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Updated: May 31, 2026
Cell-Free DNA Integrity Analysis in Urine Samples
Published on: January 5, 2017
Urinary DNA methylation biomarkers for bladder cancer diagnosis: a single center case-control study
Chao Li1, Rongjin Fang1, Jiqian Wang1
1Department of Urology, Xiamen Haicang Hospital, Xiamen, Fujian, China.
Background:
Noninvasive detection of bladder cancer remains challenging because many urine tests trade sensitivity for specificity. We evaluated whether a biologically grounded, complementary three-gene methylation panel measured in urine could improve diagnostic performance.
Methods:
We conducted a single-center 1:1 matched case-control study using clinically relevant urine samples. Urine DNA was subjected to bisulfite conversion and quantitative methylation analysis targeting three gene loci (TRPS1, HAND2, ZNF154). We evaluated the performance of individual genes and a combined panel, reporting sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), area under the receiver operating characteristic curve (AUC and ROC), and 95% confidence intervals (CI).
Results:
One hundred and seventy-two subjects (86 cases and 86 controls) with a mean age of 60.24 ± 12.54 and 59.70 ± 12.75 years old were included. TRPS1 showed the highest sensitivity at 0.97 with specificity 0.791, yielding PPV 0.82 and NPV 0.97; HAND2 maintained strong sensitivity (0.95) but lower specificity (0.56), with PPV 0.68 and NPV 0.92; and ZNF154 had sensitivity 0.93 with the lowest specificity (0.35), corresponding to PPV 0.59 and NPV 0.83. A combined methylation assay where all three genes are methylation-positive significantly improved specificity to 0.95 while maintaining acceptable sensitivity (0.86), resulting in the highest positive predictive value (0.95) and a robust negative predictive value (0.87). The ROC analysis showed strong diagnostic performance for all three urinary methylation markers: TRPS1 had the highest AUC at 0.98 (95% CI: 0.96-0.99), followed by HAND2 at 0.90 (95% CI: 0.85-0.95) and ZNF154 at 0.82 (95% CI: 0.76-0.89).
Conclusions:
A urine-based three-gene methylation panel (TRPS1, HAND2, ZNF154) demonstrates promising accuracy for bladder cancer detection, with complementary signals improving specificity. Findings are constrained by a single-center cohort and moderate size and require external, multi-center validation in the future.
