Effect of formalin fixation on DNA purity and quantity, nucleic acid, and amplicon size in cervical human papilloma virus detection

Abstract

Tissue fixation with 10% formalin and molten paraffin wax embedding (FFPE) is routinely used protocol for tissue preservation in histopathology laboratory. We therefore aimed at comparing the differences in DNA quantity, DNA purity, nucleic acid and its effect on primers (PCR) amplicon (bp) sizes between fresh cervical tissues and formalin fixed paraffin embedded (FFPE). The differences in DNA purity, quantity and nucleic acid were 2.02±0.42 versus 1.34±0.28, 47.73±37.45 vs. 21.84±25.52 (ng/µl) and 1.56±0.59 vs 0.49±0.46 between for fresh cervical tissue and FFPE respectively and were all statistically significant at p<0.005. The difference in amplification successes was higher for the 120 bp than for the 450 bp primers. The distribution of cervical human papillomavirus for fresh tissues and formalin-fixed paraffin-embedded tissues studied was 39% and 13% respectively. Although, the present results showed that PCR genomic DNA can be extracted from both fresh cervical smear and 8 years duration FFPE archived tissue blocks. Formalin fixed paraffin embedded tissue blocks is not recommended for epidemiological study for detection and typing of cervical human papillomavirus using high molecular weight  base pair primers and conventional PCR.    Key words: Amplicon size, polymerase chain reaction (PCR), cervical tissues.