Assuming a public reference sample is available to serve as a control, the objective is to select a set of controls with ancestry similar to the cases without the aid of detailed demographic records of ancestry. To this end we conduct an experiment to see how well we can match individuals in the projected sample to those in the base sample by pair matching to minimize the total pairwise distance in the eigenmap [31]; and by matching at random within each of the seven strata in POPRES and eight strata in HGDP. Distances observed for the two different matching criterion are similar (Supplementary Figure 4), which suggests that the eigenvectors are mapping populations in correspondence with subtle demographic labels.
