Smart-Plexer 2.0: Leveraging New Features of Amplification Curves to Enhance the Selection of Multiplex PCR Assays in Multi-Target Identification

Multiplex PCR plays a critical role in diagnostics by enabling the detection of multiple targets in a single reaction. However, its use is often limited by the need for multiple fluorescent channels, which are restricted in standard PCR instrumentation. Amplification curve analysis (ACA) is a data-driven multiplexing (DDM) approach that overcomes this limitation by using real-time PCR data and machine learning to differentiate targets in a single-channel, single-well format, without requiring instrument modifications. As part of this DDM strategy, we previously introduced Smart-Plexer 1.0, a tool that simulates multiplex assays using empirical singleplex data to identify optimal assay combinations in silico, maximizing kinetic feature distances between targets to support ACA-based discrimination. While Smart-Plexer 1.0 performs reliably in controlled reactions and offers a strong framework for the ACA assay design, it relies on a single kinetic feature and a median-based distance metric, which limits its accuracy in reactions with variable target concentrations or efficiencies. Here, we present Smart-Plexer 2.0, a more robust and accurate version designed to improve the performance in amplification reactions affected by such variability. This version introduces three new kinetic features that are stable across different template concentrations and uses clustering-based distance measures to better capture the variability between targets. Compared to its predecessor, Smart-Plexer 2.0 reduces accuracy variance by an order of magnitude and improves ACA classification by 1.5 and 1% in retrospective 3-plex and 7-plex assays, respectively. In a multi-experiment, cross-concentration evaluation of a newly developed 7-plex assay, it achieved 97.6% ACA accuracy, confirming its robustness across complex scenarios. Smart-Plexer 2.0 offers a reliable and scalable way to design high-performance multiplex PCR assays using standard real-time PCR instruments.