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Transferability of tag SNPs in genetic association studies in multiple populations

Nature Genetics volume 38, pages 1298–1303 (2006)Cite this article

Abstract

A general question for linkage disequilibrium–based association studies is how power to detect an association is compromised when tag SNPs are chosen from data in one population sample and then deployed in another sample. Specifically, it is important to know how well tags picked from the HapMap DNA samples capture the variation in other samples. To address this, we collected dense data uniformly across the four HapMap population samples and eleven other population samples. We picked tag SNPs using genotype data we collected in the HapMap samples and then evaluated the effective coverage of these tags in comparison to the entire set of common variants observed in the other samples. We simulated case-control association studies in the non-HapMap samples under a disease model of modest risk, and we observed little loss in power. These results demonstrate that the HapMap DNA samples can be used to select tags for genome-wide association studies in many samples around the world.

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Figure 1: Performance of tags evaluated in multiple population samples, expressed as the percentage of common SNPs (excluding the tags) captured within a given maximum r2 range (three bins: 0 < r2 < 0.5, 0.5 ≤ r2 < 0.8 and 0.8 ≤ r2 ≤ 1.0).
Figure 2: The relationship between the allele frequency observed in the HapMap reference panel (from which tags are picked) and the maximum r2 between the tags and all 'untyped' SNPs with ≥5% frequency in HGDP-YRI, CEPH-EXT, HGDP-CHB and HGDP-JPT.

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Acknowledgements

We thank M. Egyud for sharing unpublished results and all members of the collaborative Multiethnic Cohort Study and the Analysis group of the International HapMap Consortium for useful discussions. We acknowledge the support of NIH grants CA63464 and CA098758 (to B.E.H.), HL074166 (to X.Z.), CA54281 (to L.N.K.) and DK067288 (to H.N.L.); a March of Dimes grant (6-FY04-61, to J.N.H.) and a Charles E. Culpeper Scholarship of the Rockefeller Brothers Fund and a Burroughs Wellcome Fund Clinical Scholarship in Translational Research (both to D.A.).

Author information

Author notes

  1. Paul I W de Bakker, Noël P Burtt and Robert R Graham: These authors contributed equally to this work.

Authors and Affiliations

  1. Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Seven Cambridge Center, Cambridge, 02142, Massachusetts, USA

    Paul I W de Bakker, Noël P Burtt, Robert R Graham, Candace Guiducci, Roman Yelensky, Jared A Drake, Todd Bersaglieri, Johannah Butler, Robert C Onofrio, Helen N Lyon, Matthew L Freedman, Mark J Daly, Joel N Hirschhorn & David Altshuler

  2. Center for Human Genetic Research, Massachusetts General Hospital, 185 Cambridge Street, Boston, 02114-2790, Massachusetts, USA

    Paul I W de Bakker, Robert R Graham, Roman Yelensky, Stanton Young, Mark J Daly & David Altshuler

  3. Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, 02114-2790, Massachusetts, USA

    Paul I W de Bakker, Robert R Graham, Roman Yelensky, Stanton Young & David Altshuler

  4. Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA

    Paul I W de Bakker, Robert R Graham, Joel N Hirschhorn & David Altshuler

  5. Harvard-MIT Division of Health Sciences and Technology, Cambridge, Massachusetts, USA

    Roman Yelensky

  6. Divisions of Endocrinology and Genetics, Program in Genomics, Children's Hospital, Boston, 02115, Massachusetts, USA

    Jared A Drake, Todd Bersaglieri, Johannah Butler, Helen N Lyon & Joel N Hirschhorn

  7. Harvard School of Public Health, Boston, 02115, Massachusetts, USA

    Kathryn L Penney

  8. Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, 90089, California, USA

    Daniel O Stram, Christopher A Haiman & Brian E Henderson

  9. Dana-Farber Cancer Institute, Boston, 02115, Massachusetts, USA

    Matthew L Freedman

  10. Department of Preventive Medicine and Epidemiology, Loyola University, Maywood, 60153, Illinois, USA

    Xiaofeng Zhu & Richard Cooper

  11. Department of Clinical Sciences, University Hospital, Lund University, Malmö, S-20502, Sweden

    Leif Groop

  12. Department of Medicine, Helsinki University, Helsinki, Finland

    Leif Groop

  13. Cancer Research Center, University of Hawaii, Honolulu, 96813, Hawaii, USA

    Laurence N Kolonel

  14. Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA

    Mark J Daly & David Altshuler

  15. Diabetes Unit, Massachusetts General Hospital, Boston, 02114, Massachusetts, USA

    David Altshuler

Authors
  1. Paul I W de Bakker
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Contributions

H.N.L., X.Z., R.C., L.G., C.A.H., L.N.K., B.E.H. provided DNA samples; N.P.B. coordinated resequencing with R.C.O. and S.Y.; N.P.B., R.R.G., C.G., J.B., K.L.P. prepared DNA samples, designed and performed genotyping experiments; P.d.B., N.P.B., R.R.G., R.Y., J.A.D. and T.B. performed the analyses; P.d.B. wrote the paper, with contributions from N.P.B. and R.R.G.; M.L.F., C.A.H., D.O.S. and H.N.L. gave feedback and helped with revisions and M.J.D., J.N.H. and D.A. jointly directed the project.

Corresponding author

Correspondence to David Altshuler.

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Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Table 1

Summary of SNP discovery through resequencing. (PDF 25 kb)

Supplementary Table 2

Genotyping summary of all attempted SNP assays. (PDF 540 kb)

Supplementary Table 3

Genotyping summary by population. (PDF 23 kb)

Supplementary Table 4

Genotyping summary of the final data set. (PDF 24 kb)

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de Bakker, P., Burtt, N., Graham, R. et al. Transferability of tag SNPs in genetic association studies in multiple populations. Nat Genet 38, 1298–1303 (2006). https://doi.org/10.1038/ng1899

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