Clinically relevant somatic variants and genomic discordance between primary tumors and mediastinal lymph nodes in lung adenocarcinoma

Background: Histopathological evaluation, TNM classification, and mediastinal staging via endobronchial ultrasound-guided transbronchial needle aspiration provide essential guidance for therapeutic decision-making in non-small cell lung cancer (NSCLC). Genomic profiles of primary tumors (PT) and matched mediastinal lymph nodes (MLN) can uncover occult metastases, refine recurrence risk assessment, and support personalized treatment strategies in lung adenocarcinoma (LUAD). Objectives: The study aimed to investigate clinically relevant somatic variants in formalin-fixed, paraffin-embedded (FFPE) PT and scrapings of MLN cytological slide samples using next-generation sequencing (NGS) and correlated the findings with overall survival (OS). Design: We retrospectively analyzed the genomic profile of PT and MLN from Brazilian LUAD patients between 2013 and 2020. Methods: Genomic DNA (gDNA) was extracted from PT and MLN matched samples of 32 patients ( n = 64). Targeted NGS was performed using the SureSelect XTHS2 panel. We analyzed OS using Kaplan–Meier curves, and risk factors for mortality using univariate and multivariate Cox regression models. Results: Clinically significant or potentially significant variants were identified in 72% of PT and 75% of MLN, totaling 46 and 51 variants, respectively. The most frequent variants in PT involved EGFR (39.3%), TP53 (28.6%), ATM , and KRAS (21.4% in both), whereas in MLN, EGFR (35.7%), TP53 (32.1%), KRAS and BRAF (14.3% in both), and ATM (10.7%) have predominated. Co-mutations were detected in 31.3% of PT and 43.8% of MLN, with variant discordance between PT-MLN in 82.2% of cases. Conclusion: Cox regression analysis demonstrated that the presence of co-mutations in MLN was a co-factor associated with poorer OS, while no significant associations were observed for PT variants. These findings highlight distinct genomic profiles between PT and MLN. Integrating the molecular profile of MLN into staging may improve prognostic accuracy and guide treatment decisions in LUAD patients.