A Unified Multiplex Digital PCR-based Platform for Multi-class Biomarker Quantification from Low-volume Blood

Simultaneous quantification of multiple biomarker classes from blood is essential for improving diagnostic accuracy, yet current methods remain limited by low multiplexing capacity, reliance on separate instruments and workflows, and inconsistent signal readouts that hinder data integration. Here, we present FluoMag-dCoDe (Fluorescence-coded, Magnetic bead-enhanced digital Co-Detection of multi-analytes), a unified platform that converts diverse analytes into distinct fluorescence-coded DNA templates for multiplexed quantification in a single digital PCR (dPCR) reaction using a universal primer and TaqMan probe set. We demonstrate co-measurement of eight mRNA and three protein immune-response biomarkers in a two-color dPCR format. The platform achieves high quantitative fidelity with minimal cross-interference, showing strong concordance with single-plex RT-qPCR for mRNAs and superior analytical sensitivity to ELISA for proteins – including reliable detection of TRAIL where ELISA failed – from ~ 35 μL fingerstick-compatible blood volumes. By unifying mRNA and protein quantification in a single standardized readout while sustaining robust performance from low blood volumes, FluoMag-dCoDe establishes a scalable approach for high-dimensional biomarker analysis in precision diagnostics.