Siegel, R., Ma, J., Zou, Z. & Jemal, A. Cancer statistics, 2014. CA Cancer J. Clin. 64, 9–29 (2014).
Lin, K., Croswell, J.M., Koenig, H., Lam, C. & Maltz, A. in Prostate-Specific Antigen–Based Screening for Prostate Cancer: An Evidence Update for the U.S. Preventive Services Task Force (Agency for Healthcare Research and Quality, 2011).
Melnikow, J., LeFevre, M., Wilt, T.J. & Moyer, V.A. Counterpoint: randomized trials provide the strongest evidence for clinical guidelines: The US Preventive Services Task Force and Prostate Cancer Screening. Med. Care 51, 301–303 (2013).
Gomella, L.G. et al. Screening for prostate cancer: the current evidence and guidelines controversy. Can. J. Urol. 18, 5875–5883 (2011).
Lichtenstein, P. et al. 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 (2000).
Hjelmborg, J.B. et al. The heritability of prostate cancer in the Nordic Twin Study of Cancer. Cancer Epidemiol. Biomarkers Prev. 23, 2303–2310 (2014).
Al Olama, A.A. et al. Multiple loci on 8q24 associated with prostate cancer susceptibility. Nat. Genet. 41, 1058–1060 (2009).
Eeles, R.A. et al. Identification of seven new prostate cancer susceptibility loci through a genome-wide association study. Nat. Genet. 41, 1116–1121 (2009).
Eeles, R.A. et al. Multiple newly identified loci associated with prostate cancer susceptibility. Nat. Genet. 40, 316–321 (2008).
Eeles, R.A. et al. Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array. Nat. Genet. 45, 385–391 (2013).
Kote-Jarai, Z. et al. Seven prostate cancer susceptibility loci identified by a multi-stage genome-wide association study. Nat. Genet. 43, 785–791 (2011).
Schumacher, F.R. et al. Genome-wide association study identifies new prostate cancer susceptibility loci. Hum. Mol. Genet. 20, 3867–3875 (2011).
Amundadottir, L.T. et al. A common variant associated with prostate cancer in European and African populations. Nat. Genet. 38, 652–658 (2006).
Gudmundsson, J. et al. Genome-wide association study identifies a second prostate cancer susceptibility variant at 8q24. Nat. Genet. 39, 631–637 (2007).
Gudmundsson, J. et al. Genome-wide association and replication studies identify four variants associated with prostate cancer susceptibility. Nat. Genet. 41, 1122–1126 (2009).
Gudmundsson, J. et al. Common sequence variants on 2p15 and Xp11.22 confer susceptibility to prostate cancer. Nat. Genet. 40, 281–283 (2008).
Gudmundsson, J. et al. Two variants on chromosome 17 confer prostate cancer risk, and the one in TCF2 protects against type 2 diabetes. Nat. Genet. 39, 977–983 (2007).
Sun, J. et al. Evidence for two independent prostate cancer risk-associated loci in the HNF1B gene at 17q12. Nat. Genet. 40, 1153–1155 (2008).
Thomas, G. et al. Multiple loci identified in a genome-wide association study of prostate cancer. Nat. Genet. 40, 310–315 (2008).
Yeager, M. et al. Genome-wide association study of prostate cancer identifies a second risk locus at 8q24. Nat. Genet. 39, 645–649 (2007).
Duggan, D. et al. Two genome-wide association studies of aggressive prostate cancer implicate putative prostate tumor suppressor gene DAB2IP. J. Natl. Cancer Inst. 99, 1836–1844 (2007).
Haiman, C.A. et al. Genome-wide association study of prostate cancer in men of African ancestry identifies a susceptibility locus at 17q21. Nat. Genet. 43, 570–573 (2011).
Takata, R. et al. Genome-wide association study identifies five new susceptibility loci for prostate cancer in the Japanese population. Nat. Genet. 42, 751–754 (2010).
Al Olama, A.A. et al. A meta-analysis of 87,040 individuals identifies 23 new susceptibility loci for prostate cancer. Nat. Genet. 46, 1103–1109 (2014).
Witte, J.S., Visscher, P.M. & Wray, N.R. The contribution of genetic variants to disease depends on the ruler. Nat. Rev. Genet. 15, 765–776 (2014).
Gudmundsson, J. et al. A study based on whole-genome sequencing yields a rare variant at 8q24 associated with prostate cancer. Nat. Genet. 44, 1326–1329 (2012).
Cropp, C.D. et al. 8q24 risk alleles and prostate cancer in African-Barbadian men. Prostate 74, 1579–1588 (2014).
Hazelett, D.J., Coetzee, S.G. & Coetzee, G.A. A rare variant, which destroys a FoxA1 site at 8q24, is associated with prostate cancer risk. Cell Cycle 12, 379–380 (2013).
