Functional annotation of risk loci identified through genome-wide association studies for prostate cancer

Prostate

Volumn 71, Issue 9, 2011, Pages 955-963

  Lu, Yizhen ^a,b   Zhang, Zheng ^c   Yu, Hongjie ^b   Zheng, S Lily ^c   Isaacs, William B ^d   Xu, Jianfeng ^b,c,e   Sun, Jielin ^c  

^a ZHEJIANG UNIVERSITY   (China)

^b FUDAN UNIVERSITY   (China)

^c Medical Center Blvd   (United States)

^d DEPARTMENT OF PATHOLOGY   (United States)

^e VAN ANDEL RESEARCH INSTITUTE   (United States)

Author keywords

bioinformatics; functional annotation; genome wide association study; prostate cancer

Indexed keywords

ANDROGEN RECEPTOR; HEPATOCYTE NUCLEAR FACTOR 3ALPHA;

ARTICLE; BINDING SITE; BIOINFORMATICS; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENE MAPPING; GENETIC ASSOCIATION; GENETIC RISK; GENOMICS; PRIORITY JOURNAL; PROSTATE CANCER; SINGLE NUCLEOTIDE POLYMORPHISM;

GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HUMANS; LINKAGE DISEQUILIBRIUM; MALE; POLYMORPHISM, SINGLE NUCLEOTIDE; PROSTATIC NEOPLASMS; RECEPTORS, ANDROGEN;

EID: 79955592252     PISSN: 02704137     EISSN: 10970045     Source Type: Journal    
DOI: 10.1002/pros.21311     Document Type: Article

References (36)

