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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...
Autores principales: | , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2019
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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. |
format | Online Article Text |
id | pubmed-6520954 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
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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