Journal Article

Comparative high-resolution analysis of linkage disequilibrium and tag single nucleotide polymorphisms between populations in the vitamin D receptor gene

Sergey Nejentsev, Lisa Godfrey, Hywel Snook, Helen Rance, Sarah Nutland, Neil M. Walker, Alex C. Lam, Cristian Guja, Constantin Ionescu-Tirgoviste, Dag E. Undlien, Kjersti S. Rønningen, Eva Tuomilehto-Wolf, Jaakko Tuomilehto, Melanie J. Newport, David G. Clayton and John A. Todd

in Human Molecular Genetics

Volume 13, issue 15, pages 1633-1639
Published in print August 2004 | ISSN: 0964-6906
Published online June 2004 | e-ISSN: 1460-2083 | DOI: http://dx.doi.org/10.1093/hmg/ddh169
Comparative high-resolution analysis of linkage disequilibrium and tag single nucleotide polymorphisms between populations in the vitamin D receptor gene

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A genome-wide map of single nucleotide polymorphisms (SNP) and a pattern of linkage disequilibrium (LD) between their alleles are being established in three main ethnic groups. An important question is the applicability of such maps to different populations within a main ethnic group. Therefore, we have developed high-resolution SNP, haplotype and LD maps of vitamin D receptor gene region in large samples from five populations. Comparative analysis reveals that the LD patterns are identical in all four European populations tested with two small regions of 1.3 and 5.7 kb at which LD is disrupted completely resulting in three block-like regions over which there is significant and extensive LD. In an African population the pattern is similar, but two additional LD-breaking spots are also apparent. This LD pattern suggests combined action of recombination hotspots and founder effects, but cannot be explained by random recombination and genetic drift alone. Direct comparison indicates that the tag SNPs selected in one European population effectively predict the non-tag SNPs in the other Europeans, but not in the Gambians, for this region.

Journal Article.  3667 words.  Illustrated.

Subjects: Genetics and Genomics

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