Circulating tumor DNA in body fluids for molecular characterization of cancers beyond tissue and blood

Liquid biopsy using circulating tumor DNA (ctDNA) is increasingly used for cancer profiling and monitoring, but blood-based analysis may not capture tumor heterogeneity across anatomical compartments. We evaluated cell-free DNA from cerebrospinal (n = 7), pleural (n = 11), pericardial (n = 1), and ascitic (n = 26) fluids from 45 patients with advanced cancer, comparing molecular findings with matched tissue, blood, and cytology where available. Oncogenic alterations were detected in 87% of body fluid samples, with a median variant allele frequency of 3.15%. TP53 (49%), EGFR (18%), and KRAS (18%) were the most frequently altered genes, and ESCAT tier IA alterations occurred in 31.1% of patients. In six patients (13.3%), potentially targetable alterations were detected in body fluids but not in blood and/or tissue. Among five cytology-negative samples, four were ctDNA positive. These findings support body fluid ctDNA profiling as a complementary approach to tissue, plasma, and cytology, thereby warranting prospective validation.