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Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples
Y. Zhang, TM. Blomquist, R. Kusko, D. Stetson, Z. Zhang, L. Yin, R. Sebra, B. Gong, JS. Lococo, VK. Mittal, N. Novoradovskaya, JY. Yeo, N. Dominiak, J. Hipp, A. Raymond, F. Qiu, H. Arib, ML. Smith, JE. Brock, DH. Farkas, DJ. Craig, EL. Crawford,...
Jazyk angličtina Země Anglie, Velká Británie
Typ dokumentu časopisecké články, Research Support, N.I.H., Extramural, práce podpořená grantem
Grantová podpora
U24 CA086368
NCI NIH HHS - United States
U01 CA243483
NCI NIH HHS - United States
HHSF223201510172C
FDA HHS - United States
NLK
BioMedCentral
od 2001
Directory of Open Access Journals
od 2000
PubMed Central
od 2001
ProQuest Central
od 2015-01-01
Open Access Digital Library
od 2000-01-01
Open Access Digital Library
od 2000-01-01
Medline Complete (EBSCOhost)
od 2011-02-01
Health & Medicine (ProQuest)
od 2015-01-01
ROAD: Directory of Open Access Scholarly Resources
od 2001
Springer Nature OA/Free Journals
od 2000-02-01
- MeSH
- fixace tkání MeSH
- formaldehyd * MeSH
- lidé MeSH
- sekvenční analýza DNA MeSH
- vysoce účinné nukleotidové sekvenování * MeSH
- zalévání tkání do parafínu MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, N.I.H., Extramural MeSH
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.
Accugenomics Inc 1410 Commonwealth Drive Suite 105 Wilmington NC 20403 USA
Agilent Technologies 11011 N Torrey Pines Rd La Jolla CA 92037 USA
Astrazeneca Pharmaceuticals 35 Gatehouse Dr Waltham MA 02451 USA
Department of Pathology Strata Oncology Inc Ann Arbor MI 48103 USA
Department of Pathology University of Toledo 3000 Arlington Ave Toledo OH 43614 USA
Fudan Gospel Joint Research Center for Precision Medicine Fudan University Shanghai 200438 China
Human Phenome Institute Fudan University Shanghai 201203 China
Illumina Inc 5200 Illumina Way San Diego CA 92122 USA
Immuneering Corporation 245 Main St Cambridge MA 02142 USA
Lucas County Coroner's Office 2595 Arlington Ave Toledo OH 43614 USA
Massachusetts General Hospital Harvard Medical School Boston MA 02114 USA
Q2 Solutions EA Genomics 5927 S Miami Blvd Morrisville NC 27560 USA
Research and Development Burning Rock Biotech Shanghai 201114 China
Stanford Genome Technology Center Stanford University Palo Alto CA 94304 USA
Thermo Fisher Scientific 110 Miller Ave Ann Arbor MI 48104 USA
Citace poskytuje Crossref.org
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- $a 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.
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