Plant genetic engineering represents an important aspect of modern agriculture, and new genetically
modified (GM) crop varieties are entering the market on a regular basis. This necessitates the
development of high throughput multi-target analytical methods to detect and quantify their
presence for regulatory compliance. In this study, we present a multiplex dPCR method for discriminative
quantification of 19 GM soybean events and the lectin (Le1) endogene on a nanowell platebased
all-in-one dPCR system. The method consists of four 5-plex assays, taking advantage of the
platform’s multiple fluorescence detection channels. The assays complied with the minimum performance
requirements in terms of specificity, trueness, precision, sensitivity and dynamic range,
making them suitable for use in routine detection and quantification of GM crops. This method
represents the most comprehensive multi-target GM soybean quantification approach to date without
the need for prior screening and features a simplified workflow, making it suitable for widespread
adoption. Our study sets a precedent for rapid and straightforward development of multiplex dPCR
GM crop quantification assays to address the evolving demands of regulatory monitoring.