Insights into recombination from patterns of linkage disequilibrium in humans

An ability to predict levels of linkage disequilibrium (LD) between linked markers would facilitate the design of association studies and help to distinguish between evolutionary models. Unfortunately, levels of LD depend crucially on the rate of recombination, a parameter that is difficult to measure. In humans, rates of genetic exchange between markers megabases apart can be estimated from a comparison of genetic and physical maps; these large-scale estimates can then be interpolated to predict LD at smaller ("local") scales. However, if there is extensive small-scale heterogeneity, as has been recently proposed, local rates of recombination could differ substantially from those averaged over much larger distances. We test this hypothesis by estimating local recombination rates indirectly from patterns of LD in 84 genomic regions surveyed by the SeattleSNPs project in a sample of individuals of European descent and of African-Americans. We find that LD-based estimates are significantly positively correlated with map-based estimates. This implies that large-scale, average rates are informative about local rates of recombination. Conversely, although LD-based estimates are based on a number of simplifying assumptions, it appears that they capture considerable information about the underlying recombination rate or at least about the ordering of regions by recombination rate. Using LD-based estimators, we also find evidence for homologous gene conversion in patterns of polymorphism. However, as we demonstrate by simulation, inferences about gene conversion are unreliable, even with extensive data from homogeneous regions of the genome, and are confounded by genotyping error.