Tanke, H. J., Schroder, F. H., and Van Dekken, H. (2000). Identification of genetic markers for prostatic cancer progression. Lab. Invest. 80, 931-942.
4. Andreoiu, M., and Cheng, L. (2010). Multifocal prostate cancer: biologic, prognostic, and therapeutic implications. Hum. Pathol. 41, 781-793.
5. Asatiani, E., Huang, W. X., Wang, A., Rodriguez Ortner, E., Cavalli, L. R., Haddad, B. R., and Gelmann, E. P. (2005). Deletion, methylation, and expression of the NKX3.1 suppressor gene in primary human prostate cancer. Cancer Res. 65, 1164-1173.
6. Barbieri, C. E., Baca, S. C., Lawrence, M. S., Demichelis, F., Blattner, M., Theurillat, J.-P., White, T. A., Sto-janov, P., Van Allen, E., Stransky, N., Nickerson, E., Chae, S.-S., Boysen, G., Auclair, D., Onofrio, R. C., Park, K., Kitabayashi, N., MacDonald, T. Y., Sheikh, K., Vuong, T., Guiducci, C., Cibulskis, K., Sivachenko, A., Carter, S. L., Saksena, G., Voet, D., Hussain, W M., Ramos, A. H., Winckler, W., Redman, M. C., Ardlie, K., Tewari, A. K., Mosquera, J. M., Rupp, N., Wild, P. J., Moch, H., Morrissey, C., Nelson, P. S., Kantoff, P. W., Gabriel, S. B., Golub, T. R., Mey-erson, M., Lander, E. S., Getz, G., Rubin, M. A., and Garraway, L. A. (2012). Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer. Nat. Genet. (in press).
7. Berger, M. F., Lawrence, M. S., Demichelis, F., Drier, Y., Cibulskis, K., Sivachenko, A. Y., Sboner, A., Esgueva, R., Pflueger, D., Sougnez, C., Onofrio, R., Carter, S. L., Park, K., Habegger, L., Ambrogio, L., Fen-nell, T., Parkin, M., Saksena, G., Voet, D., Ramos, A. H., Pugh, T. J., Wilkinson, J., Fisher, S., Winckler, W., Mahan, S., Ardlie, K., Baldwin, J., Simons, J. W., Kitabayashi, N., Mac-donald, T. Y., Kantoff, P. W., Chin, L., Gabriel, S. B., Gerstein, M. B., Golub, T. R., Meyerson, M., Tewari, A., Lander, E. S., Getz, G., Rubin, M. A., and Garraway, L. A. (2011). The genomic complexity of primary human prostate cancer. Nature 470, 214-220.
8. Beroukhim, R., Getz, G., Nghiemphu, L., Barretina, J., Hsueh, T., Linhart, D., Vivanco, I., Lee, J. C., Huang, J. H., Alexander, S., Du, J., Kau, T., Thomas, R. K., Shah, K., Soto, H., Perner, S., Prensner, J., Debiasi, R. M., Demichelis, F., Hatton, C., Rubin, M. A., Garraway, L. A., Nelson, S. F., Liau, L., Mischel, P. S., Cloughesy, T. F., Meyerson, M., Golub, T. A., Lander, E. S., Mellinghoff, I. K., and Sellers, W R. (2007). Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc. Natl. Acad. Sci. U.S.A. 104, 20007-20012.
9. Bhatia-Gaur, R., Donjacour, A. A., Sci-avolino, P. J., Kim, M., Desai, N., Young, P., Norton, C. R., Gridley, T., Cardiff, R. D., Cunha, G. R., Abate-Shen, C., and Shen, M. M. (1999). Roles for Nkx3.1 in prostate development and cancer. Genes Dev. 13, 966-977.
10. Bookstein, R., Macgrogan, D., Hilsen-beck, S. G., Sharkey, F., and Allred, D. C. (1993). p53 is mutated in a subset of advanced-stage prostate cancers. Cancer Res. 53, 3369-3373.
11. Boormans, J. L., Korsten, H., Ziel-Van Der Made, A. C., Van Leenders, G. J., Verhagen, P. C., and Trapman, J. (2010). E17K substitution in AKT1 in prostate cancer. Br. J. Cancer 102, 1491-1494.
12. Bowen, C., and Gelmann, E. P. (2010). NKX3.1 activates cellular response to DNA damage. Cancer Res. 70, 3089-3097.
13. Brenner, J. C., Ateeq, B., Li, Y., Yocum, A. K., Cao, Q., Asangani, I. A., Patel, S., Wang, X., Liang, H., Yu, J., Palanisamy, N., Siddiqui, J., Yan, W., Cao, X., Mehra, R., Sabolch, A., Basrur, V., Lonigro, R. J., Yang, J., Tomlins, S. A., Maher, C. A., Elenitoba-Johnson, K. S., Hussain, M., Navone, N. M., Pienta, K. J., Varambally, S., Feng, F. Y., and Chinnaiyan, A. M. (2011). Mechanistic rationale for inhibition of poly(ADP-ribose) polymerase in ETS gene fusion-positive prostate cancer. Cancer Cell 19, 664-678.
