Only SNPs present on all of the applied genotyping platforms were included in the analysis. To remain in the dataset, the SNPs had to fulfill the following criteria: CR >=0.98; minor allele frequency (MAF) >=0.01; conformity with Hardy-Weinberg equilibrium (HWE; p>=1E–6) in any subsample; HWE conformity across all samples; and no significant difference in allele frequency between subsamples for controls. Cluster plots of our top findings were then assessed visually, and SNPs with poor cluster quality were removed. In 900 patients (genotyped in the follow-up study of GWAS1 with sequenom and in GWAS2 with illumina chip), replication of 140 SNPs showed 99.8% identity.
