Appropriate DNA extraction is essential for molecular research and diagnostics, as the quantity and quality of DNA affect analytical procedures such as sequencing and PCR, and thus the reliability of the results. A sufficient amount of DNA of high quality is particularly important in cancer diagnostics, where it is necessary to detect the presence of cancer markers in often small biopsy samples. If extraction is inadequate, these rare markers may be missed, leading to misdiagnosis or incorrect assessment of the effectiveness of treatment. Nevertheless, the importance of DNA extraction is still insufficiently considered in both diagnostics and preclinical research. In our study, we compared the efficiency of DNA extraction from 2D and 3D cell cultures prepared from glioblastoma brain cancer using four commercially available methods: three based on silica gel membranes and one using magnetic beads. Three different analytical techniques were used to assess the quantity and quality of extracted DNA: a fluorometry (Qubit), a spectrophotometry (NanoDrop), and automated capillary electrophoresis (TapeStation). Analysis of the results, which included quantitative assessment of extracted DNA and calculation of the coefficient of variability, showed that the DNA Mini kit (Qiagen) was the most suitable choice for DNA extraction from both 2D and 3D cell cultures. We found that extracted DNA from 2D cell cultures allows for better reproducibility of results between biological replicates compared to 3D cell cultures. The NanoDrop spectrophotometer determined higher average DNA concentrations in all samples compared to the Qubit fluorometer and the TapeStation system, regardless of the type of starting sample, indicating the sensitivity of the approach to the presence of impurities and emphasizing the importance of choosing the appropriate method. The study was carried out within the framework of the international GenomeMET project, which aims to develop metrology capabilities and establish appropriate metrology frameworks to improve the quality, traceability and reproducibility of key procedures in cancer genetic profiling.
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