A public website for the automated assessment and validation of SARS-CoV-2 diagnostic PCR assays
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 moni...
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| Veröffentlicht in: | Bioinformatics 2021-05, Vol.37 (7), p.1024-1025 |
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| creator | 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 |
| description | 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. |
| doi_str_mv | 10.1093/bioinformatics/btaa710 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_7559084</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><oup_id>10.1093/bioinformatics/btaa710</oup_id><sourcerecordid>2432857353</sourcerecordid><originalsourceid>FETCH-LOGICAL-c483t-2d070d3990dad91bc67de8d977c09189e1dd0da87272fac7c9d4ee11a1fe2a393</originalsourceid><addsrcrecordid>eNqNUU1v1DAUtBAVLS1_obI4cQn1V-L4grRalQ-pEqgfXM2L_dI1SuIldor67_Fql4reONnSm5k384aQc87ec2bkRRdimPo4j5CDSxddBtCcvSAnXDWsEqw2L8tfNrpSLZPH5HVKPxmruVLqFTmWQmvdcnlCfqzodumG4Ohv7FLISIsozRuksORY1NFTSAlTGnHKFCZPH2AIvqyNE409vVld31Tr-L0S1Ae4n2Iqhui39fWOBo_pjBz1MCR8c3hPyd3Hy9v15-rq66cv69VV5VQrcyU808xLY5gHb3jnGu2x9UZrxwxvDXLvy6jVQosenHbGK0TOgfcoQBp5Sj7sdUucEb0rbmcY7HYOI8yPNkKwzydT2Nj7-GB1XRvWqiLwdi-wS2CTK7dwGxenCV22XPOmFk0BvTtsmeOvBVO2Y0gOhwEmjEuyQknR1lrWskCbPdTNMaUZ-ycvnNldh_Z5h_bQYSGe_5vkifa3tALgB6fL9n9F_wB9qLDR</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2432857353</pqid></control><display><type>article</type><title>A public website for the automated assessment and validation of SARS-CoV-2 diagnostic PCR assays</title><source>Oxford Journals Open Access Collection</source><source>MEDLINE</source><source>EZB-FREE-00999 freely available EZB journals</source><source>PubMed Central</source><source>Alma/SFX Local Collection</source><creator>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</creator><contributor>Elofsson, Arne</contributor><creatorcontrib>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 ; Los Alamos National Lab. (LANL), Los Alamos, NM (United States) ; Elofsson, Arne</creatorcontrib><description>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.</description><identifier>ISSN: 1367-4803</identifier><identifier>EISSN: 1460-2059</identifier><identifier>EISSN: 1367-4811</identifier><identifier>DOI: 10.1093/bioinformatics/btaa710</identifier><identifier>PMID: 32777813</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Applications Notes ; Biological Science ; COVID-19 ; COVID-19 Testing ; Humans ; Polymerase Chain Reaction ; SARS-CoV-2 ; SARS2, COVID-19, assay validation, PCR ; Sensitivity and Specificity</subject><ispartof>Bioinformatics, 2021-05, Vol.37 (7), p.1024-1025</ispartof><rights>The Author(s) 2020. Published by Oxford University Press. 2020</rights><rights>The Author(s) 2020. Published by Oxford University Press.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c483t-2d070d3990dad91bc67de8d977c09189e1dd0da87272fac7c9d4ee11a1fe2a393</citedby><cites>FETCH-LOGICAL-c483t-2d070d3990dad91bc67de8d977c09189e1dd0da87272fac7c9d4ee11a1fe2a393</cites><orcidid>0000-0002-3457-1632 ; 0000-0002-7151-3108 ; 0000-0003-4290-1993 ; 0000-0003-3949-3634 ; 0000-0002-0278-8466 ; 0000000202788466 ; 0000000271513108 ; 0000000342901993 ; 0000000339493634 ; 0000000234571632</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7559084/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7559084/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,1598,27903,27904,53769,53771</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32777813$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://www.osti.gov/biblio/1716526$$D