Validation and implementation of a modular targeted capture assay for the detection of clinically significant molecular oncology alterations.
Identifieur interne : 000950 ( Main/Exploration ); précédent : 000949; suivant : 000951Validation and implementation of a modular targeted capture assay for the detection of clinically significant molecular oncology alterations.
Auteurs : Ayako J. Kuo [États-Unis] ; Vera A. Paulson [États-Unis] ; Jennifer A. Hempelmann [États-Unis] ; Mallory Beightol [États-Unis] ; Sheena Todhunter [États-Unis] ; Brice G. Colbert [États-Unis] ; Stephen J. Salipante [États-Unis] ; Eric Q. Konnick [États-Unis] ; Colin C. Pritchard [États-Unis] ; Christina M. Lockwood [États-Unis]Source :
- Practical laboratory medicine [ 2352-5517 ] ; 2020.
Abstract
Objectives
The rapid discovery of clinically significant genetic variants has translated to next-generation sequencing assays becoming out-of-date by the time they are designed, validated, and implemented. UW-OncoPlex addresses this through the adoption of a modular panel capable of redesign as significant alterations are identified. We describe the validation of OncoPlex version 6 (OPXv6) for the detection of single nucleotide variants (SNVs), insertions and deletions (indels), copy number variants (CNVs), structural variants (SVs), microsatellite instability (MSI), and tumor mutational burden (TMB) in a panel of 340 genes.
Design
One hundred twelve samples with diverse diagnoses were comprised of formalin-fixed-paraffin-embedded tissue, fresh-frozen tissue, plasma, peripheral blood, bone marrow, saliva, and cell-line DNA. Libraries were prepared from genomic and cell-free DNA, hybridized to a custom panel of xGen Lockdown probes, and sequenced on Illumina platforms. Sequences were processed through a custom bioinformatics pipeline, and variant calls were compared to prior orthogonal clinical results.
Results
Accuracy was 99% for SNVs ≥5% allele frequency, 98% for indels, 97% for SVs, 99% for CNVs, 100% for MSI, and 100% for TMB (compared to previous OncoPlex versions). Library preparation turnaround time decreased by 40%, and sequencing quality improved with a 2.5-fold increase in average sequencing coverage and 4-fold increase in percent on-target.
Conclusions
OPXv6 demonstrates improvements over prior UW-OncoPlex versions including reduced capture cost, improved sequencing quality, and decreased time to results. The modular capture probe design also provides a nimble laboratory response in addressing the expansions necessary to meet the needs of the continuously evolving field of molecular oncology.
DOI: 10.1016/j.plabm.2020.e00153
PubMed: 32123717
PubMed Central: PMC7038441
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Kuo</name><affiliation wicri:level="1"><nlm:affiliation>Department of Laboratory Medicine, University of Washington Medical Center, 1959 NE Pacific Street, Seattle, WA, 98195, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Laboratory Medicine, University of Washington Medical Center, 1959 NE Pacific Street, Seattle, WA, 98195</wicri:regionArea><wicri:noRegion>98195</wicri:noRegion></affiliation></author><author><name sortKey="Paulson, Vera A" sort="Paulson, Vera A" uniqKey="Paulson V" first="Vera A" last="Paulson">Vera A. Paulson</name><affiliation wicri:level="1"><nlm:affiliation>Department of Laboratory Medicine, University of Washington Medical Center, 1959 NE Pacific Street, Seattle, WA, 98195, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Laboratory Medicine, University of Washington Medical Center, 1959 NE Pacific Street, Seattle, WA, 98195</wicri:regionArea><wicri:noRegion>98195</wicri:noRegion></affiliation></author><author><name sortKey="Hempelmann, Jennifer A" sort="Hempelmann, Jennifer A" uniqKey="Hempelmann J" first="Jennifer A" last="Hempelmann">Jennifer A. 