Haiman, C.A. et al. Multiple regions within 8q24 independently affect risk for prostate cancer. Nat. Genet. 39, 638–644 (2007).
Barrett, J.C., Fry, B., Maller, J. & Daly, M.J. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21, 263–265 (2005).
Lindblad-Toh, K. et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature 478, 476–482 (2011).
Gnirke, A. et al. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat. Biotechnol. 27, 182–189 (2009).
Rohland, N. & Reich, D. Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture. Genome Res. 22, 939–946 (2012).
Li, Y., Sidore, C., Kang, H.M., Boehnke, M. & Abecasis, G.R. Low-coverage sequencing: implications for design of complex trait association studies. Genome Res. 21, 940–951 (2011).
Lee, S.H. et al. Estimation of SNP heritability from dense genotype data. Am. J. Hum. Genet. 93, 1151–1155 (2013).
Yang, J., Lee, S.H., Goddard, M.E. & Visscher, P.M. GCTA: a tool for genome-wide complex trait analysis. Am. J. Hum. Genet. 88, 76–82 (2011).
Gusev, A. et al. Quantifying missing heritability at known GWAS loci. PLoS Genet. 9, e1003993 (2013).
Lee, S.H., Yang, J., Goddard, M.E., Visscher, P.M. & Wray, N.R. Estimation of pleiotropy between complex diseases using single-nucleotide polymorphism–derived genomic relationships and restricted maximum likelihood. Bioinformatics 28, 2540–2542 (2012).
Eyre-Walker, A. Genetic architecture of a complex trait and its implications for fitness and genome-wide association studies. Proc. Natl. Acad. Sci. USA 107, 1752–1756 (2010).
Kichaev, G. et al. Integrating functional data to prioritize causal variants in statistical fine-mapping studies. PLoS Genet. 10, e1004722 (2014).
Hazelett, D.J. et al. Comprehensive functional annotation of 77 prostate cancer risk loci. PLoS Genet. 10, e1004102 (2014).
Bhatia, G. et al. Haplotypes of common SNPs can explain missing heritability of complex diseases. bioRxiv 10.1101/022418 (12 July 2015).
Huffman, J.E. et al. Rare and low-frequency variants and their association with plasma levels of fibrinogen, FVII, FVIII, and vWF. Blood 126, e19–e29 (2015).
Peloso, G.M. et al. Association of low-frequency and rare coding-sequence variants with blood lipids and coronary heart disease in 56,000 whites and blacks. Am. J. Hum. Genet. 94, 223–232 (2014).
Lange, L.A. et al. Whole-exome sequencing identifies rare and low-frequency coding variants associated with LDL cholesterol. Am. J. Hum. Genet. 94, 233–245 (2014).
Service, S.K. et al. Re-sequencing expands our understanding of the phenotypic impact of variants at GWAS loci. PLoS Genet. 10, e1004147 (2014).
Kolonel, L.N. et al. A multiethnic cohort in Hawaii and Los Angeles: baseline characteristics. Am. J. Epidemiol. 151, 346–357 (2000).
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
DePristo, M.A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491–498 (2011).
Browning, B.L. & Browning, S.R. A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals. Am. J. Hum. Genet. 84, 210–223 (2009).
Browning, B.L. & Browning, S.R. A fast, powerful method for detecting identity by descent. Am. J. Hum. Genet. 88, 173–182 (2011).
Baran, Y., Quintela, I., Carracedo, Á., Pasaniuc, B. & Halperin, E. Enhanced localization of genetic samples through linkage-disequilibrium correction. Am. J. Hum. Genet. 92, 882–894 (2013).
Chang, C.C. et al. Second-generation PLINK: rising to the challenge of larger and richer datasets. GigaScience 4, 7 (2015).
Willer, C.J., Li, Y. & Abecasis, G.R. METAL: fast and efficient meta-analysis of genomewide association scans. Bioinformatics 26, 2190–2191 (2010).
Oehlert, G.W. A note on the delta method. Am. Stat. 46, 27–29 (1992).
Speed, D., Hemani, G., Johnson, M.R. & Balding, D.J. Improved heritability estimation from genome-wide SNPs. Am. J. Hum. Genet. 91, 1011–1021 (2012).
Yang, L. et al. Polygenic transmission and complex neuro developmental network for attention deficit hyperactivity disorder: genome-wide association study of both common and rare variants. Am. J. Med. Genet. B. Neuropsychiatr. Genet. 162B, 419–430 (2013).
Takahata, N. Allelic genealogy and human evolution. Mol. Biol. Evol. 10, 2–22 (1993).
Lohmueller, K.E. The impact of population demography and selection on the genetic architecture of complex traits. PLoS Genet. 10, e1004379 (2014).