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

The result's identifiers

  • 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>

Alternative languages

  • 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

  • Czech description

Classification

  • Type

    J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database

  • CEP classification

  • OECD FORD branch

    10608 - Biochemistry and molecular biology

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

    2022

  • 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

    1474-7596

  • Volume of the periodical

    23

  • Issue of the periodical within the volume

    1

  • Country of publishing house

    GB - UNITED KINGDOM

  • Number of pages

    21

  • Pages from-to

    141

  • UT code for WoS article

    000818845800004

  • EID of the result in the Scopus database

    2-s2.0-85133135300