Development and Performance Evaluation of a New Test Kit for Quantifying the Degree of DNA Fragmentation

Abstract Background PCR-based genetic testing of agricultural products and foods is widely used for detecting various analytical targets such as genetically modified organisms and food allergens. However, it is difficult to obtain accurate genetic testing results from processed foods because DNA is fragmented by heat and pressure during food processing. Thus, we previously developed an analytical method to quantitatively evaluate the degree of DNA fragmentation for the purpose of QC of genetic testing for processed foods. Objective Our previous analytical method requires four PCR primer sets, resulting in high reagent costs and heavy analytical workloads. Therefore, we attempted to develop an easy-to-use test kit for quantifying the degree of DNA fragmentation and to evaluate its analytical performance. Methods To simplify the analysis procedure, we used only two primer sets. In addition, no-fragmentation control templates were prepared to obtain stable measurement results. The precision of the simplified analysis was evaluated through blind tests between laboratories. Results It was confirmed that plant species and extracted DNA concentrations had little effect on analysis with the newly developed test kit. In addition, the analytical values indicating the degree of DNA fragmentation exhibited small variability between laboratories. Conclusion We confirmed the high practicality of the developed test kit. Because DNA fragmentation in cells is a universal phenomenon, we anticipate that the test kit will be used not only for QC of genetic testing but also for food testing, medical diagnostics, and other applications in a range of fields. Highlights The newly developed test kit enables quantitative evaluation of the degree of DNA fragmentation in a simple manner.