Extraction of DNA from paraffinembedded tissues using pipette tip-based non-centrifugation method

WANG Xianwei; YUAN Fengju; CHENG Siying; YANG Zhirong; XU Pei

doi:10.3969/j.issn.1007-8096.2025.08.019

Abstract：Objective To evaluate the application effect of extracting paraffin-embedded tissue DNA based on the pipette tip-based non-centrifugation method.Methods A total of 42 paraffin-embedded tissue samples were collected,DNA extraction was performed using the pipette tip-based non-centrifugation method and centrifuge column method.The differences in DNA concentration,purity,quality,and downstream gene detection between the two methods were compared.Results The spectrophotometer detection showed that the average concentration of DNA extracted by the suction method was 18.80 ng/μ L,which was lower than the 84.01 ng/μ L by the centrifugal column method.The average values of A260/A280 extracted by the suction method and centrifugal column method were 1.9 and 1.845,respectively.The difference in DNA concentration and A260/A280 extracted by the two methods was statistically significant(P＜0.01).The Qubit test results showed that the average concentration of DNA extracted by suction method was 8.26ng/μL,which was lower than that of centrifugation column method at 35.56 ng/μL,and the difference between the two was statistically significant(P＜0.01).The average N/Q values of DNA extracted by suction and centrifugation columns were 2.631±0.839 and 2.558±0.782,respectively,with no statistically significant difference between the two(P＞0.05).There was no significant difference in the quality of DNA extracted by suction method and the results obtained by centrifugation column method.The consistency between the results of the suction type gene detection and the centrifugal column method was 100％.The external control CT values for EGFR gene detection were 27.82±1.52 and 27.89±1.26,respectively.The external control CT values for KRAS/NRAS/BRAF gene mutation combined detection were 17.52±0.80 and 17.29±0.93,respectively,and the differences were not statistically significant(P＞0.05).Conclusion The DNA concentration and purity extracted by the suction method are not as good as those of the centrifugal column method,but its DNA quality is no different from that of the centrifugal column method,which can meet the requirements of gene detection.Moreover,the extraction is simple and fast,and it is suitable for molecular pathology detection.