Genome Biology (Jun 2022)
Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples
- Yifan Zhang,
- Thomas M. Blomquist,
- Rebecca Kusko,
- Daniel Stetson,
- Zhihong Zhang,
- Lihui Yin,
- Robert Sebra,
- Binsheng Gong,
- Jennifer S. Lococo,
- Vinay K. Mittal,
- Natalia Novoradovskaya,
- Ji-Youn Yeo,
- Nicole Dominiak,
- Jennifer Hipp,
- Amelia Raymond,
- Fujun Qiu,
- Hanane Arib,
- Melissa L. Smith,
- Jay E. Brock,
- Daniel H. Farkas,
- Daniel J. Craig,
- Erin L. Crawford,
- Dan Li,
- Tom Morrison,
- Nikola Tom,
- Wenzhong Xiao,
- Mary Yang,
- Christopher E. Mason,
- Todd A. Richmond,
- Wendell Jones,
- Donald J. Johann,
- Leming Shi,
- Weida Tong,
- James C. Willey,
- Joshua Xu
Affiliations
- Yifan Zhang
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration
- Thomas M. Blomquist
- (Formerly) Department of Pathology, College of Medicine and Life Sciences, The University of Toledo
- Rebecca Kusko
- Immuneering Corporation
- Daniel Stetson
- Astrazeneca Pharmaceuticals
- Zhihong Zhang
- Research and Development, Burning Rock Biotech
- Lihui Yin
- (Formerly) Pathology and Laboratory Medicine Institute, Cleveland Clinic
- Robert Sebra
- Icahn Institute and Department of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai
- Binsheng Gong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration
- Jennifer S. Lococo
- Illumina Inc.
- Vinay K. Mittal
- Thermo Fisher Scientific
- Natalia Novoradovskaya
- Agilent Technologies
- Ji-Youn Yeo
- Department of Pathology, University of Toledo
- Nicole Dominiak
- Department of Pathology, University of Toledo
- Jennifer Hipp
- Department of Pathology, Strata Oncology, Inc.
- Amelia Raymond
- Astrazeneca Pharmaceuticals
- Fujun Qiu
- Research and Development, Burning Rock Biotech
- Hanane Arib
- Icahn Institute and Department of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai
- Melissa L. Smith
- Icahn Institute and Department of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai
- Jay E. Brock
- Pathology and Laboratory Medicine Institute, Cleveland Clinic
- Daniel H. Farkas
- Pathology and Laboratory Medicine Institute, Cleveland Clinic
- Daniel J. Craig
- Department of Medicine, College of Medicine and Life Sciences, The University of Toledo
- Erin L. Crawford
- Department of Medicine, College of Medicine and Life Sciences, The University of Toledo
- Dan Li
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration
- Tom Morrison
- Accugenomics, Inc.
- Nikola Tom
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University
- Wenzhong Xiao
- Massachusetts General Hospital, Harvard Medical School
- Mary Yang
- Department of Information Science, University of Arkansas at Little Rock
- Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University
- Todd A. Richmond
- Market & Application Development Bioinformatics, Roche Sequencing Solutions Inc.
- Wendell Jones
- Q2 Solutions - EA Genomics
- Donald J. Johann
- Winthrop P Rockefeller Cancer Institute, University of Arkansas for Medical Sciences
- Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University
- Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration
- James C. Willey
- Departments of Medicine, Pathology, and Cancer Biology, College of Medicine and Life Sciences, University of Toledo Health Sciences Campus
- Joshua Xu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration
- DOI
- https://doi.org/10.1186/s13059-022-02709-8
- Journal volume & issue
-
Vol. 23,
no. 1
pp. 1 – 21
Abstract
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
- Next-generation sequencing
- FFPE
- Preanalytics
- Precision medicine
- Oncopanel sequencing