14. Brewster, S. F., Browne, S., and Brown, K. W. (1994). Somatic allelic loss at the DCC, APC, nm23-H1 and p53 tumor suppressor gene loci in human prostatic carcinoma. J. Urol. 151, 1073-1077.
15. Brothman, A. R., Maxwell, T. M., Cui, J., Deubler, D.A., andZhu, X. L. (1999). Chromosomal clues to the development of prostate tumors. Prostate 38, 303-312.
16. Cai, C. Q., Peng, Y., Buckley, M. T., Wei, J., Chen, F., Liebes, L., Gerald, W L., Pincus, M. R., Osman, I., and Lee, P. (2008). Epidermal growth factor receptor activation in prostate cancer by three novel missense mutations. Oncogene 27, 3201-3210.
17. Cairns, P., Okami, K., Halachmi, S., Halachmi, N., Esteller, M., Herman, J. G., Jen, J., Isaacs, W. B., Bova, G. S., and Sidransky, D. (1997). Frequent inactivation of PTEN/MMAC1 in primary prostate cancer. Cancer Res. 57, 4997-5000.
18. Chen, M., Pratt, C. P., Zeeman, M. E., Schultz, N., Taylor, B. S., O'Neill, A., Castillo-Martin, M., Nowak, D. G., Naguib, A., Grace, D. M., Murn, J., Navin, N., Atwal, G. S., Sander, C., Gerald, W. L., Cordon-Cardo, C., Newton, A. C., Carver, B. S., and Trotman, L. C. (2011). Identification of PHLPP1 as a tumor suppressor reveals the role of feedback activation in PTEN-mutant prostate cancer progression. Cancer Cell 20, 173-186.
19. Chen, Y., Wang, J., Fraig, M. M., Met-calf, J., Turner, W R., Bissada, N. K., Watson, D. K., and Schwein-fest, C. W (2001). Defects of DNA mismatch repair in human prostate cancer. Cancer Res. 61, 4112-4121.
20. Chen, Z., Trotman, L. C., Shaffer, D., Lin, H. K., Dotan, Z. A., Niki, M., Koutcher, J. A., Scher, H. I., Lud-wig, T., Gerald, W., Cordon-Cardo, C., and Pandolfi, P. P. (2005). Crucial role of p53-dependent cellular senescence in suppression of Pten-deficient tumorigenesis. Nature 436, 725-730.
21. Chesire, D. R., Ewing, C. M., Sauvageot, J., Bova, G. S., and Isaacs, W B. (2000). Detection and analysis of beta-catenin mutations in prostate cancer. Prostate 45, 323-334.
22. Cho, N. Y., Choi, M., Kim, B. H., Cho, Y M., Moon, K. C., and Kang, G. H. (2006). BRAF and KRAS mutations in prostatic adenocarcinoma. Int. J. Cancer 119, 1858-1862.
23. Cronauer, M. V., Schulz, W A., Acker-mann, R., and Burchardt, M. (2005). Effects of WNT/beta-catenin pathway activation on signaling through T-cell factor and androgen receptor in prostate cancer cell lines. Int. J. Oncol. 26, 1033-1040.
24. Dahiya, R., Lee, C., Mccarville, J., Hu, W., Kaur, G., and Deng, G. (1997). High frequency of genetic instability of microsatellites in human prostatic adenocarcinoma. Int. J. Cancer 72, 762-767.
25. Demichelis, F., Fall, K., Perner, S., Andren, O., Schmidt, F., Setlur, S. R., Hoshida, Y., Mosquera, J. M., Pawi-tan, Y., Lee, C., Adami, H. O., Mucci, L. A., Kantoff, P. W., Andersson, S. O., Chinnaiyan, A. M., Johansson, J. E., and Rubin, M. A. (2007). TMPRSS2:ERG gene fusion associated with lethal prostate cancer in a watchful waiting cohort. Oncogene 26, 4596-4599.
26. DiCristofano, A., DeAcetis, M., Koff, A., Cordon-Cardo, C., and Pandolfi, P. P. (2001). Pten and p27KIP1 cooperate in prostate cancer tumor suppression in the mouse. Nat. Genet. 27, 222-224.
27. Dong, X. Y., Chen, C., Sun, X., Guo, P., Vessella, R. L., Wang, R. X., Chung, L. W., Zhou, W., and Dong, J. T. (2006). FOXO1A is a candidate for the 13q14 tumor suppressor gene inhibiting androgen receptor signaling in prostate cancer. Cancer Res. 66, 6998-7006.
28. Dreher, T., Zentgraf, H., Abel, U., Kap-peler, A., Michel, M. S., Bleyl, U., and Grobholz, R. (2004). Reduction of PTEN and p27kip1 expression correlates with tumor grade in prostate cancer. Analysis in radical prostatectomy specimens and needle biopsies. Virchows Arch. 444, 509-517.
