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Evaluating potential for whole-genome studies in Kosrae, an isolated population in Micronesia

Nature Genetics volume 38, pages 214–217 (2006)Cite this article

Abstract

Whole-genome association studies are predicted to be especially powerful in isolated populations owing to increased linkage disequilibrium (LD) and decreased allelic diversity, but this possibility has not been empirically tested1,2,3. We compared genome-wide data on 113,240 SNPs typed on 30 trios from the Pacific island of Kosrae to the same markers typed in the 270 samples from the International HapMap Project4,5. The extent of LD is longer and haplotype diversity is lower in Kosrae than in the HapMap populations. More than 98% of Kosraen haplotypes are present in HapMap populations, indicating that HapMap will be useful for genetic studies on Kosrae. The long-range LD around common alleles and limited diversity result in improved efficiency in genetic studies in this population and augments the power to detect association of 'hidden SNPs'.

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Figure 1: Allele frequency distribution.
Figure 2: Decay of linkage disequilibrium over distance.
Figure 3: Haplotype diversity.
Figure 4: Association study power comparison.

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Acknowledgements

We thank M. Sullivan for technical assistance and R. Ferrell for the Beni samples. We thank the Government and Department of Health of Kosrae for their partnership and the people of Kosrae for making this study possible. The authors thank The Starr Foundation for their support.

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Author notes

  1. Penelope E Bonnen and Itsik Pe'er: These authors contributed equally to this work.

Authors and Affiliations

  1. Rockefeller University, 1230 York Avenue, New York, 10021, New York, USA

    Penelope E Bonnen, Jackie Salit, Jennifer K Lowe, Jan L Breslow, Markus Stoffel & Jeffrey M Friedman

  2. Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, 02142, Massachusetts, USA

    Itsik Pe'er & Mark J Daly

  3. Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

    Itsik Pe'er, Robert M Plenge, Mark J Daly & David Altshuler

  4. Department of Medicine, Harvard Medical School, Boston, 02115, Massachusetts, USA

    Robert M Plenge & David Altshuler

  5. Affymetrix Inc., 3380 Central Expressway, Santa Clara, 95051, California, USA

    Michael H Shapero & Keith W Jones

  6. Departments of Medicine and Genetics, Yale University School of Medicine, New Haven, 06510, Connecticut, USA

    Richard P Lifton

  7. Howard Hughes Medical Institute, Boston, 02115, Massachusetts, USA

    Richard P Lifton & Jeffrey M Friedman

  8. Department of Genetics, Harvard Medical School, Boston, 02115, Massachusetts, USA

    David E Reich & David Altshuler

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Correspondence to Jeffrey M Friedman.

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Bonnen, P., Pe'er, I., Plenge, R. et al. Evaluating potential for whole-genome studies in Kosrae, an isolated population in Micronesia. Nat Genet 38, 214–217 (2006). https://doi.org/10.1038/ng1712

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