Linkage disequilibrium

Linkage disequilibrium (LD) refers to the correlation among neighboring alleles, reflecting common haplotype ancestry. In the May 10 Nature, Reich et al. describe a systematic, genome-wide analysis of LD within human populations (Nature 2001, 411:199-204). They analyzed 19 random chromosomal regions, each of which centers around a core SNP (single length polymorphism) in the coding region of a gene. Extensive sequencing of 44 individuals from Utah identified 272 'high frequency' SNPs at 0-160 kilobases (kb) from the core SNP. The authors measured LD between two SNPs using the classical statistic D'. They found that the LD 'half length' (the distance at which the average D' value drops below 0.5) was about 60 kb, significantly longer that previous predictions. Similar LD estimates were found for US and north-European populations, but were markedly shorter (half-length of less than 5 kb) in a Nigerian population. The authors propose that large-scale LD analysis may be applied to disease gene mapping and the study of population history.