29. Eastham, J. A., Stapleton, A. M., Gousse, A. E., Timme, T. L., Yang, G., Slawin, K. M., Wheeler, T. M., Scardino, P. T., and Thompson, T. C. (1995). Association of p53 mutations with metastatic prostate cancer. Clin. Cancer Res. 1, 1111-1118.
30. Edwards, J., Krishna, N. S., Witton, C. J., and Bartlett, J. M. (2003). Gene amplifications associated with the development of hormone-resistant prostate cancer. Clin. Cancer Res. 9, 5271-5281.
31. Emmert-Buck, M. R., Vocke, C. D., Pozzatti, R. O., Duray, P. H., Jennings, S. B., Florence, C. D., Zhuang, Z., Bostwick, D. G., Liotta, L. A., and Linehan, W M. (1995). Allelic loss on chromosome 8p12-21 in microdissected prostatic intraep-ithelial neoplasia. Cancer Res. 55, 2959-2962.
32. Febbo, P. G. (2009). Genomic approaches to outcome prediction in prostate cancer. Cancer 115, 3046-3057.
33. Gaddipati, J. P., Mcleod, D. G., Heiden-berg, H. B., Sesterhenn, I. A., Finger, M. J., Moul, J. W., and Srivastava, S. (1994). Frequent detection of codon 877 mutation in the androgen receptor gene in advanced prostate cancers. Cancer Res. 54, 2861-2864.
34. Gao, H., Ouyang, X., Banach-Petrosky, W. A., Gerald, W. L., Shen, M. M., and Abate-Shen, C. (2006). Combinatorial activities of Akt and B-Raf/Erk signaling in a mouse model of androgen-independent prostate cancer. Proc. Natl. Acad. Sci. U.S.A. 103, 14477-14482.
35. Gioeli, D., Mandell, J. W., Petroni, G. R., Frierson, H. F. Jr., and Weber, M. J. (1999). Activation of mitogen-activated protein kinase associated with prostate cancer progression. Cancer Res. 59, 279-284.
36. Glinsky, G. V., Glinskii, A. B., Stephen-son, A. J., Hoffman, R. M., and Gerald, W.L. (2004). Gene expression profiling predicts clinical outcome of prostate cancer. J. Clin. Invest. 113, 913-923.
37. Gray, I. C., Stewart, L. M., Phillips, S. M., Hamilton, J. A., Gray, N. E., Watson, G. J., Spurr, N. K., and Snary, D. (1998). Mutation and expression analysis of the putative prostate tumour-suppressor gene PTEN. Br. J. Cancer 78, 1296-1300.
38. Greenman, C., Stephens, P., Smith, R., Dalgliesh, G. L., Hunter, C., Bignell, G., Davies, H., Teague, J., Butler, A., Stevens, C., Edkins, S., O'Meara, S., Vastrik, I., Schmidt, E. E., Avis, T., Barthorpe, S., Bhamra, G., Buck, G., Choudhury, B., Clements, J., Cole, J., Dicks, E., Forbes, S., Gray, K., Halliday, K., Harrison, R., Hills, K., Hinton, J., Jenkinson, A., Jones, D., Menzies, A., Mironenko, T., Perry, J., Raine, K., Richardson, D., Shepherd, R., Small, A., Tofts, C., Varian, J., Webb, T., West, S., Widaa, S., Yates, A., Cahill, D. P., Louis, D. N., Gold-straw, P., Nicholson, A. G., Brasseur, F., Looijenga, L., Weber, B. L., Chiew, Y E., Defazio, A., Greaves, M. F., Green, A. R., Campbell, P., Birney, E., Easton, D. F., Chenevix-Trench, G., Tan, M. H., Khoo, S. K., Teh, B. T., Yuen, S. T., Leung, S. Y., Wooster, R., Futreal, P. A., and Stratton, M. R. (2007). Patterns of somatic mutation in human cancer genomes. Nature 446, 153-158.
39. Haffner, M. C., Aryee, M. J., Toubaji, A., Esopi, D. M., Albadine, R., Gurel, B., Isaacs, W. B., Bova, G. S., Liu, W., Xu, J., Meeker, A. K., Netto, G., De Marzo, A. M., Nelson, W G., and Yegnasubramanian, S. (2010). Androgen-induced TOP2B-mediated double-strand breaks and prostate cancer gene rearrangements. Nat. Genet. 42, 668-675.
40. Harbour, J. W., Onken, M. D., Rober-son, E. D., Duan, S., Cao, L., Worley, L. A., Council, M. L., Matatall, K. A., Helms, C., and Bowcock, A. M. (2010). Frequent mutation of BAP1 in metastasizing uveal melanomas. Science 330, 1410-1413.
41. Heidenberg, H. B., Sesterhenn, I. A., Gaddipati, J. P., Weghorst, C. M., Buzard, G. S., Moul, J. W., and Srivastava, S. (1995). Alteration of the tumor suppressor gene p53 in a high fraction of hormone refractory prostate cancer. J. Urol. 154, 414-421.
