[1] Ahn, J., Berndt, S.I., Wacholder, S., Kraft, P., Kibel, A.S., Yeager, M., Albanes, D., Giovannucci, E., Stampfer, M.J., Virtamo, J.,
. (2008). Variation in KLK genes, prostate-specific antigen and risk of prostate cancer.
Nat Genet 40, 1032-1034 ; author reply 1035-1036 .
10.1038/ng0908-1032[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.,
. (2011). Prostate cancer predisposition loci and risk of metastatic disease and prostate cancer recurrence.
Clin Cancer Res 17, 1075-1081 .
10.1158/1078-0432.CCR-10-0881[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.,
. (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 .
10.1093/hmg/dds425[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 .
10.1038/nrclinonc.2011.177[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 .
10.1002/pros.22532[6] Berger, M.F., Lawrence, M.S., Demichelis, F., Drier, Y., Cibulskis, K., Sivachenko, A.Y., Sboner, A., Esgueva, R., Pflueger, D., Sougnez, C.,
. (2011). The genomic complexity of primary human prostate cancer.
Nature 470, 214-220 .
10.1038/nature09744[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.,
. (2012). 8 q24 and 17q Prostate cancer susceptibility loci in a multiethnic Asian cohort(☆).
Urol Oncol .(In press).
10.1016/j.urolonc.2012.02.009[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.,
. (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 18, 1368-1375 .
10.1093/hmg/ddp035[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.,
. (2011). Validation of genome-wide prostate cancer associations in men of African descent.
Cancer Epidemiol Biomarkers Prev 20, 23-32 .
10.1158/1055-9965.EPI-10-0698[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.,
. (2012). Evaluating genetic risk for prostate cancer among Japanese and Latinos.
Cancer Epidemiol Biomarkers Prev 21, 2048-2058 .
10.1158/1055-9965.EPI-12-0598[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 .
10.1093/carcin/bgp273[12] Eeles, R.A., Kote-Jarai, Z., AlOlama, A.A., Giles, G.G., Guy, M., Severi, G., Muir, K., Hopper, J.L., Henderson, B.E., Haiman, C.A.,
. (2009). Identification of seven new prostate cancer susceptibility loci through a genome-wide association study.
Nat Genet 41, 1116-1121 .
10.1038/ng.450[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.,
. (2008). Multiple newly identified loci associated with prostate cancer susceptibility.
Nat Genet 40, 316-321 .
10.1038/ng.90[14] Elston, R.C., Lin, D., and Zheng, G. (2007). Multistage sampling for genetic studies.
Annu Rev Genomics Hum Genet 8, 327-342 .
10.1146/annurev.genom.8.080706.092357[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 .
10.1158/1055-9965.EPI-10-1299[16] FitzGerald, L.M., Zhang, X., Kolb, S., Kwon, E.M., Liew, Y.C., HurtadoColl, A., Knudsen, B.S., Ostrander, E.A., and Stanford, J.L. (2013). Investigation of the relationship between prostate cancer and MSMB and NCOA4 genetic variants and protein expression.
Hum Mutat 34, 149-156 .
10.1002/humu.22176[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.,
. (2011). Principles for the post-GWAS functional characterization of cancer risk loci.
Nat Genet 43, 513-518 .
10.1038/ng.840[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.,
. (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 .
10.1016/S1470-2045(11)70266-2[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.,
. (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).
10.1111/j.1464-410X.2012.11648.x[20] Gudmundsson, J., Sulem, P., Rafnar, T., Bergthorsson, J.T., Manolescu, A., Gudbjartsson, D., Agnarsson, B.A., Sigurdsson, A., Benediktsdottir, K.R., Blondal, T.,
. (2008). Common sequence variants on 2p15 and Xp11.22 confer susceptibility to prostate cancer.
Nat Genet 40, 281-283 .
10.1038/ng.89[21] Gudmundsson, J., Sulem, P., Steinthorsdottir, V., Bergthorsson, J.T., Thorleifsson, G., Manolescu, A., Rafnar, T., Gudbjartsson, D., Agnarsson, B.A., Baker, A.,
. (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 .
10.1038/ng2062[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.,
. (2011). Characterizing genetic risk at known prostate cancer susceptibility loci in African Americans.
PLoS Genet 7, e1001387.
10.1371/journal.pgen.1001387[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 .
10.1073/pnas.0903103106[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 .
10.1038/nrg1521[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 .
10.5808/GI.2012.10.4.220[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 .
10.1158/1055-9965.EPI-11-0312[29] Jia, P., Liu, Y., and Zhao, Z. (2012). I ntegrative pathway analysis of genome-wide association studies and gene expression data in prostate cancer.
BMC Syst Biol 6 Suppl 3, S13.
10.1186/1752-0509-6-S3-S13[30] Juran, B.D., and Lazaridis, K.N. (2011). Ge nomics in the post-GWAS era.
Semin Liver Dis 31, 215-222 .
10.1055/s-0031-1276641[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.,
. (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 .
10.1016/j.eururo.2012.05.006[32] Kerns, S.L., Stock, R., Stone, N., Buckstein, M., Shao, Y., Campbell, C., Rath, L., De Ruysscher, D., Lammering, G., Hixson, R.,
. (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 .
10.1016/j.ijrobp.2012.08.003[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). HN F1B 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). Co mparison 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 .
10.1093/carcin/bgl236[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 .
10.1056/NEJM200007133430201[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 .
10.1002/pros.21235[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 .
10.1007/s00439-012-1182-2[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 .
10.1158/0008-5472.CAN-07-2043[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.,
. (2007). Genome-wide maps of chromatin state in pluripotent and lineage-committed cells.
Nature 448, 553-560 .
