Skip to main content
SpringerLink
Log in

In silico method for inferring genotypes in pedigrees

  • Brief Communication
  • Published:

From Nature Genetics

View current issue Submit your manuscript

Abstract

Our genotype inference method combines sparse marker data from a linkage scan and high-resolution SNP genotypes for several individuals to infer genotypes for related individuals. We illustrate the method's utility by inferring over 53 million SNP genotypes for 78 children in the Centre d'Etude du Polymorphisme Humain families. The method can be used to obtain high-density genotypes in different family structures, including nuclear families commonly used in complex disease gene mapping studies.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Figure 1: Genotype inference.

Similar content being viewed by others

References

  1. Matise, T.C. et al. Am. J. Hum. Genet. 73, 271–284 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. International HapMap Consortium. Nature 426, 789–796 (2003).

  3. The International HapMap Consortium. Nature 437, 1299–1320 (2005).

  4. Gunderson, K.L., Steemers, F.J., Lee, G., Mendoza, L.G. & Chee, M.S. Nat. Genet. 37, 549–554 (2005).

    Article  CAS  PubMed  Google Scholar 

  5. Syvanen, A.C. Nat. Genet. 37, S5–10 (2005).

    Article  PubMed  Google Scholar 

  6. Matsuzaki, H. et al. Nat. Methods 1, 109–111 (2004).

    Article  CAS  PubMed  Google Scholar 

  7. Sobel, E. & Lange, K. Am. J. Hum. Genet. 58, 1323–1337 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  8. Abecasis, G.R., Cherny, S.S., Cookson, W.O. & Cardon, L.R. Nat. Genet. 30, 97–101 (2002).

    Article  CAS  PubMed  Google Scholar 

  9. Kruglyak, L., Daly, M.J., Reeve-Daly, M.P. & Lander, E.S. Am. J. Hum. Genet. 58, 1347–1363 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  10. S.A.G.E. Statistical Analysis for Genetic Epidemiology (Statistical Solutions, Cork, Ireland, 2003).

  11. Gudbjartsson, D.F., Jonasson, K., Frigge, M.L. & Kong, A. Nat. Genet. 25, 12–13 (2000).

    Article  CAS  PubMed  Google Scholar 

  12. Morley, M. et al. Nature 430, 743–747 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Abecasis, G.R., Cardon, L.R. & Cookson, W.O. Am. J. Hum. Genet. 66, 279–292 (2000).

    Article  CAS  PubMed  Google Scholar 

  14. Abecasis, G.R., Cookson, W.O. & Cardon, L.R. Eur. J. Hum. Genet. 8, 545–551 (2000).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank J. Devlin and M. Morley for technical assistance, M. Boehnke and R. Spielman for discussion and critical reading of the manuscript. This work was supported by grants from the US National Institutes of Health to G.R.A. and V.G.C.

Author information

Authors and Affiliations

  1. Department of Pediatrics, University of Pennsylvania, 3516 Civic Center Blvd., Philadelphia, 19104, Pennsylvania, USA

    Joshua T Burdick & Vivian G Cheung

  2. Department of Biostatistics and Center for Statistical Genetics, University of Michigan, 1420 Washington Heights, Ann Arbor, 48109-2029, Michigan, USA

    Wei-Min Chen & Gonçalo R Abecasis

  3. Department of Genetics, University of Pennsylvania, 3516 Civic Center Blvd., Philadelphia, 19104, Pennsylvania, USA

    Vivian G Cheung

Authors
  1. Joshua T Burdick
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Wei-Min Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Gonçalo R Abecasis
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Vivian G Cheung
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Vivian G Cheung.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Table 1

Detailed comparisons of simulated data. (PDF 61 kb)

Supplementary Table 2

Summary of chi-squares in pedigrees by inference. (PDF 43 kb)

Supplementary Methods (PDF 65 kb)

Supplementary Note (PDF 66 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Burdick, J., Chen, WM., Abecasis, G. et al. In silico method for inferring genotypes in pedigrees. Nat Genet 38, 1002–1004 (2006). https://doi.org/10.1038/ng1863

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/ng1863

  • Springer Nature America, Inc.

This article is cited by

Search

Navigation