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Tag SNP selection for Finnish individuals based on the CEPH Utah HapMap database
Author(s) -
Willer Cristen J.,
Scott Laura J.,
Bonnycastle Lori L.,
Jackson Anne U.,
Chines Peter,
Pruim Randall,
Bark Craig W.,
Tsai YaYu,
Pugh Elizabeth W.,
Doheny Kimberly F.,
Kinnunen Leena,
Mohlke Karen L.,
Valle Timo T.,
Bergman Richard N.,
Tuomilehto Jaakko,
Collins Francis S.,
Boehnke Michael
Publication year - 2006
Publication title -
genetic epidemiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.301
H-Index - 98
eISSN - 1098-2272
pISSN - 0741-0395
DOI - 10.1002/gepi.20131
Subject(s) - international hapmap project , linkage disequilibrium , single nucleotide polymorphism , minor allele frequency , genetics , biology , population , snp , tag snp , haplotype , selection (genetic algorithm) , genetic association , allele , genotype , medicine , gene , computer science , environmental health , artificial intelligence
Abstract The pattern and nature of linkage disequilibrium in the human genome is being studied and catalogued as part of the International HapMap Project [:2003 Nature 426:789–796]. A key goal of the HapMap Project is to enable identification of tag single nucleotide polymorphisms (SNPs) that capture a substantial portion of common human genetic variability while requiring only a small fraction of SNPs to be genotyped [International HapMap Consortium, 2005: Nature 437:1299–1320]. In the current study, we examined the effectiveness of using the CEU HapMap database to select tag SNPs for a Finnish sample. We selected SNPs in a 17.9‐Mb region of chromosome 14 based on pairwise linkage disequilibrium (r 2 ) estimates from the HapMap CEU sample, and genotyped 956 of these SNPs in 1,425 Finnish individuals. An excess of SNPs showed significantly different allele frequencies between the HapMap CEU and the Finnish samples, consistent with population‐specific differences. However, we observed strong correlations between the two samples for estimates of allele frequencies, r 2 values, and haplotype frequencies. Our results demonstrate that the HapMap CEU samples provide an adequate basis for tag SNP selection in Finnish individuals, without the need to create a map specifically for the Finnish population, and suggest that the four‐population HapMap data will provide useful information for tag SNP selection beyond the specific populations from which they were sampled. Genet. Epidemiol . 2006. © 2005 Wiley‐Liss, Inc.