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Player R, Verratti K, Staab A, Forsyth E, Ernlund A, Joshi MS, Dunning R, Rozak D, Grady S, Goodwin B, Sozhamannan S. Optimization of Oxford Nanopore Technology Sequencing Workflow for Detection of Amplicons in Real Time Using ONT-DART Tool. Genes (Basel) 2022; 13:genes13101785. [PMID: 36292670 PMCID: PMC9602318 DOI: 10.3390/genes13101785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/17/2022] [Accepted: 09/28/2022] [Indexed: 11/21/2022] Open
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.
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Affiliation(s)
- Robert Player
- Applied Physics Laboratory, The Johns Hopkins University, Laurel, MD 20723, USA
- Datirium, LLC, Cincinnati, OH 45226, USA
| | - Kathleen Verratti
- Applied Physics Laboratory, The Johns Hopkins University, Laurel, MD 20723, USA
| | - Andrea Staab
- Naval Surface Warfare Center, Dahlgren, VA 22448, USA
| | - Ellen Forsyth
- Applied Physics Laboratory, The Johns Hopkins University, Laurel, MD 20723, USA
| | - Amanda Ernlund
- Applied Physics Laboratory, The Johns Hopkins University, Laurel, MD 20723, USA
| | - Mihir S. Joshi
- Applied Physics Laboratory, The Johns Hopkins University, Laurel, MD 20723, USA
| | - Rebecca Dunning
- US Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, MD 21702, USA
| | - David Rozak
- US Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, MD 21702, USA
| | - Sarah Grady
- Applied Physics Laboratory, The Johns Hopkins University, Laurel, MD 20723, USA
| | - Bruce Goodwin
- Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense (JPEO-CBRND), JPL-Enabling Biotechnologies, Frederick, MD 21702, USA
| | - Shanmuga Sozhamannan
- Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense (JPEO-CBRND), JPL-Enabling Biotechnologies, Frederick, MD 21702, USA
- Logistics Management Institute, Tysons, VA 22102, USA
- Correspondence:
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