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Updated: Jul 1, 2026
Preparation of Formalin-fixed Paraffin-embedded Tissue Cores for both RNA and DNA Extraction
Published on: August 21, 2016
DNA extraction from long-term preserved formalin-fixed paraffin-embedded samples of thymic epithelial tumours - a
Duc Manh Le1,2, Thi Xuan Nguyen3, Thanh Chung Dang1
1Military Medical Hospital 103 Vietnam, Military Medical University, Hanoi, Vietnam.
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.
