DNA was extracted from peripheral blood samples at the Karolinska Institutet Biobank. Samples were genotyped in six batches at the Broad Institute using Affymetrix 5.0 (3.9%), Affymetrix 6.0 (38.6%), and Illumina OmniExpress (57.4%) chips according to the manufacturers' protocols (Supplemental Table 3). Genotype calling, quality control, and imputation were done in four sets corresponding to data from Affymetrix 5.0 (Sw1), Affymetrix 6.0 (Sw2-4), and the OmniExpress batches (Sw5, Sw6). Genotypes were called using Birdsuite (Affymetrix) or BeadStudio (Illumina). The quality control parameters applied were: SNP missingness < 0.05 (before sample removal); subject missingness < 0.02;autosomal heterozygosity deviation; SNP missingness < 0.02 (after sample removal);difference in SNP missingness between cases and controls < 0.02; and deviation from Hardy-Weinberg equilibrium (P < 10−6 in controls or P < 10−10 in cases).
