Genome-wide association studies on prostate cancer: The end or the beginning?

Protein and Cell

Volumn 4, Issue 9, 2013, Pages 677-686

  Chen, Rui ^a   Ren, Shancheng ^a   Sun, Yinghao ^a  

^a SECOND MILITARY MEDICAL UNIVERSITY   (China)

Author keywords

genome wide association study; prostate cancer

Indexed keywords

ANDROGEN; BETA MICROSEMINOPROTEIN; BIOLOGICAL MARKER; EPIDERMAL GROWTH FACTOR RECEPTOR 2; HEPATOCYTE NUCLEAR FACTOR 1BETA; PROTEIN TYROSINE KINASE INHIBITOR; SPACER DNA;

ALLELE; CANCER PROGNOSIS; CANCER RISK; CHROMOSOME PAIRING; GENE EXPRESSION; GENE FREQUENCY; GENE INTERACTION; GENE LOCUS; GENETIC ASSOCIATION; GENETIC HETEROGENEITY; GENETIC MARKER; HUMAN; INTRON; PHARMACOGENOMICS; PRIORITY JOURNAL; PROSTATE CANCER; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM; ANCESTRY GROUP; GENETIC PREDISPOSITION; GENETICS; GENOME-WIDE ASSOCIATION STUDY; MALE; PROSTATE TUMOR; TRENDS;

CONTINENTAL POPULATION GROUPS; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MALE; POLYMORPHISM, SINGLE NUCLEOTIDE; PROSTATIC NEOPLASMS;

EID: 84892866370     PISSN: 1674800X     EISSN: 16748018     Source Type: Journal    
DOI: 10.1007/s13238-013-3055-4     Document Type: Review

References (70)

