ArticleJournal of clinical microbiology2010
Improving molecular detection of fungal DNA in formalin-fixed paraffin-embedded tissues: comparison of five tissue DNA extraction methods using panfungal PCR.
Article in Journal of clinical microbiology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers, 1 of them a synthesis that pooled it.
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Who cites it
67 citing papers in PubMed, 1 synthesis or guideline pooled it, 158 citations in OpenAlex.
- Diagnostic performance of panfungal PCR on tissue specimens for the diagnosis of invasive fungal diseases: a systematic review and meta-analysis of the Fungal PCR Initiative (FPCRI).Journal of clinical microbiology · 2026Pooled it
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- 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
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- Beyond conventional approaches: Enhancing photodynamic therapy for refractory feline sporotrichosis caused byMedical mycology case reports · 2024Article
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- Fluconazole and echinocandin resistance ofEpidemiology and infection · 2023Observational
- Application of Real-Time PCR Assays for the Diagnosis of Histoplasmosis in Human FFPE Tissues Using Three Molecular Targets.Journal of fungi (Basel, Switzerland) · 2023Article
- Fungal Integrated Histomolecular Diagnosis Using Targeted Next-Generation Sequencing on Formalin-Fixed Paraffin-Embedded Tissues.Journal of clinical microbiology · 2023Article
- Detection and identification ofFrontiers in cellular and infection microbiology · 2023Article
- Nucleic Acid-Based Detection ofJournal of fungi (Basel, Switzerland) · 2022Review
- Nested PCR Detection ofVeterinary sciences · 2022Article
- Molecular Diagnosis of Two Major Implantation Mycoses: Chromoblastomycosis and Sporotrichosis.Journal of fungi (Basel, Switzerland) · 2022Review
- Evaluating a semi-nested PCR to support histopathology reports of fungal rhinosinusitis in formalin-fixed paraffin-embedded tissue samples.Journal of clinical laboratory analysis · 2022Article
- Microbiological and Molecular Diagnosis of Mucormycosis: From Old to New.Microorganisms · 2021Review
- Recognition of Diagnostic Gaps for Laboratory Diagnosis of Fungal Diseases: Expert Opinion from the Fungal Diagnostics Laboratories Consortium (FDLC).Journal of clinical microbiology · 2021Article
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- Molecular Techniques for Genus and Species Determination of Fungi From Fresh and Paraffin-Embedded Formalin-Fixed Tissue in the Revised EORTC/MSGERC Definitions of Invasive Fungal Infection.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2021Article
- Nested PCR for the Diagnosis of Feline Sporotrichosis From Formalin-Fixed and Paraffin-Embedded Samples Using Different DNA Extraction Protocols.Frontiers in veterinary science · 2021Article
- Development of a Sensitive and Specific Novel qPCR Assay for Simultaneous Detection and Differentiation of Mucormycosis and Aspergillosis by Melting Curve Analysis.Frontiers in fungal biology · 2021Article
7 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA extraction from formalin-fixed paraffin-embedded (FFPE) tissues is difficult and requires special protocols in order to extract small amounts of DNA suitable for amplification. Most described methods report an amplification success rate between 60 and 80%; therefore, there is a need to improve molecular detection and identification of fungi in FFPE tissue. Eighty-one archived FFPE tissues with a positive Gomori methenamine silver (GMS) stain were evaluated using five different commercial DNA extraction kits with some modifications. Three different panfungal PCR assays were used to detect fungal DNA, and two housekeeping genes were used to assess the presence of amplifiable DNA and to detect PCR inhibitors. The sensitivities of the five extraction protocols were compared, and the quality of DNA detection (calculated for each kit as the number of housekeeping gene PCR-positive samples divided by the total number of samples) was 60 to 91% among the five protocols. The efficiencies of the three different panfungals used (calculated as the number of panfungal-PCR-positive samples divided by the number of housekeeping gene PCR-positive samples) were 58 to 93%. The panfungal PCR using internal transcribed spacer 3 (ITS3) and ITS4 primers yielded a product in most FFPE tissues. Two of the five DNA extraction kits (from TaKaRa and Qiagen) showed similar and promising results. However, one method (TaKaRa) could extract fungal DNA from 69 of the 74 FFPE tissues from which a housekeeping gene could be amplified and was also cost-effective, with a nonlaborious protocol. Factors such as sensitivity, cost, and labor will help guide the selection of the most appropriate method for the needs of each laboratory.
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