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

2.50
Hdl Handle:
http://hdl.handle.net/11287/596928
Title:
Pitfalls of haplotype phasing from amplicon-based long-read sequencing.
Authors:
Laver, T W; Caswell, Richard C; Moore, K A; Poschmann, J; Johnson, M B; Owens, Martina; Ellard, Sian ( 0000-0002-7620-5526 ) ; Paszkiewicz, K H; Weedon, M N
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:
Nature
Journal:
Scientific reports
Issue Date:
17-Feb-2016
URI:
http://hdl.handle.net/11287/596928
DOI:
10.1038/srep21746
PubMed ID:
26883533
Additional Links:
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.
Type:
Journal Article; Report
Language:
en
ISSN:
2045-2322
Appears in Collections:
Molecular Genetics; Molecular Genetics; Honorary contracts publications; 2016 RD&E publications

Full metadata record

DC FieldValue Language
dc.contributor.authorLaver, T Wen
dc.contributor.authorCaswell, Richard Cen
dc.contributor.authorMoore, K Aen
dc.contributor.authorPoschmann, Jen
dc.contributor.authorJohnson, M Ben
dc.contributor.authorOwens, Martinaen
dc.contributor.authorEllard, Sianen
dc.contributor.authorPaszkiewicz, K Hen
dc.contributor.authorWeedon, M Nen
dc.date.accessioned2016-02-22T14:54:36Zen
dc.date.available2016-02-22T14:54:36Zen
dc.date.issued2016-02-17en
dc.identifier.citationPitfalls of haplotype phasing from amplicon-based long-read sequencing. 2016, 6:21746 Sci Repen
dc.identifier.issn2045-2322en
dc.identifier.pmid26883533en
dc.identifier.doi10.1038/srep21746en
dc.identifier.urihttp://hdl.handle.net/11287/596928en
dc.description.abstractThe 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
dc.language.isoenen
dc.publisherNatureen
dc.relation.urlhttp://dx.doi.org/10.1038/srep21746en
dc.rightsArchived 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/en
dc.subjectWessex Classification Subject Headings::Oncology. Pathology.::Geneticsen
dc.titlePitfalls of haplotype phasing from amplicon-based long-read sequencing.en
dc.typeJournal Articleen
dc.typeReporten
dc.identifier.journalScientific reportsen
dc.description.noteThis article is available via Open Access. Click on the 'Additional Link' above to access the full-text from the publisher's site.en
dc.type.versionPublisheden

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