1. Ahn, J., Berndt, S. I., Wacholder, S., Kraft, P., Kibel, A. S., Yeager, M., Albanes, D., Giovannucci, E., Stampfer, M. J., Virtamo, J., et al. (2008). Variation in KLK genes, prostate-specific antigen and risk of prostate cancer. Nat Genet 40, 1032-1034; author reply 1035-1036.
2. Ahn, J., Kibel, A. S., Park, J. Y., Rebbeck, T. R., Rennert, H., Stanford, J. L., Ostrander, E. A., Chanock, S., Wang, M. H., Mittal, R. D., et al. (2011). Prostate cancer predisposition loci and risk of metastatic disease and prostate cancer recurrence. Clin Cancer Res 17, 1075-1081.
3. Amin Al Olama, A., Kote-Jarai, Z., Schumacher, F. R., Wiklund, F., Berndt, S. I., Benlloch, S., Giles, G. G., Severi, G., Neal, D. E., Hamdy, F. C., et al. (2013). A meta-analysis of genome-wide association studies to identify prostate cancer susceptibility loci associated with aggressive and non-aggressive disease. Hum Mol Genet 22, 408-415.
4. Arteaga, C. L., Sliwkowski, M. X., Osborne, C. K., Perez, E. A., Puglisi, F., and Gianni, L. (2012). Treatment of HER2-positive breast cancer: current status and future perspectives. Nat Rev Clin Oncol 9, 16-32.
5. Bensen, J. T., Xu, Z., Smith, G. J., Mohler, J. L., Fontham, E. T., and Taylor, J. A. (2013). Genetic polymorphism and prostate cancer aggressiveness: a case-only study of 1, 536 GWAS and candidate SNPs in African-Americans and European-Americans. Prostate 73, 11-22.
6. Berger, M. F., Lawrence, M. S., Demichelis, F., Drier, Y., Cibulskis, K., Sivachenko, A. Y., Sboner, A., Esgueva, R., Pflueger, D., Sougnez, C., et al. (2011). The genomic complexity of primary human prostate cancer. Nature 470, 214-220.
7. Chan, J. Y., Li, H., Singh, O., Mahajan, A., Ramasamy, S., Subramaniyan, K., Kanesvaran, R., Sim, H. G., Chong, T. W., Teo, Y. Y., et al. (2012). 8q24 and 17q Prostate cancer susceptibility loci in a multiethnic Asian cohort({star operator}). Urol Oncol. (In press).
8. Chang, B. L., Cramer, S. D., Wiklund, F., Isaacs, S. D., Stevens, V. L., Sun, J., Smith, S., Pruett, K., Romero, L. M., Wiley, K. E., et al. (2009). 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 i18, 1368-1375.
9. Chang, B. L., Spangler, E., Gallagher, S., Haiman, C. A., Henderson, B., Isaacs, W., Benford, M. L., Kidd, L. R., Cooney, K., Strom, S., et al. (2011). Validation of genome-wide prostate cancer associations in men of African descent. Cancer Epidemiol Biomarkers Prev 20, 23-32.
10. Cheng, I., Chen, G. K., Nakagawa, H., He, J., Wan, P., Laurie, C. C., Shen, J., Sheng, X., Pooler, L. C., Crenshaw, A. T., et al. (2012). Evaluating genetic risk for prostate cancer among Japanese and Latinos. Cancer Epidemiol Biomarkers Prev 21, 2048-2058.
11. Chung, C. C., Magalhaes, W. C., Gonzalez-Bosquet, J., and Chanock, S. J. (2010). Genome-wide association studies in cancer-current and future directions. Carcinogenesis 31, 111-120.
12. Eeles, R. A., Kote-Jarai, Z., Al Olama, A. A., Giles, G. G., Guy, M., Severi, G., Muir, K., Hopper, J. L., Henderson, B. E., Haiman, C. A., et al. (2009). Identification of seven new prostate cancer susceptibility loci through a genome-wide association study. Nat Genet 41, 1116-1121.
13. Eeles, R. A., Kote-Jarai, Z., Giles, G. G., Olama, A. A., Guy, M., Jugurnauth, S. K., Mulholland, S., Leongamornlert, D. A., Edwards, S. M., Morrison, J., et al. (2008). Multiple newly identified loci associated with prostate cancer susceptibility. Nat Genet 40, 316-321.