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Colbert</name><affiliation wicri:level="1"><nlm:affiliation>Department of Laboratory Medicine, University of Washington Medical Center, 1959 NE Pacific Street, Seattle, WA, 98195, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Laboratory Medicine, University of Washington Medical Center, 1959 NE Pacific Street, Seattle, WA, 98195</wicri:regionArea><wicri:noRegion>98195</wicri:noRegion></affiliation></author><author><name sortKey="Salipante, Stephen J" sort="Salipante, Stephen J" uniqKey="Salipante S" first="Stephen J" last="Salipante">Stephen J. Salipante</name><affiliation wicri:level="1"><nlm:affiliation>Department of Laboratory Medicine, University of Washington Medical Center, 1959 NE Pacific Street, Seattle, WA, 98195, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Laboratory Medicine, University of Washington Medical Center, 1959 NE Pacific Street, Seattle, WA, 98195</wicri:regionArea><wicri:noRegion>98195</wicri:noRegion></affiliation></author><author><name sortKey="Konnick, Eric Q" sort="Konnick, Eric Q" uniqKey="Konnick E" first="Eric Q" last="Konnick">Eric Q. Konnick</name><affiliation wicri:level="1"><nlm:affiliation>Department of Laboratory Medicine, University of Washington Medical Center, 1959 NE Pacific Street, Seattle, WA, 98195, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Laboratory Medicine, University of Washington Medical Center, 1959 NE Pacific Street, Seattle, WA, 98195</wicri:regionArea><wicri:noRegion>98195</wicri:noRegion></affiliation></author><author><name sortKey="Pritchard, Colin C" sort="Pritchard, Colin C" uniqKey="Pritchard C" first="Colin C" last="Pritchard">Colin C. Pritchard</name><affiliation wicri:level="1"><nlm:affiliation>Department of Laboratory Medicine, University of Washington Medical Center, 1959 NE Pacific Street, Seattle, WA, 98195, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Laboratory Medicine, University of Washington Medical Center, 1959 NE Pacific Street, Seattle, WA, 98195</wicri:regionArea><wicri:noRegion>98195</wicri:noRegion></affiliation></author><author><name sortKey="Lockwood, Christina M" sort="Lockwood, Christina M" uniqKey="Lockwood C" first="Christina M" last="Lockwood">Christina M. Lockwood</name><affiliation wicri:level="1"><nlm:affiliation>Department of Laboratory Medicine, University of Washington Medical Center, 1959 NE Pacific Street, Seattle, WA, 98195, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Laboratory Medicine, University of Washington Medical Center, 1959 NE Pacific Street, Seattle, WA, 98195</wicri:regionArea><wicri:noRegion>98195</wicri:noRegion></affiliation></author></analytic><series><title level="j">Practical laboratory medicine</title><idno type="ISSN">2352-5517</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>Objectives</b></p><p>The rapid discovery of clinically significant genetic variants has translated to next-generation sequencing assays becoming out-of-date by the time they are designed, validated, and implemented. UW-OncoPlex addresses this through the adoption of a modular panel capable of redesign as significant alterations are identified. We describe the validation of OncoPlex version 6 (OPXv6) for the detection of single nucleotide variants (SNVs), insertions and deletions (indels), copy number variants (CNVs), structural variants (SVs), microsatellite instability (MSI), and tumor mutational burden (TMB) in a panel of 340 genes.</p></div><div type="abstract" xml:lang="en"><p><b>Design</b></p><p>One hundred twelve samples with diverse diagnoses were comprised of formalin-fixed-paraffin-embedded tissue, fresh-frozen tissue, plasma, peripheral blood, bone marrow, saliva, and cell-line DNA. Libraries were prepared from genomic and cell-free DNA, hybridized to a custom panel of xGen Lockdown probes, and sequenced on Illumina platforms. Sequences were processed through a custom bioinformatics pipeline, and variant calls were compared to prior orthogonal clinical results.</p></div><div type="abstract" xml:lang="en"><p><b>Results</b></p><p>Accuracy was 99% for SNVs ≥5% allele frequency, 98% for indels, 97% for SVs, 99% for CNVs, 100% for MSI, and 100% for TMB (compared to previous OncoPlex versions). Library preparation turnaround time decreased by 40%, and sequencing quality improved with a 2.5-fold increase in average sequencing coverage and 4-fold increase in percent on-target.