Genotyping was performed by the Partners Biobank using the Illumina Multi-Ethnic Global (MEG) array and its pre-release forms MEGA and MEGA Ex (Illumina, Inc., San Diego, CA). SNPs with low genotyping quality were removed during quality control processing. The Biobank team used Illumina’s manual clustering process and the Michigan Imputation Server (MIS) for quality control. Samples with a discrepancy between reported and predicted sex were first removed. Subsequently, the team removed sites with invalid alleles, duplicate, monomorphic, indel, allele mismatch, or a low call rate (less than 90%). SNPs that were not in the 1000 Genomes reference panel were also removed. Imputation to the 1000 Genomes panel was performed using the Michigan Imputation Server and haplotype phasing was performed using SHAPEIT(Delaneau et al., 2011).
