BIOM-44. UTILIZING ALIGNMENT-FREE CLASSIFICATION OF CELL-FREE DNA SEQUENCING READS TO MONITOR TUMOR BURDEN IN PRIMARY BRAIN TUMORS

Abstract Cell-free DNA (cfDNA) are short acellular fragments of DNA found in the circulation. It has emerged as a promising diagnostic tool for the early detection and follow-up of tumor-derived biomarkers in many cancer types, but primary brain tumors remain challenging to monitor using this approach. Allegedly limited by the blood-brain-barrier, detection rates of tumor-derived cfDNA range from 25-50% in plasma and 60-80% in CSF samples using conventional read alignment and variant calling approaches, sowing doubt in the utility of cfDNA-based monitoring of primary brain tumors. In this study, we sought to investigate the effectiveness of a novel alignment-free read classifier to detect tumor-derived cfDNA (ctDNA) sequencing reads and quantify tumor burden. Our dataset comprises plasma (n = 101) and CSF (n = 15) samples collected from n = 24 patients with primary brain tumors, including both adult (n = 8) and pediatric (n = 16) patients. In our cohort, n = 6 patients (25%) were diagnosed with a diffuse midline glioma, n = 13 (54%) high-grade glioma, n = 4 (17%) medulloblastoma, and n = 1 (4%) ependymoma. Applying read classification, we detected ctDNA reads at varying abundances across all cfDNA samples examined (n = 116/116, 100%), highlighting the potential to track sequence-based tumor signals from liquid biopsies using our approach. At several plasma timepoints across patients, an increase in ctDNA signal correlated with clinical progression and a decrease in signal aligned with the absence of residual tumor. In several patient datasets, ctDNA signal was higher in CSF samples compared to plasma, consistent with findings reported in the literature. Our method has the potential to accurately and specifically quantify tumor signals in cfDNA, offering a sensitive and mutation-agnostic approach for tracking tumor dynamics across various brain tumor subtypes. Further investigations with larger patient cohorts and more comprehensive data analysis to validate these findings are actively underway.