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

Author
Organization
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. European Journal of Human Genetics (2010) 18, 569-574; doi:10.1038/ejhg.2009.210; published online 25 November 2009
Keywords
COMPLEX DISEASE, ISOLATED POPULATIONS, WHOLE-GENOME, INDIVIDUALS, EUROPE, TRAITS, population isolates, linkage disequilibrium, genome-wide association studies, Saami, MAPPING GENES, LINKAGE DISEQUILIBRIUM, HEARING IMPAIRMENT, DRIFT

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MLA
Huyghe, Jeroen R, Erik Fransen, Samuli Hannula, et al. “Genome-wide SNP Analysis Reveals No Gain in Power for Association Studies of Common Variants in the Finnish Saami.” EUROPEAN JOURNAL OF HUMAN GENETICS 18.5 (2010): 569–574. Print.
APA
Huyghe, J. R., Fransen, E., Hannula, S., Van Laer, L., Van Eyken, E., Maki-Torkko, E., Lysholm-Bernacchi, A., et al. (2010). Genome-wide SNP analysis reveals no gain in power for association studies of common variants in the Finnish Saami. EUROPEAN JOURNAL OF HUMAN GENETICS, 18(5), 569–574.
Chicago author-date
Huyghe, Jeroen R, Erik Fransen, Samuli Hannula, Lut Van Laer, Els Van Eyken, Elina Maki-Torkko, Alan Lysholm-Bernacchi, et al. 2010. “Genome-wide SNP Analysis Reveals No Gain in Power for Association Studies of Common Variants in the Finnish Saami.” European Journal of Human Genetics 18 (5): 569–574.
Chicago author-date (all authors)
Huyghe, Jeroen R, Erik Fransen, Samuli Hannula, Lut Van Laer, Els Van Eyken, Elina Maki-Torkko, Alan Lysholm-Bernacchi, Pekka Aikio, Dietrich A Stephan, Martti Sorri, Matthew J Huentelman, and Guy Van Camp. 2010. “Genome-wide SNP Analysis Reveals No Gain in Power for Association Studies of Common Variants in the Finnish Saami.” European Journal of Human Genetics 18 (5): 569–574.
Vancouver
1.
Huyghe JR, Fransen E, Hannula S, Van Laer L, Van Eyken E, Maki-Torkko E, et al. Genome-wide SNP analysis reveals no gain in power for association studies of common variants in the Finnish Saami. EUROPEAN JOURNAL OF HUMAN GENETICS. 2010;18(5):569–74.
IEEE
[1]
J. R. Huyghe et al., “Genome-wide SNP analysis reveals no gain in power for association studies of common variants in the Finnish Saami,” EUROPEAN JOURNAL OF HUMAN GENETICS, vol. 18, no. 5, pp. 569–574, 2010.
@article{946081,
  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. European Journal of Human Genetics (2010) 18, 569-574; doi:10.1038/ejhg.2009.210; published online 25 November 2009},
  author       = {Huyghe, Jeroen R and Fransen, Erik and Hannula, Samuli and Van Laer, Lut and Van Eyken, Els and Maki-Torkko, Elina and Lysholm-Bernacchi, Alan and Aikio, Pekka and Stephan, Dietrich A and Sorri, Martti and Huentelman, Matthew J and Van Camp, Guy},
  issn         = {1018-4813},
  journal      = {EUROPEAN JOURNAL OF HUMAN GENETICS},
  keywords     = {COMPLEX DISEASE,ISOLATED POPULATIONS,WHOLE-GENOME,INDIVIDUALS,EUROPE,TRAITS,population isolates,linkage disequilibrium,genome-wide association studies,Saami,MAPPING GENES,LINKAGE DISEQUILIBRIUM,HEARING IMPAIRMENT,DRIFT},
  language     = {eng},
  number       = {5},
  pages        = {569--574},
  title        = {Genome-wide SNP analysis reveals no gain in power for association studies of common variants in the Finnish Saami},
  url          = {http://dx.doi.org/10.1038/ejhg.2009.210},
  volume       = {18},
  year         = {2010},
}

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