A Comparison of Linkage Disequilibrium Patterns and Estimated Population Recombination Rates across Multiple Populations

Large-scale studies of linkage disequilibrium (LD) have shown considerable variation in the extent and distribution of pairwise LD within and between populations. Taken at face value, these results suggest that genomewide LD maps for one population may not be generalizable to other populations. However, at least part of this diversity is due to some undesirable features of pairwise LD measures, which are well documented for the D′ and r2 measures. In this report, we compare patterns of LD derived from pairwise measures with statistical estimates of population recombination rates (ρ) along a 10-Mb stretch of chromosome 20 in four population samples, comprising East Asians, African Americans, and U.K. and U.S. individuals of western European descent. The results reveal the expected variability of D′ within and between populations but show better concordance in estimates of r2 for the same markers across the population samples. Estimates of ρ correlate well across populations, but there is still evidence of population-specific spikes and troughs in ρ values. We conclude that it is unlikely that a single haplotype map will provide a definitive guide for association studies of many populations; rather, multiple maps will need to be constructed to provide the best-possible guides for gene mapping