Despite some different choices of SNPs to be typed—either tag-SNPs chosen to capture substantial variability of the common SNPs in the HapMap, or randomly selected SNPs, or a combination of both strategies—all of the major genotyping platforms that are currently available offer similar coverage of common variants in the HapMap [46,55]. The coverage ranges between 500,000 and 1,000,000 SNPs per sample, and these numbers continue to steadily increase. Initial estimates suggested that, for example, the Illumina humanhap 300 array captured 75% of HapMap common SNPs with an allelic correlation of 80% in subjects of European ancestry, but the coverage was only 28% in subjects of African ancestry. The 80% allelic correlation is a measure of the LD between two SNPs that is based on the correlation coefficient r2 (see Table I) and measures the correlation of two SNP alleles on the same chromosome [56]. Equivalent arrays produced by Affymetrix had lower coverage of common SNPs for Europeans but higher coverage for Africans [55]. These figures are higher in denser arrays, with a clear gain of coverage in African subjects, so