View this record in Osti.gov$$Hfree_for_read</backlink></links><search><contributor>Elofsson, Arne</contributor><creatorcontrib>Li, Po-E</creatorcontrib><creatorcontrib>Myers y Gutiérrez, Adán</creatorcontrib><creatorcontrib>Davenport, Karen</creatorcontrib><creatorcontrib>Flynn, Mark</creatorcontrib><creatorcontrib>Hu, Bin</creatorcontrib><creatorcontrib>Lo, Chien-Chi</creatorcontrib><creatorcontrib>Player Jackson, Elais</creatorcontrib><creatorcontrib>Shakya, Migun</creatorcontrib><creatorcontrib>Xu, Yan</creatorcontrib><creatorcontrib>Gans, Jason D</creatorcontrib><creatorcontrib>Chain, Patrick S G</creatorcontrib><creatorcontrib>Los Alamos National Lab. (LANL), Los Alamos, NM (United States)</creatorcontrib><title>A public website for the automated assessment and validation of SARS-CoV-2 diagnostic PCR assays</title><title>Bioinformatics</title><addtitle>Bioinformatics</addtitle><description>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.</description><subject>Applications Notes</subject><subject>Biological Science</subject><subject>COVID-19</subject><subject>COVID-19 Testing</subject><subject>Humans</subject><subject>Polymerase Chain Reaction</subject><subject>SARS-CoV-2</subject><subject>SARS2, COVID-19, assay validation, PCR</subject><subject>Sensitivity and Specificity</subject><issn>1367-4803</issn><issn>1460-2059</issn><issn>1367-4811</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>EIF</sourceid><recordid>eNqNUU1v1DAUtBAVLS1_obI4cQn1V-L4grRalQ-pEqgfXM2L_dI1SuIldor67_Fql4reONnSm5k384aQc87ec2bkRRdimPo4j5CDSxddBtCcvSAnXDWsEqw2L8tfNrpSLZPH5HVKPxmruVLqFTmWQmvdcnlCfqzodumG4Ohv7FLISIsozRuksORY1NFTSAlTGnHKFCZPH2AIvqyNE409vVld31Tr-L0S1Ae4n2Iqhui39fWOBo_pjBz1MCR8c3hPyd3Hy9v15-rq66cv69VV5VQrcyU808xLY5gHb3jnGu2x9UZrxwxvDXLvy6jVQosenHbGK0TOgfcoQBp5Sj7sdUucEb0rbmcY7HYOI8yPNkKwzydT2Nj7-GB1XRvWqiLwdi-wS2CTK7dwGxenCV22XPOmFk0BvTtsmeOvBVO2Y0gOhwEmjEuyQknR1lrWskCbPdTNMaUZ-ycvnNldh_Z5h_bQYSGe_5vkifa3tALgB6fL9n9F_wB9qLDR</recordid><startdate>20210517</startdate><enddate>20210517</enddate><creator>Li, Po-E</creator><creator>Myers y Gutiérrez, Adán</creator><creator>Davenport, Karen</creator><creator>Flynn, Mark</creator><creator>Hu, Bin</creator><creator>Lo, Chien-Chi</creator><creator>Player Jackson, Elais</creator><creator>Shakya, Migun</creator><creator>Xu, Yan</creator><creator>Gans, Jason D</creator><creator>Chain, Patrick S G</creator><general>Oxford University Press</general><scope>TOX</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>OTOTI</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-3457-1632</orcidid><orcidid>https://orcid.org/0000-0002-7151-3108</orcidid><orcidid>https://orcid.org/0000-0003-4290-1993</orcidid><orcidid>https://orcid.org/0000-0003-3949-3634</orcidid><orcidid>https://orcid.org/0000-0002-0278-8466</orcidid><orcidid>https://orcid.org/0000000202788466</orcidid><orcidid>https://orcid.org/0000000271513108</orcidid><orcidid>https://orcid.org/0000000342901993</orcidid><orcidid>https://orcid.org/0000000339493634</orcidid><orcidid>https://orcid.org/0000000234571632</orcidid></search><sort><creationdate>20210517</creationdate><title>A public website for the automated assessment and validation of SARS-CoV-2 diagnostic PCR assays</title><author>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</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c483t-2d070d3990dad91bc67de8d977c09189e1dd0da87272fac7c9d4ee11a1fe2a393</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Applications