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Human Molecular Genetics, 2003, Vol. 12, No. 1 33-40
© 2003 Oxford University Press

Recombination hotspots rather than population history dominate linkage disequilibrium in the MHC class II region

Liisa Kauppi1, Antti Sajantila2 and Alec J. Jeffreys1,*

1Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK and 2Department of Forensic Medicine, University of Helsinki, Helsinki, Finland

Received August 2, 2002; Accepted November 5, 2002

Recombination, demographic history, drift and selection influence the extent of linkage disequilibrium (LD) in the human genome, but their relative contributions remain unclear. To investigate the effect of meiotic recombination versus population history on LD, three populations with different demographic histories (UK north Europeans, Saami and Zimbabweans) were genotyped for high-frequency single-nucleotide polymorphisms (SNPs) across a 75 kb DNA segment of the MHC class II region. This region spans three well-characterized recombination hotspots and a 60 kb long LD block. Despite a high level of underlying haplotype diversity and considerable divergence in haplotype composition between populations, all three populations showed very similar patterns of LD. Surprisingly, the entire 60 kb LD block was present even in Africans, although it was relatively difficult to detect owing to a systematic deficiency of high frequency SNPs. In contrast, DNA within recombination hotspots did not show this low nucleotide diversity in Africans. Thus, while population history has some influence on LD, our findings suggest that recombination hotspots play a major global role in shaping LD patterns as well as helping to maintain localized SNP diversity in this region of the MHC.

* To whom correspondence should be addressed. Tel: +44 1162523435; Fax: +44 1162523378; Email: ajj{at}le.ac.uk


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