Decoding long nanopore sequencing reads of natural DNA

Andrew H. Laszlo, Ian M. Derrington, Brian C. Ross, Henry Brinkerhoff, Andrew Adey, Ian C. Nova, Jonathan M. Craig, Kyle W. Langford, Jenny Mae Samson, Riza Daza, Kenji Doering, Jay Shendure, Jens H. Gundlach

Research output: Contribution to journalArticle

202 Citations (Scopus)

Abstract

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, which 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 a foundation for nanopore sequencing of long, natural DNA strands.

Original languageEnglish (US)
Pages (from-to)829-833
Number of pages5
JournalNature Biotechnology
Volume32
Issue number8
DOIs
StatePublished - 2014
Externally publishedYes

Fingerprint

Nanopores
Decoding
DNA
Ions
Genes
Genome
Nucleotides
Bacteriophage phi X 174
Bacteriophages
Polymorphism
DNA Sequence Analysis
Costs and Cost Analysis
Molecules
Costs

ASJC Scopus subject areas

  • Applied Microbiology and Biotechnology
  • Biotechnology
  • Molecular Medicine
  • Bioengineering
  • Biomedical Engineering

Cite this

Laszlo, A. H., Derrington, I. M., Ross, B. C., Brinkerhoff, H., Adey, A., Nova, I. C., ... Gundlach, J. H. (2014). Decoding long nanopore sequencing reads of natural DNA. Nature Biotechnology, 32(8), 829-833. https://doi.org/10.1038/nbt.2950

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.

In: Nature Biotechnology, Vol. 32, No. 8, 2014, p. 829-833.

Research output: Contribution to journalArticle

Laszlo, AH, Derrington, IM, Ross, BC, Brinkerhoff, H, Adey, A, Nova, IC, Craig, JM, Langford, KW, Samson, JM, Daza, R, Doering, K, Shendure, J & Gundlach, JH 2014, 'Decoding long nanopore sequencing reads of natural DNA', Nature Biotechnology, vol. 32, no. 8, pp. 829-833. https://doi.org/10.1038/nbt.2950
Laszlo AH, Derrington IM, Ross BC, Brinkerhoff H, Adey A, Nova IC et al. Decoding long nanopore sequencing reads of natural DNA. Nature Biotechnology. 2014;32(8):829-833. https://doi.org/10.1038/nbt.2950
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. In: Nature Biotechnology. 2014 ; Vol. 32, No. 8. pp. 829-833.
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