42. Holcomb, I. N., Young, J. M., Cole-man, I. M., Salari, K., Grove, D. I., Hsu, L., True, L. D., Roudier, M. P., Morrissey, C. M., Higano, C. S., Nelson, P. S., Vessella, R. L., and Trask, B. J. (2009). Comparative analyses of chromosome alterations in soft-tissue metastases within and across patients with castration-resistant prostate cancer. Cancer Res. 69, 7793-7802.
43. Hyytinen, E. R., Frierson, H. F. Jr., Boyd, J. C., Chung, L. W., and Dong, J. T. (1999). Three distinct regions of allelic loss at 13q14, 13q21-22, and 13q33 in prostate cancer. Genes Chromosomes Cancer 25, 108-114.
44. Jemal, A., Bray, F., Center, M. M., Ferlay, J., Ward, E., and Forman, D. (2011). Global cancer statistics. CA Cancer J. Clin. 61, 69-90.
45. Jenkins, R. B., Qian, J., Lieber, M. M., and Bostwick, D. G. (1997). and American men. Prostate 30, 53-57.
46. Kumar, A., White, T. A., Mackenzie, A. P., Clegg, N., Lee, C., Dumpit, R. F., Coleman, I., Ng, S. B., Sali-pante, S. J., Rieder, M. J., Nick-erson, D. A., Corey, E., Lange, P. H., Morrissey, C., Vessella, R. L., Nelson, P. S., and Shendure, J. (2011). Exome sequencing identifies a spectrum of mutation frequencies in advanced and lethal prostate cancers. Proc. Natl. Acad. Sci. U.S.A. 108, 17087-17092.
47. Kumar-Sinha, C., Tomlins, S. A., and Chinnaiyan, A. M. (2008). Recurrent gene fusions in prostate cancer. Nat. Rev. Cancer8, 497-511.
48. Kwabi-Addo, B., Wang, J., Erdem, H., Vaid, A., Castro, P., Ayala, G., and Ittmann, M. (2004). The expression of Sprouty 1, an inhibitor of fibroblast growth factor signal transduction, is decreased in human prostate cancer. Cancer Res. 64, 4728-4735.
49. Lapointe, J., Li, C., Giacomini, C. P., Salari, K., Huang, S., Wang, P., Ferrari, M., Hernandez-Boussard, T., Bro oks, J. D., and Pollack, J. R. (2007). Genomic profiling reveals alternative genetic pathways of prostate tumorigenesis. Cancer Res. 67, 8504-8510.
50. Lapointe, J., Li, C., Higgins, J. P., Van De Rijn, M., Bair, E., Montgomery, K., Ferrari, M., Egevad, L., Ray-ford, W., Bergerheim, U., Ekman, P., Demarzo, A. M., Tibshirani, R., Bot-stein, D., Brown, P. O., Brooks, J. D., and Pollack, J. R. (2004). Gene expression profiling identifies clinically relevant subtypes of prostate cancer. Proc. Natl. Acad. Sci. U.S.A. 101, 811-816.
51. Linja, M. J., and Visakorpi, T. (2004). Alterations of androgen receptor in prostate cancer. J. Steroid Biochem. Mol. Biol. 92, 255-264.
52. Liu, W., Laitinen, S., Khan, S., Vihi-nen, M., Kowalski, J., Yu, G., Chen, L., Ewing, C. M., Eisenberger, M. A., Carducci, M. A., Nelson, W G., Yeg-nasubramanian, S., Luo, J., Wang, Y., Xu, J., Isaacs, W B., Visakorpi, T., and Bova, G. S. (2009). Copy number analysis indicates monoclonal origin of lethal metastatic prostate cancer. Nat.Med. 15, 559-565.
53. Majumder, P. K., Grisanzio, C., O'Connell, F., Barry, M., Brito, J. M., Xu, Q., Guney, I., Berger, R., Herman, P., Bikoff, R., Fedele, G., Baek, W K., Wang, S., Ellwood-Yen, K., Wu, H., Sawyers, C. L., Signoretti, S., Hahn, W. C., Loda, M., and Sellers, W R. (2008). A prostatic intraepithe-lial neoplasia-dependent p27 Kip1 checkpoint induces senescence and inhibits cell proliferation and cancer progression. Cancer Cell 14, 146-155.
54. Mardis, E. R., Ding, L., Dooling, D. J., Larson, D. E., Mclellan, M. D., Chen, K., Koboldt, D. C., Fulton, R. S., Delehaunty, K. D., McGrath, S. D., Fulton, L. A., Locke, D. P., Magrini, V J., Abbott, R. M., Vickery, T. L., Reed, J. S., Robinson, J. S., Wylie, T., Smith, S. M., Carmichael, L., Eldred, J. M., Harris, C. C., Walker, J., Peck, J. B., Du, F., Dukes, A. F., Sanderson, G. E., Brummett, A. M., Clark, E., McMichael, J. F., Meyer, R. J., Schindler, J. K., Pohl, C. S., Wal-lis, J. W., Shi, X., Lin, L., Schmidt, H., Tang, Y., Haipek, C., Wiechert, M. E., Ivy, J. V., Kalicki, J., Elliott, G., Ries, R. E., Payton, J. E., West-ervelt, P., Tomasson, M. H., Watson, M. A., Baty, J., Heath, S., Shannon, W D., Nagarajan, R., Link, D. C., Walter, M. J., Graubert, T. A., Dipersio, J. F., Wilson, R. K., and Ley, T. J. (2009). Recurring mutations found by sequencing an acute myeloid leukemia genome. N Engl. J. Med. 361, 1058-1066.
