Quality control (QC) was first carried out on three batches of samples that may differ in key variables: 1) all cases, LifeGene-EGOS controls, and LifeGene-NORDiC, 2) LifeGene-ANGI-Wave-1 controls, and 3) LifeGene-ANGI-Wave-2 controls. We employed the following QC steps using PLINK 2.0 (Supplementary Materials Tables S1–S3): individuals were removed who had a genotype non-call rate > 0.05, were discrepant for nominal versus genetically-determined sex, or had low heterozygosity (< −3SD or > +3SD from the mean); a SNP was removed if its non-call rate for genotypes was > 0.05, its MAF < 0.01, or it had Hardy–Weinberg equilibrium (HW) p-value < 0.00125. Gemtools was used to choose individuals with European ancestry where indicated (Supplementary Materials Figure S1).
