Urinary Cell-Free DNA Fragmentomics Detects Multiple Urologic Cancers and May Reduce Unnecessary Prostate Biopsies

Urinary cell-free DNA (ucfDNA) represents a completely noninvasive yet underutilized biospecimen for molecular diagnostics. Our group previously demonstrated that fragmentomic features of plasma cell-free DNA enable direct inference of underlying DNA methylation signals. However, the relationship between DNA methylation and fragmentomic patterns in urine, as well as their potential clinical utility, remains unexplored.

We developed FRAGmentomics-based Methylation Analysis for ucfDNA (termed uFRAGMA) and evaluated its performance using 400 ucfDNA samples from patients with bladder, prostate, and kidney cancers, as well as non-cancer subjects. The ucfDNA fragmentation patterns around cancer-associated cytosine-phosphate-guanine (CpG) sites were used for cancer detection and differentiation.

uFRAGMA demonstrated robust diagnostic performance across urological malignancies, achieving an area under the curve (AUC) of 0.98 for bladder cancer detection and 0.93 for kidney cancer detection. In the context of prostate cancer screening, uFRAGMA could potentially reduce unnecessary prostate biopsies by 67.5% among patients with elevated prostate-specific antigen (PSA) levels (>4 ng/mL), who would otherwise be at risk of overtreatment. Furthermore, we developed a tumor-of-origin classifier for urologic malignancies, attaining classification accuracies ranging from 71% to 92%.

Our findings from this proof-of-concept study suggest that fragmentomics analysis of ucfDNA may provide a clinically meaningful, noninvasive strategy for cancer detection, localization, and risk stratification of urologic cancers, with potential to refine existing clinical practices and reduce unnecessary tissue biopsies.