55. McKie, A. B., Douglas, D. A., Olijs-lagers, S., Graham, J., Omar, M. M., Heer, R., Gnanapragasam, V J., Robson, C. N., and Leung, H. Y. (2005). Epigenetic inactivation of the human sprouty2 (hSPRY2) homo-logue in prostate cancer. Oncogene24, 2166-2174.
56. McMenamin, M. E., Soung, P., Perera, S., Kaplan, I., Loda, M., and Sellers, W. R. (1999). Loss of PTEN expression in paraffin-embedded primary prostate cancer correlates with high Gleason score and advanced stage. Cancer Res. 59, 4291-4296.
57. Mehra, R., Han, B., Tomlins, S. A., Wang, L., Menon, A., Wasco, M. J., Shen, R., Montie, J. E., Chinnaiyan, A. M., and Shah, R. B. (2007). Heterogeneity of TMPRSS2 gene rearrangements in multifocal prostate adenocarcinoma: molecular evidence for an independent group of diseases. Cancer Res. 67, 7991-7995.
58. Min, J., Zaslavsky, A., Fedele, G., Mclaughlin, S. K., Reczek, E. E., De Raedt, T., Guney, I., Strochlic, D. E., Macconaill, L. E., Beroukhim, R., Bronson, R. T., Ryeom, S., Hahn, W. C., Loda, M., and Cichowski, K. (2010). An oncogene-tumor suppressor cascade drives metastatic prostate cancer by coordinately activating Ras and nuclear factor-kappaB. Nat. Med. 16, 286-294.
59. Mirchandani, D., Zheng, J., Miller, G. J., Ghosh, A. K., Shibata, D. K., Cote, R. J., and Roy-Burman, P. (1995). Heterogeneity in intratumor distribution of p53 mutations in human prostate cancer. Am. J. Pathol. 147, 92-101.
60. Navone, N. M., Labate, M. E., Tron-coso, P., Pisters, L. L., Conti, C. J., Von Eschenbach, A. C., and Logothetis, C. J. (1999). p53 mutations in prostate cancer bone metastases suggest that selected p53 mutants in the primary site define foci with metastatic potential.J. Urol. 161, 304-308.
61. Oda, K., Stokoe, D., Taketani, Y., and Mccormick, E (2005). High frequency of coexistent mutations of PIK3CA and PTEN genes in endome-trial carcinoma. Cancer Res. 65, 10669-10673.
62. Osborne, C. S., Chakalova, L., Brown, K. E., Carter, D., Horton, A., Debrand, E., Goyenechea, B., Mitchell, J. A., Lopes, S., Reik, W., and Fraser, P. (2004). Active genes dynamically colocalize to shared sites of ongoing transcription. Nat. Genet. 36, 1065-1071.
63. Ouyang, X., Deweese, T. L., Nelson, W. G., and Abate-Shen, C. (2005). Loss-of-function of Nkx3.1 promotes increased oxidative damage in prostate carcinogenesis. Cancer Res. 65, 6773-6779.
64. Paez, J. G., Janne, P. A., Lee, J. C., Tracy, S., Greulich, H., Gabriel, S., Herman, P., Kaye, F. J., Lindeman, N., Boggon, T. J., Naoki, K., Sasaki, H., Fujii, Y., Eck, M. J., Sellers, W R., Johnson, B. E., and Meyerson, M. (2004). EGFR mutations in lung cancer: correlation with clinical response to gefitinib therapy. Science 304, 1497-1500.
65. Palanisamy, N., Ateeq, B., Kalyana-Sundaram, S., Pflueger, D., Ram-narayanan, K., Shankar, S., Han, B., Cao, Q., Cao, X., Suleman, K., Kumar-Sinha, C., Dhanasekaran, S. M., Chen, Y B., Esgueva, R., Baner-jee, S., Lafargue, C. J., Siddiqui, J., Demichelis, F., Moeller, P., Bismar, T. A., Kuefer, R., Fullen, D. R., Johnson, T. M., Greenson, J. K., Giordano, T. J., Tan, P., Tomlins, S. A., Varam-bally, S., Rubin, M. A., Maher, C. A., and Chinnaiyan, A. M. (2010). Rearrangements of the RAF kinase pathway in prostate cancer, gastric cancer and melanoma. Nat. Med. 16, 793-798.
