Evidence map›Paper›PMID 24964173›Full record

ArticleNature biotechnology2014

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 and 3 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature biotechnology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 191 papers.

0numbers the graph read from it
0cells of the map it votes in
191citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

191 citing papers in PubMed.

  1. Nanopore Sequencing for Chikungunya Virus: Principles and Application.Methods in molecular biology (Clifton, N.J.) · 2027
    Article
  2. Review
  3. Review
  4. Article
  5. Article
  6. Article
  7. Article
  8. Article
  9. Article
  10. Review
  11. Review
  12. Replication-coupled hemimethylation inFrontiers in microbiology · 2026
    Review
  13. Article
  14. Review
  15. Article
  16. Review
  17. Article
  18. Article
  19. Review
  20. Article

131 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

13 authors.

Andrew H LaszloDepartment of Physics, University of Washington, Seattle, Washington, USA.
Ian M DerringtonDepartment of Physics, University of Washington, Seattle, Washington, USA.
Brian C RossDepartment of Physics, University of Washington, Seattle, Washington, USA.
Henry BrinkerhoffDepartment of Physics, University of Washington, Seattle, Washington, USA.ORCID 0000000327358048
Andrew AdeyDepartment of Genome Sciences, University of Washington, Seattle, Washington, USA.
Ian C NovaDepartment of Physics, University of Washington, Seattle, Washington, USA.
Jonathan M CraigDepartment of Physics, University of Washington, Seattle, Washington, USA.
Kyle W LangfordDepartment of Physics, University of Washington, Seattle, Washington, USA.
Jenny Mae SamsonDepartment of Physics, University of Washington, Seattle, Washington, USA.
Riza DazaDepartment of Genome Sciences, University of Washington, Seattle, Washington, USA.
Kenji DoeringDepartment of Physics, University of Washington, Seattle, Washington, USA.
Jay ShendureDepartment of Genome Sciences, University of Washington, Seattle, Washington, USA.
Jens H GundlachDepartment of Physics, University of Washington, Seattle, Washington, USA.

Funding

Nanopore sequencing of DNA with MspAR01HG005115 · NHGRI · UNIVERSITY OF WASHINGTON · PI GUNDLACH, JENS, LASZLO, ANDREW · 2009 to 2024
$14.0M
Optimization of Processive Enzymes for DNA Sequencing using NanoporesR01HG006321 · NHGRI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI AKESON, MARK A · 2011 to 2013
$3.6M
Massively Parallel Contiguity MappingR01HG006283 · NHGRI · UNIVERSITY OF WASHINGTON · PI SHENDURE, JAY ASHOK · 2011 to 2016
$3.4M
NHGRI NIH HHS R01 HG005115NHGRI NIH HHS R01HG005115NHGRI NIH HHS R01 HG006283NHGRI NIH HHS R01HG006283NHGRI NIH HHS R01 HG006321NHGRI NIH HHS R01HG006321
6 · The paper itself

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.

Indexed as

NanoporesDNASequence Analysis, DNADNA

Identifiers

PMID24964173
PMCPMC4126851

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.