Venous blood samples were taken at the time of the participation in the CoLaus study. Nuclear DNA was extracted from whole blood. Participants consented for the genetic data to be used for the study of cardiovascular risk factors and psychiatric disorders. The samples were genotyped on the Affymetrix GeneChip Human Mapping 500K Array Set according to the Affymetrix published protocol. Genotypes were determined by the Bayesian Robust Linear Model with Mahalanobis Distance algorithm (BRLMM). Details of the genotyping procedures are given by Li [35]. A QC procedure was carried out on the sample to remove SNPs with poor amplification and individuals with an excess of missing genotypes. First, a total of 60,545 SNPs with >5% missing genotypes were removed. Next, 4 individuals with missingness >5% among the remaining SNPs were excluded. This left 2,235 individuals genotyped at 430,193 autosomal SNPs. An additional 9,828 SNPs were available on the X chromosome, but only in 2,168 individuals. Overall we flagged 1,893 autosomal SNPs showing significant deviation from HWE (p<10−4). None of the SNPs highlighted here were among these 1,893.
