Abstract | The formalin fixed paraffin-embedded tissues (FFPET) represent an important source of biological material. However, the quality of the extracted DNA from such biopsies is often poor probably because of the type of fixative, fixation duration, block age and persistence of paraffin residues. The objective of the current study was to compare two deparaffinization techniques in combination with three extraction methods in order to select the best one to be used in routine diagnosis. Two deparaffinization techniques; xylene and temperature were tested. They were combined with three commonly used extraction methods namely phenol-chloroform, the commercial kit QIAamp DNA Mini Kit (Qiagen) and the salting-out method. Thirteen samples of FFPET, among which three infected by Entamoeba histolytica, were used for this evaluation. The quantity and quality of obtained DNA were measured using NanoDrop. The IL6 human gene was also amplified for further validation. The combination temperature/commercial kit revealed the most efficient with good DNA yield and high purity (p≤0,001). It also provided the best success rate of PCR amplification. This method is simple and does not use toxic substances. Amplification products confirmed the presence of Entamoeba histolytica in 2 out of 3 amoebiasis biopsies tested. The combination temperature/commercial kit allows the DNA extraction with good quantities and high purity from FFPET. Such biological samples may represent a possible alternative in research and diagnosis.
Keywords | Deparaffinization, DNA extraction, PCR, IL6 gene, Entamoeba histolytica