Chromato-Kinetic Fingerprinting Enables Multiomic Digital Counting of Single Disease Biomarker Molecules

Early and personalized intervention in complex diseases requires robust molecular diagnostics, yet the simultaneous detection of diverse biomarkers─microRNAs (miRNAs), mutant DNAs, and proteins─remains challenging due to low abundance and preprocessing incompatibilities. We present Biomarker Single-molecule Chromato-kinetic multi-Omics Profiling and Enumeration (Bio-SCOPE), a triple-modality, multiplexed detection platform that integrates both chromatic and kinetic fingerprinting for nanoscale molecular profiling through digital encoding. Bio-SCOPE achieves femtomolar sensitivity, single-base mismatch specificity, and minimal matrix interference, enabling precise, parallel quantification of potentially up to nine biomarkers in a single sample with single-molecule resolution. We demonstrate its versatility in accurately detecting low-abundance miRNA signatures from human tissues, identifying upregulated miRNAs in the plasma of prostate cancer patients, and measuring elevated interleukin-6 (IL-6) and <i>hsa</i>-miR-21 levels in cytokine release syndrome patients. By seamlessly integrating multiomic biomarker panels on a unified, high-precision platform, Bio-SCOPE offers a comprehensive approach for molecular diagnostics and precision medicine.