66. Parsons, D. W., Jones, S., Zhang, X., Lin, J. C., Leary, R. J., Angenendt, P., Mankoo, P., Carter, H., Siu, I. M., Gallia, G. L., Olivi, A., Mclendon, R., Rasheed, B. A., Keir, S., Nikolskaya, T., Nikolsky, Y., Busam, D. A., Tek-leab, H., Diaz, L. A. Jr., Hartigan, J., Smith, D. R., Strausberg, R. L., Marie, S. K., Shinjo, S. M., Yan, H., Riggins, G. J., Bigner, D. D., Karchin, R., Papadopoulos, N., Parmigiani, G., Vogelstein, B., Velculescu, V. E., and Kinzler, K. W. (2008). An integrated genomic analysis of human glioblas-toma multiforme. Science 321, 1807-1812.
67. Phillips, S. M., Morton, D. G., Lee, S. J., Wallace, D. M., and Neoptolemos, J. P. (1994). Loss of heterozygosity of the retinoblastoma and adenomatous polyposis susceptibility gene loci and in chromosomes 10p, 10q and 16q in human prostate cancer. Br. J. Urol. 73, 390-395.
68. Pleasance, E. D., Cheetham, R. K., Stephens, P. J., Mcbride, D. J., Humphray, S. J., Greenman, C. D., Varela, I., Lin, M. L., Ordonez, G. R., Bignell, G. R., Ye, K., Alipaz, J., Bauer, M. J., Beare, D., Butler, A., Carter, R. J., Chen, L., Cox, A. J., Edkins, S., Kokko-Gonzales, P. I., Gormley, N. A., Grocock, R. J., Hau-denschild, C. D., Hims, M. M., James, T., Jia, M., Kingsbury, Z., Leroy, C., Marshall, J., Menzies, A., Mudie, L. J., Ning, Z., Royce, T., Schulz-Trieglaff, O. B., Spiridou, A., Steb-bings, L. A., Szajkowski, L., Teague, J., Williamson, D., Chin, L., Ross, M. T., Campbell, P. J., Bentley, D. R., Futreal, P. A., and Stratton, M. R. (2010). A comprehensive catalogue of somatic mutations from a human cancer genome. Nature 463, 191-196.
69. Pleasance, E. D., Stephens, P. J., O'Meara, S., Mcbride, D. J., Meyn-ert, A., Jones, D., Lin, M. L., Beare, D., Lau, K. W., Greenman, C., Varela, I., Nik-Zainal, S., Davies, H. R., Ordonez, G. R., Mudie, L. J., Latimer, C., Edkins, S., Stebbings, L., Chen, L., Jia, M., Leroy, C., Marshall, J., Menzies, A., Butler, A., Teague, J. W., Mangion, J., Sun, Y. A., Mclaughlin, S. F., Peckham, H. E., Tsung, E. F., Costa, G. L., Lee, C. C., Minna, J. D., Gazdar, A., Birney, E., Rhodes, M. D., Mckernan, K. J., Stratton, M. R., Futreal, P. A., and Campbell, P. J. (2010b). A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature 463, 184-190.
70. Prins, G. S., and Putz, O. (2008). Molecular signaling pathways that regulate prostate gland development. Differentiation 76, 641-659.
71. Qian, J., Bostwick, D. G., Takahashi, S., Borell, T. J., Herath, J. F., Lieber, M. M., and Jenkins, R. B. (1995). Chromosomal anomalies in prostatic intraepithelial neoplasia and carcinoma detected by fluorescence in situ hybridization. Cancer Res. 55, 5408-5414.
72. Robbins, C.M., Tembe, W. A., Baker, A., Sinari, S., Moses, T. Y., Beckstrom-Sternberg, S., Beckstrom-Sternberg, J., Barrett, M., Long, J., Chinnaiyan, A., Lowey, J., Suh, E., Pearson, J. V., Craig, D. W., Agus, D. B., Pienta, K. J., and Carpten, J. D. (2011). Copy number and targeted mutational analysis reveals novel somatic events in metastatic prostate tumors. Genome Res. 21, 47-55.
73. Roychowdhury, S., Iyer, M. K., Robinson, D. R., Lonigro, R. J., Wu, Y. M., Cao, X., Kalyana-Sundaram, S., Sam, L., Balbin, O. A., Quist, M. J., Barrette, T., Everett, J., Siddiqui, J., Kunju, L. P., Navone, N., Araujo, J. C., Troncoso, P., Logothetis, C. J., Innis, J. W., Smith, D. C., Lao, C. D., Kim, S. Y., Roberts, J. S., Gruber, S. B., Pienta, K. J., Talpaz, M., and Chinnaiyan, A. M. (2011). Personalized oncology through inte-grative high-throughput sequencing: a pilot study. Sci. Transl. Med. 3
74. Ruiz, C., Lenkiewicz, E., Evers, L., Holley, T., Robeson, A., Kiefer, J., Demeure, M. J., Hollingsworth, M. A., Shen, M., Prunkard, D., Rabi-novitch, P. S., Zellweger, T., Mousses, S., Trent, J. M., Carpten, J. D., Bubendorf, L., Von Hoff, D., and Barrett, M. T. (2011). Advancing a clinically relevant perspective of the clonal nature of cancer. Proc. Natl. Acad. Sci. U.S.A. 108, 12054-12059.
75. Sato, K., Qian, J., Slezak, J. M., Lieber, M. M., Bostwick, D. G., Bergstralh, E. J., and Jenkins, R. B. (1999). Clinical significance of alterations of chromosome 8 in high-grade, advanced, nonmetastatic prostate carcinoma. J. Natl. Cancer Inst. 91, 1574-1580.
76. Sboner, A., Demichelis, F., Calza, S., Pawitan, Y., Setlur, S. R., Hoshida, Y., Perner, S., Adami, H. O., Fall, K., Mucci, L. A., Kantoff, P. W., Stampfer, M., Andersson, S. O., Varenhorst, E., Johansson, J. E., Gerstein, M. B., Golub, T. R., Rubin, M. A., and Andren, O. (2010). Molecular sampling of prostate cancer: a dilemma for predicting disease progression. BMC Med. Genomics 3, 8. doi: 10.1186/1755-8794-3-8
77. Sharma, A., Yeow, W S., Ertel, A., Coleman, I., Clegg, N., Thangavel, C., Morrissey C, Zhang, X., Com-stock, C. E., Witkiewicz, A. K., Gomella, L., Knudsen, E. S., Nelson, P. S., and Knudsen, K. E. (2010). The retinoblastoma tumor suppressor controls androgen signaling and human prostate cancer progression. J. Clin. Invest. 120, 4478-4492.
78. Singh, D., Febbo, P. G., Ross, K., Jackson, D. G., Manola, J., Ladd, C., Tamayo, P., Renshaw, A. A., D'Amico, A. V., Richie, J. P., Lander, E. S., Loda, M., Kantoff, P. W., Golub, T. R., and Sellers, W R. (2002). Gene expression correlates of clinical prostate cancer behavior. Cancer Cell 1, 203-209.
79. Sircar, K., Yoshimoto, M., Monzon, F. A., Koumakpayi, I. H., Katz, R. L., Khanna, A., Alvarez, K., Chen, G., Darnel, A. D., Aprikian, A. G., Saad, F., Bismar, T. A., and Squire, J. A. (2009). PTEN genomic deletion is associated with p-Akt and AR signalling in poorer outcome, hormone refractory prostate cancer. J. Pathol. 218, 505-513.
80. Sun, X., Huang, J., Homma, T., Kita, D., Klocker, H., Schafer, G., Boyle, P., and Ohgaki, H. (2009). Genetic alterations in the PI3K pathway in prostate cancer. Anticancer Res. 29, 1739-1743.
81. Taylor, B. S., Schultz, N., Hieronymus, H., Gopalan, A., Xiao, Y., Carver, B. S., Arora, V K., Kaushik, P., Cerami, E., Reva, B., Antipin, Y., Mitsiades, N., Landers, T., Dolgalev, I., Major, J. E., Wilson, M., Socci, N. D., Lash, A. E., Heguy, A., Eastham, J. A., Scher, H. I., Reuter, V E., Scardino, P. T., Sander, C., Sawyers, C. L., and Gerald, W L. (2010). Integrative genomic profiling of human prostate cancer. Cancer Cell 18, 11-22.
82. Tomlins, S. A., Laxman, B., Dhana-sekaran, S. M., Helgeson, B. E., Cao, X., Morris, D. S., Menon, A., Jing, X., Cao, Q., Han, B., Yu, J., Wang, L., Montie, J. E., Rubin, M. A., Pienta, K. J., Roulston, D., Shah, R. B., Varambally, S., Mehra, R., and Chinnaiyan, A. M. (2007). Distinct classes of chromosomal rearrangements create oncogenic ETS gene fusions in prostate cancer. Nature 448, 595-599.
83. Tomlins, S. A., Rhodes, D. R., Perner, S., Dhanasekaran, S. M., Mehra, R., Sun, X. W., Varambally, S., Cao, X., Tchinda, J., Kuefer, R., Lee, C., Montie, J. E., Shah, R. B., Pienta, K. J., Rubin, M. A., and Chinnaiyan, A. M. (2005). Recurrent fusion of TMPRSS2 and ETS transcription fac tor genes in prostate cancer. Science 310, 644-648.
84. Tricoli, J. V., Gumerlock, P. H., Yao, J. L., Chi, S. G., D'Souza, S. A., Nestok, B. R., and Devere White, R. W. (1996). Alterations of the retinoblas toma gene in human prostate ade-nocarcinoma. Genes Chromosomes Cancer 15, 108-114.
85. True, L., Coleman, I., Hawley, S., Huang, C. Y., Gifford, D., Coleman, R., Beer, T. M., Gelmann, E., Datta, M., Mostaghel, E., Knudsen, B., Lange, P., Vessella, R., Lin, D., Hood, L., and Nelson, P. S. (2006). A molec ular correlate to the Gleason grading system for prostate adenocarcinoma. Proc. Natl. Acad. Sci. U.S.A. 103, 10991-10996.
86. Truica, C. I., Byers, S., and Gelmann, E. P. (2000). Beta-catenin affects androgen receptor transcriptional activity and ligand specificity. Cancer Res. 60, 4709-4713.