10.1038/nature06008[41] Miyamoto, Y., Shi, D., Nakajima, M., Ozaki, K., Sudo, A., Kotani, A., Uchida, A., Tanaka, T., Fukui, N., Tsunoda, T.,
. (2008). Common variants in DVWA on chromosome 3p24.3 are associated with susceptibility to knee osteoarthritis.
Nat Genet 40, 994-998 .
10.1038/ng.176[42] Nam, R.K., Zhang, W., Siminovitch, K., Shlien, A., Kattan, M.W., Klotz, L.H., Trachtenberg, J., Lu, Y., Zhang, J., Yu, C.,
. (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 .
10.4161/cbt.12.11.18366[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.,
. (2010). Refining the prostate cancer genetic association within the JAZF1 gene on chromosome 7p15.2.
Cancer Epidemiol Biomarkers Prev 19, 1349-1355 .
10.1158/1055-9965.EPI-09-1181[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 .
10.1007/s00439-012-1221-z[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.,
. (2008). Common variants in the GDF5-UQCC region are associated with variation in human height.
Nat Genet 40, 198-203 .
10.1038/ng.74[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.,
. (2011). Genome-wide association study identifies new prostate cancer susceptibility loci.
Hum Mol Genet 20, 3867-3875 .
10.1093/hmg/ddr295[48] Seng, K.C., and Seng, C.K. (2008). Th e success of the genome-wide association approach: a brief story of a long struggle.
Eur J Hum Genet 16, 554-564 .
10.1038/ejhg.2008.12[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.,
. (2006). Variants in the prostate-specific antigen (PSA) gene and prostate cancer risk, survival, and circulating PSA.
Cancer Epidemiol Biomarkers Prev 15, 1142-1147 .
10.1158/1055-9965.EPI-05-0984[50] Siegel, R., Naishadham, D., and Jemal, A. (2013). Ca ncer statistics, 2013.
CA Cancer J Clin 63, 11-30 .
10.3322/caac.21166[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 .
10.1073/pnas.0906067107[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 .
10.1200/JCO.2009.25.7816[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 .
10.1002/pros.21094[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.,
. (2007). Replicating genotype-phenotype associations.
Nature 447, 655-660 .
10.1038/447655a[55] Takata, R., Akamatsu, S., Kubo, M., Takahashi, A., Hosono, N., Kawaguchi, T., Tsunoda, T., Inazawa, J., Kamatani, N., Ogawa, O.,
. (2010). Genome-wide association study identifies five new susceptibility loci for prostate cancer in the Japanese population.
Nat Genet 42, 751-754 .
10.1038/ng.635[56] Thomas, G., Jacobs, K.B., Yeager, M., Kraft, P., Wacholder, S., Orr, N., Yu, K., Chatterjee, N., Welch, R., Hutchinson, A.,
. (2008). Multiple loci identified in a genome-wide association study of prostate cancer.
Nat Genet 40, 310-315 .
10.1038/ng.91[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.,
. (2009). Germline genetic variation in an organic anion transporter polypeptide associated with methotrexate pharmacokinetics and clinical effects.
J Clin Oncol 27, 5972-5978 .
10.1200/JCO.2008.20.4156[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 .
10.1200/JCO.2009.24.1968[59] Wang, M., Liu, F., Hsing, A.W., Wang, X., Shao, Q., Qi, J., Ye, Y., Wang, Z., Chen, H., Gao, X.,
. (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 .
10.1093/carcin/bgr279[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 .
10.1101/gr.105361.110[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 .
10.1038/nrg3352[62] Wright, J.B., Brown, S.J., and Cole, M.D. (2010). Upregulation of cMYC in cis through a large chromatin loop linked to a cancer riskassociated single-nucleotide polymorphism in colorectal cancer cells.
Mol Cell Biol 30, 1411-1420 .
10.1128/MCB.01384-09[63] Xu, J., Mo, Z., Ye, D., Wang, M., Liu, F., Jin, G., Xu, C., Wang, X., Shao, Q., Chen, Z.,
. (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 .
10.1038/ng.2424[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.,
. (2010). In herited genetic variant predisposes to aggressive but not indolent prostate cancer.
Proc Natl Acad Sci U S A 107, 2136-2140 .
10.1073/pnas.0914061107[65] Yaspan, B.L., and Veatch, O.J. (2011). Strategies for pathway analysis from GWAS data.
Curr Protoc Hum Genet. Chapter 1, Unit1.20.
10.1002/0471142905.hg0120s71[66] Yeager, M., Chatterjee, N., Ciampa, J., Jacobs, K.B., Gonzalez-Bosquet, J., Hayes, R.B., Kraft, P., Wacholder, S., Orr, N., Berndt, S.,
. (2009). Identification of a new prostate cancer susceptibility locus on chromosome 8q24.
Nat Genet 41, 1055-1057 .
10.1038/ng.444[67] Yeager, M., Orr, N., Hayes, R.B., Jacobs, K.B., Kraft, P., Wacholder, S., Minichiello, M.J., Fearnhead, P., Yu, K., Chatterjee, N.,
. (2007). Genome-wide association study of prostate cancer identifies a second risk locus at 8q24.
Nat Genet 39, 645-649 .
10.1038/ng2022[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.,
. (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 .
10.1016/j.lungcan.2008.10.016[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.,
. (2008). Meta-analysis of genome-wide association data and largescale replication identifies additional susceptibility loci for type 2 diabetes.
Nat Genet 40, 638-645 .
10.1038/ng.120[70] Zheng, J., Liu, F., Lin, X., Wang, X., Ding, Q., Jiang, H., Chen, H., Lu, D., Jin, G., Hsing, A.W.,
. (2012). Predictive performance of prostate cancer risk in Chinese men using 33 reported prostate cancer risk-associated SNPs.
Prostate 72, 577-583 .
10.1002/pros.21462