Based on published candidate gene association studies, gene expression studies, and pathway analysis we constructed a list of 848 candidate genes of interest in prostate cancer. Using GenePipe, 542 genes were excluded because none of the GWAS SNPs in these genes had a P-value ≤0.05 and there were sufficient GWAS SNPs to capture (at r2 ≥ 0.8) more than 50% of common (MAF ≥ 0.05) SNPs in Europeans. For the remaining 306 genes, 822 non-redundant SNPs were selected as outlined in Figure 1 with the following GenePipe parameter values: gene upstream region = 5 kb, gene downstream region = 1 kb, MAF = 0.05 for all SNPs, weight = 3 for any predicted functional SNP and small P-value SNPs, weight = 1 for all other SNPs, r2 threshold = 0.8, minimum number of SNPs tagged by each selected tag SNP = 3, minimum number of tag SNPs/gene = 1, and maximum number of tag SNPs/gene = 5.
