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

Kód výsledku v 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>

Výsledek na webu

<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>

Jazyk výsledku

angličtina

Název v původním jazyce

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

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

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

Popis výsledku anglicky

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.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10608 - Biochemistry and molecular biology

Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2022

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

GENOME BIOLOGY

ISSN

1474-760X

e-ISSN

1474-7596

Svazek periodika

23

Číslo periodika v rámci svazku

1

Stát vydavatele periodika

GB - Spojené království Velké Británie a Severního Irska

Počet stran výsledku

21

Strana od-do

141

Kód UT WoS článku

000818845800004

EID výsledku v databázi Scopus

2-s2.0-85133135300