by Justin Jackson , Medical Xpress

DNA, which has a double-helix structure, can have many genetic mutations and variations. Credit: NIH

Researchers led by the University of Ulsan College of Medicine, Korea, have checked the performance of a noninvasive urinary DNA methylation test for bladder cancer diagnosis.

Findings indicate that the test demonstrated 89.2% sensitivity and 87.8% specificity for detecting high-grade or invasive bladder cancer, surpassing the nuclear matrix protein 22 (NMP22) and urine cytology tests in sensitivity still suboptimal for reliable diagnostic testing.

Bladder cancer is the fourth most diagnosed cancer in men in the United States, with an estimated 83,190 new cases annually. Early detection is critical to preventing muscle-invasive bladder cancer, which often requires radical cystectomy and increases mortality risk.

Cystoscopy, while invasive and comparatively expensive, remains the gold standard for diagnosis. Urine cytology is a widely used adjunct diagnostic tool, but its clinical use is restricted due to limited sensitivity in detecting low-grade tumors and high false negatives.

In the study, “Urinary DNA Methylation Test for Bladder Cancer Diagnosis,” published in JAMA Oncology, researchers enrolled 1,099 participants aged 40 years or older with hematuria who underwent cystoscopy within three months.

Urine samples were collected before cystoscopy and analyzed for PENK methylation, NMP22, and cytology. Pathological confirmation of bladder cancer was conducted by an independent pathologist blinded to the urine test results. Sensitivity, specificity, positive predictive value, and negative predictive value were evaluated for each diagnostic method.

Among the 1,099 participants, 219 were ultimately diagnosed with bladder cancer (via cystoscopy), including 176 with high-grade or invasive disease.

Urinary DNA methylation testing identified 157 of 176 cases of high-grade or invasive bladder cancer, with 19 false negatives. It achieved a sensitivity of 89.2% (95% CI, 84.6–93.8%) and a specificity of 87.8% (95% CI, 85.6–89.9%), implying that 113 (12.2%) would have received a false positive cancer result. For all stages of bladder cancer, sensitivity was 78.1% (95% CI, 72.6–83.6%), and specificity was 88.8% (95% CI, 86.7–90.8%).

The test’s negative predictive value for high-grade or invasive bladder cancer was 97.6%, while the positive predictive value was 61.3%, meaning that about 61 out of 100 positive test results truly reflect the presence of the cancer, with roughly 39% being false positives.

Compared to the NMP22 and urine cytology tests, the urinary DNA methylation test showed significantly higher sensitivity. The NMP22 test had a sensitivity of 51.5% for high-grade or invasive bladder cancer, while urine cytology had a sensitivity of 39.7%.

Both alternative tests had higher specificity than the urinary DNA methylation test, with urine cytology achieving 99.5% specificity (95% CI, 99.0–100%) for patients without high-grade or invasive bladder cancer.

The study also evaluated combinations of the urinary DNA methylation test with the NMP22 and urine cytology tests. When combined with NMP22, sensitivity increased to 91.8% (95% CI, 87.7–95.9%), but specificity decreased to 81.6% (95% CI, 79.0–84.2%). Similar results were observed when combining the urinary DNA methylation test with urine cytology.

Relying on the urinary DNA methylation method test alone, out of 1,099 individuals, around 952 would have received a correct diagnosis. 48 individuals (with all cancer types) would have been falsely reported as cancer free, 99 to 113 would have been falsely diagnosed with cancer.

Based on the study data, there is a 14-patient difference between calculations derived from the positive predictive value (PPV) and those based on specificity. A PPV of 61.3% with 157 true positives among high-grade or invasive bladder cancer cases suggests that 256 individuals tested positive.

In contrast, a specificity of 87.8% applied to 923 participants without high-grade or invasive cancer indicates roughly 113 false positives, yielding an expected total of 270 positive results. Study authors did not reconcile this 14-patient discrepancy in the published report.

Data handling nuances such as rounding, differing analytic subsets, or specific exclusion criteria might account for the variation. Future research should detail these aspects to ensure transparent reporting of diagnostic performance.

The testing method showed high sensitivity and negative predictive value, yet its positive predictive value was less than optimal. If multiple diagnostic testing methods can be used in combination, relying on each test’s diagnostic strength, there could eventually be a reduction in cystoscopy as a result.

In the meantime, the stochastic nature of sensitivity and specificity in the current validation attempt leaves a lot of room for diagnostic discrepancies.

Genomictree Inc. (Republic of Korea) supplied the urinary DNA methylation tests.

More information: In Gab Jeong et al, Urinary DNA Methylation Test for Bladder Cancer Diagnosis, JAMA Oncology (2025). DOI: 10.1001/jamaoncol.2024.6160

Journal information:JAMA Oncology

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