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23 January 2019

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Int J Med Sci 2014; 11(5):494-499. doi:10.7150/ijms.8842

Research Paper

Comparison of Methods for the Extraction of DNA from Formalin-Fixed, Paraffin-Embedded Archival Tissues

Burcu Sengüven1✉, Emre Baris1, Tulin Oygur1, Mehmet Berktas2

1. Department of Oral Pathology, Faculty of Dentistry, Gazi University, Ankara, Turkey;
2. Pharmacoeconomy and Pharmacoepidemiology Research Center (PEPIRC), Yeditepe University, Istanbul, Turkey.


Aim: Discussing a protocol involving xylene-ethanol deparaffinization on slides followed by a kit-based extraction that allows for the extraction of high quality DNA from FFPE tissues.

Methods: DNA was extracted from the FFPE tissues of 16 randomly selected blocks. Methods involving deparaffinization on slides or tubes, enzyme digestion overnight or for 72 hours and isolation using phenol chloroform method or a silica-based commercial kit were compared in terms of yields, concentrations and the amplifiability.

Results: The highest yield of DNA was produced from the samples that were deparaffinized on slides, digested for 72 hours and isolated with a commercial kit. Samples isolated with the phenol-chloroform method produced DNA of lower purity than the samples that were purified with kit. The samples isolated with the commercial kit resulted in better PCR amplification.

Conclusion: Silica-based commercial kits and deparaffinized on slides should be considered for DNA extraction from FFPE.

Keywords: DNA extraction, formalin fixed paraffin-embedded tissues.

This is an open access article distributed under the terms of the Creative Commons Attribution (CC BY-NC) License. See for full terms and conditions.
How to cite this article:
Sengüven B, Baris E, Oygur T, Berktas M. Comparison of Methods for the Extraction of DNA from Formalin-Fixed, Paraffin-Embedded Archival Tissues. Int J Med Sci 2014; 11(5):494-499. doi:10.7150/ijms.8842. Available from