Figure 4

The individual participants are represented by rectangular shapes distributed by the strength of their separation in three dimensions: along the first factor (abscissa), second factor (ordinate), and third factor (depth). This factor analysis is based on vectors fitted to the individual allele frequencies of each SNP. The percentage of inertia for each factor is provided on each of the axes and correspond to the eigenvalue vectors.

(A) The analysis utilized the set of 2,657 random SNPs. In the upper panel, the European ancestry groups, Italy (ITN), Spain (SPN), eastern European American (EEURA), western European American (WEURA), Sweden (SWD), and Amerindian (AMI) are indicated by color code, and show that the ITN and SPN participants are mostly distinct from the other European populations examined. The eigenvalue vectors for factors 1–3 were 0.0234, 0.0024, and 0.0019, respectively. In the bottom panel, the same groups are shown without the AMI participants. The eigenvalue vectors for factors 1–3 were 0.0033, 0.0022, and 0.0014, respectively.

(B) The analysis was performed using 749 SNPs chosen for European substructure information. The country of origin is shown by the color coding indicated in the upper panel. Except for the Spanish, Italian (1), and Swedish groups, the participants in (B) do not overlap with those in (A), and were European Americans self-reported as having four grandparents with the same country of origin. The Italian (2) group were Italian Americans. The bottom right of (B) shows a different three-dimensional view (factor 3 as ordinate), and the bottom left of (B) shows factor 4. The vector eigenvalues for factors 1–4 were 0.0059, 0.0026, 0.0017, and 0.0016, respectively.