JCO precision oncology · 2026
Integrated Methylation and Copy Number Analysis for Noninvasive Bladder Cancer Detection in Urine.
СтатьяНазвание и аннотация: Перевод в очереди
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Beijert Irene J, Wever Birgit M M, Moldovan Norbert, van den Burgt Yara, Nouwens Annick, van der Pol Ymke, Hentschel Anouk E, Bosschieter Judith, Lissenberg-Witte Birgit, Kauer Paul C, van Moorselaar R Jeroen A, Mouliere Florent, Nieuwenhuijzen Jakko A, Steenbergen Renske D M
Аннотация
PURPOSE: The molecular analysis of urine cell-free DNA offers a noninvasive tool to advanced bladder cancer (BC) management. Assessment of somatic copy number aberration (SCNA) and DNA methylation analysis have emerged as promising approaches for BC detection. Here, we developed an integrated analysis to assess both SCNA and targeted methylation changes from the same template molecules, which we named the integrated sequencing-based copy number and methylation analysis in urine (iSECURE) method.
MATERIALS AND METHODS: Urine samples of 30 patients with primary BC, 28 patients with recurrent BC, and 31 hematuria controls were collected at home. Copy number profiling and tumor fraction (TF) estimation were performed by shallow whole-genome enzymatic methyl sequencing. Methylation sequencing libraries were also used for the measurement of a previously validated three-gene methylation marker panel (GALR1/HAND2/NRN1) by the quantitative methylation-specific polymerase chain reaction. Diagnostic accuracy was evaluated by logistic regression analysis using Youden's index for sensitivity and specificity and validated using leave-one-out cross-validation (LOOCV).
RESULTS: TF and methylation levels were significantly higher in patients with BC compared with controls (P < .0001). The individual assays yielded an AUC of 0.91 at 79% sensitivity and 97% specificity for the methylation marker panel and 0.81 at 74% sensitivity and 87% specificity for copy number profiling. The iSECURE workflow yielded a higher diagnostic accuracy with an AUC of 0.94 at 88% sensitivity (90% for primary tumors and 86% for recurrent tumors) and 94% specificity. LOOCV demonstrated an AUC of 0.91 at 84% sensitivity and 90% specificity.
CONCLUSION: We developed a single workflow for copy number profiling and targeted methylation analysis, requiring less input DNA and hands-on time. The high accuracy of iSECURE in home-collected urine samples for detecting both primary and recurrent BC underscores its clinical potential.
MATERIALS AND METHODS: Urine samples of 30 patients with primary BC, 28 patients with recurrent BC, and 31 hematuria controls were collected at home. Copy number profiling and tumor fraction (TF) estimation were performed by shallow whole-genome enzymatic methyl sequencing. Methylation sequencing libraries were also used for the measurement of a previously validated three-gene methylation marker panel (GALR1/HAND2/NRN1) by the quantitative methylation-specific polymerase chain reaction. Diagnostic accuracy was evaluated by logistic regression analysis using Youden's index for sensitivity and specificity and validated using leave-one-out cross-validation (LOOCV).
RESULTS: TF and methylation levels were significantly higher in patients with BC compared with controls (P < .0001). The individual assays yielded an AUC of 0.91 at 79% sensitivity and 97% specificity for the methylation marker panel and 0.81 at 74% sensitivity and 87% specificity for copy number profiling. The iSECURE workflow yielded a higher diagnostic accuracy with an AUC of 0.94 at 88% sensitivity (90% for primary tumors and 86% for recurrent tumors) and 94% specificity. LOOCV demonstrated an AUC of 0.91 at 84% sensitivity and 90% specificity.
CONCLUSION: We developed a single workflow for copy number profiling and targeted methylation analysis, requiring less input DNA and hands-on time. The high accuracy of iSECURE in home-collected urine samples for detecting both primary and recurrent BC underscores its clinical potential.