Related Experiment Video
Updated: Jun 6, 2026
Preparation of Formalin-fixed Paraffin-embedded Tissue Cores for both RNA and DNA Extraction
Published on: August 21, 2016
DNA extraction from formalin-fixed laryngeal biopsies: Comparison of techniques
Mariela C Torrente1, Carolina Ríos, Carlos Misad
1Departamento de Otorrinolaringología, Hospital San Juan de Dios, Facultad de Medicina, Universidad de Chile, Santiago, Chile. mtorrente@med.uchile.cl
Conclusion:
PCR-quality DNA could be extracted from formalin-fixed paraffin-embedded (FFPE) samples with amplicons of at least 390 bp. Paraffin removal was not a necessary step. Proteinase K digestion was as efficient as the commercial kit for DNA extraction with a lower cost.
Objectives:
To compare different DNA extraction protocols for FFPE samples and to describe the suitability of the extracted DNA for PCR reactions.
Methods:
For deparaffinization the following techniques were compared: alkaline heat, xylene, and no removal. For DNA extraction, proteinase K digestion and organic extraction were compared. A commercial extraction kit was included as standard. DNA quality was assessed by PCR amplification of the HFE gene, for amplicons of 208 and 390 bp.
Results:
Extraction with the commercial kit and proteinase K digestion were more efficient than other techniques, with no statistical difference between them for both amplicons. The proteinase K digestion buffer had a cost of U$ 0.2 per sample and the commercial kit of U$7 per sample.
Insights
DNA extraction from formalin-fixed paraffin-embedded (FFPE) samples is efficient using Proteinase K digestion, yielding PCR-ready DNA. This method is cost-effective and bypasses the need for paraffin removal.
Area of Science:
- Molecular Biology
- Genetics
- Biochemistry
Background:
- Formalin-fixed paraffin-embedded (FFPE) tissues are valuable for molecular analysis.
- Efficient DNA extraction from FFPE samples is crucial for downstream applications like PCR.
- Optimizing DNA extraction protocols can improve yield, quality, and cost-effectiveness.
Purpose of the Study:
- To compare various DNA extraction protocols for FFPE samples.
- To evaluate the suitability of extracted DNA for Polymerase Chain Reaction (PCR).
- To identify cost-effective methods for DNA extraction from FFPE specimens.
Main Methods:
- Comparison of deparaffinization techniques: alkaline heat, xylene, and no removal.
- Evaluation of DNA extraction methods: Proteinase K digestion and organic extraction.
- Assessment of DNA quality via PCR amplification of the HFE gene (208 and 390 bp amplicons).
- Inclusion of a commercial extraction kit as a standard.
Main Results:
- Proteinase K digestion and a commercial kit showed comparable efficiency in DNA extraction.
- Both methods successfully generated PCR-quality DNA with amplicons up to 390 bp.
- Proteinase K digestion significantly reduced costs (U$ 0.2/sample) compared to the commercial kit (U$ 7/sample).
- Paraffin removal was not essential for successful DNA extraction.
Conclusions:
- PCR-quality DNA can be reliably extracted from FFPE samples using Proteinase K digestion.
- Paraffin removal is an unnecessary step in DNA extraction from FFPE samples.
- Proteinase K digestion offers a cost-effective and efficient alternative to commercial kits for FFPE DNA extraction.
