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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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Formato: | Online Artículo Texto |
Lenguaje: | English |
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F1000Research
2012
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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. |
format | Online Article Text |
id | pubmed-3945748 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | F1000Research |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT olivergavinr considerationsforclinicalreadalignmentandmutationalprofilingusingnextgenerationsequencing |