Can tissue deparaffinization influence the extracted DNA for forensic purposes?

In forensic genetics, sometimes the biological specimen available for DNA extraction is biopsy tissue taken in life from deceased subjects and then fixed in formalin and embedded in paraffin (FFPE). Degradation and chemical alteration of DNA caused by treatment of tissue with formalin and paraffin is an event reported in the literature, even if the influence of exposure time and intensity of the phenomenon are still uncertain. This results in obtaining DNA of degraded quality, the quantity of which is for sure affected by paraffin hindering its release from the tissues in the lysis step. Therefore, pretreatment of the biological sample, i.e. deparaffinization, may assume a relevant role in the subsequent DNA extraction and amplification steps. In this study, five different tissue deparaffinization protocols were compared to determine which was the most appropriate for the aim, exploiting two tissue samples (lung and kidney), FFPE over the next 24 h, taken during autopsies on two male cadavers. The deparaffinization protocols involved the use of the standard procedure with xylene and 100% ethanol and four methods in which paraffin solubilizing solvents were used, i.e. chloroform and white mineral oil. Then, DNA extraction was performed by employing the QIAamp DNA FFPE Tissue Kit, modifying the procedure only in the post-lysis step, in which the provided treatment at 90°C for 1 h was omitted, proceeding with incubation at 70°C for 24 h, after addition of Tris 1M to the lysate. Extracted DNA was quantified and normalized to 1 ng/µl and then submitted for amplification with two forensic kits. Amplicons were genotyped in capillary electrophoresis and fragment analysis was conducted with the GeneMapper ID-X v1.6 software. The two panels of Short Tandem Repeats yielded reproducible, albeit partial, genetic profiles, referable to 12/13 loci (molecular weight <300 bp), and showed no significant differences correlated with the adopted deparaffinization procedure. Therefore, while being aware that the study needs to implement the number of samples, it seems reasonable to assume that deparaffinization can also be carried out by procedures other than the standard one, using solvents with low toxic characteristics.