Initial QC control in the QIMR sample was applied separately to different genotype platform data and different projects. Data were checked for ancestry outliers, Mendelian errors, HWE failure (excluded if P<10−6) and minor allele frequency. After separate QC checks, Illumina and Affymetrix data were imputed separately by MACH using the data from the European HM2. SNPs with an imputation quality score (r2) >0.3 were retained, resulting in 2 380 486 Illumina and 2 369 130 Affymetrix SNPs. In addition, QC using individuals that were imputed on both the Illumina and the Affymetrix platforms, SNPs were only retained if they had high concordance rates for the most probable genotype, and had a minor allele frequency>0.01. In total, 1 252 387 SNPs were available for association analyses. More details on QC procedures in the QIMR sample can be found in Verweij et al.18
