DNA samples were genotyped on three related platforms: cases on Affymetrix 500K and 5.0, and controls on Affymetrix 6.0, resulting in 382,598 SNPs that were assayed on all three platforms and that passed QC for the MGS/GenRED controls. To ensure consistency of results, we then excluded SNPs for all samples in the STAR*D analysis based on cross-platform data as follows:
