Comparative Analysis of DNA Extraction Methods from Formalin-Fixed and Paraffin-Embedded Echinococcus Cyst Tissue for Molecular Identification
Main Article Content
Aidana Tautanova
Department of Microbiology and Virology, Astana Medical University, Astana, Kazakhstan
tautanovaidana@gmail.com
Karina Jazina
Laboratory of Biodiversity and Genetic Resources, National Center for Biotechnology, Astana, Kazakhstan
Dzhazinak01@gmail.com
Rabiga Uakhit
Laboratory of Biodiversity and Genetic Resources, National Center for Biotechnology, Astana, Kazakhstan
erken.uakhitrabiga@gmail.com
Ainur Smagulova
Laboratory of Biodiversity and Genetic Resources, National Center for Biotechnology, Astana, Kazakhstan
smagulova0114@gmail.com
Marat Dusmagambetov
Department of Microbiology and Virology, Astana Medical University, Astana, Kazakhstan
dusmagambetov.m@amu.kzAbstract
Archived formalin-fixed and paraffin-embedded (FFPE) samples of echinococcal cysts represent a valuable biological resource for molecular epidemiological studies of infections caused by parasites of the genus Echinococcus. However, formalin fixation and prolonged storage significantly affect DNA quality, leading to DNA fragmentation and the formation of cross-links between nucleic acids and proteins. The aim of this study was to comparatively evaluate the efficiency of DNA extraction methods from FFPE material of echinococcal cysts and to assess their suitability for molecular identification of the pathogen. The chitinous laminated layers of echinococcal cysts isolated from FFPE samples were selected as the study material. The results demonstrated that the DNA extraction method incorporating xylene-based deparaffinization yielded higher DNA concentrations ranging from 13.1 to 1161.8 ng/µL and superior nucleic acid purity. In contrast, DNA extracted using the Raissol Bio kit showed low concentrations ranging from 0.6 to 10.2 ng/µL and evidence of protein and organic contamination, which potentially inhibited PCR amplification. The application of xylene deparaffinization ensured complete paraffin removal and preservation of DNA integrity, enabling successful molecular identification. For molecular-genetic identification, a marker fragment of the mitochondrial cox1 gene was used. The obtained results highlight the potential of optimized DNA extraction protocols for FFPE material and expand the possibilities for laboratory diagnostics and retrospective molecular epidemiological investigations of echinococcosis.
Article Details
Accepted 2026-07-02
Published 2026-07-02
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