87. van 't Veer, L. J., Dai, H., Van De Vijver, M. J., He, Y D., Hart, A. A., Mao, M., Peterse, H. L., Van Der Kooy, K., Marton, M. J., Witteveen, A. T., Schreiber, G. J., Kerkhoven, R. M., Roberts, C., Linsley, P. S., Bernards, R., and Friend, S. H. (2002). Gene expression profiling predicts clinical outcome of breast cancer. Nature 415, 530-536.
88. Vasudevan, K. M., Barbie, D. A., Davies, M. A., Rabinovsky, R., Mcnear, C. J., Kim, J. J., Hennessy, B. T., Tseng, H., Pochanard, P., Kim, S. Y., Dunn, I. E, Schinzel, A. C., Sandy, P., Hoersch, S., Sheng, Q., Gupta, P. B., Boehm, J. S., Reiling, J. H., Silver, S., Lu, Y., Stemke-Hale, K., Dutta, B., Joy, C., Sahin, A. A., Gonzalez-Angulo, A. M., Lluch, A., Rameh, L. E., Jacks, T., Root, D. E., Lander, E. S., Mills, G. B., Hahn, W C, Sellers, W. R., and Garraway, L. A. (2009). AKT-independent signaling downstream of oncogenic PIK3CA mutations in human cancer. Cancer Cell 16, 21-32.
89. Vis, A. N., Noordzij, M. A., Fitoz, K., Wildhagen, M. F., Schroder, F. H., and Van Der Kwast, T. H. (2000). Prognostic value of cell cycle proteins p27(kip1) and MIB-1, and the cell adhesion protein CD44s in surgically treated patients with prostate cancer. J. Urol. 164, 2156-2161.
90. Visakorpi, T., Kallioniemi, A. H., Syvanen, A. C., Hyytinen, E. R., Karhu, R., Tammela, T., Isola, J. J., and Kallioniemi, O. P. (1995). Genetic changes in primary and recurrent prostate cancer by comparative genomic hybridization. Cancer Res. 55, 342-347.
91. Vocke, C. D., Pozzatti, R. O., Bostwick, D. G., Florence, C. D., Jennings, S. B., Strup, S. E., Duray, P. H., Liotta, L. A., Emmert-Buck, M. R., and Linehan, W. M. (1996). Analysis of 99 micro dissected prostate carcinomas reveals a high frequency of allelic loss on chromosome 8p12-21. Cancer Res. 56, 2411-2416.
92. Voeller, H. J., Truica, C. I., and Gelmann, E. P. (1998). Beta-catenin mutations in human prostate cancer. Cancer Res. 58, 2520-2523.
93. Wang, X. S., Shankar, S., Dhanasekaran, S. M., Ateeq, B., Sasaki, A. T., Jing, X., Robinson, D., Cao, Q., Prensner, J. R., Yocum, A. K., Wang, R., Fries, D. F., Han, B., Asangani, I. A., Cao, X., Li, Y., Omenn, G. S., Pflueger, D., Gopalan, A., Reuter, V. E., Kahoud, E. R., Cantley, L. C., Rubin, M. A., Palanisamy, N., Varambally, S., and Chinnaiyan, A. M. (2011). Charac terization of KRAS rearrangements in metastatic prostate cancer. Cancer Discov. 1, 35-43.
94. Watanabe, M., Shiraishi, T., Yatani, R., Nomura, A. M., and Stemmermann, G. N. (1994). International comparison on ras gene mutations in latent prostate carcinoma. Int. J. Cancer 58, 174-178.
95. Wu, X., Hepner, K., Castelino-Prabhu, S., Do, D., Kaye, M. B., Yuan, X. J., Wood, J., Ross, C., Sawyers, C. L., and Whang, Y. E. (2000). Evidence for regulation of the PTEN tumor suppressor by a membrane-localized multi-PDZ domain containing scaffold protein MAGI-2. Proc. Natl. Acad. Sci. U.S.A. 97, 4233-4238.
96. Yardy, G. W., Bicknell, D. C., Wilding, J. L., Bartlett, S., Liu, Y., Winney, B., Turner, G. D., Brewster, S. F., and Bodmer, W F. (2009). Mutations in the AXIN1 gene in advanced prostate cancer. Eur. Urol. 56, 486-494.
97. Yardy, G. W., and Brewster, S. F. (2005). Wnt signalling and prostate cancer. Prostate Cancer Prostatic Dis. 8, 119-126.
98. Yegnasubramanian, S., Kowalski, J., Gonzalgo, M. L., Zahurak, M., Piantadosi, S., Walsh, P. C., Bova, G. S., De Marzo, A. M., Isaacs, W B., and Nelson, W. G. (2004). Hyper-methylation of CpG islands in primary and metastatic human prostate cancer. Cancer Res. 64, 1975-1986.
99. Zitzelsberger, H., Engert, D., Walch, A., Kulka, U., Aubele, M., Hofler, H., Bauchinger, M., and Werner, M. (2001). Chromosomal changes during development and progression of prostate adenocarcinomas. Br. J. Cancer 84, 202-208.