Introduction

Thymic epithelial tumours (TET) are a rare, histologically varied group of malignancies, classified by the World Health Organization into 5 subtypes ranging from indolent to aggressive forms. Formalin-fixed paraffin-embedded (FFPE) tissues represent the conventional approach for preserving TET tissues in pathology archives, ensuring long-term stability. Advancements in molecular techniques have significantly improved the molecular analysis in TET. Their efficacy is dependent upon the extraction of high-quality DNA from FFPE samples. The formalin-fixed paraffin-embedded preservation method and extended storage duration, however, pose challenges for molecular analysis because of DNA crosslinking, fragmentation, and reduced recovery efficiency and purity.

Material and methods

This investigation evaluated the performance of 3 commercial DNA extraction kits: the QIAamp® DNA FFPE Tissue Kit, the GeneJET® FFPE DNA Purification Kit, and the MasterPure™ Complete DNA and RNA Purification Kit, across 20 FFPE and 3 fresh TET samples, representing various sexes, ages, histological subtypes, and preservation conditions. The evaluation of DNA yield, purity, and compatibility for subsequent applications was conducted for each method.

Results

The QIAamp kit produced the most substantial and reliable DNA yields of 1785.5 ng (Qubit) and 3280 ng (NanoDrop), along with a high level of purity. The DNA has been determined to be appropriate for polymerase chain reaction, Sanger sequencing, and whole genome sequencing regarding its quality and quantity.

Conclusions

The QIAamp kit demonstrates superior performance compared to the others, providing high- quality DNA that is suitable for all molecular applications across all TET subtypes and sample conditions.