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Human Molecular Genetics, 2003, Vol. 12, No. 7 771-776
DOI: 10.1093/hmg/ddg088
© 2003 Oxford University Press

Linkage disequilibrium patterns of the human genome across populations

Sagiv Shifman1,2, Jane Kuypers3, Mark Kokoris3, Benjamin Yakir4 and Ariel Darvasi1,2,*

1The Life Sciences Institute, The Hebrew University of Jerusalem, Jerusalem 91904, Israel, 2IDgene Pharmaceuticals Ltd, Jerusalem 91344, Israel, 3QIAGEN Genomics Inc., 1725 220th St SE, Bothell, WA 98021, USA and 4Department of Statistics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel

Received December 9, 2002; Revised January 30, 2003; Accepted February 5, 2003

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 r 2) 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.

* To whom correspondence should be addressed. Tel: +972 26595600; Fax: +972 26595601; Email: arield{at}cc.huji.ac.il


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