Evidence map›Paper›PMID 36292670›Full record

ArticleGenes2022

Optimization of Oxford Nanopore Technology Sequencing Workflow for Detection of Amplicons in Real Time Using ONT-DART Tool.

Robert Player, Kathleen Verratti, Andrea Staab, Ellen Forsyth, Amanda Ernlund, Mihir S Joshi, Rebecca Dunning, David Rozak, Sarah Grady, Bruce Goodwin and 1 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genes, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
1.0field-weighted citation impact, top 23% of its field
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

4 citing papers in PubMed, 6 citations in OpenAlex.

  1. Article
  2. Review
  3. Review
  4. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

11 authors at 4 institutions in 1 country.

Robert PlayerApplied Physics Laboratory, The Johns Hopkins University, Laurel, MD 20723, USA.ORCID 0000-0001-5872-259X
Kathleen VerrattiApplied Physics Laboratory, The Johns Hopkins University, Laurel, MD 20723, USA.
Andrea StaabNaval Surface Warfare Center, Dahlgren, VA 22448, USA.
Ellen ForsythApplied Physics Laboratory, The Johns Hopkins University, Laurel, MD 20723, USA.
Amanda ErnlundApplied Physics Laboratory, The Johns Hopkins University, Laurel, MD 20723, USA.ORCID 0000-0003-1113-4103
Mihir S JoshiApplied Physics Laboratory, The Johns Hopkins University, Laurel, MD 20723, USA.
Rebecca DunningUS Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, MD 21702, USA.
David RozakUS Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, MD 21702, USA.
Sarah GradyApplied Physics Laboratory, The Johns Hopkins University, Laurel, MD 20723, USA.
Bruce GoodwinJoint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense (JPEO-CBRND), JPL-Enabling Biotechnologies, Frederick, MD 21702, USA.
Shanmuga SozhamannanJoint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense (JPEO-CBRND), JPL-Enabling Biotechnologies, Frederick, MD 21702, USA.ORCID 0000-0002-6762-7874
Johns Hopkins University Applied Physics Laboratory · USUnited States Army Medical Research Institute of Infectious Diseases · USLogistics Management Institute (United States) · USNaval Surface Warfare Center · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

An optimized, well-tested and validated targeted genomic sequencing-based high-throughput assay is currently not available ready for routine biodefense and biosurveillance applications. Earlier, we addressed this gap by developing and establishing baseline comparisons of a multiplex end-point Polymerase Chain Reaction (PCR) assay followed by Oxford Nanopore Technology (ONT) based amplicon sequencing to real time PCR and customized data processing. Here, we expand upon this effort by identifying the optimal ONT library preparation method for integration into a novel software platform ONT-DART (ONT-Detection of Amplicons in Real-Time). ONT-DART is a dockerized, real-time, amplicon-sequence analysis workflow that is used to reproducibly process and filter read data to support actionable amplicon detection calls based on alignment metrics, within sample statistics, and no-template control data. This analysis pipeline was used to compare four ONT library preparation protocols using R9 and Flongle (FL) flow cells. The two 4-Primer methods tested required the shortest preparation times (5.5 and 6.5 h) for 48 libraries but provided lower fidelity data. The Native Barcoding and Ligation methods required longer preparation times of 8 and 12 h, respectively, and resulted in higher overall data quality. On average, data derived from R9 flow cells produced true positive calls for target organisms more than twice as fast as the lower throughput FL flow cells. These results suggest that utilizing the R9 flowcell with an ONT Native Barcoding amplicon library method in combination with ONT-DART platform analytics provides the best sequencing-based alternative to current PCR-based biodetection methods.

Indexed as

NanoporesHigh-Throughput Nucleotide SequencingMultiplex Polymerase Chain ReactionTechnologyWorkflowbiodefensebiodetectionbiosurveillancebiothreat agentsoxford nanopore sequencingreal-time Sequencingsequencing library preparation

Identifiers

PMID36292670
PMCPMC9602318
OpenAlexW4303685756

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.