Journal Article

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

Liisa Kauppi, Antti Sajantila and Alec J. Jeffreys

in Human Molecular Genetics

Volume 12, issue 1, pages 33-40
Published in print January 2003 | ISSN: 0964-6906
Published online January 2003 | e-ISSN: 1460-2083 | DOI: https://dx.doi.org/10.1093/hmg/ddg008
Recombination hotspots rather than population history dominate linkage disequilibrium in the MHC class II region

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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.

Journal Article.  5817 words.  Illustrated.

Subjects: Genetics and Genomics

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