A public website for the automated assessment and validation of SARS-CoV-2 diagnostic PCR assays.
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.
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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