</p></div><div type="abstract" xml:lang="en"><p><b>Conclusions</b></p><p>OPXv6 demonstrates improvements over prior UW-OncoPlex versions including reduced capture cost, improved sequencing quality, and decreased time to results. The modular capture probe design also provides a nimble laboratory response in addressing the expansions necessary to meet the needs of the continuously evolving field of molecular oncology.</p></div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">32123717</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>28</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">2352-5517</ISSN><JournalIssue CitedMedium="Print"><Volume>19</Volume><PubDate><Year>2020</Year><Month>Mar</Month></PubDate></JournalIssue><Title>Practical laboratory medicine</Title><ISOAbbreviation>Pract Lab Med</ISOAbbreviation></Journal><ArticleTitle>Validation and implementation of a modular targeted capture assay for the detection of clinically significant molecular oncology alterations.</ArticleTitle><Pagination><MedlinePgn>e00153</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.plabm.2020.e00153</ELocationID><Abstract><AbstractText Label="Objectives" NlmCategory="UNASSIGNED">The rapid discovery of clinically significant genetic variants has translated to next-generation sequencing assays becoming out-of-date by the time they are designed, validated, and implemented. UW-OncoPlex addresses this through the adoption of a modular panel capable of redesign as significant alterations are identified. We describe the validation of OncoPlex version 6 (OPXv6) for the detection of single nucleotide variants (SNVs), insertions and deletions (indels), copy number variants (CNVs), structural variants (SVs), microsatellite instability (MSI), and tumor mutational burden (TMB) in a panel of 340 genes.</AbstractText><AbstractText Label="Design" NlmCategory="UNASSIGNED">One hundred twelve samples with diverse diagnoses were comprised of formalin-fixed-paraffin-embedded tissue, fresh-frozen tissue, plasma, peripheral blood, bone marrow, saliva, and cell-line DNA. Libraries were prepared from genomic and cell-free DNA, hybridized to a custom panel of xGen Lockdown probes, and sequenced on Illumina platforms. Sequences were processed through a custom bioinformatics pipeline, and variant calls were compared to prior orthogonal clinical results.</AbstractText><AbstractText Label="Results" NlmCategory="UNASSIGNED">Accuracy was 99% for SNVs ≥5% allele frequency, 98% for indels, 97% for SVs, 99% for CNVs, 100% for MSI, and 100% for TMB (compared to previous OncoPlex versions). Library preparation turnaround time decreased by 40%, and sequencing quality improved with a 2.5-fold increase in average sequencing coverage and 4-fold increase in percent on-target.</AbstractText><AbstractText Label="Conclusions" NlmCategory="UNASSIGNED">OPXv6 demonstrates improvements over prior UW-OncoPlex versions including reduced capture cost, improved sequencing quality, and decreased time to results. The modular capture probe design also provides a nimble laboratory response in addressing the expansions necessary to meet the needs of the continuously evolving field of molecular oncology.</AbstractText><CopyrightInformation>© 2020 The Authors.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Kuo</LastName><ForeName>Ayako J</ForeName><Initials>AJ</Initials><AffiliationInfo><Affiliation>Department of Laboratory Medicine, University of Washington Medical Center, 1959 NE Pacific Street, Seattle, WA, 98195, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Paulson</LastName><ForeName>Vera A</ForeName><Initials>VA</Initials><AffiliationInfo><Affiliation>Department of Laboratory Medicine, University of Washington Medical Center, 1959 NE Pacific Street, Seattle, WA, 98195, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hempelmann</LastName><ForeName>Jennifer A</ForeName><Initials>JA</Initials><AffiliationInfo><Affiliation>Department of Laboratory Medicine, University of Washington Medical Center, 1959 NE Pacific Street, Seattle, WA, 98195, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Beightol</LastName><ForeName>Mallory</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Laboratory Medicine, University of Washington Medical Center, 1959 NE Pacific Street, Seattle, WA, 