ArticleGenome biology2022
Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples.
Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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Who cites it
8 citing papers in PubMed, 13 citations in OpenAlex.
- Enhanced recovery of high-quality DNA from limited FFPE tissue for advancing cancer genomics.Scientific reports · 2026Article
- Leukemic Transdifferentiation: From Pathological Plasticity to Dendritic Cell-Based Immunotherapy.Biomedicines · 2025Review
- Evaluation of false positive and false negative errors in targeted next generation sequencing.Genome biology · 2025Article
- A critical spotlight on the paradigms of FFPE-DNA sequencing.Nucleic acids research · 2023Review
- Residual Humidity in Paraffin-Embedded Tissue Reduces Nucleic Acid Stability.International journal of molecular sciences · 2023Article
- Clinical Circulating Tumor DNA Testing for Precision Oncology.Cancer research and treatment · 2023Article
- Consistency and reproducibility of large panel next-generation sequencing: Multi-laboratory assessment of somatic mutation detection on reference materials with mismatch repair and proofreading deficiency.Journal of advanced research · 2023Article
- FDA-led consortium studies advance quality control of targeted next generation sequencing assays for precision oncology.Precision cancer medicine · 2021Article
Corrections and comments
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Authors and funding
35 authors at 18 institutions in 3 countries.
Funding
Abstract
backgroundClinical 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.
resultsTissue 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.
conclusionsTo assure reliable results, we recommend avoiding the block surface portion and restricting mutation detection to genomic regions of high confidence.
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