Effect of digestion time on quality of FFPE-derived DNA during DNA extraction
ZHANG Keping
XU Jie
ZHAO Panpan
HUANG Yongjun
Abstract：Objective To investigate the effect of the duration of the lysis digestion step during DNA extraction on the quality of DNA from formalin-fixed paraffin-embedded (FFPE) samples. Methods A fresh tonsil tissue sample with dimensions of 1 cm × 1 cm × 0.3 cm was fixed in 4% neutral buffered formalin for 24 hours, followed by dehydration and embedding. Fifty unstained slides were obtained by continuous sectioning. These slides were divided into five groups (A to E), labeled as A1 to A5, B1 to B5, etc. Group A used a standard digestion protocol (i.e., overnight digestion at 56°C for approximately 16 hours), while groups B, C, D, and E had digestion times of 24 hours, 48 hours, 72 hours, and 7 days, respectively. DNA was then extracted from all samples, and its concentration and optical density (OD) ratio were measured to evaluate DNA quality and integrity. Results As the digestion time increased, the concentration of FFPE-derived DNA showed an upward trend; however, the effect of digestion time on improving DNA purity was not significant. Notably, prolonged digestion led to a decrease in DNA integrity. Nevertheless, FFPE DNA digested for up to one week could still serve as a viable material for subsequent analyses such as next-generation sequencing (NGS). Conclusion Controlling the digestion time during DNA isolation from FFPE specimens is crucial to ensure the acquisition of high-quality DNA, thereby enhancing the accuracy of subsequent experimental tests.
Keywords：Formalin-Fixed Paraffin-Embedded (FFPE)DNAExtractionProteinase KLysis Digestion
Publication Date：2025-10-28
Online Publishing Date：2025-11-06(First online date of this platform, not the publication date of the document)
Pages：3( 1376-1378 )