Principal components analysis (PCA) was conducted using the smartpca program in the Eigensoft 3.0 package (Patterson et al., 2006) to determine whether correction for admixture was necessary. The kill r2 setting of 0.8 was used to remove 307 SNPs in high LD with others in the panel for the examination of admixture. PCA using data from the remaining 1123 SNPs found that comparisons of cases to neighborhood controls did not require inclusion of principal components as covariates. The breakdown of self-reported ancestry, available for 590 individuals with PTSD, is 68.6% European, 5.1% Asian, 1.4% Aboriginal, and 24.9% mixed. The similar breakdown available for 1011 individuals without PTSD is 76.1% European, 7.0% Asian, 1.8% Aboriginal, and 15.1% mixed.
