Clinical utility of comprehensive genomic profiling versus Oncomine Dx target test in pathological stage II–III non-small cell lung cancer

Abstract

Abstract The next-generation sequencing (NGS)–based Oncomine Dx Target Test (ODxTT) is the standard tool for guiding postoperative adjuvant therapy in patients with non-small cell lung cancer (NSCLC) in Japan. To advance precision oncology, we evaluated the clinical utility of an in-house comprehensive genomic profiling (CGP) assay, Rapid-Neo, as a complementary approach to ODxTT in surgically resected NSCLC. Patients with pathological stage II–III NSCLC who underwent anatomical surgical resection between December 2019 and May 2024 were included. Resected specimens underwent genomic analysis using both ODxTT and Rapid-Neo CGP. We evaluated the mutational concordance and the frequency of additional actionable alterations identified by CGP. Among 68 eligible patients, driver mutation results were concordant in 64 (94.1%) cases. Crucially, CGP rescued one patient for targeted therapy by detecting an EGFR mutation where ODxTT failed due to insufficient DNA. CGP also identified rare EGFR variants not covered by ODxTT in two cases, although it failed to detect a RET fusion in one patient. Furthermore, CGP revealed additional actionable alterations, such as tumor suppressor gene mutations, in 57 patients (83.8%). Our in-house CGP shows high concordance with ODxTT and serves as a powerful complementary tool. These findings support a strategic testing algorithm where CGP is incorporated for patients with negative or inconclusive ODxTT results, or at the time of recurrence, to maximize opportunities for individualized therapy in resected NSCLC.