After merging samples from all platforms, SNPs with an MAF difference >0.15 between case-case or control-control platforms were flagged, as were SNPs with >1% Mendelian errors in a parallel sample of 400 OCD trios genotyped simultaneously with the TS cases (Stewart et al., accompanying manuscript). Any SNP not present on the three major common platforms (550v1, 610-Quad, 1M) was removed, leaving 496 877 SNPs for population-specific QC.
