Figure 2.
Estimation of European Ancestry using Exome Chip Genotypes
Grey symbols represent 1,000 reference individuals randomly selected from the POPRES data. Colored symbols represent the remaining 385 POPRES individuals who constitute the test set. Population abbreviations and colors follow Novembre et al.29
(A) Estimated ancestry based on all 318,682 SNPs genotyped in the POPRES data with K = K′ = 2.
(B–D) Estimated ancestry based on 3,983 exome chip SNPs shared with the original POPRES data.
(B) K = K′ = 2 and t0 = 0.5112 compared to estimates based on genome-wide SNPs in (A).
(C) K = K′ = 20 and t0 = 0.7946 when comparing top two PCs to estimates in (A).
(D) K = 2, K′ = 20, and t0 = 0.8135 compared to estimates based on genome-wide SNPs in (A).
(E–G) Estimated ancestry based on 19,123 exome chip SNPs shared with the imputed POPRES data.
(E) K = K′ = 2 and t0 = 0.5594 compared to estimates based on genome-wide SNPs in (A).
(F) K = K′ = 20 and t0 = 0.9042 when comparing top two PCs to estimates in (A).
(G) K = 2, K′ = 20, and t0 = 0.9087 compared to estimates based on genome-wide SNPs in (A).