In silico method for inferring genotypes in pedigrees

Article metrics

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.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Figure 1: Genotype inference.

References

  1. 1

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

  2. 2

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

  3. 3

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

  4. 4

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

  5. 5

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

  6. 6

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

  7. 7

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

  8. 8

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

  9. 9

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

  10. 10

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

  11. 11

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

  12. 12

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

  13. 13

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

  14. 14

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

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

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

Download citation

Further reading