A total of 53,338 PAGE and GRP samples were genotyped on the MEGA array at the CIDR, of which 52,878 samples successfully passed the quality control process of the CIDR. Genotyping data that passed initial quality control at CIDR were released to the quality assurance and quality control analysis team at the University of Washington Genetic Analysis Center, after which the data were further cleaned according to previously described methods38 and genotypes for 51,520 subjects were returned. A total of 1,705,969 SNPs were genotyped on the MEGA. Quality control of genotyped variants was completed by filtering through various criteria, including the exclusion of (1) CIDR technical filters; (2) variants with missing call rate ≥ 2%; (3) variants with more than 6 discordant calls in 988 study duplicates; (4) variants with more than 1 Mendelian error in 282 trios and 1,439 duos; (5) variants with a Hardy–Weinberg P < 1 × 10−4; (6) SNPs with sex difference in allele frequency ≥ 0.2 for autosomes or XY; (7) SNPs with sex difference in heterozygosity > 0.3 for autosomes or XY; and (8)
