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Updated: Sep 1, 2025
Preparation of Formalin-fixed Paraffin-embedded Tissue Cores for both RNA and DNA Extraction
Published on: August 21, 2016
Unveiling the arcanum of formalin-fixed paraffin-embedded archival tissue blocks: A valuable resource for genomic DNA
Sameera Begum1, Vishnudas Prabhu1, Varshasnata Mohanty2
1Department of Oral Pathology, Yenepoya Dental College, Yenepoya (Deemed to be University), Mangaluru, Karnataka, India.
Background:
Formalin-fixed paraffin-embedded (FFPE) tissue blocks are routinely preserved after pathological diagnosis and possess tremendous potential for biomarker discovery. These archival samples are prone to degradation on prolonged storage due to the formalin cross-linking.
Aims:
This study aimed to evaluate whether the storage period of the formalin-fixed paraffin-embedded tumor blocks had a significant impact on the yield and purity of the isolated DNA archived for 11 years.
Settings And Design:
A retrospective study was carried out in the Department of Oral Pathology and Microbiology in accordance with the Institutional Ethics Committee.
Materials And Methods:
Genomic DNA extraction was performed using TaKaRa DEXPAT Easy DNA kit from 40 FFPE tissue blocks of oral squamous cell carcinoma archived for 11 years (2006-2017). NanoDrop spectrophotometer was used to determine the DNA yield (A260) and purity (A260/A280 ratio). The quality of DNA fragments was validated using agarose gel electrophoresis.
Statistical Analysis Used:
Statistical analysis was obtained by SPSS 22, MS Excel and analyzed using the analysis of variance (ANOVA) test. P < 0.05 was set for statistical significance.
Results:
There was no statistically significant difference observed both in terms of DNA yield (P = 0.996) and purity (P = 0.997) of FFPE tumor blocks archived for 11 years among the study groups.
Conclusions:
It was concluded that, irrespective of years of storage of the FFPE, it is possible to extract genomic DNA and use it for molecular studies.
