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Improved whole-chromosome phasing for disease and population genetic studies

Nature Methods volume 10, pages 5–6 (2013)Cite this article

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Methods that can accurately estimate haplotypes from single-nucleotide polymorphism (SNP) genotype data are important because they are widely used in many areas of genetic analysis. Examples include the creation of haplotype reference panels, pre-phasing1 before genotype imputation in genome-wide association studies (GWAS), and population genetic analysis. The task is an inverse problem in which we observe a set of SNP genotypes in a sample, typically using a genome-wide SNP microarray, and wish to infer the underlying haplotypes carried by the study individuals.

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Figure 1: Accuracy and computational performance.

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Acknowledgements

J.M. and O.D. acknowledge support from the Medical Research Council (G0801823). O.D. acknowledges support from Peptinov SAS (France). Thanks to B. Howie, C. Churchhouse and J. O'Connell for comments on this paper and to A. Cox (Illumina Cambridge Ltd) for providing the high-coverage trio sequence data set. The Vietnamese cohort was provided by A. Alcais (Institut National de la Santé de la Recherche Médicale, Paris, France) and E. Schurr (McGill Centre for the Study of Host Resistance, Montreal, Canada). This study uses data from the Wellcome Trust Case Control Consortium.

Author information

Author notes

  1. Jean-Francois Zagury and Jonathan Marchini: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Statistics, University of Oxford, Oxford, UK

    Olivier Delaneau & Jonathan Marchini

  2. Chaire de Bioinformatique, Laboratoire Génomique, Bioinformatique, et Applications (EA 4627), Conservatoire National des Arts et Métiers, Paris, France

    Jean-Francois Zagury

  3. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK

    Jonathan Marchini

Authors
  1. Olivier Delaneau
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  2. Jean-Francois Zagury
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  3. Jonathan Marchini
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Corresponding authors

Correspondence to Jean-Francois Zagury or Jonathan Marchini.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Table 1, Supplementary Figures 1–7, Supplementary Methods and Supplementary Notes 1 and 2 (PDF 7498 kb)

Supplementary Software

SHAPEIT2 software (ZIP 1281 kb)

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Delaneau, O., Zagury, JF. & Marchini, J. Improved whole-chromosome phasing for disease and population genetic studies. Nat Methods 10, 5–6 (2013). https://doi.org/10.1038/nmeth.2307

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