Contemporary Oncology
eISSN: 1897-4309
ISSN: 1428-2526
Contemporary Oncology/Współczesna Onkologia
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4/2025
vol. 29
 
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abstract:
Original paper

DNA extraction from long-term preserved formalin-fixed paraffinembedded samples of thymic epithelial tumours – a performance comparison of three commercial kits

Duc Manh Le
1, 2
,
Thi Xuan Nguyen
3
,
Thanh Chung Dang
1
,
Ngoc Dung Tran
1
,
Ngoc Lan Nguyen
4
,
Thai Tra Dang
1
,
Thu Hien Nguyen
1
,
Huy Hoang Nguyen
3
,
Duc Quan Nguyen
3
,
Thi Trang Do
3, 5

  1. Military Medical Hospital 103 Vietnam, Military Medical University, Hanoi, Vietnam 10000
  2. Research Centre 69, Ho Chi Minh President Mausoleum Command, Hanoi, Vietnam 10000
  3. Insitute of Biology, Vietnam Academy of Science and Technology, Nghia Do, Hanoi, Vietnam 10000
  4. Hanoi Medical University, No.1 Ton That Tung Street, Kim Lien, Hanoi, Vietnam 10000
  5. Publishing House for Science and Technology, Vietnam Academy of Science and Technology, Nghia Do, Hanoi, Vietnam 10000
Contemp Oncol (Pozn) 2025; 29 (4): 341–346
DOI: https://doi.org/10.5114/wo.2025.156116
Online publish date: 2025/11/11
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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.

keywords:

thymic epithelial tumour, FFPE samples, DNA extraction, commercial kits, comparative analysis
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