In both GWAS discovery samples, genotyping was carried out using the Affymetrix Genome-Wide Human SNP Array 6.0. Besides 906 703 SNP probes (869 747 autosomal), this chip contains 943 390 non-polymorphic additional probes (888 023 autosomal) for copy number analyses (http://www.affymetrix.com). The autosomal fluorescent intensities at the non-polymorphic probes were used as a measure of copy number variance for the primary statistical analysis. This was done to avoid the loss of information and power related to CNV calling (36,37). The intensity values were extracted from the individual CEL files utilizing the R-package ‘affxparser’. We normalized the raw intensities of the case–control GWAS sample by performing quantile normalization (38) to address potential chip effects. In case of the family-based GWAS sample, we analysed the raw fluorescent intensities since the family-based design allows for controlling the inter-individual variability.
