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A public website for the automated assessment and validation of SARS-CoV-2 diagnostic PCR assays.
Li, Po-E; Myers Y Gutiérrez, Adán; Davenport, Karen; Flynn, Mark; Hu, Bin; Lo, Chien-Chi; Player Jackson, Elais; Shakya, Migun; Xu, Yan; Gans, Jason D; Chain, Patrick S G.
  • Li PE; Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
  • Myers Y Gutiérrez A; Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
  • Davenport K; Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
  • Flynn M; Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
  • Hu B; Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
  • Lo CC; Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
  • Player Jackson E; Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
  • Shakya M; Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
  • Xu Y; Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
  • Gans JD; Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
  • Chain PSG; Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
Bioinformatics ; 37(7): 1024-1025, 2021 05 17.
Article in English | MEDLINE | ID: covidwho-706027
ABSTRACT

SUMMARY:

Polymerase chain reaction-based assays are the current gold standard for detecting and diagnosing SARS-CoV-2. However, as SARS-CoV-2 mutates, we need to constantly assess whether existing PCR-based assays will continue to detect all known viral strains. To enable the continuous monitoring of SARS-CoV-2 assays, we have developed a web-based assay validation algorithm that checks existing PCR-based assays against the ever-expanding genome databases for SARS-CoV-2 using both thermodynamic and edit-distance metrics. The assay-screening results are displayed as a heatmap, showing the number of mismatches between each detection and each SARS-CoV-2 genome sequence. Using a mismatch threshold to define detection failure, assay performance is summarized with the true-positive rate (recall) to simplify assay comparisons. AVAILABILITY AND IMPLEMENTATION The assay evaluation website and supporting software are Open Source and freely available at https//covid19.edgebioinformatics.org/#/assayValidation, https//github.com/jgans/thermonucleotide BLAST and https//github.com/LANL-Bioinformatics/assay_validation. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Subject(s)

Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Experimental Studies / Prognostic study Limits: Humans Language: English Journal: Bioinformatics Journal subject: Medical Informatics Year: 2021 Document Type: Article Affiliation country: Bioinformatics

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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Experimental Studies / Prognostic study Limits: Humans Language: English Journal: Bioinformatics Journal subject: Medical Informatics Year: 2021 Document Type: Article Affiliation country: Bioinformatics