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Whole-genome haplotyping using long reads and statistical methods

Nature Biotechnology volume 32, pages 261–266 (2014)Cite this article

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Abstract

The rapid growth of sequencing technologies has greatly contributed to our understanding of human genetics. Yet, despite this growth, mainstream technologies have not been fully able to resolve the diploid nature of the human genome. Here we describe statistically aided, long-read haplotyping (SLRH), a rapid, accurate method that uses a statistical algorithm to take advantage of the partially phased information contained in long genomic fragments analyzed by short-read sequencing. For a human sample, as little as 30 Gbp of additional sequencing data are needed to phase genotypes identified by 50× coverage whole-genome sequencing. Using SLRH, we phase 99% of single-nucleotide variants in three human genomes into long haplotype blocks 0.2–1 Mbp in length. We apply our method to determine allele-specific methylation patterns in a human genome and identify hundreds of differentially methylated regions that were previously unknown. SLRH should facilitate population-scale haplotyping of human genomes.

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Figure 1: SLRH.
Figure 2: Haplotyping results at several accuracy thresholds.
Figure 3: Haplotyping performance from 30 Gbp of sequencing.
Figure 4: Genome browser view of differentially methylated regions at the promoter of the H19 gene.

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Sequence Read Archive

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Acknowledgements

We thank C. Pan for assistance in coordinating contacts and discussions. This work is funded by US National Institutes of Health grants HL107393-02, HG004558-05, and the Genetics Department of Stanford University.

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Author notes

  1. Volodymyr Kuleshov, Dan Xie, Rui Chen and Dmitry Pushkarev: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Computer Science, Stanford University, Stanford, California, USA

    Volodymyr Kuleshov

  2. Illumina Inc., San Diego, California, USA

    Volodymyr Kuleshov, Dmitry Pushkarev, Tim Blauwkamp & Michael Kertesz

  3. Department of Genetics, Stanford University School of Medicine, Stanford, California, USA

    Volodymyr Kuleshov, Dan Xie, Rui Chen, Zhihai Ma & Michael Snyder

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  1. Volodymyr Kuleshov
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Contributions

D.P. and M.K. developed the laboratory preparation protocol. V.K. developed the Prism phasing algorithm. Z.M. and R.C. performed the Methyl-seq experiments. T.B. prepared the phasing libraries. V.K., D.X. and D.P. performed computational analysis. V.K., D.X. and M.S. wrote the manuscript. R.C. and M.K. reviewed and revised the manuscript. M.K. and M.S. supervised the research.

Corresponding author

Correspondence to Michael Snyder.

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Competing interests

V.K., D.P., T.B. and M.K. performed the research at Moleculo Inc. (acquired by Illumina Inc.). D.P., T.B. and M.K. are employed by Illumina Inc. and V.K. is a consultant to Illumina Inc. M.K., D.P., T.B. and V.K. are listed as inventors on a patent filed for the SLRH technology. The library preparation protocol is covered by US and international patents with numbers 61/532,882 and 13/608,778 on which D.P. and M.K. are listed as inventors. The SLRH technology is offered commercially by Illumina Inc.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–5, Supplementary Tables 1–15 and Supplementary Note (PDF 1431 kb)

List of DMRs

List of DMRs (XLSX 106 kb)

Prism source code

Prism Source Code (ZIP 181 kb)

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Kuleshov, V., Xie, D., Chen, R. et al. Whole-genome haplotyping using long reads and statistical methods. Nat Biotechnol 32, 261–266 (2014). https://doi.org/10.1038/nbt.2833

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