To obtain consistent ancestry-informative covariates, we carried out a final principal components analysis (PCA)30 of all subjects, using the 82,361 autosomal SNPs common to the three datasets. Subjects who were outliers to the distributions of the two largest components were excluded (no additional STAR*D cases had to be excluded beyond those noted above), and the first ten PC scores were entered into the analyses as covariates to correct for population substructure.