14. Elston, R. C., Lin, D., and Zheng, G. (2007). Multistage sampling for genetic studies. Annu Rev Genomics Hum Genet 8, 327-342.
15. FitzGerald, L. M., Kwon, E. M., Conomos, M. P., Kolb, S., Holt, S. K., Levine, D., Feng, Z., Ostrander, E. A., and Stanford, J. L. (2011). Genome-wide association study identifies a genetic variant associated with risk for more aggressive prostate cancer. Cancer Epidemiol Biomarkers Prev 20, 1196-1203.
16. FitzGerald, L. M., Zhang, X., Kolb, S., Kwon, E. M., Liew, Y. C., Hurtado-Coll, A., Knudsen, B. S., Ostrander, E. A., and Stanford, J. L. (2013). In vestigation of the relationship between prostate cancer and MSMB and NCOA4 genetic variants and protein expression. Hum Mutat 34, 149-156.
17. Freedman, M. L., Monteiro, A. N., Gayther, S. A., Coetzee, G. A., Risch, A., Plass, C., Casey, G., De Biasi, M., Carlson, C., Duggan, D., et al. (2011). Principles for the post-GWAS functional characterization of cancer risk loci. Nat Genet 43, 513-518.
18. Garcia-Donas, J., Esteban, E., Leandro-Garcia, L. J., Castellano, D. E., del Alba, A. G., Climent, M. A., Arranz, J. A., Gallardo, E., Puente, J., Bellmunt, J., et al. (2011). Single nucleotide polymorphism associations with response and toxic effects in patients with advanced renal-cell carcinoma treated with first-line sunitinib: a multicentre, observational, prospective study. Lancet Oncol 12, 1143-1150.
19. Goh, C. L., Saunders, E. J., Leongamornlert, D. A., Tymrakiewicz, M., Thomas, K., Selvadurai, E. D., Woode-Amissah, R., Dadaev, T., Mahmud, N., Castro, E., et al. (2013). Clinical implications of family history of prostate cancer and genetic risk single nucleotide polymorphism (SNP) profiles in an active surveillance cohort. BJU Int. (In Press).
20. Gudmundsson, J., Sulem, P., Rafnar, T., Bergthorsson, J. T., Manolescu, A., Gudbjartsson, D., Agnarsson, B. A., Sigurdsson, A., Benediktsdottir, K. R., Blondal, T., et al. (2008). Common sequence variants on 2p15 and Xp11. 22 confer susceptibility to prostate cancer. Nat Genet 40, 281-283.
21. Gudmundsson, J., Sulem, P., Steinthorsdottir, V., Bergthorsson, J. T., Thorleifsson, G., Manolescu, A., Rafnar, T., Gudbjartsson, D., Agnarsson, B. A., Baker, A., et al. (2007). Two variants on chromosome 17 confer prostate cancer risk, and the one in TCF2 protects against type 2 diabetes. Nat Genet 39, 977-983.
22. Haiman, C. A., Chen, G. K., Blot, W. J., Strom, S. S., Berndt, S. I., Kittles, R. A., Rybicki, B. A., Isaacs, W. B., Ingles, S. A., Stanford, J. L., et al. (2011). Characterizing genetic risk at known prostate cancer susceptibility loci in African Americans. PLoS Genet 7, e1001387.
23. Hawkins, R. D., Hon, G. C., and Ren, B. (2010). Next-generation genomics: an integrative approach. Nat Rev Genet 11, 476-486.
24. Hindorff, L. A., Sethupathy, P., Junkins, H. A., Ramos, E. M., Mehta, J. P., Collins, F. S., and Manolio, T. A. (2009). Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci U S A 106, 9362-9367.
25. Hirschhorn, J. N., and Daly, M. J. (2005). Genome-wide association studies for common diseases and complex traits. Nat Rev Genet 6, 95-108.
26. Hooker, S., Hernandez, W., Chen, H., Robbins, C., Torres, J. B., Ahaghotu, C., Carpten, J., and Kittles, R. A. (2010). Replication of prostate cancer risk loci on 8q24, 11q13, 17q12, 19q33, and Xp11 in African Americans. Prostate 70, 270-275.
27. Ikegawa, S. (2012). A short history of the genome-wide association study: where we were and where we are going. Genomics Inform 10, 220-225.