Notes</topic><topic>Biological Science</topic><topic>COVID-19</topic><topic>COVID-19 Testing</topic><topic>Humans</topic><topic>Polymerase Chain Reaction</topic><topic>SARS-CoV-2</topic><topic>SARS2, COVID-19, assay validation, PCR</topic><topic>Sensitivity and Specificity</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Li, Po-E</creatorcontrib><creatorcontrib>Myers y Gutiérrez, Adán</creatorcontrib><creatorcontrib>Davenport, Karen</creatorcontrib><creatorcontrib>Flynn, Mark</creatorcontrib><creatorcontrib>Hu, Bin</creatorcontrib><creatorcontrib>Lo, Chien-Chi</creatorcontrib><creatorcontrib>Player Jackson, Elais</creatorcontrib><creatorcontrib>Shakya, Migun</creatorcontrib><creatorcontrib>Xu, Yan</creatorcontrib><creatorcontrib>Gans, Jason D</creatorcontrib><creatorcontrib>Chain, Patrick S G</creatorcontrib><creatorcontrib>Los Alamos National Lab. (LANL), Los Alamos, NM (United States)</creatorcontrib><collection>Oxford Journals Open Access Collection</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>OSTI.GOV</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Bioinformatics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Li, Po-E</au><au>Myers y Gutiérrez, Adán</au><au>Davenport, Karen</au><au>Flynn, Mark</au><au>Hu, Bin</au><au>Lo, Chien-Chi</au><au>Player Jackson, Elais</au><au>Shakya, Migun</au><au>Xu, Yan</au><au>Gans, Jason D</au><au>Chain, Patrick S G</au><au>Elofsson, Arne</au><aucorp>Los Alamos National Lab. (LANL), Los Alamos, NM (United States)</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>A public website for the automated assessment and validation of SARS-CoV-2 diagnostic PCR assays</atitle><jtitle>Bioinformatics</jtitle><addtitle>Bioinformatics</addtitle><date>2021-05-17</date><risdate>2021</risdate><volume>37</volume><issue>7</issue><spage>1024</spage><epage>1025</epage><pages>1024-1025</pages><issn>1367-4803</issn><eissn>1460-2059</eissn><eissn>1367-4811</eissn><abstract>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.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>32777813</pmid><doi>10.1093/bioinformatics/btaa710</doi><tpages>2</tpages><orcidid>https://orcid.org/0000-0002-3457-1632</orcidid><orcidid>https://orcid.org/0000-0002-7151-3108</orcidid><orcidid>https://orcid.org/0000-0003-4290-1993</orcidid><orcidid>https://orcid.org/0000-0003-3949-3634</orcidid><orcidid>https://orcid.org/0000-0002-0278-8466</orcidid><orcidid>https://orcid.org/0000000202788466</orcidid><orcidid>https://orcid.org/0000000271513108</orcidid><orcidid>https://orcid.org/0000000342901993</orcidid><orcidid>https://orcid.org/0000000339493634</orcidid><orcidid>https://orcid.org/0000000234571632</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1367-4803 |
| ispartof | Bioinformatics, 2021-05, Vol.37 (7), p.1024-1025 |
| issn | 1367-4803 1460-2059 1367-4811 |
| language | eng |
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| source | Oxford Journals Open Access Collection; MEDLINE; EZB-FREE-00999 freely available EZB journals; PubMed Central; Alma/SFX Local Collection |
| subjects | Applications Notes Biological Science COVID-19 COVID-19 Testing Humans Polymerase Chain Reaction SARS-CoV-2 SARS2, COVID-19, assay validation, PCR Sensitivity and Specificity |
| title | A public website for the automated assessment and validation of SARS-CoV-2 diagnostic PCR assays |
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