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    Pitfalls of haplotype phasing from amplicon-based long-read sequencing.

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    Open Access article (402.7Kb)
    URI
    http://hdl.handle.net/11287/596928
    Author
    Laver, T. W.
    Caswell, Richard C.
    Moore, K. A.
    Poschmann, J
    Johnson, M B
    Owens, Martina
    Ellard, Sian
    Paszkiewicz, K H
    Weedon, M. N.
    Date
    2016-02-17
    Journal
    Scientific reports
    Type
    Journal Article
    Report
    Publisher
    Nature
    DOI
    10.1038/srep21746
    Rights
    Archived with thanks to Scientific reports. This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
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    Abstract
    The long-read sequencers from Pacific Bioscience (PacBio) and Oxford Nanopore Technologies (ONT) offer the opportunity to phase mutations multiple kilobases apart directly from sequencing reads. In this study, we used long-range PCR with ONT and PacBio sequencing to phase two variants 9 kb apart in the RET gene. We also re-analysed data from a recent paper which had apparently successfully used ONT to phase clinically important haplotypes at the CYP2D6 and HLA loci. From these analyses, we demonstrate PCR-chimera formation during PCR amplification and reference alignment bias are pitfalls that need to be considered when attempting to phase variants using amplicon-based long-read sequencing technologies. These methodological pitfalls need to be avoided if the opportunities provided by long-read sequencers are to be fully exploited.
    Citation
    Pitfalls of haplotype phasing from amplicon-based long-read sequencing. 2016, 6:21746 Sci Rep
    Publisher URL
    http://dx.doi.org/10.1038/srep21746
    Note
    This article is available via Open Access. Click on the 'Additional Link' above to access the full-text from the publisher's site.
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    • 2016 RD&E publications
    • Honorary contracts publications
    • Molecular Genetics

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