28. Ishak, M. B., and Giri, V. N. (2011). A systematic review of replication studies of prostate cancer susceptibility genetic variants in high-risk men originally identified from genome-wide association studies. Cancer Epidemiol Biomarkers Prev 20, 1599-1610.
29. Jia, P., Liu, Y., and Zhao, Z. (2012). Integrative pathway analysis of genome-wide association studies and gene expression data in prostate cancer. BMC Syst Biol 6Suppl 3, S13.
30. Juran, B. D., and Lazaridis, K. N. (2011). Genomics in the post-GWAS era. Semin Liver Dis 31, 215-222.
31. Kader, A. K., Sun, J., Reck, B. H., Newcombe, P. J., Kim, S. T., Hsu, F. C., D'Agostino, R. B., Jr., Tao, S., Zhang, Z., Turner, A. R., et al. (2012). Potential impact of adding genetic markers to clinical parameters in predicting prostate biopsy outcomes in men following an initial negative biopsy: findings from the REDUCE trial. Eur Urol 62, 953-961.
32. Kerns, S. L., Stock, R., Stone, N., Buckstein, M., Shao, Y., Campbell, C., Rath, L., De Ruysscher, D., Lammering, G., Hixson, R., et al. (2013). A 2-stage genome-wide association study to identify single nucleotide polymorphisms associated with development of erectile dysfunction following radiation therapy for prostate cancer. Int J Radiat Oncol Biol Phys 85, e21-28.
33. Kim, H. J., Bae, J. S., Lee, J., Chang, I. H., Kim, K. D., Shin, H. D., Han, J. H., Lee, S. Y., Kim, W., and Myung, S. C. (2011). HNF1B polymorphism associated with development of prostate cancer in Korean patients. Urology 78, 969. e1-6.
34. Konety, B. R., Bird, V. Y., Deorah, S., and Dahmoush, L. (2005). Comparison of the incidence of latent prostate cancer detected at autopsy before and after the prostate specific antigen era. J Urol 174, 1785-1788; discussion 1788.
35. Lai, J., Kedda, M. A., Hinze, K., Smith, R. L., Yaxley, J., Spurdle, A. B., Morris, C. P., Harris, J., and Clements, J. A. (2007). PSA/KLK3 AREI promoter polymorphism alters androgen receptor binding and is associated with prostate cancer susceptibility. Carcinogenesis 28, 1032-1039.
36. Lichtenstein, P., Holm, N. V., Verkasalo, P. K., Iliadou, A., Kaprio, J., Koskenvuo, M., Pukkala, E., Skytthe, A., and Hemminki, K. (2000). Environmental and heritable factors in the causation of cancer-analyses of cohorts of twins from Sweden, Denmark, and Finland. N Engl J Med 343, 78-85.
37. Liu, H., Wang, B., and Han, C. (2011). Meta-analysis of genome-wide and replication association studies on prostate cancer. Prostate 71, 209-224.
38. Lou, H., Li, H., Yeager, M., Im, K., Gold, B., Schneider, T. D., Fraumeni, J. F., Jr., Chanock, S. J., Anderson, S. K., and Dean, M. (2012). Promoter variants in the MSMB gene associated with prostate cancer regulate MSMB/NCOA4 fusion transcripts. Hum Genet 131, 1453-1466.
39. 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.
40. Mikkelsen, T. S., Ku, M., Jaffe, D. B., Issac, B., Lieberman, E., Giannoukos, G., Alvarez, P., Brockman, W., Kim, T. K., Koche, R. P., et al. (2007). Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448, 553-560.
41. Miyamoto, Y., Shi, D., Nakajima, M., Ozaki, K., Sudo, A., Kotani, A., Uchida, A., Tanaka, T., Fukui, N., Tsunoda, T., et al. (2008). Common variants in DVWA on chromosome 3p24. 3 are associated with susceptibility to knee osteoarthritis. Nat Genet 40, 994-998.
42. Nam, R. K., Zhang, W., Siminovitch, K., Shlien, A., Kattan, M. W., Klotz, L. H., Trachtenberg, J., Lu, Y., Zhang, J., Yu, C., et al. (2011). New variants at 10q26 and 15q21 are associated with aggressive prostate cancer in a genome-wide association study from a prostate biopsy screening cohort. Cancer Biol Ther 12, 997-1004.
