Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14740%2F21%3A00120110" target="_blank" >RIV/00216224:14740/21:00120110 - isvavai.cz</a>
Result on the web
<a href="https://genomebiology.biomedcentral.com/track/pdf/10.1186/s13059-021-02315-0.pdf" target="_blank" >https://genomebiology.biomedcentral.com/track/pdf/10.1186/s13059-021-02315-0.pdf</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1186/s13059-021-02315-0" target="_blank" >10.1186/s13059-021-02315-0</a>
Alternative languages
Result language
angličtina
Original language name
Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions
Original language description
BackgroundTargeted sequencing using oncopanels requires comprehensive assessments of accuracy and detection sensitivity to ensure analytical validity. By employing reference materials characterized by the U.S. Food and Drug Administration-led SEquence Quality Control project phase2 (SEQC2) effort, we perform a cross-platform multi-lab evaluation of eight Pan-Cancer panels to assess best practices for oncopanel sequencing.ResultsAll panels demonstrate high sensitivity across targeted high-confidence coding regions and variant types for the variants previously verified to have variant allele frequency (VAF) in the 5-20% range. Sensitivity is reduced by utilizing VAF thresholds due to inherent variability in VAF measurements. Enforcing a VAF threshold for reporting has a positive impact on reducing false positive calls. Importantly, the false positive rate is found to be significantly higher outside the high-confidence coding regions, resulting in lower reproducibility. Thus, region restriction and VAF thresholds lead to low relative technical variability in estimating promising biomarkers and tumor mutational burden.ConclusionThis comprehensive study provides actionable guidelines for oncopanel sequencing and clear evidence that supports a simplified approach to assess the analytical performance of oncopanels. It will facilitate the rapid implementation, validation, and quality control of oncopanels in clinical use.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
30204 - Oncology
Result continuities
Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)
Others
Publication year
2021
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
GENOME BIOLOGY
ISSN
1474-760X
e-ISSN
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Volume of the periodical
22
Issue of the periodical within the volume
1
Country of publishing house
GB - UNITED KINGDOM
Number of pages
23
Pages from-to
109
UT code for WoS article
000641654300001
EID of the result in the Scopus database
2-s2.0-85104386329