Validation of NTRK Fusion Detection Using an Ultrarapid, Fully Automated Cartridge-Based PCR Assay

NTRK gene fusions are rare but actionable oncogenic drivers, and their timely detection is critical for guiding tyrosine receptor kinase-targeted therapy. Conventional methods, such as immunohistochemistry, fluorescence in situ hybridization, RT-PCR, and next-generation sequencing (NGS), can be limited by variable sensitivity, cost, and slow turnaround. The Idylla GeneFusion Assay-a rapid, fully automated cartridge-based platform that infers NTRK1/2/3 fusions through 3' to 5' expression imbalance-was evaluated across a retrospective, fusion-enriched cohort of 193 tissue and cytology specimens from The MD Anderson Cancer Center and Mayo Clinic, all with prior RNA-based NGS profiling. Of 108 NTRK gene fusions detected by NGS, 67 (62.0%) were reported as detected by Idylla. Restricting analysis to definitive detected and not detected results (n = 147), the assay demonstrated high concordance with NGS, with positive and negative percentage agreement of 95.7% and 100%, respectively, and strongest performance for NTRK3. Including equivocal results as positive increased sensitivity (positive percentage agreement, 96.3%) with a modest specificity reduction (negative percentage agreement, 93.9%; n = 190). Most invalid results reflected RNA degradation and resolved with freshly cut sections. These findings support the Idylla GeneFusion Assay as a rapid, practical frontline tool for NTRK fusion detection, particularly with limited tissue or need for expedited decisions, with reflex NGS recommended for equivocal cases or fusion partner identification.