such SNPs. The third, linkage pipeline uses a user-provided list of linkage regions to select small P-value GWAS SNPs for each linkage region. The web application has information on all SNPs in HapMap and dbSNP and automatically constructs ethnic-specific LD relationships from both sources provided that the SNPs have population data available. In this way, SNPs that were not genotyped in a GWAS, but are in LD with a SNP that was genotyped, can be screened appropriately and GWAS data generated in one ethnic group can be used to pick SNPs in one or more other ethnic groups. We illustrate this application using prostate cancer as an example in which we start with a set of a priori candidate genes, prostate cancer GWAS data, and a set of linkage regions, and use the pipelines to select a small panel of 1361 SNPs. We evaluate the utility of the application against the results of a follow-up validation study that screened a much larger panel of ∼27 000 SNPs genotyped in ∼8000 cases and controls and find that we included five of the seven SNPs found to be associated with prostate cancer.
