Innovative biomarker discovery: A non-invasive, comprehensive tumor characterization approach with plasma and urine from breast cancer patients

Background: Circulating cell-free DNA (cfDNA) profiling from blood plasma has demonstrated considerable potential for clinical applications in breast cancer, yet urinary cfDNA remains less explored. In a previous pilot study of plasma-derived and matching urinary cfDNA (n=30), we have found plasma and urines may be complementary liquid biopsy samples for molecular profiling. Methods: In this study, we expand to a larger patient cohort. To enhance the sensitivity of the assay, we utilized direct preservation with Urinary Analyte Stabilizer, which led to improved yield and quality of cfDNA from urine samples. We conducted an extensive analysis of 150 matched plasma and urine samples from breast cancer patients utilizing QIAGEN's QIAseq Human Breast Cancer Panel, Element Biosciences' Aviti system, CLC secondary analysis and QCI Interpret bioinformatic solutions.Results: The cfDNA levels in urine were increased compared to plasma but with minimal correlation between the two body fluids. Compared to the pilot study the validation study achieved improved sequencing precision and enhanced variant detection and identification. Both cfDNA sources led to quantitatively and qualitatively comparable results with a median number of 137 vs. 131 somatic variants in plasma vs. urine. Further, 53% of the variants had a super low abundance with VAF< 3%. The variants were similarly distributed in matching plasma and urinary cfDNA samples (5 vs. 4% pathogenic, 15 vs. 17% likely pathogenic, 73 vs. 76% VUS). We found 571 shared variants among both body fluids with a median of 14 shared pathogenic variants per sample. Conclusion: Unlocking the clinical utility of urinary cfDNA as a non-invasive approach could redefine liquid biopsy strategies, offering a more comprehensive and dynamic view of tumor evolution and therapeutic response.