1. Yeager M, Orr N, Hayes RB, Jacobs KB, Kraft P, Wacholder S, Minichiello MJ, Fearnhead P, Yu K, Chatterjee N, Wang Z, Welch R, Staats BJ, Calle EE, Feigelson HS, Thun MJ, Rodriguez C, Albanes D, Virtamo J, Weinstein S, Schumacher FR, Giovannucci E, Willett WC, Cancel-Tassin G, Cussenot O, Valeri A, Andriole GL, Gelmann EP, Tucker M, Gerhard DS, Fraumeni JF Jr, Hoover R, Hunter DJ, Chanock SJ, Thomas G,. Genome-wide association study of prostate cancer identifies a second risk locus at 8q24. Nat Genet 2007; 39: 645-649. (Pubitemid 46676108)
2. Gudmundsson J, Sulem P, Steinthorsdottir V, et al. Two variants on chromosome 17 confer prostate cancer risk, and the one in TCF2 protects against type 2 diabetes. Nat Genet 2007; 39: 977-983. (Pubitemid 47185170)
3. Duggan D, Zheng SL, Knowlton M, et al. Two genome-wide association studies of aggressive prostate cancer implicate putative prostate tumor suppressor gene DAB2IP. J Natl Cancer Inst 2007; 99: 1836-1844. (Pubitemid 351767196)
4. Thomas G, Jacobs KB, Yeager M, et al. Multiple loci identified in a genome-wide association study of prostate cancer. Nat Genet 2008; 40: 310-315. (Pubitemid 351311773)
5. Gudmundsson J, Sulem P, Rafnar T, et al. Common sequence variants on 2p15 and Xp11.22 confer susceptibility to prostate cancer. Nat Genet 2008; 40: 281-283. (Pubitemid 351311771)
6. Eeles RA, Kote-Jarai Z, Giles GG, et al. Multiple newly identified loci associated with prostate cancer susceptibility. Nat Genet 2008; 40: 316-321. (Pubitemid 351311772)
7. Yeager M, Chatterjee N, Ciampa J, et al. Identification of a new prostate cancer susceptibility locus on chromosome 8q24. Nat Genet 2009; 41: 1055-1057.
8. Gudmundsson J, Sulem P, Gudbjartsson DF, et al. Genome-wide association and replication studies identify four variants associated with prostate cancer susceptibility. Nat Genet 2009; 41: 1122-1126.
9. Eeles RA, Kote-Jarai Z, Al Olama AA, et al. Identification of seven new prostate cancer susceptibility loci through a genome-wide association study. Nat Genet 2009; 41: 1116-1121.
10. Ghoussaini M, Song H, Koessler T, Al Olama AA, Kote-Jarai Z, Driver KE, Pooley KA, Ramus SJ, Kjaer SK, Hogdall E, DiCioccio RA, Whittemore AS, Gayther SA, Giles GG, Guy M, Edwards SM, Morrison J, Donovan JL, Hamdy FC, Dearnaley DP, Ardern-Jones AT, Hall AL, O'Brien LT, Gehr-Swain BN, Wilkinson RA, Brown PM, Hopper JL, Neal DE, Pharoah PD, Ponder BA, Eeles RA, Easton DF, Dunning AM,. UK Genetic Prostate Cancer Study Collaborators/British Association of Urological Surgeons' Section of Oncology; UK ProtecT Study Collaborators. Multiple loci with different cancer specificities within the 8q24 gene desert. J Natl Cancer Inst 2008; 100 (13): 962-966. Epub 2008 Jun 24.
11. Lou H, Yeager M, Li H, Bosquet JG, Hayes RB, Orr N, Yu K, Hutchinson A, Jacobs KB, Kraft P, Wacholder S, Chatterjee N, Feigelson HS, Thun MJ, Diver WR, Albanes D, Virtamo J, Weinstein S, Ma J, Gaziano JM, Stampfer M, Schumacher FR, Giovannucci E, Cancel-Tassin G, Cussenot O, Valeri A, Andriole GL, Crawford ED, Anderson SK, Tucker M, Hoover RN, Fraumeni JF, Jr., Thomas G, Hunter DJ, Dean M, Chanock SJ,. Fine mapping and functional analysis of a common variant in MSMB on chromosome 10q11.2 associated with prostate cancer susceptibility. Proc Natl Acad Sci USA 2009; 106 (19): 7933-7938. Epub 2009 Apr 21.
12. Chang BL, Cramer SD, Wiklund F, Isaacs SD, Stevens VL, Sun J, Smith S, Pruett K, Romero LM, Wiley KE, Kim ST, Zhu Y, Zhang Z, Hsu FC, Turner AR, Adolfsson J, Liu W, Kim JW, Duggan D, Carpten J, Zheng SL, Rodriguez C, Isaacs WB, Grönberg H, Xu J,. Fine mapping association study and functional analysis implicate a SNP in MSMB at 10q11 as a causal variant for prostate cancer risk. Hum Mol Genet 2009; 18 (7): 1368-1375. Epub 2009 Jan 19.
13. The ENCODE Project Consortium. The ENCODE Project Consortium Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007; 447 (7146): 799-816.
14. Euskirchen GM, Rozowsky JS, Wei CL, Lee WH, Zhang ZD, Hartman S, Emanuelsson O, Stolc V, Weissman S, Gerstein MB, Ruan Y, Snyder M,. Mapping of transcription factor binding regions in mammalian cells by ChIP: Comparison of array- and sequencing-based technologies. Genome Res 2007; 17 (6): 898-909. (Pubitemid 46919724)
15. Wang Q, Li W, Zhang Y, Yuan X, Xu K, Yu J, et al. Androgen receptor regulates a distinct transcription program in androgen-independent prostate cancer. Cell 2009; 138 (2): 245-256.
16. Carroll JS, Meyer CA, Song J, Li W, Geistlinger TR, Eeckhoute J, Brodsky AS, Keeton EK, Fertuck KC, Hall GF, Wang Q, Bekiranov S, Sementchenko V, Fox EA, Silver PA, Gingeras TR, Liu XS, Brown M,. Genome-wide analysis of estrogen receptor binding sites. Nat Genet 2006; 38: 1289-1297. (Pubitemid 44646291)
