Abstract 5882: A novel NGS-based assay in kit format for tumor-independent cancer monitoring, and evaluation of patient treatment response using cfDNA genomic alteration and methylation duo analysis
Authors: Tali Azenkot, Grace Zhao, Heng Wang, Xiaomu Chen, Margherita Corioni, Michael Ruvolo, Teressa Celma, Jeff Pawelek, Aswati Aravind, Douglas Roberts, Yun Bao, Bram Herman, Annie Wu, William Mitchell, Kathryn Gold, Lyudmila Bazhenova, Shengrong Lin, Sandip Patel
Journal: Cancer Research (2025)

Abstract Introduction: While circulating tumor DNA-based tests have shown promise in evaluating treatment response, predicting prognosis, and detecting measurable residual disease, tumor-informed personalized strategies have limitations. For example, the need for large tumor samples and the complexity and high cost of personalized testing can be barriers to clinical use. Commercially available genomic and methylation tumor-independent assays require large panels and sample splitting, further limiting their practicality. Both these assays require samples to be sent to centralized CLIA-certified labs. To address these challenges, we explored the Agilent Avida target enrichment technology in a small sample of patients with non-small cell lung cancer (NSCLC). This kit-based solution reduces sequencing costs, is compatible with automation systems like the Agilent Bravo NGS Workstation, and enables decentralized, faster molecular analysis. Methods: We applied the Agilent Avida circulating cell-free DNA (cfDNA) genomic alteration and methylation combined analysis for tumor-independent cancer monitoring in patients with NSCLC. First, we demonstrated the differential hypermethylation cancer-specific signal in 4 different lung cancer tumors, with low background noise in normal lung tissues, non-cancerous pathological lung tissue, control peripheral blood mononuclear cells, and cfDNA. We then showed feasibility of this cfDNA technology in patients with stage I through III NSCLC. In 4 patients with stage III NSCLC, plasma samples were collected before and 1-3 months after initiating immunotherapy treatment to assess whether the assays correlated with known clinical and imaging markers of disease response. Results: Using 1 mL of plasma from NSCLC patients, we detected cancer in 8 of 10 stage I patients and 10 of 11 stage II patients. Fifteen of 16 control samples were below the cutoff threshold. Among 4 patients with stage III NSCLC, we performed cfDNA Duo analysis, capturing both DNA mutations and methylation information from one input without sample splitting. The combined genomic and methylation analysis provided information on actionable mutations and tumor mutation burden for these patients. The overall methylation signal correlated with CT imaging-based tumor changes for most cases. Conclusion: Our results demonstrate the feasibility of the Agilent-Avida DNA/methylation DUO kit for tumor-independent cancer monitoring in patients with NSCLC undergoing immunotherapy treatment. Citation Format: Tali Azenkot, Grace Zhao, Heng Wang, Xiaomu Chen, Margherita Corioni, Michael Ruvolo, Teressa Celma, Jeff Pawelek, Aswati Aravind, Douglas Roberts, Yun Bao, Bram Herman, Annie Wu, William Mitchell, Kathryn Gold, Lyudmila Bazhenova, Shengrong Lin, Sandip Patel. A novel NGS-based assay in kit format for tumor-independent cancer monitoring, and evaluation of patient treatment response using cfDNA genomic alteration and methylation duo analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 5882.