Infinium global screening array v1

The Infinium Global Screening Array v1.0 (Illumina, San Diego CA, USA) was used to characterize variation at 690,364 markers across the genome according to manufacturer’s guidelines. Individuals with low genotyping rates (<95%) and single nucleotide polymorphisms (SNPs) showing significant deviation from Hardy-Weinberg equilibrium (HWE, p-value < 1×10⁻³⁰) were excluded. Similarly, SNPs with high rates of missing data (>5%) were excluded. Quality control of genetic data was performed using PLINK 1.9 (Chang et al., 2015 (link)). Imputation of additional variants was performed using the Sanger Imputation Service with Haplotype Reference Consortium (release 1.1; http://www.haplotype-reference-consortium.org/participating-cohorts) panel (McCarthy et al., 2016 (link)). SNPs with imputation accuracy score of less than 0.8 were excluded. Imputed genotype probabilities were converted to hard-called genotypes using posterior genotype probability above 0.90. Population structure was described using principal component analysis (Patterson et al., 2006 (link)) of a pruned set of genotyped SNPs with a minor allele frequency > 5% in low linkage disequilibrium (r²<0.20) with a 50 kilobase sliding window and an increment of 5 SNPs. Population structure was best described by the first three principal component scores (PC1, PC2, PC3), which were included as covariates in specified analyses.