Reconstructed Ancestral Sequences Improve Pathogen Identification Using Resequencing DNA Microarrays

We describe the benefit of using reconstructed ancestral sequences (RAS) on resequencing microarrays for rapid pathogen identification, with Enterobacteriaceae rpoB sequences as a model. Our results demonstrate a sharp improvement of call rate and accuracy when using RASs as compared to extant seque...

Descripción completa

Detalles Bibliográficos
Autores principales: Berthet, Nicolas, Deletoile, Alexis, Passet, Virginie, Kennedy, Giulia C., Manuguerra, Jean-Claude, Cole, Stewart T., Brisse, Sylvain
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2010
Materias:
Research Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3004854/
https://www.ncbi.nlm.nih.gov/pubmed/21187950
http://dx.doi.org/10.1371/journal.pone.0015243
_version_ 1782194039584456704
author Berthet, Nicolas
Deletoile, Alexis
Passet, Virginie
Kennedy, Giulia C.
Manuguerra, Jean-Claude
Cole, Stewart T.
Brisse, Sylvain
author_facet Berthet, Nicolas
Deletoile, Alexis
Passet, Virginie
Kennedy, Giulia C.
Manuguerra, Jean-Claude
Cole, Stewart T.
Brisse, Sylvain
author_sort Berthet, Nicolas
collection PubMed
description We describe the benefit of using reconstructed ancestral sequences (RAS) on resequencing microarrays for rapid pathogen identification, with Enterobacteriaceae rpoB sequences as a model. Our results demonstrate a sharp improvement of call rate and accuracy when using RASs as compared to extant sequences. This improvement was attributed to the lower sequence divergence of RASs, which also expanded the sequence space covered by the microarray. Extension of this novel microarray design strategy to viruses, antimicrobial resistance elements or toxins is straightforward.
format Text
id pubmed-3004854
institution National Center for Biotechnology Information
language English
publishDate 2010
publisher Public Library of Science
record_format MEDLINE/PubMed
spelling pubmed-30048542010-12-27 Reconstructed Ancestral Sequences Improve Pathogen Identification Using Resequencing DNA Microarrays Berthet, Nicolas Deletoile, Alexis Passet, Virginie Kennedy, Giulia C. Manuguerra, Jean-Claude Cole, Stewart T. Brisse, Sylvain PLoS One Research Article We describe the benefit of using reconstructed ancestral sequences (RAS) on resequencing microarrays for rapid pathogen identification, with Enterobacteriaceae rpoB sequences as a model. Our results demonstrate a sharp improvement of call rate and accuracy when using RASs as compared to extant sequences. This improvement was attributed to the lower sequence divergence of RASs, which also expanded the sequence space covered by the microarray. Extension of this novel microarray design strategy to viruses, antimicrobial resistance elements or toxins is straightforward. Public Library of Science 2010-12-20 /pmc/articles/PMC3004854/ /pubmed/21187950 http://dx.doi.org/10.1371/journal.pone.0015243 Text en Berthet et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Berthet, Nicolas
Deletoile, Alexis
Passet, Virginie
Kennedy, Giulia C.
Manuguerra, Jean-Claude
Cole, Stewart T.
Brisse, Sylvain
Reconstructed Ancestral Sequences Improve Pathogen Identification Using Resequencing DNA Microarrays
title Reconstructed Ancestral Sequences Improve Pathogen Identification Using Resequencing DNA Microarrays
title_full Reconstructed Ancestral Sequences Improve Pathogen Identification Using Resequencing DNA Microarrays
title_fullStr Reconstructed Ancestral Sequences Improve Pathogen Identification Using Resequencing DNA Microarrays
title_full_unstemmed Reconstructed Ancestral Sequences Improve Pathogen Identification Using Resequencing DNA Microarrays
title_short Reconstructed Ancestral Sequences Improve Pathogen Identification Using Resequencing DNA Microarrays
title_sort reconstructed ancestral sequences improve pathogen identification using resequencing dna microarrays
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3004854/
https://www.ncbi.nlm.nih.gov/pubmed/21187950
http://dx.doi.org/10.1371/journal.pone.0015243
work_keys_str_mv AT berthetnicolas reconstructedancestralsequencesimprovepathogenidentificationusingresequencingdnamicroarrays
AT deletoilealexis reconstructedancestralsequencesimprovepathogenidentificationusingresequencingdnamicroarrays
AT passetvirginie reconstructedancestralsequencesimprovepathogenidentificationusingresequencingdnamicroarrays
AT kennedygiuliac reconstructedancestralsequencesimprovepathogenidentificationusingresequencingdnamicroarrays
AT manuguerrajeanclaude reconstructedancestralsequencesimprovepathogenidentificationusingresequencingdnamicroarrays
AT colestewartt reconstructedancestralsequencesimprovepathogenidentificationusingresequencingdnamicroarrays
AT brissesylvain reconstructedancestralsequencesimprovepathogenidentificationusingresequencingdnamicroarrays

Ejemplares similares