A ligase-mediated encoding system for rapid, multiplex single-nucleotide variant detection

Accurate detection of single-nucleotide variants (SNV) is critical for genetic disease diagnosis and cancer profiling, yet existing methods often lack the combination of specificity, multiplexing capacity, and rapid workflow required for clinical application. Here, we report a ligase-mediated encoding (LmCo) system that integrates ligase chain reaction (LCR) for single-base discrimination with hybridization chain reaction (HCR) for signal amplification and multicolor fluorescence encoding. The system achieves a detection limit of 0.1626 fM and enables reliable identification of mutant alleles at frequencies as low as 0.0001% variant allele fraction, substantially outperforming conventional methods. LmCo simultaneously detects six or more SNV targets in a single closed-tube reaction with minimal crosstalk, demonstrates robust stability in complex matrices, and achieves 96.7% accuracy in simulated clinical samples. This platform provides a rapid, sensitive, and highly multiplexed solution for SNV detection in molecular diagnostics and precision medicine.