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Interpreting Viral Deep Sequencing Data with GLUE

Using deep sequencing technologies such as Illumina’s platform, it is possible to obtain reads from the viral RNA population revealing the viral genome diversity within a single host. A range of software tools and pipelines can transform raw deep sequencing reads into Sequence Alignment Mapping (SAM...

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Autores principales: Singer, Joshua B., Thomson, Emma C., Hughes, Joseph, Aranday-Cortes, Elihu, McLauchlan, John, da Silva Filipe, Ana, Tong, Lily, Manso, Carmen F., Gifford, Robert J., Robertson, David L., Barnes, Eleanor, Ansari, M. Azim, Mbisa, Jean L., Bibby, David F., Bradshaw, Daniel, Smith, David
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6520954/
https://www.ncbi.nlm.nih.gov/pubmed/30987147
http://dx.doi.org/10.3390/v11040323
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author Singer, Joshua B.
Thomson, Emma C.
Hughes, Joseph
Aranday-Cortes, Elihu
McLauchlan, John
da Silva Filipe, Ana
Tong, Lily
Manso, Carmen F.
Gifford, Robert J.
Robertson, David L.
Barnes, Eleanor
Ansari, M. Azim
Mbisa, Jean L.
Bibby, David F.
Bradshaw, Daniel
Smith, David
author_facet Singer, Joshua B.
Thomson, Emma C.
Hughes, Joseph
Aranday-Cortes, Elihu
McLauchlan, John
da Silva Filipe, Ana
Tong, Lily
Manso, Carmen F.
Gifford, Robert J.
Robertson, David L.
Barnes, Eleanor
Ansari, M. Azim
Mbisa, Jean L.
Bibby, David F.
Bradshaw, Daniel
Smith, David
author_sort Singer, Joshua B.
collection PubMed
description Using deep sequencing technologies such as Illumina’s platform, it is possible to obtain reads from the viral RNA population revealing the viral genome diversity within a single host. A range of software tools and pipelines can transform raw deep sequencing reads into Sequence Alignment Mapping (SAM) files. We propose that interpretation tools should process these SAM files, directly translating individual reads to amino acids in order to extract statistics of interest such as the proportion of different amino acid residues at specific sites. This preserves per-read linkage between nucleotide variants at different positions within a codon location. The samReporter is a subsystem of the GLUE software toolkit which follows this direct read translation approach in its processing of SAM files. We test samReporter on a deep sequencing dataset obtained from a cohort of 241 UK HCV patients for whom prior treatment with direct-acting antivirals has failed; deep sequencing and resistance testing have been suggested to be of clinical use in this context. We compared the polymorphism interpretation results of the samReporter against an approach that does not preserve per-read linkage. We found that the samReporter was able to properly interpret the sequence data at resistance-associated locations in nine patients where the alternative approach was equivocal. In three cases, the samReporter confirmed that resistance or an atypical substitution was present at NS5A position 30. In three further cases, it confirmed that the sofosbuvir-resistant NS5B substitution S282T was absent. This suggests the direct read translation approach implemented is of value for interpreting viral deep sequencing data.
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spelling pubmed-65209542019-06-03 Interpreting Viral Deep Sequencing Data with GLUE Singer, Joshua B. Thomson, Emma C. Hughes, Joseph Aranday-Cortes, Elihu McLauchlan, John da Silva Filipe, Ana Tong, Lily Manso, Carmen F. Gifford, Robert J. Robertson, David L. Barnes, Eleanor Ansari, M. Azim Mbisa, Jean L. Bibby, David F. Bradshaw, Daniel Smith, David Viruses Article Using deep sequencing technologies such as Illumina’s platform, it is possible to obtain reads from the viral RNA population revealing the viral genome diversity within a single host. A range of software tools and pipelines can transform raw deep sequencing reads into Sequence Alignment Mapping (SAM) files. We propose that interpretation tools should process these SAM files, directly translating individual reads to amino acids in order to extract statistics of interest such as the proportion of different amino acid residues at specific sites. This preserves per-read linkage between nucleotide variants at different positions within a codon location. The samReporter is a subsystem of the GLUE software toolkit which follows this direct read translation approach in its processing of SAM files. We test samReporter on a deep sequencing dataset obtained from a cohort of 241 UK HCV patients for whom prior treatment with direct-acting antivirals has failed; deep sequencing and resistance testing have been suggested to be of clinical use in this context. We compared the polymorphism interpretation results of the samReporter against an approach that does not preserve per-read linkage. We found that the samReporter was able to properly interpret the sequence data at resistance-associated locations in nine patients where the alternative approach was equivocal. In three cases, the samReporter confirmed that resistance or an atypical substitution was present at NS5A position 30. In three further cases, it confirmed that the sofosbuvir-resistant NS5B substitution S282T was absent. This suggests the direct read translation approach implemented is of value for interpreting viral deep sequencing data. MDPI 2019-04-03 /pmc/articles/PMC6520954/ /pubmed/30987147 http://dx.doi.org/10.3390/v11040323 Text en © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Singer, Joshua B.
Thomson, Emma C.
Hughes, Joseph
Aranday-Cortes, Elihu
McLauchlan, John
da Silva Filipe, Ana
Tong, Lily
Manso, Carmen F.
Gifford, Robert J.
Robertson, David L.
Barnes, Eleanor
Ansari, M. Azim
Mbisa, Jean L.
Bibby, David F.
Bradshaw, Daniel
Smith, David
Interpreting Viral Deep Sequencing Data with GLUE
title Interpreting Viral Deep Sequencing Data with GLUE
title_full Interpreting Viral Deep Sequencing Data with GLUE
title_fullStr Interpreting Viral Deep Sequencing Data with GLUE
title_full_unstemmed Interpreting Viral Deep Sequencing Data with GLUE
title_short Interpreting Viral Deep Sequencing Data with GLUE
title_sort interpreting viral deep sequencing data with glue
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6520954/
https://www.ncbi.nlm.nih.gov/pubmed/30987147
http://dx.doi.org/10.3390/v11040323
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