Manipulating Analytical Bias in GMO Quantification for Processed Foods by Adjusting PCR Amplicon Sizes

BACKGROUND: A wide range of foods containing genetically modified organisms (GMOs) are commercially available. To verify the accuracy of GMO labeling, real-time PCR is used to quantify GMO content in raw materials. However, DNA fragmentation during food processing can introduce analytical bias, making it difficult to accurately assess GMO content in processed foods. OBJECTIVE: This study aimed to establish a method to accurately evaluate food labeling suitability by inferring the GMO content at the raw material stage from the measurement results of processed foods. METHODS: Model processed foods (heat-treated soybeans) containing GM events were prepared and analyzed using a GMO quantification method incorporating taxon-specific real-time PCR with longer amplicons. RESULTS: We observed that the calculated GMO content increased with the length of the amplicon used in the taxon-specific PCR assay. This finding indicates that GMO content can be artificially influenced by modifying the amplicon size. When a longer amplicon was deliberately employed, the GMO content calculated for the processed food always exceeded that of the raw material. CONCLUSIONS: The use of longer amplicons in taxon-specific PCR can lead to an overestimation of GMO content at the raw material stage based on the measurements from processed foods. If the overestimated value remains below the labeling threshold, the appropriateness of GMO labeling can still be confirmed. The proposed method offers a simplified and practical approach for use in routine inspections. HIGHLIGHTS: The developed method enables direct analysis of processed foods to assess GMO labeling appropriateness. It eliminates the need to obtain raw materials or conduct multiple analyses. The approach simplifies GMO quantification in inspection laboratories by reducing procedural complexity.