An overview of SNP genotyping, quality control (QC), and imputation is given in eTable 2. QC of genotype data was performed in each study independently, using comparable but study specific criteria. Basic QC steps included checks for European ancestry, sex inconsistencies, Mendelian errors, and high genome-wide homozygosity. Checks for relatedness were carried out in those samples that aimed to include unrelated individuals only. Genotype data were further checked based on Hardy–Weinberg Equilibrium (HWE), minor allele frequencies (MAF), SNP and sample call rates. Genotype data were imputed using the 1000G phase 1 version 3 (build 37, hg19) reference panel with standard software packages such as IMPUTE, MACH or Minimac (see eTable 2).
