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PCA-Correlated SNPs for Structure Identification in Worldwide Human Populations

Figure 4

Analysis of 1.7 Million SNPs Typed on the HapMap Han Chinese and Japanese populations (Available from the HapMap Database)

(A) Projection of all 90 Han Chinese and Japanese individuals on the top two principal components using PCA on all available SNPs

(B) k-Means clustering on panel (A).

(C) Average correlation coefficient between true and predicted membership of an individual to the Japanese of Han Chinese populations, using PCA and k-means clustering on all available SNPs and sets of 50 to 1,000 PCA-correlated, high-In or random SNPs (random selection was repeated 30 times). The dotted line represents a decline in the performance of high-In SNPs due to the detection of a very large number of significant principal components; see Results for details.

Figure 4

doi: https://doi.org/10.1371/journal.pgen.0030160.g004