Deep oncopanel sequencing reveals fixation time- and within block position-dependent quality degradation in FFPE processed samples Article Swipe
Yifan Zhang
,
Thomas M. Blomquist
,
Rebecca Kusko
,
Daniel Stetson
,
Zhihong Zhang
,
Lihui Yin
,
Robert Sebra
,
Binsheng Gong
,
Jennifer S. LoCoco
,
Vinay Kumar Mittal
,
Natalia Novoradovskaya
,
Ji‐Youn Yeo
,
Nicole Dominiak
,
Jennifer Hipp
,
Amelia Raymond
,
Fujun Qiu
,
Hanane Arib
,
Melissa Smith
,
Jay E. Brock
,
Daniel H. Farkas
,
Daniel J. Craig
,
Erin L. Crawford
,
Dan Li
,
Tom Morrison
,
Nikola Tom
,
Wenzhong Xiao
,
Mary Qu Yang
,
Christopher E. Mason
,
Todd Richmond
,
Wendell Jones
,
Donald J. Johann
,
Leming Shi
,
Weida Tong
,
James C. Willey
,
Joshua Xu
·
YOU?
·
· 2021
· Open Access
·
· DOI: https://doi.org/10.1101/2021.04.06.438687
YOU?
·
· 2021
· Open Access
·
· DOI: https://doi.org/10.1101/2021.04.06.438687
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.
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Concepts
Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/2021.04.06.438687
- https://www.biorxiv.org/content/biorxiv/early/2021/04/07/2021.04.06.438687.full.pdf
- OA Status
- green
- Cited By
- 4
- References
- 31
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W3148759568
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W3148759568Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1101/2021.04.06.438687Digital Object Identifier
- Title
-
Deep oncopanel sequencing reveals fixation time- and within block position-dependent quality degradation in FFPE processed samplesWork title
- Type
-
preprintOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2021Year of publication
- Publication date
-
2021-04-07Full publication date if available
- Authors
-
Yifan Zhang, Thomas M. Blomquist, Rebecca Kusko, Daniel Stetson, Zhihong Zhang, Lihui Yin, Robert Sebra, Binsheng Gong, Jennifer S. LoCoco, Vinay Kumar Mittal, Natalia Novoradovskaya, Ji‐Youn Yeo, Nicole Dominiak, Jennifer Hipp, Amelia Raymond, Fujun Qiu, Hanane Arib, Melissa Smith, Jay E. Brock, Daniel H. Farkas, Daniel J. Craig, Erin L. Crawford, Dan Li, Tom Morrison, Nikola Tom, Wenzhong Xiao, Mary Qu Yang, Christopher E. Mason, Todd Richmond, Wendell Jones, Donald J. Johann, Leming Shi, Weida Tong, James C. Willey, Joshua XuList of authors in order
- Landing page
-
https://doi.org/10.1101/2021.04.06.438687Publisher landing page
- PDF URL
-
https://www.biorxiv.org/content/biorxiv/early/2021/04/07/2021.04.06.438687.full.pdfDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
greenOpen access status per OpenAlex
- OA URL
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https://www.biorxiv.org/content/biorxiv/early/2021/04/07/2021.04.06.438687.full.pdfDirect OA link when available
- Concepts
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Fixation (population genetics), Deep sequencing, Block (permutation group theory), Computational biology, DNA sequencing, Biology, Genetics, DNA, Gene, Mathematics, Genome, GeometryTop concepts (fields/topics) attached by OpenAlex
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4Total citation count in OpenAlex
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2022: 2, 2021: 2Per-year citation counts (last 5 years)
- References (count)
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31Number of works referenced by this work
- Related works (count)
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10Other works algorithmically related by OpenAlex
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| corresponding_institution_ids | https://openalex.org/I1304557061, https://openalex.org/I1320320070, https://openalex.org/I90871651 |
| citation_normalized_percentile.value | 0.518304 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |