Comparative high-resolution analysis of linkage disequilibrium and tag single nucleotide polymorphisms between populations in the vitamin D receptor gene.
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.
Nejentsev
Sergey
S
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
Godfrey
Lisa
L
Snook
Hywel
H
Rance
Helen
H
Nutland
Sarah
S
Walker
Neil M
NM
Lam
Alex C
AC
Guja
Cristian
C
Ionescu-Tirgoviste
Constantin
C
Undlien
Dag E
DE
Rønningen
Kjersti S
KS
Tuomilehto-Wolf
Eva
E
Tuomilehto
Jaakko
J
Newport
Melanie J
MJ
Clayton
David G
DG
Todd
John A
JA
D002881:Chromosomes, Human, Pair 12; D005714:Gambia; D006801:Humans; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide; D018167:Receptors, Calcitriol / Q000235:genetics*; D006113:United Kingdom
D018167:Receptors, Calcitriol