Dataset Information

Genome-wide SNP analysis reveals no gain in power for association studies of common variants in the Finnish Saami.

ABSTRACT: The Saami from Fennoscandia are believed to represent an ancient, genetically isolated population with no evidence of population expansion. Theoretical work has indicated that under this demographic scenario, extensive linkage disequilibrium (LD) is generated by genetic drift. Therefore, it has been suggested that the Saami would be particularly suited for genetic association studies, offering a substantial power advantage and allowing more economic study designs. However, no study has yet assessed this claim. As part of a GWAS for a complex trait, we evaluated the relative power for association studies of common variants in the Finnish Saami. LD patterns in the Saami were very similar to those in the non-African HapMap reference panels. Haplotype diversity was reduced and, on average, levels of LD were higher in the Saami as compared with those in the HapMap panels. However, using a 'hidden' SNP approach we show that this does not translate into a power gain in association studies. Contrary to earlier claims, we show that for a given set of common SNPs, genomic coverage attained in the Saami is similar to that in the non-African HapMap panels. Nevertheless, the reduced haplotype diversity could potentially facilitate gene identification, especially if multiple rare variants play a role in disease etiology. Our results further indicate that the HapMap is a useful resource for genetic studies in the Saami.

SUBMITTER: Huyghe JR

PROVIDER: S-EPMC2987317 | biostudies-literature | 2010 May

REPOSITORIES: biostudies-literature

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Genome-wide SNP analysis reveals no gain in power for association studies of common variants in the Finnish Saami.

Huyghe Jeroen R JR Fransen Erik E Hannula Samuli S Van Laer Lut L Van Eyken Els E Mäki-Torkko Elina E Lysholm-Bernacchi Alana A Aikio Pekka P Stephan Dietrich A DA Sorri Martti M Huentelman Matthew J MJ Van Camp Guy G

European journal of human genetics : EJHG 20091125 5

The Saami from Fennoscandia are believed to represent an ancient, genetically isolated population with no evidence of population expansion. Theoretical work has indicated that under this demographic scenario, extensive linkage disequilibrium (LD) is generated by genetic drift. Therefore, it has been suggested that the Saami would be particularly suited for genetic association studies, offering a substantial power advantage and allowing more economic study designs. However, no study has yet asses ...[more]

PMID: 19935831

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Dataset Information

Genome-wide SNP analysis reveals no gain in power for association studies of common variants in the Finnish Saami.

Publications

Genome-wide SNP analysis reveals no gain in power for association studies of common variants in the Finnish Saami.

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