Several investigations have found that the SNPs typically used in GWA studies are in various ways not representative58,59. They can have comparatively higher minor allele frequency (MAF) in Europeans and therefore higher expected heterozygosity than might be predicted on the basis of what is known about other types of markers that have less ascertainment bias (Fig. 3). These observations, which result from a likely focus on populations of European ancestry in the initial detection of SNPs, in turn affect the relative proportion of the genome suited to mapping in different populations. Because of ascertainment effects in the development of marker panels, the fraction of the genome that lies within a specified physical distance of at least one variable marker in a standard panel can vary across populations. Additionally, the LD statistic r2 that measures whether a locus is “covered” by a panel, typically on the basis of its maximal LD with some marker from the panel60, depends on marker allele frequencies61,62, with intermediate-MAF markers having greater potential to produce high r2 values with markers at a range of other minor
