Pitfalls of haplotype phasing from amplicon-based long-read sequencing
dc.contributor.author | Laver, TW | |
dc.contributor.author | Caswell, RC | |
dc.contributor.author | Moore, KA | |
dc.contributor.author | Poschmann, J | |
dc.contributor.author | Johnson, MB | |
dc.contributor.author | Owens, MM | |
dc.contributor.author | Ellard, S | |
dc.contributor.author | Paszkiewicz, KH | |
dc.contributor.author | Weedon, MN | |
dc.date.accessioned | 2019-10-22T10:06:35Z | |
dc.date.issued | 2016-02-17 | |
dc.description.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. | en_GB |
dc.description.sponsorship | Wellcome Trust | en_GB |
dc.identifier.citation | Vol. 6, article 21746 | en_GB |
dc.identifier.doi | 10.1038/srep21746 | |
dc.identifier.grantnumber | WT097835MF | en_GB |
dc.identifier.uri | http://hdl.handle.net/10871/39293 | |
dc.language.iso | en | en_GB |
dc.publisher | Nature Research | en_GB |
dc.rights | © 2016 The Author(s). 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/ | en_GB |
dc.title | Pitfalls of haplotype phasing from amplicon-based long-read sequencing | en_GB |
dc.type | Article | en_GB |
dc.date.available | 2019-10-22T10:06:35Z | |
dc.description | This is the final version. Available on open access from Nature Research via the DOI in this record | en_GB |
dc.identifier.eissn | 2045-2322 | |
dc.identifier.journal | Scientific Reports | en_GB |
dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | en_GB |
pubs.euro-pubmed-id | MED:26883533 | |
dcterms.dateAccepted | 2016-01-26 | |
rioxxterms.version | VoR | en_GB |
rioxxterms.licenseref.startdate | 2016-02-17 | |
rioxxterms.type | Journal Article/Review | en_GB |
refterms.dateFCD | 2019-10-22T10:03:24Z | |
refterms.versionFCD | VoR | |
refterms.dateFOA | 2019-10-22T10:06:39Z | |
refterms.panel | A | en_GB |
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Except where otherwise noted, this item's licence is described as © 2016 The Author(s). This work is licensed under a Creative Commons Attribution 4.0 International License. The images
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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/