PT  - JOURNAL ARTICLE
AU  - SEQC2 Oncopanel Sequencing Working Group
AU  - Yifan Zhang
AU  - Thomas M. Blomquist
AU  - Rebecca Kusko
AU  - Daniel Stetson
AU  - Zhihong Zhang
AU  - Lihui Yin
AU  - Robert Sebra
AU  - Binsheng Gong
AU  - Jennifer S. LoCoco
AU  - Vinay K. Mittal
AU  - Natalia Novoradovskaya
AU  - Ji-Youn Yeo
AU  - Nicole Dominiak
AU  - Jennifer Hipp
AU  - Amelia Raymond
AU  - Fujun Qiu
AU  - Hanane Arib
AU  - Melissa L. Smith
AU  - Jay E. Brock
AU  - Daniel H. Farkas
AU  - Daniel J. Craig
AU  - Erin L. Crawford
AU  - Dan Li
AU  - Tom Morrison
AU  - Nikola Tom
AU  - Wenzhong Xiao
AU  - Mary Yang
AU  - Christopher E. Mason
AU  - Todd A. Richmond
AU  - Wendell Jones
AU  - Donald J. Johann, Jr
AU  - Leming Shi
AU  - Weida Tong
AU  - James C. Willey
AU  - Joshua Xu
TI  - Deep oncopanel sequencing reveals fixation time- and within block position-dependent quality degradation in FFPE processed samples
AID  - 10.1101/2021.04.06.438687
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.04.06.438687
4099  - http://biorxiv.org/content/early/2021/04/07/2021.04.06.438687.short
4100  - http://biorxiv.org/content/early/2021/04/07/2021.04.06.438687.full
AB  - 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 normal 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. Tissue sections that failed more frequently showed low cellularity, lower than recommended library preparation DNA input, or target sequencing depth. Importantly, sections from block surfaces were more likely to show FFPE-specific errors, akin to “edge effects” seen in histology, and the depth of formalin damage was related to fixation time. To assure reliable results, we recommend avoiding the block surface portion and restricting mutation detection to genomic regions of high confidence.Competing Interest StatementThe authors have declared no competing interest.