SNPs. Three of the five SNPs were selected by GenePipe, one was selected by GenomePipe and three were selected by LinkagePipe. Of the two SNPs that were missed, rs10486567 in JAZF1 was not in our candidate gene list because at the time we constructed the gene list, JAZF1 had not previously been reported in the literature as having any association with prostate cancer. The other SNP, rs10896449, was not located in a known gene or linkage region. Although the very small panel of SNPs selected by the algorithm cannot substitute for massive follow-up genotyping, it performs very well with 2.5% (709 vs. 26 958) of the GWAS SNPs, and in addition dedicates almost half of the SNPs to new functional and candidate gene polymorphisms that were unexplored in the half million GWAS SNP panel.
