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Decoding long nanopore sequencing reads of natural DNA

Nanopore sequencing of DNA is a single-molecule technique that may achieve long reads, low cost and high speed with minimal sample preparation and instrumentation. Here, we build on recent progress with respect to nanopore resolution and DNA control to interpret the procession of ion current levels...

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Autores principales: Laszlo, Andrew H., Derrington, Ian M., Ross, Brian C., Brinkerhoff, Henry, Adey, Andrew, Nova, Ian C., Craig, Jonathan M., Langford, Kyle W., Samson, Jenny Mae, Daza, Riza, Doering, Kenji, Shendure, Jay, Gundlach, Jens H.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4126851/
https://www.ncbi.nlm.nih.gov/pubmed/24964173
http://dx.doi.org/10.1038/nbt.2950
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author Laszlo, Andrew H.
Derrington, Ian M.
Ross, Brian C.
Brinkerhoff, Henry
Adey, Andrew
Nova, Ian C.
Craig, Jonathan M.
Langford, Kyle W.
Samson, Jenny Mae
Daza, Riza
Doering, Kenji
Shendure, Jay
Gundlach, Jens H.
author_facet Laszlo, Andrew H.
Derrington, Ian M.
Ross, Brian C.
Brinkerhoff, Henry
Adey, Andrew
Nova, Ian C.
Craig, Jonathan M.
Langford, Kyle W.
Samson, Jenny Mae
Daza, Riza
Doering, Kenji
Shendure, Jay
Gundlach, Jens H.
author_sort Laszlo, Andrew H.
collection PubMed
description Nanopore sequencing of DNA is a single-molecule technique that may achieve long reads, low cost and high speed with minimal sample preparation and instrumentation. Here, we build on recent progress with respect to nanopore resolution and DNA control to interpret the procession of ion current levels observed during the translocation of DNA through the pore MspA. As approximately four nucleotides affect the ion current of each level, we measured the ion current corresponding to all 256 four-nucleotide combinations (quadromers). This quadromer map is highly predictive of ion current levels of previously unmeasured sequences derived from the bacteriophage phi X 174 genome. Furthermore, we show nanopore sequencing reads of phi X 174 up to 4,500 bases in length that can be unambiguously aligned to the phi X 174 reference genome, and demonstrate proof-of-concept utility with respect to hybrid genome assembly and polymorphism detection. This work provides the foundation for nanopore sequencing of long, complex, natural DNA strands.
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spelling pubmed-41268512015-02-01 Decoding long nanopore sequencing reads of natural DNA Laszlo, Andrew H. Derrington, Ian M. Ross, Brian C. Brinkerhoff, Henry Adey, Andrew Nova, Ian C. Craig, Jonathan M. Langford, Kyle W. Samson, Jenny Mae Daza, Riza Doering, Kenji Shendure, Jay Gundlach, Jens H. Nat Biotechnol Article Nanopore sequencing of DNA is a single-molecule technique that may achieve long reads, low cost and high speed with minimal sample preparation and instrumentation. Here, we build on recent progress with respect to nanopore resolution and DNA control to interpret the procession of ion current levels observed during the translocation of DNA through the pore MspA. As approximately four nucleotides affect the ion current of each level, we measured the ion current corresponding to all 256 four-nucleotide combinations (quadromers). This quadromer map is highly predictive of ion current levels of previously unmeasured sequences derived from the bacteriophage phi X 174 genome. Furthermore, we show nanopore sequencing reads of phi X 174 up to 4,500 bases in length that can be unambiguously aligned to the phi X 174 reference genome, and demonstrate proof-of-concept utility with respect to hybrid genome assembly and polymorphism detection. This work provides the foundation for nanopore sequencing of long, complex, natural DNA strands. 2014-06-25 2014-08 /pmc/articles/PMC4126851/ /pubmed/24964173 http://dx.doi.org/10.1038/nbt.2950 Text en http://www.nature.com/authors/editorial_policies/license.html#terms Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:http://www.nature.com/authors/editorial_policies/license.html#terms
spellingShingle Article
Laszlo, Andrew H.
Derrington, Ian M.
Ross, Brian C.
Brinkerhoff, Henry
Adey, Andrew
Nova, Ian C.
Craig, Jonathan M.
Langford, Kyle W.
Samson, Jenny Mae
Daza, Riza
Doering, Kenji
Shendure, Jay
Gundlach, Jens H.
Decoding long nanopore sequencing reads of natural DNA
title Decoding long nanopore sequencing reads of natural DNA
title_full Decoding long nanopore sequencing reads of natural DNA
title_fullStr Decoding long nanopore sequencing reads of natural DNA
title_full_unstemmed Decoding long nanopore sequencing reads of natural DNA
title_short Decoding long nanopore sequencing reads of natural DNA
title_sort decoding long nanopore sequencing reads of natural dna
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4126851/
https://www.ncbi.nlm.nih.gov/pubmed/24964173
http://dx.doi.org/10.1038/nbt.2950
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