title: 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.
authors: Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.
authors: Jeroen R
authors: JR
authors: Huyghe
authors: Erik
authors: E
authors: Fransen
authors: Samuli
authors: S
authors: Hannula
authors: Lut
authors: L
authors: Van Laer
authors: Els
authors: E
authors: Van Eyken
authors: Elina
authors: E
authors: Mäki-Torkko
authors: Alana
authors: A
authors: Lysholm-Bernacchi
authors: Pekka
authors: P
authors: Aikio
authors: Dietrich A
authors: DA
authors: Stephan
authors: Martti
authors: M
authors: Sorri
authors: Matthew J
authors: MJ
authors: Huentelman
authors: Guy
authors: G
authors: Van Camp
mesh_terms: D000368:Aged; D002887:Chromosomes, Human, Pair 18 / Q000235:genetics; D005006:Ethnicity / Q000235:genetics*; D005387:Finland; D005787:Gene Frequency / Q000235:genetics; D056726:Genetic Association Studies / Q000379:methods*; D015894:Genome, Human / Q000235:genetics*; D006239:Haplotypes / Q000235:genetics; D006801:Humans; D015810:Linkage Disequilibrium / Q000235:genetics; D008875:Middle Aged; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D044465:White People / Q000235:genetics*