Abstract
BACKGROUND: Rearranged during transfection (RET) fusion is a key driver in non-small cell lung cancer (NSCLC). Accurate detection is essential for targeted therapeutic strategies, and its reliability varies with the diagnostic methods employed. This study systematically compares the concordance of various molecular profiling techniques for identifying RET fusions in early-stage NSCLC. METHODS: This retrospective study included 40 NSCLC patients with RET fusions (RET+) identified by DNA sequencing (DNA-seq). Comprehensive detection was conducted using fluorescence in situ hybridization (FISH) and RNA sequencing (RNA-seq), incorporating both targeted RNA-seq and whole-transcriptome sequencing (WTS). Clinical and molecular features were evaluated for associations with fusion types. RESULTS: Patients were predominantly female (67.5%) and never-smokers (87.5%), with a median age of 53 years. All patients underwent FISH, while 39 cases underwent RNA-seq, with one excluded due to RNA quality control failure. The most common fusions were KIF5B::RET and CCDC6::RET (89.7%), alongside noncanonical fusion partners such as ERC1 (5.0%) and CCDC186 (2.5%). WTS achieved a 79.5% (31/39) RET+ detection rate. Targeted RNA-seq uncovered an additional five RET+ cases missed by WTS. Concordance rates for fusion detection were 92.3% between DNA-seq and RNA-seq, 84.6% between RNA-seq and FISH, and 82.5% between DNA-seq and FISH. Interestingly, patients exhibiting nonreciprocal RET translocations were significantly younger (P=0.03) and presented a lower Ki67 proliferation index (P=0.03). CONCLUSIONS: Our findings underscore the complexity of RET fusion characterization and the necessity for a comprehensive diagnostic approach, which enhances the identification of both canonical and noncanonical alterations. This supports precision oncology initiatives aimed at optimizing treatment outcomes for RET+ NSCLC patients.