DNA extraction from formalin-fixed laryngeal biopsies: Comparison of techniques

Abstract

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.

Keywords::

• Paraffin embedding
• cancer
• PCR

Acknowledgments

This work was supported by a grant from the Sociedad Chilena de Otorrinolaringología.

Declaration of interest: The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.