Abstract 4549: Impact of an ultrasensitive ctDNA test on MRD detection in real world clinical patient testing
Authors: Rachel Marty Pyke, Steven Dea, Fábio C.P. Navarro, Charles W. Abbott, Sherif El-Refai, Yi Chen, Janet Lai, Gabor Bartha, John M. Lyle, Jason Harris, Georges Azzi, Sean M. Boyle, Richard O. Chen
Journal: Cancer Research (2025)

Abstract Circulating tumor DNA (ctDNA) is a non-invasive biomarker increasingly used to detect residual or recurrent disease and to monitor patient response to therapy. However, there is a need for more sensitive tests that can achieve earlier detection of disease. The NeXT Personal® Dx (NPDx) ctDNA MRD test uses paired tumor and normal whole genome sequencing (WGS) to design a bespoke panel of up to ∼1800 variants and relies on advanced noise suppression to achieve ultrasensitive detection down to ∼1 part per million (PPM) of ctDNA (1x10-6 tumor fraction) with high analytical specificity (&amp;gt;99.9%). Here, we describe the real world performance for a set of cancer patients (&amp;gt;15 cancer types) profiled using the NPDx test. For this study we have included 1693 plasma timepoints from 700 patients (range of 1 to 21 timepoints per patient), with the highest proportion of patients having breast, lung or colorectal cancer. The plasma timepoints have a median LOD of 1.93 PPM (IQR:1.55-2.78 PPM). Notably 41.6% of MRD+ samples were detected at low traces of ctDNA below 100 PPM, in the ultrasensitive range; moreover, a majority (50.4%) of the ultrasensitive detections are at or below 15 PPM, further highlighting the impact of a highly sensitive assay for MRD profiling. We also examined performance in specific challenging situations. NPDx tests performed well with challenging FFPE tumor samples (low tumor DIN &amp;lt;=3 indicating some sample degradation or low tumor fraction &amp;lt;=30%), achieving low LODs (median = 2.97 and 2.56 PPM, respectively). The WGS-based panel design allowed NPDx to achieve ultrasensitivity on low TMB tumors (&amp;lt;=2 mutation/MB, median LOD = 2.90 PPM) through utilization of variants from intergenic regions (95% MRD panel variants were from non-exonic regions) that would largely be unavailable to exome-based tests. Testing was performed across a wide range of cell free DNA (cfDNA) inputs (range 2-30 ng, median = 14 ng). Even with low cfDNA inputs (&amp;lt;=3ng, 5.25% of cohort), NPDx still achieved a low median LOD of 2.63 PPM. Two case studies demonstrate the impact of ultrasensitive MRD testing with patients. A 50-year-old woman with stage 1B endometrial cancer was monitored using NPDx following hysterectomy and brachytherapy, and ctDNA was detected in the ultrasensitive range (&amp;lt;50 PPM in this case). Reflex imaging revealed a new nodule leading to additional therapy and ctDNA clearance. In a second case, a woman in her 70s with stage 1 HER2+ breast cancer who underwent standard lumpectomy and adjuvant treatment was found with persistent low levels of ctDNA (between 25-30 PPM) detected with NPDx over a period of five months. Reflex imaging revealed a new nodule leading to additional radiation therapy, with plans for chemotherapy. These cases illustrate how NPDx's ultrasensitive detection capabilities can impact patient management in a real world setting. Citation Format: Rachel Marty Pyke, Steven Dea, Fábio C.P. Navarro, Charles W. Abbott, Sherif El-Refai, Yi Chen, Janet Lai, Gabor Bartha, John M. Lyle, Jason Harris, Georges Azzi, Sean M. Boyle, Richard O. Chen. Impact of an ultrasensitive ctDNA test on MRD detection in real world clinical patient testing [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 4549.