sample of major depressive disorder cases only, more stringent QC criteria were applied. We had 327 individuals genotyped on both the Illumina and the Affymetrix platform, allowing for cross project QC. These checks led us to a more stringent value (>0.02; using the Birdseed program) for the genotype confidence score for the Affymetrix data for selecting which SNPs to include in our dataset. After QC control of the individual projects, the data from the different Illumina projects were combined and additional QC was applied to this combined dataset.
