Figure 1

Minor allele frequency comparison for different populations typed on the Omni5 chip. We compared the distribution of minor allele frequencies for black Sowetan (BSO; n = 94) individuals to those generated in-house, by Illumina, for the CEU, CHB, JPT and YRI populations. Note that minor allele designation was dependent on genotyping frequencies per population, thus the minor allele per SNP may be different between populations. BSO individuals had an increased fraction of SNPs with minor allele frequencies between 0 and 2.5%, as well as a lower proportion of monomorphic SNPs (0 MAF), when compared to their African counterparts, the Yoruba (n = 55). Between frequencies of 2.5 and 10%, the YRI had a marginally larger fraction of SNPs, but levels remained comparable between the two African groups for common variants with frequencies between 10 and 50%. Performance was best for CEU (n = 113), with a low percentage of monomorphic SNPs and a significantly greater proportion of rare (1-5%) markers. Conversely, Asian [CHB (n = 44) and JPT (n = 40)] populations fared poorly, with over half of all markers on the Omni5 panel lacking variation.