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Considerations for clinical read alignment and mutational profiling using next-generation sequencing

Next-generation sequencing technologies are increasingly being applied in clinical settings, however the data are characterized by a range of platform-specific artifacts making downstream analysis problematic and error- prone. One major application of NGS is in the profiling of clinically relevant m...

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Autor principal: Oliver, Gavin R
Formato: Online Artículo Texto
Lenguaje:English
Publicado: F1000Research 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3945748/
https://www.ncbi.nlm.nih.gov/pubmed/24627757
http://dx.doi.org/10.12688/f1000research.1-2.v2
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author Oliver, Gavin R
author_facet Oliver, Gavin R
author_sort Oliver, Gavin R
collection PubMed
description Next-generation sequencing technologies are increasingly being applied in clinical settings, however the data are characterized by a range of platform-specific artifacts making downstream analysis problematic and error- prone. One major application of NGS is in the profiling of clinically relevant mutations whereby sequences are aligned to a reference genome and potential mutations assessed and scored. Accurate sequence alignment is pivotal in reliable assessment of potential mutations however selection of appropriate alignment tools is a non-trivial task complicated by the availability of multiple solutions each with its own performance characteristics. Using targeted analysis of BRCA1 as an example, we have simulated and mutated a test dataset based on Illumina sequencing technology. Our findings reveal key differences in the abilities of a range of common commercial and open source alignment tools to facilitate accurate downstream detection of a range of mutations. These observations will be of importance to anyone using NGS to profile mutations in clinical or basic research.
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spelling pubmed-39457482014-03-12 Considerations for clinical read alignment and mutational profiling using next-generation sequencing Oliver, Gavin R F1000Res Research Article Next-generation sequencing technologies are increasingly being applied in clinical settings, however the data are characterized by a range of platform-specific artifacts making downstream analysis problematic and error- prone. One major application of NGS is in the profiling of clinically relevant mutations whereby sequences are aligned to a reference genome and potential mutations assessed and scored. Accurate sequence alignment is pivotal in reliable assessment of potential mutations however selection of appropriate alignment tools is a non-trivial task complicated by the availability of multiple solutions each with its own performance characteristics. Using targeted analysis of BRCA1 as an example, we have simulated and mutated a test dataset based on Illumina sequencing technology. Our findings reveal key differences in the abilities of a range of common commercial and open source alignment tools to facilitate accurate downstream detection of a range of mutations. These observations will be of importance to anyone using NGS to profile mutations in clinical or basic research. F1000Research 2012-09-20 /pmc/articles/PMC3945748/ /pubmed/24627757 http://dx.doi.org/10.12688/f1000research.1-2.v2 Text en Copyright: © 2012 Oliver GR http://creativecommons.org/licenses/by/3.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. http://creativecommons.org/publicdomain/zero/1.0/ Data associated with the article are available under the terms of the Creative Commons Zero "No rights reserved" data waiver (CC0 1.0 Public domain dedication).
spellingShingle Research Article
Oliver, Gavin R
Considerations for clinical read alignment and mutational profiling using next-generation sequencing
title Considerations for clinical read alignment and mutational profiling using next-generation sequencing
title_full Considerations for clinical read alignment and mutational profiling using next-generation sequencing
title_fullStr Considerations for clinical read alignment and mutational profiling using next-generation sequencing
title_full_unstemmed Considerations for clinical read alignment and mutational profiling using next-generation sequencing
title_short Considerations for clinical read alignment and mutational profiling using next-generation sequencing
title_sort considerations for clinical read alignment and mutational profiling using next-generation sequencing
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3945748/
https://www.ncbi.nlm.nih.gov/pubmed/24627757
http://dx.doi.org/10.12688/f1000research.1-2.v2
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