Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

In silico method for inferring genotypes in pedigrees


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, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Get just this article for as long as you need it


Prices may be subject to local taxes which are calculated during checkout

Figure 1: Genotype inference.


  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


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


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).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing