Fusion Gene Detection in Driver Mutation-Negative Melanomas Using RNA-Based Anchored Multiplex Polymerase Chain Reaction

Abstract

Advanced melanoma is typically treated with immune checkpoint inhibitors (ICIs) and targeted therapies. However, their efficacy is limited in acral and mucosal melanomas, which are more prevalent in non-White populations and often exhibit low tumor mutational burden and lack BRAF mutations. Fusion genes, widely used as therapeutic targets in other cancers, may represent alternative targets in these melanoma subtypes. This study aimed to detect fusion genes in Japanese melanomas lacking major driver mutations (BRAF, RAS, NF1, or KIT) using a custom RNA-based anchored multiplex polymerase chain reaction (AMP) panel. RNA extracted from 14 tumors, primarily formalin-fixed paraffin-embedded specimens, was analyzed using a custom Archer FUSIONPlex panel. Libraries were successfully generated in 80% of cases, and two in-frame fusions—MAD1L1::BRAF and CIC::MEGF8—were identified (17%). MAD1L1::BRAF retained the BRAF kinase domain and may be targetable by MEK inhibitors. CIC::MEGF8, a novel fusion in melanoma, may result in transcriptional dysregulation through CIC loss of function. This Method paper outlines the AMP workflow, including troubleshooting strategies and quality control criteria, and demonstrates its applicability to clinical samples. Our findings support the utility of RNA-based fusion detection in driver-negative melanomas and the potential of fusion genes as actionable targets.