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In silico method for inferring genotypes in pedigrees

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.

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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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