98195, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Todhunter</LastName><ForeName>Sheena</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Laboratory Medicine, University of Washington Medical Center, 1959 NE Pacific Street, Seattle, WA, 98195, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Colbert</LastName><ForeName>Brice G</ForeName><Initials>BG</Initials><AffiliationInfo><Affiliation>Department of Laboratory Medicine, University of Washington Medical Center, 1959 NE Pacific Street, Seattle, WA, 98195, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Salipante</LastName><ForeName>Stephen J</ForeName><Initials>SJ</Initials><AffiliationInfo><Affiliation>Department of Laboratory Medicine, University of Washington Medical Center, 1959 NE Pacific Street, Seattle, WA, 98195, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Konnick</LastName><ForeName>Eric Q</ForeName><Initials>EQ</Initials><AffiliationInfo><Affiliation>Department of Laboratory Medicine, University of Washington Medical Center, 1959 NE Pacific Street, Seattle, WA, 98195, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pritchard</LastName><ForeName>Colin C</ForeName><Initials>CC</Initials><AffiliationInfo><Affiliation>Department of Laboratory Medicine, University of Washington Medical Center, 1959 NE Pacific Street, Seattle, WA, 98195, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lockwood</LastName><ForeName>Christina M</ForeName><Initials>CM</Initials><AffiliationInfo><Affiliation>Department of Laboratory Medicine, University of Washington Medical Center, 1959 NE Pacific Street, Seattle, WA, 98195, USA.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>02</Month><Day>03</Day></ArticleDate></Article><MedlineJournalInfo><Country>Netherlands</Country><MedlineTA>Pract Lab Med</MedlineTA><NlmUniqueID>101690848</NlmUniqueID><ISSNLinking>2352-5517</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Assay validation</Keyword><Keyword MajorTopicYN="N">Molecular diagnostics</Keyword><Keyword MajorTopicYN="N">Molecular oncology</Keyword><Keyword MajorTopicYN="N">Next generation sequencing</Keyword><Keyword MajorTopicYN="N">OncoPlex</Keyword><Keyword MajorTopicYN="N">Precision medicine</Keyword></KeywordList><CoiStatement>The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: CC Pritchard and SJ Salipante: consult for Promega EQ Konnick: Travel & honoraria – Ventana, Medscape, Roche, Genentech CM Lockwood: spouse is employed by Bayer.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>09</Month><Day>04</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2019</Year><Month>12</Month><Day>24</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>01</Month><Day>16</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>3</Month><Day>4</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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Kuo</name></noRegion><name sortKey="Beightol, Mallory" sort="Beightol, Mallory" uniqKey="Beightol M" first="Mallory" last="Beightol">Mallory Beightol</name><name sortKey="Colbert, Brice G" sort="Colbert, Brice G" uniqKey="Colbert B" first="Brice G" last="Colbert">Brice G. Colbert</name><name sortKey="Hempelmann, Jennifer A" sort="Hempelmann, Jennifer A" uniqKey="Hempelmann J" first="Jennifer A" last="Hempelmann">Jennifer A. Hempelmann</name><name sortKey="Konnick, Eric Q" sort="Konnick, Eric Q" uniqKey="Konnick E" first="Eric Q" last="Konnick">Eric Q. Konnick</name><name sortKey="Lockwood, Christina M" sort="Lockwood, Christina M" uniqKey="Lockwood C" first="Christina M" last="Lockwood">Christina M. Lockwood</name><name sortKey="Paulson, Vera A" sort="Paulson, Vera A" uniqKey="Paulson V" first="Vera A" last="Paulson">Vera A. Paulson</name><name sortKey="Pritchard, Colin C" sort="Pritchard, Colin C" uniqKey="Pritchard C" first="Colin C" last="Pritchard">Colin C. Pritchard</name><name sortKey="Salipante, Stephen J" sort="Salipante, Stephen J" uniqKey="Salipante S" first="Stephen J" last="Salipante">Stephen J. Salipante</name><name sortKey="Todhunter, Sheena" sort="Todhunter, Sheena" uniqKey="Todhunter S" first="Sheena" last="Todhunter">Sheena Todhunter</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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