43. Panagopoulos, I., Moller, E., Collin, A., and Mertens, F. (2008). The POU5F1P1 pseudogene encodes a putative protein similar to POU5F1 isoform 1. Oncol Rep 20, 1029-1033.
44. Prokunina-Olsson, L., Fu, Y. P., Tang, W., Jacobs, K. B., Hayes, R. B., Kraft, P., Berndt, S. I., Wacholder, S., Yu, K., Hutchinson, A., et al. (2010). Refining the prostate cancer genetic association within the JAZF1 gene on chromosome 7p15. 2. Cancer Epidemiol Biomarkers Prev 19, 1349-1355.
45. Ritchie, M. D. (2012). The success of pharmacogenomics in moving genetic association studies from bench to bedside: study design and implementation of precision medicine in the post-GWAS era. Hum Genet 131, 1615-1626.
46. Sanna, S., Jackson, A. U., Nagaraja, R., Willer, C. J., Chen, W. M., Bonnycastle, L. L., Shen, H., Timpson, N., Lettre, G., Usala, G., et al. (2008). Common variants in the GDF5-UQCC region are associated with variation in human height. Nat Genet 40, 198-203.
47. Schumacher, F. R., Berndt, S. I., Siddiq, A., Jacobs, K. B., Wang, Z., Lindstrom, S., Stevens, V. L., Chen, C., Mondul, A. M., Travis, R. C., et al. (2011). Genome-wide association study identifies new prostate cancer susceptibility loci. Hum Mol Genet 20, 3867-3875.
48. Seng, K. C., and Seng, C. K. (2008). The success of the genome-wide association approach: a brief story of a long struggle. Eur J Hum Genet 16, 554-564.
49. Severi, G., Hayes, V. M., Neufing, P., Padilla, E. J., Tilley, W. D., Eggleton, S. A., Morris, H. A., English, D. R., Southey, M. C., Hopper, J. L., et al. (2006). Variants in the prostate-specific antigen (PSA) gene and prostate cancer risk, survival, and circulating PSA. Cancer Epidemiol Biomarkers Prev 15, 1142-1147.
50. Siegel, R., Naishadham, D., and Jemal, A. (2013). Cancer statistics, 2013. CA Cancer J Clin 63, 11-30.
51. Sotelo, J., Esposito, D., Duhagon, M. A., Banfield, K., Mehalko, J., Liao, H., Stephens, R. M., Harris, T. J., Munroe, D. J., and Wu, X. (2010). Long-range enhancers on 8q24 regulate c-Myc. Proc Natl Acad Sci U S A 107, 3001-3005.
52. Stadler, Z. K., Thom, P., Robson, M. E., Weitzel, J. N., Kauff, N. D., Hurley, K. E., Devlin, V., Gold, B., Klein, R. J., and Offit, K. (2010). Genome-wide association studies of cancer. J Clin Oncol 28, 4255-4267.
53. Stevens, V. L., Ahn, J., Sun, J., Jacobs, E. J., Moore, S. C., Patel, A. V., Berndt, S. I., Albanes, D., and Hayes, R. B. (2010). HNF1B and JAZF1 genes, diabetes, and prostate cancer risk. Prostate 70, 601-607.
54. Studies, N.-N. W. G. o. R. i. A., Chanock, S. J., Manolio, T., Boehnke, M., Boerwinkle, E., Hunter, D. J., Thomas, G., Hirschhorn, J. N., Abecasis, G., Altshuler, D., et al. (2007). Replicating genotype-phenotype associations. Nature 447, 655-660.
55. Takata, R., Akamatsu, S., Kubo, M., Takahashi, A., Hosono, N., Kawaguchi, T., Tsunoda, T., Inazawa, J., Kamatani, N., Ogawa, O., et al. (2010). Genome-wide association study identifies five new susceptibility loci for prostate cancer in the Japanese population. Nat Genet 42, 751-754.
56. Thomas, G., Jacobs, K. B., Yeager, M., Kraft, P., Wacholder, S., Orr, N., Yu, K., Chatterjee, N., Welch, R., Hutchinson, A., et al. (2008). Multiple loci identified in a genome-wide association study of prostate cancer. Nat Genet 40, 310-315.