17. Xu J, Sun J, Kader AK, Lindström S, Wiklund F, Hsu FC, Johansson JE, Zheng SL, Thomas G, Hayes RB, Kraft P, Hunter DJ, Chanock SJ, Isaacs WB, Grönberg H,. Estimation of absolute risk for prostate cancer using genetic markers and family history. Prostate 2009; 69 (14): 1565-1572.
18. Hsu FC, Sun J, Zhu Y, Kim ST, Jin T, Zhang Z, Wiklund F, Kader AK, Zheng SL, Isaacs W, Grönberg H, Xu J,. Comparison of two methods for estimating absolute risk of prostate cancer based on single nucleotide polymorphisms and family history. Cancer Epidemiol Biomarkers Prev 2010; 19 (4): 1083-1088.
19. Sun J, Kader AK, Hsu FC, Kim ST, Zhu Y, Turner AR, Jin T, Zhang Z, Adolfsson J, Wiklund F, Zheng SL, Isaacs WB, Grönberg H, Xu J,. Inherited genetic markers discovered to date are able to identify a significant number of men at considerably elevated risk for prostate cancer. Prostate 2010; [Epub ahead of print].
20. Thompson IM, Goodman PJ, Tangen CM,. et al. The influence of finasteride on the development of prostate cancer. N Engl J Med 2003; 349: 215-224. (Pubitemid 36859473)
21. Andriole GA, Bostwick D, Brawley OW,. The influence of dutasteride on the risk of biopsy-detectable prostate cancer: Outcomes of the REduction by DUtasteride of Prostate Cancer Events (REDUCE) study. N Engl J Med 2010; 362 (13): 1192-1202.
22. Johnson WE, Li W, Meyer CA, Gottardo R, Carroll JS, Brown M, Liu XS,. Model-based analysis of tiling-arrays for ChIP-chip. Proc Natl Acad Sci USA 2006; 103 (33): 12457-12462. (Pubitemid 44267281)
23. Carroll JS, Liu XS, Brodsky AS, Li W, Meyer CA, Szary AJ, Eeckhoute J, Shao W, Hestermann EV, Geistlinger TR, Fox EA, Silver PA, Brown M,. Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1. Cell 2005; 122 (1): 33-43. (Pubitemid 40977938)
24. Wang Q, Li W, Liu XS, Carroll JS, Jänne OA, Keeton EK, Chinnaiyan AM, Pienta KJ, Brown M,. A hierarchical network of transcription factors governs androgen receptor-dependent prostate cancer growth. Mol Cell 2007; 27 (3): 380-392. (Pubitemid 47126935)
25. Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, Swarbreck D, Rossier C, Ucla C, Hubbard T, Antonarakis SE, Guigo R,. GENCODE: Producing a reference annotation for ENCODE. Genome Biol 2006; 7 (Suppl 1): S41-S49. Epub 2006 Aug 7.
26. Gardiner-Garden M, Frommer M,. CpG islands in vertebrate genomes. J Mol Biol 1987; 196 (2): 261-282. (Pubitemid 17122132)
27. Washietl S, Pedersen JS, Korbel JO, Stocsits C, Gruber AR, Hackermüller J, Hertel J, Lindemeyer M, Reiche K, Tanzer A, Ucla C, Wyss C, Antonarakis SE, Denoeud F, Lagarde J, Drenkow J, Kapranov P, Gingeras TR, Guigõ R, Snyder M, Gerstein MB, Reymond A, Hofacker IL, Stadler PF,. Structured RNAs in the ENCODE selected regions of the human genome. Genome Res 2007; 17 (6): 852-864. (Pubitemid 46919720)
28. Down TA, Hubbard TJP,. Computational detection and location of transcription start sites in mammalian genomic DNA. Genome Res 2002; 12 (3): 458-461. (Pubitemid 34233021)
29. Davuluri RV, Grosse I, Zhang MQ,. Computational identification of promoters and first exons in the human genome. Nat Genet 2001; 29 (4): 412-417. Erratum in: Nat Genet 2002 Nov;32(3): 459. (Pubitemid 34326691)
30. Guelen L, Pagie L, Brasset E, Meuleman W, Faza MB, Talhout W, Eussen BH, de Klein A, Wessels L, de Laat W, van Steensel B,. Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature 2008; 453: 948-951. (Pubitemid 351832561)
31. Pennacchio LA, Ahituv N, Moses AM, Prabhakar S, Nobrega MA, Shoukry M, Minovitsky S, Dubchak I, Holt A, Lewis KD, et al. In vivo enhancer analysis of human conserved non-coding sequences. Nature 2006; 444 (7118): 499-502. (Pubitemid 44809068)
32. Cheng Y, Miura RM, Tian B,. 2006; Prediction of mRNA polyadenylation sites by support vector machine. Bioinformatics 22: 2320-2325. (Pubitemid 44566959)
33. Lewis BP, Burge CB, Bartel DP,. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA. Targets Cell 2005; 120: 15-20. (Pubitemid 40094598)
34. Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, Bartel DP,. Micro RNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell 2007; 27 (1): 91-105. (Pubitemid 46991392)
35. Friedman RC, Farh KK, Burge CB, Bartel DP,. Most mammalian mRNAs are conserved targets of microRNAs genome research. Genome Res 2009; 19: 92-105.
36. Down TA, Hubbard TJ,. Computational detection and location of transcription start sites in mammalian genomic DNA. Genome Res 2002; 12 (3): 458-461. (Pubitemid 34233021)