@article{30a6c7a8aa8f46d7a2ca91d5832f17e8,
title = "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. 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.",
keywords = "Cancer genomics, FFPE, Next-generation sequencing, Oncopanel sequencing, Preanalytics, Precision medicine",
author = "Yifan Zhang and Blomquist, {Thomas M.} and Rebecca Kusko and Daniel Stetson and Zhihong Zhang and Lihui Yin and Robert Sebra and Binsheng Gong and Lococo, {Jennifer S.} and Mittal, {Vinay K.} and Natalia Novoradovskaya and Yeo, {Ji Youn} and Nicole Dominiak and Jennifer Hipp and Amelia Raymond and Fujun Qiu and Hanane Arib and Smith, {Melissa L.} and Brock, {Jay E.} and Farkas, {Daniel H.} and Craig, {Daniel J.} and Crawford, {Erin L.} and Dan Li and Tom Morrison and Nikola Tom and Wenzhong Xiao and Mary Yang and Mason, {Christopher E.} and Richmond, {Todd A.} and Wendell Jones and Johann, {Donald J.} and Leming Shi and Weida Tong and Willey, {James C.} and Joshua Xu",
note = "Funding Information: Part of this work was carried out with the support to Thomas Blomquist through the University of Toledo College of Medicine Academic Affiliation with ProMedica research funds. James C. Willey was supported by a sub-contract from NCI 5U24CA086368 and NHGRI 1U01CA243483 and from the George Isaac Endowed Chair for Cancer Research. Leming Shi was supported by the National Key R&D Project of China (2018YFE0201600), the National Natural Science Foundation of China (31720103909), and the Shanghai Municipal Science and Technology Major Project (2017SHZDZX01). Donald J. Johann, Jr., acknowledges the support by FDA BAA grant HHSF223201510172C. Nikola Tom was supported by research infrastructure EATRIS-CZ, ID number LM2018133 funded by MEYS CR and MEYS CR project CEITEC 2020 (LQ1601). Funding Information: All SEQC2 participants freely donated their time, reagents, and computing resources for the completion and analysis of this project. This manuscript was previously reviewed at another journal, and no review history is available. Stephanie McClelland and Barbara Cheifet were the primary editor of this article and managed its editorial process and peer review in collaboration with the rest of the editorial team. The views presented in this article do not necessarily reflect those of the US Food and Drug Administration. Any mention of commercial products is for clarification and is not intended as an endorsement. Publisher Copyright: {\textcopyright} 2022, The Author(s).",
year = "2022",
month = dec,
doi = "10.1186/s13059-022-02709-8",
language = "English",
volume = "23",
journal = "Genome Biology",
issn = "1474-7596",
publisher = "BioMed Central Ltd.",
number = "1",
}