Spatial and temporal tumor heterogeneity representation in liquid biopsies of pediatric precision oncology patients

Biopsies of high-risk pediatric tumors are challenging and often provide limited molecular insights due to spatial and temporal heterogeneity. Liquid biopsies, particularly cell-free DNA (cfDNA) analysis, offer a non-invasive alternative to detect tumor subclones and refine diagnostics. This study evaluates cfDNA as a liquid biopsy analyte to improve non-invasive tumor characterization and detect mutations. As part of the INFORM program, cfDNA from 130 patients was analyzed using optimized extraction, whole-genome, methylome, whole-exome, and targeted sequencing. cfDNA data were compared with tissue analyses to improve the characterization of tumor heterogeneity. Low-coverage whole-genome sequencing (lcWGS) showed high sensitivity for circulating tumor DNA (ctDNA) detection. Combining fragment length analysis with copy-number-variation (CNV) profiling improved plasma-based tumor detection, enabling non-invasive identification in 93% of patients. In a Wilms tumor patient, liquid biopsy identified subclones that were missed by tissue biopsy. cfDNA analysis provides insights into tumor heterogeneity, detects previously hidden subclones, and may reveal new therapeutic targets.

Publication History

Article published online:
09 May 2025