A Comparison and Integration of MiSeq and MinION Platforms for Sequencing Single Source and Mixed Mitochondrial Genomes

Single source and multiple donor (mixed) samples of human mitochondrial DNA were analyzed and compared using the MinION and the MiSeq platforms. A generalized variant detection strategy was employed to provide a cursory framework for evaluating the reliability and accuracy of mitochondrial sequences...

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Autores principales: Lindberg, Michael R., Schmedes, Sarah E., Hewitt, F. Curtis, Haas, Jamie L., Ternus, Krista L., Kadavy, Dana R., Budowle, Bruce
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2016
Materias:
Research Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5147911/
https://www.ncbi.nlm.nih.gov/pubmed/27936026
http://dx.doi.org/10.1371/journal.pone.0167600
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author Lindberg, Michael R.
Schmedes, Sarah E.
Hewitt, F. Curtis
Haas, Jamie L.
Ternus, Krista L.
Kadavy, Dana R.
Budowle, Bruce
author_facet Lindberg, Michael R.
Schmedes, Sarah E.
Hewitt, F. Curtis
Haas, Jamie L.
Ternus, Krista L.
Kadavy, Dana R.
Budowle, Bruce
author_sort Lindberg, Michael R.
collection PubMed
description Single source and multiple donor (mixed) samples of human mitochondrial DNA were analyzed and compared using the MinION and the MiSeq platforms. A generalized variant detection strategy was employed to provide a cursory framework for evaluating the reliability and accuracy of mitochondrial sequences produced by the MinION. The feasibility of long-read phasing was investigated to establish its efficacy in quantitatively distinguishing and deconvolving individuals in a mixture. Finally, a proof-of-concept was demonstrated by integrating both platforms in a hybrid assembly that leverages solely mixture data to accurately reconstruct full mitochondrial genomes.
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spelling pubmed-51479112016-12-28 A Comparison and Integration of MiSeq and MinION Platforms for Sequencing Single Source and Mixed Mitochondrial Genomes Lindberg, Michael R. Schmedes, Sarah E. Hewitt, F. Curtis Haas, Jamie L. Ternus, Krista L. Kadavy, Dana R. Budowle, Bruce PLoS One Research Article Single source and multiple donor (mixed) samples of human mitochondrial DNA were analyzed and compared using the MinION and the MiSeq platforms. A generalized variant detection strategy was employed to provide a cursory framework for evaluating the reliability and accuracy of mitochondrial sequences produced by the MinION. The feasibility of long-read phasing was investigated to establish its efficacy in quantitatively distinguishing and deconvolving individuals in a mixture. Finally, a proof-of-concept was demonstrated by integrating both platforms in a hybrid assembly that leverages solely mixture data to accurately reconstruct full mitochondrial genomes. Public Library of Science 2016-12-09 /pmc/articles/PMC5147911/ /pubmed/27936026 http://dx.doi.org/10.1371/journal.pone.0167600 Text en © 2016 Lindberg 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 (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Lindberg, Michael R.
Schmedes, Sarah E.
Hewitt, F. Curtis
Haas, Jamie L.
Ternus, Krista L.
Kadavy, Dana R.
Budowle, Bruce
A Comparison and Integration of MiSeq and MinION Platforms for Sequencing Single Source and Mixed Mitochondrial Genomes
title A Comparison and Integration of MiSeq and MinION Platforms for Sequencing Single Source and Mixed Mitochondrial Genomes
title_full A Comparison and Integration of MiSeq and MinION Platforms for Sequencing Single Source and Mixed Mitochondrial Genomes
title_fullStr A Comparison and Integration of MiSeq and MinION Platforms for Sequencing Single Source and Mixed Mitochondrial Genomes
title_full_unstemmed A Comparison and Integration of MiSeq and MinION Platforms for Sequencing Single Source and Mixed Mitochondrial Genomes
title_short A Comparison and Integration of MiSeq and MinION Platforms for Sequencing Single Source and Mixed Mitochondrial Genomes
title_sort comparison and integration of miseq and minion platforms for sequencing single source and mixed mitochondrial genomes
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5147911/
https://www.ncbi.nlm.nih.gov/pubmed/27936026
http://dx.doi.org/10.1371/journal.pone.0167600
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