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In silico method for inferring genotypes in pedigrees

Nature Genetics volume 38, pages 1002–1004 (2006)Cite this article

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.

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Figure 1: Genotype inference.

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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
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  2. Wei-Min Chen
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  3. Gonçalo R Abecasis
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  4. Vivian G Cheung
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Corresponding author

Correspondence to Vivian G Cheung.

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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)

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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

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