Abstract 1129: Analytical and clinical sensitivity of tumor-informed and tumor-naïve ctDNA residual disease detection during neoadjuvant immune checkpoint inhibition in resectable cancers

Abstract Background: Circulating tumor DNA (ctDNA) has become a key biomarker for minimally invasive detection of residual disease during neoadjuvant immunotherapy. However, its integration into routine clinical decision-making remains limited by modest sensitivity and the practical constraints of current assays. Methods: We performed multi-modality matched tumor, white blood cell (WBC), and cell-free DNA (cfDNA) next-generation sequencing (NGS) of 520 biospecimens (56 tumor, 105 WBC, 359 plasma) from 32 patients with operable gastroesophageal (GE) cancer (NCT03044613) and 30 patients with resectable pleural mesothelioma (PM; NCT03918252). ctDNA residual disease analyses were performed at baseline, before each cycle of neoadjuvant immunotherapy, and preoperatively. For the tumor-informed approach, whole genome sequencing (WGS) data of matched tumor, WBC, and cfDNA (80x, 40x, and 30x coverage) were integrated through a random forest machine learning model and calibrated using a reference set of noncancerous cfDNA to determine cfDNA tumor fraction (TF). In parallel, we performed orthogonal tumor-naïve, fixed-gene-panel targeted error-correction NGS of cfDNA and WBC (30,000x), filtering germline and clonal hematopoiesis variants. Results: Overall, the tumor-informed assay showed significantly higher sensitivity, evidenced by a higher ctDNA detection rate at all evaluated timepoints compared to the tumor-naïve assay. In the GE cohort, the tumor-informed assay detected ctDNA for 22 of 25 (88%), 20 of 25 (80%), 18 of 26 (69%), and 5 of 21 (24%) patients at baseline, cycle 2, cycle 3, and preoperatively, respectively. By contrast, 13 of 30 (43%), 12 of 30 (40%), 11 of 30 (37%), and 5 of 25 (20%) had detectable ctDNA by the tumor-naïve assay at corresponding timepoints. In detectable cases, cfDNA TFs were highly concordant between approaches (R = 0.85, p 0.001). In the PM cohort, 12 of 26 (46%), 11 of 25 (44%), 7 of 21 (33%), and 13 of 25 (52%) had ctDNA detected by the tumor-informed assay at baseline, cycle 2, cycle 3, and preoperatively, respectively. Having demonstrated higher analytical sensitivity with the tumor-informed approach in the GE cohort, we applied the tumor-naïve approach only in cases with detectable ctDNA by the tumor-informed assay. Of these, 6 of 14 (43%), 6 of 13 (46%), 5 of 8 (63%), and 7 of 15 (47%) had ctDNA detected at corresponding timepoints. cfDNA TFs were concordant at timepoints when ctDNA was detectable by both approaches (R = 0.63, p = 0.002). Tumor-informed ctDNA residual disease preoperatively was associated with shorter progression-free survival (log-rank, p = 0.0059). Conclusion: Tumor-informed WGS-based liquid biopsies reliably measure ctDNA residual disease during neoadjuvant immunotherapy, demonstrating greater sensitivity compared to a tumor-naïve approach, supporting their clinical value. Citation Format: Paul K. Lee, Blair V. Landon, Ezgi Oner, Jaime Wehr, Qiong Meng, Amna Jamali, Mimi Najjar, Gavin Pereira, Samira Hosseini-Nami, Rachel Keogh, Chen Hu, Ronan J. Kelly, Joshua E. Reuss, Patrick M. Forde, Mark Sausen, Vincent K. Lam, Robert B. Scharpf, Noushin Niknafs, Valsamo (Elsa) Anagnostou. Analytical and clinical sensitivity of tumor-informed and tumor-naïve ctDNA residual disease detection during neoadjuvant immune checkpoint inhibition in resectable cancers abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 1129.