In 139 clinical tumor samples with orthogonal FISH validation at MET, ERBB2, and MTAP, PScnv showed improved accuracy and robustness over existing methods that do not require patient-matched normal samples, provided that a pre-built PoN cohort is available.<h4>Availability</h4>Source code is available for academic use at https://github.com/lvws/PScnv. This evidence concerns the gene MTAP and neoplasm.