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Updated: May 23, 2026
Preparation of Formalin-fixed Paraffin-embedded Tissue Cores for both RNA and DNA Extraction
Published on: August 21, 2016
Microwave heating of long-term formalin-fixed surgical pathology specimens improves quality of extracted DNA
Shanshui Wu1, Xin Qian, Xinchun Yu
1Department of Oncology, Quzhou Municipal Hospital, Quzhou, Zhejiang Province, PR China.
Abstract:
A large amount of DNA of high quality is essential for molecular analysis. The amount of DNA in routine paraffin sections is small. Surgical specimens retained in formalin for the long-term (several months) left over from the sampling required for wax embedding can be referred to as "long-term formalin-fixed" specimens, and clearly this material is a rich source of DNA; however, it is difficult to extract. In the current study, we designed a microwave-heating method for DNA extraction from these specimens. We found that the heating procedure achieved greater DNA yields than a common nonheating method used for comparison (DNA contents mean±SD, heating 2.16±0.95 μg/μL vs. common 1.75±0.90 μg/μL, P<0.05). Fluorescence multiplex polymerase chain reaction-capillary electrophoresis successfully detected microsatellite instability (MSI) in the DNA samples derived from this heating procedure (98.4%, 689 of 700 sample tests), at significantly higher levels than from the conventional method (82.3%, 247 of 300 sample tests, P<0.05). We identified 10 (14.3%) MSI with high frequency and 6 (8.6%) MSI with low frequency colorectal cancers. MSI with high frequency cancers showed distinct clinicopathologic features including higher incidence of right-sided location, high histologic grade, mucin-production, and prominent intraepithelial lymphocyte infiltration. We concluded that the microwave-heating method was efficient for DNA isolation from long-term formalin-fixed tissue samples. The successful fluorescence multiplex polymerase chain reaction-capillary electrophoresis analysis in these samples might facilitate MSI detection in clinical practice.
Insights
A novel microwave-heating method efficiently extracts high-quality DNA from long-term formalin-fixed tissues. This DNA enables accurate microsatellite instability (MSI) detection, aiding colorectal cancer diagnosis and characterization.
Area of Science:
- Molecular Biology
- Genetics
- Histopathology
Background:
- High-quality DNA is crucial for molecular analyses.
- Routine paraffin sections yield limited DNA.
- Long-term formalin-fixed tissues offer abundant DNA but pose extraction challenges.
Purpose of the Study:
- To develop an efficient DNA extraction method for long-term formalin-fixed specimens.
- To evaluate the efficacy of a microwave-heating technique for DNA isolation.
- To assess the utility of extracted DNA for microsatellite instability (MSI) detection.
Main Methods:
- A microwave-heating method was designed for DNA extraction from long-term formalin-fixed tissues.
- DNA yields were compared between the microwave-heating method and a conventional non-heating method.
- Microsatellite instability (MSI) was detected using fluorescence multiplex polymerase chain reaction-capillary electrophoresis.
Main Results:
- The microwave-heating method yielded significantly greater DNA amounts compared to the non-heating method (2.16±0.95 μg/μL vs. 1.75±0.90 μg/μL, P<0.05).
- MSI detection rates were significantly higher using DNA from the heating method (98.4%) versus the conventional method (82.3%, P<0.05).
- High-frequency MSI was identified in 14.3% of colorectal cancers, correlating with specific clinicopathologic features.
Conclusions:
- The microwave-heating method is an efficient technique for DNA isolation from long-term formalin-fixed tissue samples.
- This method facilitates successful molecular analysis, including MSI detection.
- The findings may enhance MSI detection in clinical practice for colorectal cancer management.
