Integrated Methylation and Copy Number Analysis for Noninvasive Bladder Cancer Detection in Urine

Area of Science:

• Urology
• Oncology
• Molecular Diagnostics

Background:

• Urine cell-free DNA (cfDNA) analysis is a noninvasive tool for advanced bladder cancer (BC) management.
• Somatic copy number aberration (SCNA) and DNA methylation analysis are promising for BC detection.

Purpose of the Study:

• To develop an integrated analysis method (iSECURE) for simultaneous SCNA and targeted methylation assessment from urine cfDNA.
• To evaluate the diagnostic accuracy of iSECURE for primary and recurrent BC detection.

Main Methods:

• Developed the integrated sequencing-based copy number and methylation analysis in urine (iSECURE) method.
• Analyzed urine samples from 30 primary BC, 28 recurrent BC patients, and 31 controls using shallow whole-genome enzymatic methyl sequencing and quantitative methylation-specific PCR for a three-gene panel.
• Evaluated diagnostic accuracy using logistic regression and leave-one-out cross-validation (LOOCV).

Main Results:

• iSECURE demonstrated high diagnostic accuracy with an AUC of 0.94 at 88% sensitivity and 94% specificity.
• The methylation marker panel achieved an AUC of 0.91 (79% sensitivity, 97% specificity), and copy number profiling yielded an AUC of 0.81 (74% sensitivity, 87% specificity).
• LOOCV confirmed strong performance with an AUC of 0.91 (84% sensitivity, 90% specificity).

Conclusions:

• The iSECURE workflow offers a single, efficient method for copy number profiling and targeted methylation analysis from urine cfDNA.
• iSECURE shows high accuracy in detecting both primary and recurrent bladder cancer in home-collected samples, highlighting its clinical utility.