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Deparaffinization and Lysis by Hydrothermal Pressure (Pressure Cooking) Coupled With Chaotropic Salt Column Purification: A Rapid and Efficient Method of DNA Extraction From Formalin-fixed Paraffin-embedded Tissue

Zhong, Haohao MS*; Liu, Yan MD, PhD*; Talmor, Monica MS; Wu, Bingquan MD*; Hui, Pei MD, PhD

Diagnostic Molecular Pathology: March 2013 - Volume 22 - Issue 1 - p 52–58
doi: 10.1097/PDM.0b013e318263f092
Original Articles

We report a hydrothermal pressure method (pressure cooking) for simultaneous deparaffinization and lysis of formalin-fixed paraffin-embedded tissue followed by conventional chaotropic salt column purification to obtain high-quality DNA. Using this method, the release of DNA occurred within the first minute of treatment, reaching the maximum at 5 minutes. An optimal treatment window was between 5 and 30 minutes. The extracted DNA was of high quality as determined by the 260/280 absorbance ratios, and the quantity of DNA extracted was linear with the input tissue amount. In paired sample experiments (N=19), the quantity of DNA extracted by hydrothermal pressure treatment was comparable to that obtained through the conventional xylene deparaffinization and protease K digestion method. The integrity of the recovered DNA was also comparable, evidenced by polymerase chain reaction amplifications of variable-sized amplicons in tissue samples archived from 0.2 to 22 years (N=14). The high quality of DNA was further confirmed by polymerase chain reaction amplification and Sanger sequencing analysis of representative exons of the EGFR gene in human non–small cell lung cancer tissue samples. In summary, this novel method offers DNA release from formalin-fixed paraffin-embedded tissue with unprecedented simplicity, speed, biohazard safety, and cost-efficiency. Combined with chaotropic salt column purification, high-quality DNA can be prepared for downstream applications in <30 minutes.

*Department of Pathology, Health Science Center, Peking University, Beijing, China

Department of Pathology, Yale University School of Medicine, New Haven, CT

The authors declare no conflict of interest.

Reprints: Pei Hui, MD, PhD, Department of Pathology, Yale University School of Medicine, BML 254B, 310 Cedar Street, New Haven, CT 06520-8023 (e-mail:

© 2013 Lippincott Williams & Wilkins, Inc.