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Tag SNP selection for Finnish individuals based on the CEPH Utah HapMap database
Cristen J Willer1, Laura J Scott, Lori L Bonnycastle
1Department of Biostatistics and Center for Statistical Genetics, University of Michigan, 1420 Washington Heights, Ann Arbor, MI 48109, USA. cristen@umich.edu
Genetic Epidemiology
|December 24, 2005
Summary
The International HapMap Project
Area of Science:
- Human genetics
- Population genetics
- Genomic research
Background:
- The International HapMap Project catalogs human genome linkage disequilibrium.
- A primary goal is to identify tag single nucleotide polymorphisms (SNPs) to efficiently capture genetic variation.
Purpose of the Study:
- To assess the utility of the CEU HapMap database for selecting tag SNPs in a Finnish population.
- To evaluate population-specific differences in SNP selection strategies.
Main Methods:
- Selected tag SNPs in a 17.9-Mb region of chromosome 14 using CEU HapMap data.
- Genotyped 956 SNPs in 1,425 Finnish individuals.
- Analyzed allele frequencies, linkage disequilibrium (r(2)), and haplotype frequencies.
Main Results:
- Observed population-specific allele frequency differences between CEU and Finnish samples.
- Found strong correlations in allele frequencies, r(2) values, and haplotype frequencies between the two populations.
- Demonstrated that CEU HapMap data is adequate for tag SNP selection in Finnish individuals.
Conclusions:
- The HapMap CEU samples provide a suitable basis for tag SNP selection in Finnish populations.
- HapMap data can be broadly applied for tag SNP selection beyond the sampled populations.
- Eliminates the need for a population-specific map for Finnish tag SNP selection.