We first examined our samples for non-European ancestry, using multidimensional scaling after ‘seeding’ our data with those from the three HapMap analysis panels (see Supplementary Fig. 5 and Methods), and excluded 153 individuals on this basis. We next looked for evidence of population heterogeneity by studying allele frequency differences between the 12 broad geographical regions (defined in Supplementary Fig. 4). The results for these 11-d.f. tests and associated quantile-quantile plots are shown in Fig. 2. Widespread small differences in allele frequencies are evident as an increased slope of the line (Fig. 2b); in addition, a few loci show much larger differences (Fig. 2a and Supplementary Fig. 6).
