Emerging cfDNA technologies in glioblastoma through fragmentomics and sonobiopsy

Glioblastoma (GBM) is difficult to monitor using liquid biopsy because the tumor-derived fraction of circulating cell-free DNA (cfDNA), i.e., circulating tumor DNA (ctDNA), is often very low in plasma and because spatial and temporal heterogeneity complicate single-variant tracking. This narrative review critically compares mutation-based, methylation-based, fragmentomic, and signal-enhancing approaches, with explicit separation of evidence generated in GBM from findings derived from broader glioma, other central nervous system (CNS) tumor, or non-CNS cancer cohorts. A structured narrative search of PubMed, Google Scholar, and reference lists was used to identify clinically and methodologically informative studies, primarily from 2015 to 2025; earlier landmark studies were retained where necessary for historical or methodological context. Evidence was categorized as GBM-specific, mixed glioma/CNS, preclinical, or extrapolated from non-CNS cancer and assessed for analytical performance, sampling design, confirmation of tumor origin, biological plausibility, and stage of clinical validation. GBM-specific studies show that targeted mutation assays can be informative when a recurrent or tissue-defined alteration is available, but plasma sensitivity is highly assay-, variant-, disease-, and tumor-fraction dependent. CSF generally provides higher tumor-derived fractions and stronger tissue concordance than plasma, although it is less suitable for routine serial sampling. Methylation profiling offers multilocus and tissue-of-origin information, whereas fragmentomic analysis provides mutation-agnostic features; however, direct prospective GBM validation is substantially stronger for selected CSF genomic and methylation approaches than for plasma fragmentomics, for which several proposed advantages remain extrapolated from other cancers. Focused ultrasound (FUS)-enabled sonobiopsy can transiently enrich circulating biomarkers in early-phase studies, but reproducibility, optimal sampling time, tumor-specific signal gain, repeated-use safety, and clinical utility remain incompletely defined. Mutation-based, methylation-based, and fragmentomic assays should be viewed as complementary rather than hierarchical strategies. Their value depends on biofluid, disease setting, prior tissue information, and the clinical question. Sonobiopsy and other signal-enhancing methods remain investigational. Prospective multicenter validation, harmonized pre-analytical and analytical workflows, and evidence of clinical utility and cost-effectiveness are required before cfDNA-guided decisions can enter routine GBM care.