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 TRK-targeted therapy. Conventional methods such as immunohistochemistry, fluorescence in situ hybridization, reverse transcription polymerase chain reaction, and next-generation sequencing can be limited by variable sensitivity, cost, and slow turnaround times. We evaluated the Idylla GeneFusion Assay—a rapid, fully automated cartridge-based platform that infers NTRK1/2/3 fusions through 3'–5' expression imbalance—across a retrospective, fusion-enriched cohort of 193 tissue and cytology specimens from MD Anderson Cancer Center and Mayo Clinic, all of which had prior RNA-based next-generation sequencing profiling. Of 108 NTRK gene fusions detected by next-generation sequencing profiling, 67 (62.0%) were reported as " Detected " by the Idylla GeneFusion Assay. When analysis was restricted to definitive " Detected " and " Not Detected" results (n=147), the assay demonstrated high concordance with next-generation sequencing, with positive percent agreement and negative percent agreement of 95.7% and 100%, respectively, with the strongest performance for NTRK3 . Including " Equivocal " results as positive increased sensitivity (positive percent agreement 96.3%) with a modest reduction in specificity (negative percent agreement 93.9%, n=190). Most " Invalid " results were attributable to RNA degradation and resolved with freshly cut sections. These findings support the Idylla GeneFusion Assay as a rapid and practical frontline tool for NTRK fusion detection, particularly in settings with limited tissue or need for expedited decision-making, with reflex next-generation sequencing recommended for " Equivocal " cases or when fusion partner identification is required.