ArticlePloS one2013
Improved PCR performance using template DNA from formalin-fixed and paraffin-embedded tissues by overcoming PCR inhibition.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 papers.
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Who cites it
82 citing papers in PubMed, 152 citations in OpenAlex.
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- Evaluating the mechanism of indigo-mediated PCR inhibition and validation of nano-based mitigation for forensic STR profiling.International journal of legal medicine · 2026Article
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- Novel apicomplexan in the critically endangered Leadbeater's possum,International journal for parasitology. Parasites and wildlife · 2026Article
- Diagnostic accuracy of chip hybridization from formalin-fixed paraffin embedded bioptic specimens in a cohort with predominantly extrapulmonary mycobacterial disease.BMC microbiology · 2026Article
- Subtype-Dependent Expression Patterns of Core Hippo Pathway Components in Thymic Epithelial Tumors (TETs): An RT-qPCR Study.Biomedicines · 2026Article
- Noninfectious Necrotizing Aortitis With Predominantly Neutrophilic Infiltrate.Case reports in pathology · 2026Article
- Generative and integrative modeling for transcriptomics with formalin fixed paraffin embedded material.Journal of translational medicine · 2025Article
- Challenges and predictive value of morphologic features in panfungal sequencing of formalin-fixed, paraffin-embedded tissues: A 5-year retrospective study.American journal of clinical pathology · 2025Article
- The Diagnostic Utility of PCR in FFPE Skin Biopsies with Inconclusive Histopathology for Suspected Cutaneous Leishmaniasis: A Pilot Study from Colombia.Tropical medicine and infectious disease · 2025Article
- Cervical Actinomycosis Diagnosed via Metagenomic Next-Generation Sequencing of Formalin-Fixed Paraffin-Embedded Tissue: A Case Report and Literature Review.Microorganisms · 2025Article
- Partial Alpha-Tubulin Gene Amplification by Nested PCR in Fresh Biological Samples and Formalin-Fixed, Paraffin-Embedded Tissues for Paracoccidioides spp. Identification.Mycopathologia · 2025Article
- Nanoparticle-assisted PCR: fundamentals, mechanisms, and forensic implications.International journal of legal medicine · 2025Review
- Impact of commercial RNA extraction methods on the recovery of human RNA sequence data from archival fixed tissues.BioTechniques · 2025Article
- Systematic comparison of quantity and quality of RNA recovered with commercial FFPE tissue extraction kits.Journal of translational medicine · 2025Article
- Detection ofFrontiers in veterinary science · 2025Article
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- Analysis of DNA Methylation in Gliomas: Assessment of Preanalytical Variables.Laboratory investigation; a journal of technical methods and pathology · 2024Article
- InDEL instability in two different tumoral tissues and its forensic significance.Forensic science, medicine, and pathology · 2024Article
- Apolipoprotein-E genotyping in formalin-fixed and paraffin-embedded post-mortem brain tissue.Brain pathology (Zurich, Switzerland) · 2024Article
22 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Formalin-fixed and paraffin-embedded (FFPE) tissues represent a valuable source for biomarker studies and clinical routine diagnostics. However, they suffer from degradation of nucleic acids due to the fixation process. Since genetic and epigenetic studies usually require PCR amplification, this degradation hampers its use significantly, impairing PCR robustness or necessitating short amplicons. In routine laboratory medicine a highly robust PCR performance is mandatory for the clinical utility of genetic and epigenetic biomarkers. Therefore, methods to improve PCR performance using DNA from FFPE tissue are highly desired and of wider interest. The effect of template DNA derived from FFPE tissues on PCR performance was investigated by means of qPCR and conventional PCR using PCR fragments of different sizes. DNA fragmentation was analyzed via agarose gel electrophoresis. This study showed that poor PCR amplification was partly caused by inhibition of the DNA polymerase by fragmented DNA from FFPE tissue and not only due to the absence of intact template molecules of sufficient integrity. This PCR inhibition was successfully minimized by increasing the polymerase concentration, dNTP concentration and PCR elongation time thereby allowing for the robust amplification of larger amplicons. This was shown for genomic template DNA as well as for bisulfite-converted template DNA required for DNA methylation analyses. In conclusion, PCR using DNA from FFPE tissue suffers from inhibition which can be alleviated by adaptation of the PCR conditions, therefore allowing for a significant improvement of PCR performance with regard to variability and the generation of larger amplicons. The presented solutions to overcome this PCR inhibition are of tremendous value for clinical chemistry and laboratory medicine.
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