Human Molecular Genetics Advance Access published online on June 2, 2004
Human Molecular Genetics, doi:10.1093/hmg/ddh169
© 2004 by Oxford University Press
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1 Juvenile Diabetes Research Foundation / Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC building, Addenbrooke's Hospital, Cambridge, CB2 2XY, UK
* To whom correspondence should be addressed. E-mail: sergey.nejentsev{at}cimr.cam.ac.uk.
A genome-wide map of single nucleotide polymorphisms (SNPs) and a pattern of linkage disequilibrium (LD) between their alleles is 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 the vitamin D receptor gene region in large samples from five populations. Comparative analysis reveals that LD patterns are identical in all four European populations tested with two small regions of 1.3 kb and 5.7 kb at which LD is completely disrupted 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 only. Direct comparison indicates that tag SNPs selected in one European population effectively predict non-tag SNPs in other Europeans, but not in the Gambians, for this region.
Article
Comparative high-resolution analysis of linkage disequilibrium and tag single nucleotide polymorphisms between populations in the vitamin D receptor gene
2 Juvenile Diabetes Research Foundation / Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
3 Clinic of Diabetes, Institute of Diabetes, Nutrition and Metabolic Diseases "N. Paulescu", Bucharest, Romania
4 Institute of Medical Genetics, Ulleval University Hospital, University of Oslo, Oslo, Norway
5 Laboratory of Molecular Epidemiology, Division of Epidemiology, Norwegian Institute of Public Health, Oslo, Norway
6 Diabetes and Genetic Epidemiology Unit, National Public Health Institute, Helsinki, Finland
7 Diabetes and Genetic Epidemiology Unit, National Public Health Institute, Helsinki, Finland; Department of Public Health, University of Helsinki, Helsinki, Finland
8 Department of Medicine, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
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