57. Trevino, L. R., Shimasaki, N., Yang, W., Panetta, J. C., Cheng, C., Pei, D., Chan, D., Sparreboom, A., Giacomini, K. M., Pui, C. H., et al. (2009). Germline genetic variation in an organic anion transporter polypeptide associated with methotrexate pharmacokinetics and clinical effects. J Clin Oncol 27, 5972-5978.
58. Vickers, A., Cronin, A., Roobol, M., Savage, C., Peltola, M., Pettersson, K., Scardino, P. T., Schroder, F., and Lilja, H. (2010). Reducing unnecessary biopsy during prostate cancer screening using a four-kallikrein panel: an independent replication. J Clin Oncol 28, 2493-2498.
59. Wang, M., Liu, F., Hsing, A. W., Wang, X., Shao, Q., Qi, J., Ye, Y., Wang, Z., Chen, H., Gao, X., et al. (2012). Replication and cumulative effects of GWAS-identified genetic variations for prostate cancer in Asians: a case-control study in the ChinaPCa consortium. Carcinogenesis 33, 356-360.
60. Wasserman, N. F., Aneas, I., and Nobrega, M. A. (2010). An 8q24 gene desert variant associated with prostate cancer risk confers differential in vivo activity to a MYC enhancer. Ge nome Res 20, 1191-1197.
61. Wheeler, H. E., Maitland, M. L., Dolan, M. E., Cox, N. J., and Ratain, M. J. (2013). Cancer pharmacogenomics: strategies and challenges. Nat Rev Genet 14, 23-34.
62. Wright, J. B., Brown, S. J., and Cole, M. D. (2010). Upregulation of c-MYC in cis through a large chromatin loop linked to a cancer risk-associated single-nucleotide polymorphism in colorectal cancer cells. Mol Cell Biol 30, 1411-1420.
63. Xu, J., Mo, Z., Ye, D., Wang, M., Liu, F., Jin, G., Xu, C., Wang, X., Shao, Q., Chen, Z., et al. (2012). Genome-wide association study in Chinese men identifies two new prostate cancer risk loci at 9q31. 2 and 19q13. 4. Nat Genet 44, 1231-1235.
64. Xu, J., Zheng, S. L., Isaacs, S. D., Wiley, K. E., Wiklund, F., Sun, J., Kader, A. K., Li, G., Purcell, L. D., Kim, S. T., et al. (2010). Inherited genetic variant predisposes to aggressive but not indolent prostate cancer. Proc Natl Acad Sci U S A 107, 2136-2140.
65. Yaspan, B. L., and Veatch, O. J. (2011). Strategies for pathway analysis from GWAS data. Curr Protoc Hum Genet. Chapter 1, Unit1. 20.
66. Yeager, M., Chatterjee, N., Ciampa, J., Jacobs, K. B., Gonzalez-Bosquet, J., Hayes, R. B., Kraft, P., Wacholder, S., Orr, N., Berndt, S., et al. (2009). Identification of a new prostate cancer susceptibility locus on chromosome 8q24. Nat Genet 41, 1055-1057.
67. Yeager, M., Orr, N., Hayes, R. B., Jacobs, K. B., Kraft, P., Wacholder, S., Minichiello, M. J., Fearnhead, P., Yu, K., Chatterjee, N., et al. (2007). Genome-wide association study of prostate cancer identifies a second risk locus at 8q24. Nat Genet 39, 645-649.
68. Yi, H. G., Kim, H. J., Kim, Y. J., Han, S. W., Oh, D. Y., Lee, S. H., Kim, D. W., Im, S. A., Kim, T. Y., Kim, C. S., et al. (2009). Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) are effective for leptomeningeal metastasis from non-small cell lung cancer patients with sensitive EGFR mutation or other predictive factors of good response for EGFR TKI. Lung Cancer 65, 80-84.
69. Zeggini, E., Scott, L. J., Saxena, R., Voight, B. F., Marchini, J. L., Hu, T., de Bakker, P. I., Abecasis, G. R., Almgren, P., Andersen, G., et al. (2008). Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes. Nat Genet 40, 638-645.
70. Zheng, J., Liu, F., Lin, X., Wang, X., Ding, Q., Jiang, H., Chen, H., Lu, D., Jin, G., Hsing, A. W., et al. (2012). Predictive performance of prostate cancer risk in Chinese men using 33 reported prostate cancer risk-associated SNPs. Prostate 72, 577-583.