Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14740%2F22%3A00126461" target="_blank" >RIV/00216224:14740/22:00126461 - isvavai.cz</a>
Result on the web
<a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02709-8" target="_blank" >https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02709-8</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1186/s13059-022-02709-8" target="_blank" >10.1186/s13059-022-02709-8</a>

Result language
angličtina
Original language name
Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples
Original language description
Background Clinical laboratories routinely use formalin-fixed paraffin-embedded (FFPE) tissue or cell block cytology samples in oncology panel sequencing to identify mutations that can predict patient response to targeted therapy. To understand the technical error due to FFPE processing, a robustly characterized diploid cell line was used to create FFPE samples with four different pre-tissue processing formalin fixation times. A total of 96 FFPE sections were then distributed to different laboratories for targeted sequencing analysis by four oncopanels, and variants resulting from technical error were identified. Results Tissue sections that fail more frequently show low cellularity, lower than recommended library preparation DNA input, or target sequencing depth. Importantly, sections from block surfaces are more likely to show FFPE-specific errors, akin to "edge effects" seen in histology, while the inner samples display no quality degradation related to fixation time. Conclusions To assure reliable results, we recommend avoiding the block surface portion and restricting mutation detection to genomic regions of high confidence.
Czech name
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Czech description
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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
10608 - Biochemistry and molecular biology

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)

Publication year
2022
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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