Genotyping was accomplished via a 723,305-SNP Affymetrix Axiom biobank array, customized for the MVP32. The first MVP data release (used here) includes genotyping data from 360,062 individuals. After quality control, there were 353,948 samples and 657,459 SNPs remaining. Of these, 187,644 subjects had available PCL scores. Population group assignment is discussed below. Due to missing PCL scores or covariate information, GWAS analysis considered 146,660 EA samples and 19,983 AA samples. The MVP genotype data were imputed through Minimac334 using data from the 1000 Genomes Project reference panel (version 3), resulting in imputed genotypes for 49,134,253 SNPs. QC thresholds for post-imputation data were: info score R2 >0.9, MAF>0.01, and Hardy-Weinberg equilibrium test p-value >1 × 10−6. Samples with call rate >98.5% and SNPs with minor allele frequency (MAF) >2×10−6 were retained.
