Urine cfDNA workflow for epigenomic profiling.

Urine cell-free DNA (cfDNA) holds great promise as a non-invasive biomarker for diagnosis, prognosis and treatment monitoring of diseases. However, its clinical utility is challenged by high nuclease activity and rapid degradation, necessitating an optimized urine cfDNA workflow. We evaluated a workflow for urine cfDNA methylation and fragmentation profiling, comparing PAXgene Urine Technology, with Streck Urine Preserve and unstabilized urine, using enzymatic methyl sequencing of cfDNA from healthy individuals, across multiple urine storage time points (immediate, 6 h, and 72 h). Urine stabilization significantly improved cfDNA yield and preserved cfDNA fragment sizes, while unstabilized samples exhibited marked degradation and reduced sequencing quality. Methylation analysis revealed high concordance between stabilized samples, with subtle divergence after 72 h. In contrast, unstabilized samples showed widespread methylation changes. Biological patterns were retained in stabilized urine cfDNA. Our study underscores the importance of well-designed (pre)analytical urine workflows to allow urine cfDNA (epi)genomic analyses.

• Type: Epigenetics
• Archive: European Genome-phenome Archive (EGA)