Remarkably, we observed that imputed genotypes could also be used to obtain very accurate estimates of LD between pairs of untyped markers, or of LD between a genotyped marker and an untyped marker. As shown in Figure 2, estimates of LD between two SNPs obtained using imputed data are much closer to the results obtained by actually genotyping the two SNPs than estimates obtained by looking up the two markers in the HapMap CEU database (Supplementary Figure 2 shows a similar comparison for D’ estimates). Even with some imprecision in estimates of individual genotypes, the increased sample size compensates to reduce variation in the estimated LD measures.
