We implemented a series of filtering steps to select a pruned set of high-quality variants from the 1,584,609 variants detected across the cohort. Variants were excluded if they (1) failed VQSR; (2) lay within the highly variable HLA, LCT, 8p and 17q regions; (3) had MAF below 5% or deviation from Hardy-Weinberg Equilibrium below p < 1.0 E-4; or (4) had linkage disequilibrium r2 value above 0.2 within 0.1 megabase sliding windows. In total, 16,187 variants passed all filters, and 12,100 variants overlapped with variants detected in the 1000 Genomes samples of known ethnicities. The genotypes of the ADSP samples were combined with those of the 1000 Genomes samples at these 12,100 loci. PCs of the genotypes were then computed and plotted using the software plinkQC (https://meyer-lab-cshl.github.io/plinkQC/). The first four PCs of the ADSP genotypes had eigenvalues above 1 and were retained as covariates in the association analyses.

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