ArticlePloS one2017
Assessment of the quality of DNA from various formalin-fixed paraffin-embedded (FFPE) tissues and the use of this DNA for next-generation sequencing (NGS) with no artifactual mutation.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed, 113 citations in OpenAlex.
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- Cell-Free DNA-Based Theranostics for Inflammatory Disorders.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Validation of an Adapted NGS-Based Clonality Assay for MRD Monitoring in B-ALL Using Archived and Follow-Up Samples.EJHaem · 2025Article
- Clinical utility of targeted RNA sequencing in cancer molecular diagnostics.Nature medicine · 2025Article
- Exploring HPV-linked head and neck cancer in Southern Punjab, Pakistan: Insights from HPV-16 phylogenetic analysis.Journal of Taibah University Medical Sciences · 2025Article
- Evaluation of whole-genome enrichment and sequencing ofiScience · 2024Article
- Structural Features of Connective Tissue Formed around Resin Implants Subcutaneously Embedded in Dairy Cows.Animals : an open access journal from MDPI · 2023Article
- Article
- DNA methylation profiling to determine the primary sites of metastatic cancers using formalin-fixed paraffin-embedded tissues.Nature communications · 2023Article
- A critical spotlight on the paradigms of FFPE-DNA sequencing.Nucleic acids research · 2023Review
- Developing an effective quality evaluation strategy of next-generation sequencing for accurate detecting non-small cell lung cancer samples with variable characteristics: a real-world clinical practice.Journal of cancer research and clinical oncology · 2023Article
- Multi-Gene Next-Generation Sequencing Panel for Analysis ofInternational journal of molecular sciences · 2023Article
- The DNA integrity number and concentration are useful parameters for successful comprehensive genomic profiling test for cancer using formalin-fixed paraffin embedded tissue.Pathology international · 2023Article
- Expert opinion on NSCLC small specimen biomarker testing - Part 1: Tissue collection and management.Virchows Archiv : an international journal of pathology · 2022Review
- Doing more with less: multiple uses of a single slide in veterinary cytology. A practical approach.Veterinary research communications · 2022Review
- Effect of Antigen Retrieval on Genomic DNA From Immunodissected Samples.The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society · 2022Article
- Presence of a mouse mammary tumour virus-like in feline lymphomas: a preliminary study.Infectious agents and cancer · 2022Review
- Validation of AmpliSeq NGS Panel forLife (Basel, Switzerland) · 2022Article
- Direct molecular evidence for both multicentric and monoclonal carcinogenesis followed by transdifferentiation from hepatocellular carcinoma to cholangiocarcinoma in a case of metachronous liver cancer.Oncology letters · 2022Article
- Case report:Frontiers in oncology · 2022Article
Corrections and comments
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Authors and funding
11 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Formalin-fixed, paraffin-embedded (FFPE) tissues used for pathological diagnosis are valuable for studying cancer genomics. In particular, laser-capture microdissection of target cells determined by histopathology combined with FFPE tissue section immunohistochemistry (IHC) enables precise analysis by next-generation sequencing (NGS) of the genetic events occurring in cancer. The result is a new strategy for a pathological tool for cancer diagnosis: 'microgenomics'. To more conveniently and precisely perform microgenomics, we revealed by systematic analysis the following three details regarding FFPE DNA compared with paired frozen tissue DNA. 1) The best quality of FFPE DNA is obtained by tissue fixation with 10% neutral buffered formalin for 1 day and heat treatment of tissue lysates at 95°C for 30 minutes. 2) IHC staining of FFPE tissues decreases the quantity and quality of FFPE DNA to one-fourth, and antigen retrieval (at 120°C for 15 minutes, pH 6.0) is the major reason for this decrease. 3) FFPE DNA prepared as described herein is sufficient for NGS. For non-mutated tissue specimens, no artifactual mutation occurs during FFPE preparation, as shown by precise comparison of NGS of FFPE DNA and paired frozen tissue DNA followed by validation. These results demonstrate that even FFPE tissues used for routine clinical diagnosis can be utilized to obtain reliable NGS data if appropriate conditions of fixation and validation are applied.
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