Journal Article

Linkage disequilibrium patterns of the human genome across populations

Sagiv Shifman, Jane Kuypers, Mark Kokoris, Benjamin Yakir and Ariel Darvasi

in Human Molecular Genetics

Volume 12, issue 7, pages 771-776
Published in print April 2003 | ISSN: 0964-6906
Published online April 2003 | e-ISSN: 1460-2083 | DOI: http://dx.doi.org/10.1093/hmg/ddg088
Linkage disequilibrium patterns of the human genome across populations

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We studied the patterns of linkage disequilibrium (LD) in the human genome among three populations: African Americans, Caucasians and Ashkenazi Jews. These three populations represent admixed, outbred and isolated populations, respectively. The study examined defined chromosomal regions across the whole genome. We found that SNP allele frequencies are highly correlated between Ashkenazi Jews and Caucasians and somewhat distinct in African Americans. In addition, Ashkenazi Jews have a modest increase in LD compared with Caucasians, and both have greater LD than African Americans. The three populations differed more significantly with regard to haplotype heterogeneity. We found, as expected, that Ashkenazi Jews display the greatest extent of homogeneity and African Americans the greatest extent of heterogeneity. We found that most of the variance in LD can be attributed to the difference between regions and markers rather than to that between different population types. The average recombination rates estimated by low-resolution genetic maps can only explain a small fraction of the variance between regions. We found that LD (in terms of r2) decreases as a function of distance even within the so-called ‘haplotype blocks’. This has significant consequences when using LD mapping for the genetic dissection of complex traits, as higher density SNP maps will be required to scan the genome.

Journal Article.  4011 words.  Illustrated.

Subjects: Genetics and Genomics

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