We used principal component analysis (PCA) to characterize residual population structure in the subset of 23andMe participants with European ancestry. We computed principal components using 82,654 SNPs that were genotyped on all 23andMe array designs, with Hardy-Weinberg P > 1e–40, minor allele frequency > 0.01, call rate > 99%, and excluding regions of extended long range linkage disequilibrium. We used the ARPACK library34 to compute principal components using data for 519,914 individuals across all array designs; additional individuals were then projected onto this set of eigenvectors.
