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High-resolution whole-genome haplotyping using limited seed data

Nature Methods volume 10, pages 6–7 (2013)Cite this article

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To the Editor:

The term 'haplotype' refers to a group of alleles inherited on the same chromosome. Although most sequencing technologies cannot resolve which chromosomal copy a given sequence comes from, the value of haplotype information for genetic studies is increasingly being appreciated by researchers. Haplotypes are important for inferring disease status, determining which allele combinations tend to segregate together and helping to 'fill in' or impute missing values in regions that lack genotype information to power association studies. Statistical methods exist that can resolve or 'phase' haplotypes, but these have been limited to short sequence stretches and can be computationally demanding. Technical difficulties still exist for obtaining accurate whole-genome and long-range haplotypes experimentally1,2.

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Figure 1: The principle behind HiFi.

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Acknowledgements

This work was supported by US National Institutes of Health grants (R21HG006173, RC4MD005964, HL003676, RR014758, RR003034, GM74913, G12MD007602, U54MD007588), an American Heart Association grant (09GRNT2300003), and in part by the Baltimore Research Enhancement Award Program in Stroke of the Baltimore Department of Veterans Affairs. We also want to thank G.H. Gibbons for his critical discussions.

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Authors and Affiliations

  1. Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, Georgia, USA

    Weinian Rao, Yamin Ma, Li Ma, Qiling Li & Qing Song

  2. Independent investigator, Atlanta, Georgia, USA.,

    Jian Zhao

  3. Department of Orthopaedic Surgery, University of Tennessee Health Science Center, Memphis, Tennessee, USA

    Weikuan Gu

  4. Section of Statistical Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA

    Kui Zhang

  5. Department of Microbiology, Biochemistry & Immunology, Morehouse School of Medicine, Atlanta, Georgia, USA

    Vincent C Bond

Authors
  1. Weinian Rao
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  2. Yamin Ma
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  3. Li Ma
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  8. Vincent C Bond
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  9. Qing Song
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Corresponding author

Correspondence to Qing Song.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–4, Supplementary Tables 1–11, Supplementary Methods, Supplementary Discussion and Supplementary Note (PDF 527 kb)

Supplementary Software

HiFi software (ZIP 105 kb)

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Rao, W., Ma, Y., Ma, L. et al. High-resolution whole-genome haplotyping using limited seed data. Nat Methods 10, 6–7 (2013). https://doi.org/10.1038/nmeth.2308

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