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PVAmpliconFinder: a workflow for the identification of human papillomaviruses from high-throughput amplicon sequencing
BACKGROUND: The detection of known human papillomaviruses (PVs) from targeted wet-lab approaches has traditionally used PCR-based methods coupled with Sanger sequencing. With the introduction of next-generation sequencing (NGS), these approaches can be revisited to integrate the sequencing power of...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7282039/ https://www.ncbi.nlm.nih.gov/pubmed/32513098 http://dx.doi.org/10.1186/s12859-020-03573-8 |
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author | Robitaille, Alexis Brancaccio, Rosario N. Dutta, Sankhadeep Rollison, Dana E. Leja, Marcis Fischer, Nicole Grundhoff, Adam Gheit, Tarik Tommasino, Massimo Olivier, Magali |
author_facet | Robitaille, Alexis Brancaccio, Rosario N. Dutta, Sankhadeep Rollison, Dana E. Leja, Marcis Fischer, Nicole Grundhoff, Adam Gheit, Tarik Tommasino, Massimo Olivier, Magali |
author_sort | Robitaille, Alexis |
collection | PubMed |
description | BACKGROUND: The detection of known human papillomaviruses (PVs) from targeted wet-lab approaches has traditionally used PCR-based methods coupled with Sanger sequencing. With the introduction of next-generation sequencing (NGS), these approaches can be revisited to integrate the sequencing power of NGS. Although computational tools have been developed for metagenomic approaches to search for known or novel viruses in NGS data, no appropriate tool is available for the classification and identification of novel viral sequences from data produced by amplicon-based methods. RESULTS: We have developed PVAmpliconFinder, a data analysis workflow designed to rapidly identify and classify known and potentially new Papillomaviridae sequences from NGS amplicon sequencing with degenerate PV primers. Here, we describe the features of PVAmpliconFinder and its implementation using biological data obtained from amplicon sequencing of human skin swab specimens and oral rinses from healthy individuals. CONCLUSIONS: PVAmpliconFinder identified putative new HPV sequences, including one that was validated by wet-lab experiments. PVAmpliconFinder can be easily modified and applied to other viral families. PVAmpliconFinder addresses a gap by providing a solution for the analysis of NGS amplicon sequencing, increasingly used in clinical research. The PVAmpliconFinder workflow, along with its source code, is freely available on the GitHub platform: https://github.com/IARCbioinfo/PVAmpliconFinder. |
format | Online Article Text |
id | pubmed-7282039 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-72820392020-06-10 PVAmpliconFinder: a workflow for the identification of human papillomaviruses from high-throughput amplicon sequencing Robitaille, Alexis Brancaccio, Rosario N. Dutta, Sankhadeep Rollison, Dana E. Leja, Marcis Fischer, Nicole Grundhoff, Adam Gheit, Tarik Tommasino, Massimo Olivier, Magali BMC Bioinformatics Methodology Article BACKGROUND: The detection of known human papillomaviruses (PVs) from targeted wet-lab approaches has traditionally used PCR-based methods coupled with Sanger sequencing. With the introduction of next-generation sequencing (NGS), these approaches can be revisited to integrate the sequencing power of NGS. Although computational tools have been developed for metagenomic approaches to search for known or novel viruses in NGS data, no appropriate tool is available for the classification and identification of novel viral sequences from data produced by amplicon-based methods. RESULTS: We have developed PVAmpliconFinder, a data analysis workflow designed to rapidly identify and classify known and potentially new Papillomaviridae sequences from NGS amplicon sequencing with degenerate PV primers. Here, we describe the features of PVAmpliconFinder and its implementation using biological data obtained from amplicon sequencing of human skin swab specimens and oral rinses from healthy individuals. CONCLUSIONS: PVAmpliconFinder identified putative new HPV sequences, including one that was validated by wet-lab experiments. PVAmpliconFinder can be easily modified and applied to other viral families. PVAmpliconFinder addresses a gap by providing a solution for the analysis of NGS amplicon sequencing, increasingly used in clinical research. The PVAmpliconFinder workflow, along with its source code, is freely available on the GitHub platform: https://github.com/IARCbioinfo/PVAmpliconFinder. BioMed Central 2020-06-08 /pmc/articles/PMC7282039/ /pubmed/32513098 http://dx.doi.org/10.1186/s12859-020-03573-8 Text en © The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Methodology Article Robitaille, Alexis Brancaccio, Rosario N. Dutta, Sankhadeep Rollison, Dana E. Leja, Marcis Fischer, Nicole Grundhoff, Adam Gheit, Tarik Tommasino, Massimo Olivier, Magali PVAmpliconFinder: a workflow for the identification of human papillomaviruses from high-throughput amplicon sequencing |
title | PVAmpliconFinder: a workflow for the identification of human papillomaviruses from high-throughput amplicon sequencing |
title_full | PVAmpliconFinder: a workflow for the identification of human papillomaviruses from high-throughput amplicon sequencing |
title_fullStr | PVAmpliconFinder: a workflow for the identification of human papillomaviruses from high-throughput amplicon sequencing |
title_full_unstemmed | PVAmpliconFinder: a workflow for the identification of human papillomaviruses from high-throughput amplicon sequencing |
title_short | PVAmpliconFinder: a workflow for the identification of human papillomaviruses from high-throughput amplicon sequencing |
title_sort | pvampliconfinder: a workflow for the identification of human papillomaviruses from high-throughput amplicon sequencing |
topic | Methodology Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7282039/ https://www.ncbi.nlm.nih.gov/pubmed/32513098 http://dx.doi.org/10.1186/s12859-020-03573-8 |
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