Haplotype blocks and linkage disequilibrium in the human genome

Linkage disequilibrium (LD) is the nonrandom association of alleles at different sites.Recent studies have proposed that patterns of LD in the human genome can be summarized by a series of discrete haplotype blocks: regions of high LD that are separated from other haplotype blocks by many historical recombination events.Patterns of LD and the fit of the haplotype-block model vary tremendously from region to region: some show extensive well-defined haplotype blocks, while others contain essentially no haplotype blocks.This variability across regions is probably the result of several factors, which include large-scale variation in recombination rates (apparent from genetic maps), fine-scale variation in recombination rates (for example, hotspots) and the inherent stochasticity of LD.Simulations indicate that although recombination hotspots generally create haplotype-block boundaries, the converse is not true: most haplotype-block boundaries do not occur at hotspotsThe identification of haplotype blocks will be of some use for future association studies, but there will be a substantial fraction of the genome (not covered by large haplotype blocks) for which other approaches will be useful.