About: PCR diagnostics: In silico validation by an automated tool using freely available software programs

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An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	PCR diagnostics: In silico validation by an automated tool using freely available software programs
Creator	Kooi, Engbert Van Rijn, Piet Van Weezep, Erik
source	Elsevier; Medline; PMC
abstract	Abstract PCR diagnostics are often the first line of laboratory diagnostics and are regularly designed to either differentiate between or detect all pathogen variants of a family, genus or species. The ideal PCR test detects all variants of the target pathogen, including newly discovered and emerging variants, while closely related pathogens and their variants should not be detected. This is challenging as pathogens show a high degree of genetic variation due to genetic drift, adaptation and evolution. Therefore, frequent re-evaluation of PCR diagnostics is needed to monitor its usefulness. Validation of PCR diagnostics recognizes three stages, in silico, in vitro and in vivo validation. In vitro and in vivo testing are usually costly, labour intensive and imply a risk of handling dangerous pathogens. In silico validation reduces this burden. In silico validation checks primers and probes by comparing their sequences with available nucleotide sequences. In recent years the amount of available sequences has dramatically increased by high throughput and deep sequencing projects. This makes in silico validation more informative, but also more computing intensive. To facilitate validation of PCR tests, a software tool named PCRv was developed. PCRv consists of a user friendly graphical user interface and coordinates the use of the software programs ClustalW and SSEARCH in order to perform in silico validation of PCR tests of different formats. Use of internal control sequences makes the analysis compliant to laboratory quality control systems. Finally, PCRv generates a validation report that includes an overview as well as a list of detailed results. In-house developed, published and OIE-recommended PCR tests were easily (re-) evaluated by use of PCRv. To demonstrate the power of PCRv, in silico validation of several PCR tests are shown and discussed.
has issue date	2019-08-31(xsd:dateTime)
bibo:doi	10.1016/j.jviromet.2019.05.002
bibo:pmid	31095975
has license	els-covid
sha1sum (hex)	9c5ee28376fc314e26bd3ea5f6dc7a5d356d9175
schema:url	https://doi.org/10.1016/j.jviromet.2019.05.002
resource representing a document's title	PCR diagnostics: In silico validation by an automated tool using freely available software programs
has PubMed Central identifier	PMC7113775
has PubMed identifier	31095975
schema:publication	Journal of Virological Methods
resource representing a document's body	covid:9c5ee28376fc314e26bd3ea5f6dc7a5d356d9175#body_text
is schema:about of	named entity 'validation' named entity 'PCR' named entity 'recognizes' named entity 'perform' named entity 'MONITOR' named entity 'LABORATORY' named entity 'SOFTWARE TOOL' named entity 'USUALLY' named entity 'INFORMATIVE' named entity 'TARGET' named entity 'INCREASED' named entity 'RELATED' named entity 'CLUSTALW' named entity 'TESTS' named entity 'DUE TO' named entity 'NUCLEOTIDE SEQUENCES' named entity 'IN VITRO' named entity 'THEIR' named entity 'HIGH' named entity 'RE-EVALUATION' named entity 'PRIMERS' named entity 'EASILY' named entity 'PUBLISHED' named entity 'DIFFERENTIATE' named entity 'ADAPTATION' named entity 'YEARS' named entity 'PERFORM' named entity 'CONTROL SYSTEMS' named entity 'EVOLUTION' named entity 'DEGREE' named entity 'VALIDATION' named entity 'REGULARLY' named entity 'INTERNAL' named entity 'CONTROL SEQUENCES' named entity 'S T' named entity 'POWER' named entity 'PCR' named entity 'PATHOGEN' named entity 'COMPLIANT' named entity 'AVAILABLE' named entity 'LINE' named entity 'USE OF' named entity 'DETECT' named entity 'DEEP SEQUENCING' named entity 'GENETIC VARIATION' named entity 'OVERVIEW' named entity 'FAMILY' named entity 'IN VIVO TESTING' named entity 'ORDER' named entity 'NEWLY DISCOVERED' named entity 'EVALUATED' named entity 'SPECIES' named entity 'DETAILED' named entity 'PROBES' named entity 'USER' named entity 'LIST' named entity 'HIGH THROUGHPUT' named entity 'HANDLING' named entity 'RECENT' named entity 'ANALYSIS' named entity 'GENUS' named entity 'IDEAL' named entity 'NAMED' named entity 'IN-HOUSE' named entity 'TEST' named entity 'PATHOGENS' named entity 'BURDEN' named entity 'FORMATS' named entity 'ITS' named entity 'RECOMMENDED' named entity 'LABOUR' named entity 'REPORT' named entity 'EITHER' named entity 'GENETIC DRIFT' named entity 'DIFFERENT' named entity 'COMPUTING' named entity 'SOFTWARE' named entity 'PROGRAMS' named entity 'IN VIVO'

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