Integrated Plasma and Urinary Cell-free DNA Profiling Enables Noninvasive Molecular Detection from Ta to T4 Bladder Cancer

Background and Objective: Due to the heterogeneity of bladder cancer, minimally invasive molecular profiling may improve tumor characterization at the time of diagnosis. We evaluated whether integrated genomic and fragmentomic profiling of plasma and urinary circulating tumor DNA (ctDNA) detects BC-derived signals for diagnosis and disease stratification across all tumor stages. Methods: In this real-world cohort, 202 plasma and urine samples were obtained from 33 patients with non-muscle-invasive BC (NMIBC), mostly Ta tumors, and 15 patients with muscle-invasive BC (MIBC), as well as from 58 cancer-free controls. Low-coverage whole-genome sequencing was performed to assess ctDNA fragmentation, chromosomal instability and copy number variations. Matched tumor tissue was analyzed to evaluate concordance between liquid biopsy and tissue-derived molecular alterations. Key Findings and Limitations: Complementary genomic and fragmentomic profiling of cfDNA achieved detection rates of 75.8% in NMIBC patients and 91.7% in MIBC patients with paired plasma and urine. Distinct differences were observed between MIBC, NMIBC and cancer-free controls, consistent with increasing ctDNA signals during disease progression. Tumor tissue analysis confirmed BC-associated molecular alterations. Limitations include the single-center design and limited sample size. Conclusions and Clinical Implications: Multimodal profiling of plasma and urinary cfDNA enabled the detection of tumor-derived molecular signals for all bladder cancer stages, including early-stage disease. By integrating genomic and fragmentomic features, this minimally invasive approach provides molecular tumor characterization at the time of diagnosis and may support future risk-adapted diagnostic, therapeutic and surveillance strategies.