Genotype Quality Control and Imputation

All participants were genotyped upon consent using common single nucleotide polymorphism (SNP) arrays including Affymetrix Affy60 and Axiom, and Illumina HumanHap550 (v1, v3), Human610-Quad (v1), and HumanOmniExpress. We applied pre-imputation quality control measures to our genotype data, including removing SNPs with minor allele frequencies (MAF) < 5%, Hardy–Weinberg equilibrium p values < 1.0e − 4, and call rates < 95%. We phased and imputed the genotype data using the Haplotype Reference Consortium reference panel version r1.1 2016 available on the Michigan Imputation server [40 (link)]. After imputation, we further removed duplicated and strand-ambiguous SNPs, as well as SNPs with MAF < 0.01 or an imputation quality score below 0.8. Samples genotyped using different arrays were processed in separate batches.