We have used the GWAS data from the Cancer Genetics Markers of Susceptibility (CGEMS) project on prostate cancer (4) to demonstrate the utility of our method. This GWAS genotyped 550 K SNPs in 1172 prostate cancer cases and 1157 controls of European origin. We used our web utility to construct a small SNP genotyping panel for a genetic association study on prostate cancer in African-American and European-American men.
