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. 2022 Apr-Jun;26(2):289.
doi: 10.4103/jomfp.jomfp_424_20. Epub 2022 Jun 28.

Unveiling the arcanum of formalin-fixed paraffin-embedded archival tissue blocks: A valuable resource for genomic DNA extraction

Sameera Begum  1 , Vishnudas Prabhu  1 , Varshasnata Mohanty  2 , K Krishnaraj Upadhyaya  3 , Riaz Abdulla  1
Affiliations

Unveiling the arcanum of formalin-fixed paraffin-embedded archival tissue blocks: A valuable resource for genomic DNA extraction

Sameera Begum et al. J Oral Maxillofac Pathol. 2022 Apr-Jun.

Abstract

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.

Keywords: DNA; NanoDrop; formalin-fixed; oral squamous cell carcinoma; storage; tumor blocks.

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Conflict of interest statement

There are no conflicts of interest.

Figures

Figure 1
Figure 1
Represents mean DNA yield between groups
Figure 2
Figure 2
Represents mean DNA purity between groups
Figure 3
Figure 3
Different aspects of the spectrophotometric curve: (a) a negative extraction control, with very low DNA yield and purity; (b) lower DNA yield (117 ng/μL) but good purity (1.08); (c) one oral squamous cell carcinoma case with very good DNA yield (337.9 ng/μL) and purity (1.21); (d) one oral squamous cell carcinoma case with a very good DNA yield (533.5 ng/μL) but lower purity (0.5); (e) one oral squamous cell carcinoma case with a very good DNA yield (490.9ng/μL) but lower purity (0.48)
Figure 4
Figure 4
DNA bands visualized under ultraviolet light after agarose gel electrophoresis
See this image and copyright information in PMC

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