DNA Extraction from Archived Paraffin Embedded Tissues: A Comparative Study Using Three Different Extraction Method-Extraction of DNA from Paraffin Embedded Tissues

Abstract

Objective: Formalin fixed paraffin embedded (FFPE) tissue is a valuable source of nucleic acids required
for various molecular studies. The purpose of the present study was to extract Deoxyribonucleic acid (DNA)
from archival retrieved FFPE oral squamous cell carcinoma tissues using three different extraction method
(salting out, commercial kit and microwave method) and to compare the yield of DNA extracted by these
method.
Method and Material: 30 oral squamous cell carcinoma paraffin embedded tissue blocks were categorized
into three groups based on the duration of storage as Group A(<2 years), B(2-4 years) and C(4-6years). The
tissue sections made from these blocks were subjected to three DNA extraction method and the DNA yield
was measured using a spectrophotometer. The extracted DNA was checked by successful amplification of
p53 gene using Polymerase Chain Reaction followed by gel electrophoresis. The values of DNA yield and
purity were statistically analysed and the level of significance was set at P?0.05.
Results: The DNA yield was above 3?g in all the three extraction method. On multiple comparison, the
mean DNA yield was statistically significant (P value<0.05) among the three method in Group A. Also, the
DNA yield was found to be higher in salting out method though successful amplification was obtained from
the extracted DNA in other extraction method as well.
Conclusions: DNA was successfully extracted from all the tissue samples using all the three method. Salting
out method yielded the maximum amount of DNA compared to the other method and shall be a good cost
effective alternative.