Haplotypes, hotspots, and a multilocus model for linkage disequilibrium

Abstract

Current methods for understanding the relationship between LD and the underlying recombination rate are limited. The most common approach is to compute a measure of LD between every pair of sites in the region, and to form a graphical display of the results. However, it is typically difficult to assess the significance of observed patterns. More sophisticated coalescent-based statistical methods for estimating local recombination rate from patterns of LD are either computationally impractical for moderate-sized regions, or suffer from loss of information by using only a summary of the data. Furthermore, they all assume constant recombination rate, making them poor tools for studying local recombination rates. Here we propose a novel computationally-tractable model for LD across multiple loci. We apply this model to the problem of inferring recombination rates from population data, and in particular to identifying variation in the local recombination rate (”hotspots” and”coldspots”) long chromosomes. We outline how this model might be used to develop more powerful methods for LD mapping.