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

ABSTRACT:

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. Importantl

SUBMITTER: Zhang Y 

PROVIDER: S-EPMC9241261 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature