Impact of specimen age on its DNA quality for Formalin-Fixed Paraffin-Embedded HPV specimens

Abstract

Formalin fixation and paraffin embedding (FFPE) allows the storage of diagnostic and surplus tissue in archival banks. Therefore, FFPE is now a standard method for long-term preservation of tissue biopsies as FFPE of samples preserves the morphology of tissue. Unfortunately, the FFPE process engenders chemical changes and degradation in tissue macromolecules that can pose threats to reliable subsequent analysis. DNA, while more resistant to FFPE in comparison to RNA and protein, is also subject to such chemical formations and degradation. This study provides robust findings about the relationship between DNA quality and specimen age from 10252 FFPE HPV specimens. This paper suggests that there is a perceptible degrading effect in DNA quality as specimens age. This study suggests that the biospecimen may begin to take on new characteristics after certain storage years, and such changes may result in inaccurate determinations of the molecular characteristics of the biospecimen during analysis. Results from this study demonstrate that older HPV specimens are more inclined to be tested negative or inadequate from commercial HPV genotyping assays. Same findings are conferred when multiple genotyping assays are involved with HPV testing. Also, older HPV samples typify fewer HPV types compared to younger HPV samples. The results from this study will be useful to enhance potential scope for next fixation methods such as ethanol fixation that may be equally useful for both molecular profiling and histology as FFPE.