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| Status |
Public on Jan 24, 2021 |
| Title |
A Multiplexed, Next-Generation Sequencing Platform for High-Throughput Detection of SARS-CoV-2 [pilot cohort] |
| Organisms |
Homo sapiens; synthetic construct; synthetic RNA |
| Experiment type |
Other
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| Summary |
Population scale sweeps of viral pathogens, such as SARS-CoV-2, require high intensity testing for effective management. However, reliable systems affording parallel testing of thousands of patients for pathogen infection have not yet been routinely employed. Here we describe “Systematic Parallel Analysis of RNA coupled to Sequencing for Covid-19 screening” (C19-SPAR-Seq), a multiplexed, readily automated platform for SARS-CoV-2 detection capable of analyzing tens of thousands of patient samples in a single instrument run. To address strict requirements for control of assay parameters and output demanded by clinical diagnostics, we employed a control-based Precision-Recall and Receiver Operator Characteristics (coPR) analysis to assign run-specific quality control metrics. C19-SPAR-Seq coupled to coPR on a trial cohort of several hundred patients performed with a specificity of 100% and sensitivity of 91% on samples with low viral loads. Our study thus establishes the feasibility of employing C19-SPAR-Seq for the large-scale monitoring of SARS-CoV-2 and other pathogens.
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| Overall design |
Highly parallelized RT-PCR amplification of SARS-CoV-2 sequences from patient swabs coupled to next-generation sequencing (NGS) for multiplexed samples.
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| Contributor(s) |
Aynaud MM, Hernandez JJ, Barutcu S, Braunschweig U, Chan K, Pearson JD, Trcka D, Han H, Prosser S, Kim J, Barrios-Rodiles M, Jen M, Song S, Shen J, Bruce C, Hazlett B, Poutanen S, Attisano L, Bremner R, Mazzulli T, Blencowe BJ, Pelletier L, Wrana JL |
| Citation(s) |
33658502 |
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| Submission date |
Oct 25, 2020 |
| Last update date |
Apr 06, 2021 |
| Contact name |
Jeff Wrana |
| E-mail(s) |
wrana@lunenfeld.ca
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| Organization name |
Lunenfeld Tanenbaum Research Institute
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| Street address |
600 Unv Ave
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| City |
Toronto |
| State/province |
ON |
| ZIP/Postal code |
M5G 1X5 |
| Country |
Canada |
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| Platforms (3) |
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| Samples (862)
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| This SubSeries is part of SuperSeries: |
| GSE160036 |
A Multiplexed, Next-Generation Sequencing Platform for High-Throughput Detection of SARS-CoV-2 |
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| Relations |
| BioProject |
PRJNA671689 |
| SRA |
SRP288484 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE160033_Pilot_ReadCount_Table.csv.gz |
7.3 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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