Tag SNP selection for Finnish individuals based on the CEPH Utah HapMap database

Cristen J. Willer, Laura J. Scott, Lori L. Bonnycastle, Anne U. Jackson, Peter Chines, Randall Pruim, Craig W. Bark, Ya Yu Tsai, Elizabeth W. Pugh, Kimberly F. Doheny, Leena Kinnunen, Karen L. Mohlke, Timo T. Valle, Richard N. Bergman, Jaakko Tuomilehto, Francis S. Collins, Michael Boehnke

Research output: Contribution to journalArticlepeer-review

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 (r2) 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, r2 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.

Original languageEnglish (US)
Pages (from-to)180-190
Number of pages11
JournalGenetic epidemiology
Volume30
Issue number2
DOIs
StatePublished - Feb 2006

Keywords

  • Finland
  • HapMap
  • Haplotype
  • Linkage disequilibrium

ASJC Scopus subject areas

  • Epidemiology
  • Genetics(clinical)

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