e20021 Background: Recent studies substantiate the circulating tumor cells (CTCs) as biological markers for the cancer progression and metastasis. Nevertheless, isolating CTCs is challenging due to their relatively low abundance in the bloodstream. The innovative CTC detection and characterization method, iDXGate TO by BeyondDx, has overcome these challenges, facilitating the seamless identification of genomic alterations, deepening understanding of the functions of CTCs in cancer progression. Methods: In this study, a total of 50 patients diagnosed with early-stage lung cancer, without a history of anticancer therapy at Seoul National University Bundang Hospital from August 2023 to December 2023 participated to compare the genomic alterations between primary cancer tissue and CTCs. Resected tumor tissues and whole blood were collected during surgery, and DNA was freshly extracted and transferred. iDXGate TO, designed specifically for early-stage lung cancer, employs EpCAM, EGFR, and HER2 Biomarkers for targeted capture of circulating tumor cells (CTCs). Targeted sequencing was performed on the genomic DNA extracted from both cancer tissues and CTCs of each patient. Out of the CTC samples, 16 were excluded due to insufficient DNA. Results: Detailed analysis involved sequencing data from 34 CTC samples and 50 tissue samples. CTCs exhibited 100% (34/34) likely pathogenic alterations, compared to 42.00% (21/50) in tissues. Predominant genomic alterations in CTCs included MSH6 (100.0%), FANCE (91.2%), CDK12 (85.3%), HNF1A (85.3%), AXIN2 (82.4%), and FLCN (79.4%). Tissues were frequently associated with EGFR (40.0%), TP53 (34.0%), FAT1 (18.0%), LRP1B (16.0%), NOTCH3 (16.0%), and KMT2D (16.0%). Alterations in MSH6, FANCE, and CDK12 underscore the critical role of DNA repair mechanisms in CTCs, contributing to genomic instability. Alterations in HNF1A suggest implications in metabolic regulation, influencing the tumor microenvironment. Alterations in AXIN2 and FLCN hint at involvement in Wnt signaling and cellular growth regulation, potentially contributing to tumorigenesis. Conclusions: The iDXGate TO selectively identifies tumor-specific circulating tumor cells (CTCs) and explores a new realm of liquid biopsy through molecular and phenotypic integrated analysis. Detection of altered genes in CTCs highlights the molecular heterogeneity. Further exploration of these genetic alterations could offer valuable insights into the underlying mechanisms propelling cancer progression. Additionally, CTCs could serve as pivotal biomarkers for real-time monitoring of tumor evolution, potentially guiding the development of targeted therapies tailored to the specific genomic landscape of CTCs.