Abstract 7823: Ultrasensitive abnormal DNA methylation detection in plasma samples from patients with three different childhood sarcomas.

Abstract Introduction: Early and accurate detection of Ewing sarcoma (EWS), Osteosarcoma (OS), Rhabdomyosarcoma (RMS), is critical because these aggressive pediatric and adolescent malignancies progress rapidly, often metastasize at diagnosis, and require timely, targeted therapy to improve survival and reduce long-term morbidity. Aberrant cell-free DNA (cfDNA) methylation pattern profiling holds great promise for the non-invasive detection and monitoring of cancer. However, sarcomas generally shed less DNA into the bloodstream than other cancers, making them particularly challenging cases that require highly sensitive detection methods. Here, we used an ultrasensitive cfDNA methylation assay to detect abnormal methylation patterns in archival plasma samples from seven patients representing three sarcoma subtypes. We observed robust aberrant methylation patterns in all samples, highlighting the potential of epigenetic alterations as a non-invasive indicator of tumor burden. Methods: Longitudinal plasma samples were obtained from seven sarcoma patients: 3 patients with EWS 2 with OS and 2 with RMS. Samples were variously collected post-surgery and radiation treatment, when there was no evidence of disease, or at the time of relapse. cfDNA methylation was profiled using PredicineALERT™, a panel-based DNA methylation assay designed to detect abnormally methylated genomic fragments relative to a background model constructed from healthy-donor plasma. Importantly, only 1 ml of archival plasma stored in Acid-Citrate-Dextrose was used. Results: Differentially methylated fragments (DMFs) were detected across the genome in all sarcoma samples, with DMF counts markedly higher than those observed in healthy-donor controls. Sarcoma samples clustered distinctly away from the controls, with patient samples grouping together and showing evidence of subtype-specific DMF patterns. DMF dynamics also corresponded with disease progression in that signal decreased for patients in remission and increased in cases showing relapse. Conclusion: This study demonstrates the utility of cfDNA methylation profiling for sensitive, non-invasive detection and tracking of disease in childhood sarcoma patients. Future work will include generating corresponding tumor-tissue methylation libraries to confirm that plasma-derived methylation signatures are subtype-specific and biologically representative and evaluation of an extend longitudinal biobank of pediatric sarcoma patients. Citation Format: Giancarlo Bonora, Ziqi Zhu, Binggang Xiang, Kemin Zhou, Pan Du, Soumya Turaga, Glenson Samuel, Andrew Godwin. Ultrasensitive abnormal DNA methylation detection in plasma samples from patients with three different childhood sarcomas 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 7823.