ArticleBiology methods & protocols2022
An efficient procedure for the recovery of DNA from formalin-fixed paraffin-embedded tissue sections.
Article in Biology methods & protocols, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Article
- BRAFVeterinary research communications · 2026Article
- Genotypic spectrum and prevalence of HPV associated with cervical cancer in Palestine.BMC infectious diseases · 2025Article
- Enabling whole genome sequencing analysis from FFPE specimens in clinical oncology.Nature communications · 2025Article
- Article
- Response to primary canine core vaccination in 10-month-old seronegative dogs treated with three times the recommended therapeutic dose of Ilunocitinib tablets (Zenrelia™).BMC veterinary research · 2025Article
- The mutational landscape and actionable targets of gallbladder cancer: an ancestry-informed and comparative analysis of a Chilean population.Frontiers in oncology · 2025Article
- A cost-effective and scalable approach for DNA extraction from FFPE tissues.Biology methods & protocols · 2025Article
- Spatial transcriptomics in cancer research and potential clinical impact: a narrative review.Journal of cancer research and clinical oncology · 2024Review
- Emerging Approaches to Profile Accessible Chromatin from Formalin-Fixed Paraffin-Embedded Sections.Epigenomes · 2024Review
- Comprehensive Diagnosis, Treatment, and Outcome ofPathogens (Basel, Switzerland) · 2024Article
- Epigenomic analysis of formalin-fixed paraffin-embedded samples by CUT&Tag.Nature communications · 2023Article
- Colorectal Cancer Archaeome: A Metagenomic Exploration, Tunisia.Current issues in molecular biology · 2023Article
Corrections and comments
- Erratum issued
Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
With the advent of new molecular diagnostic techniques, retrieving DNA from the formalin-fixed paraffin-embedded (FFPE) tissues has become an essential yet challenging step for efficient downstream processes. Owing to low quality and quantity of DNA retrieved from the FFPE sections, the process is often impractical and needs significant improvements. Here, we established an efficient method for the purification of DNA from FFPE specimens by optimizing incubation temperature, incubation time, and the concentration of a formalin scavenger tris(hydroxymethyl)aminomethane (Tris) for reverse-crosslinking. The optimized method, named "Highly concentrated Tris-mediated DNA extraction" (HiTE), yielded three times the DNA yield per tissue slice compared with a representative DNA extraction kit. Moreover, the use of HiTE-extracted DNA increased the yield of the sequencing library three times and accordingly yielded a log higher and more reproducible sequencing library compared with that obtained using the commonly used commercial kit. The sequencing library prepared from HiTE-extracted FFPE-DNA had longer inserts and produced reads that evenly covered the reference genome. Successful application of HiTE-extracted FFPE-DNA for whole-genome and targeted gene panel sequencing indicates its practical usability.
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