title: Comparative high-resolution analysis of linkage disequilibrium and tag single nucleotide polymorphisms between populations in the vitamin D receptor gene.
abstract: 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.
authors.affiliation: Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, UK. sergey.nejentsev@cimr.cam.ac.uk
authors.forename: Sergey
authors.initials: S
authors.lastname: Nejentsev
authors.forename: Lisa
authors.initials: L
authors.lastname: Godfrey
authors.forename: Hywel
authors.initials: H
authors.lastname: Snook
authors.forename: Helen
authors.initials: H
authors.lastname: Rance
authors.forename: Sarah
authors.initials: S
authors.lastname: Nutland
authors.forename: Neil M
authors.initials: NM
authors.lastname: Walker
authors.forename: Alex C
authors.initials: AC
authors.lastname: Lam
authors.forename: Cristian
authors.initials: C
authors.lastname: Guja
authors.forename: Constantin
authors.initials: C
authors.lastname: Ionescu-Tirgoviste
authors.forename: Dag E
authors.initials: DE
authors.lastname: Undlien
authors.forename: Kjersti S
authors.initials: KS
authors.lastname: Rønningen
authors.forename: Eva
authors.initials: E
authors.lastname: Tuomilehto-Wolf
authors.forename: Jaakko
authors.initials: J
authors.lastname: Tuomilehto
authors.forename: Melanie J
authors.initials: MJ
authors.lastname: Newport
authors.forename: David G
authors.initials: DG
authors.lastname: Clayton
authors.forename: John A
authors.initials: JA
authors.lastname: Todd
mesh_terms: D002881:Chromosomes, Human, Pair 12; D005714:Gambia; D006801:Humans; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide; D018167:Receptors, Calcitriol / Q000235:genetics*; D006113:United Kingdom
chemical_list: D018167:Receptors, Calcitriol