Noninvasive Detection of Urothelial Carcinoma by Cost-effective Low-coverage Whole-genome Sequencing from Urine-Exfoliated Cell DNA

Abstract

Purpose: Urothelial carcinoma is a malignant cancer with frequent chromosomal aberrations. Here, we investigated the application of a cost-effective, low-coverage whole-genome sequencing technology in detecting all chromosomal aberrations.Experimental Design: Patients with urothelial carcinomas and nontumor controls were prospectively recruited in clinical trial NCT03998371. Urine-exfoliated cell DNA was analyzed by Illumina HiSeq XTen, followed by genotyping with a customized bioinformatics workflow named Urine Exfoliated Cells Copy Number Aberration Detector (UroCAD).Results: In the discovery phase, urine samples from 126 patients with urothelial carcinomas and 64 nontumor disease samples were analyzed. Frequent chromosome copy-number changes were found in patients with tumor as compared with nontumor controls. A novel diagnosis model, UroCAD, was built by incorporating all the autosomal chromosomal changes. The model reached performance of AUC ¼ 0.92 (95% confidence interval, 89.4%-97.3%). At the optimal cutoff, |Z| ≥ 3.21, the sensitivity, specificity, and accuracy were 82.5%, 96.9%, and 89.0%, respectively. The prediction positivity was found correlated with tumor grade (P ¼ 0.01). In the external validation cohort of 95 participants, the UroCAD assay identified urothelial carcinomas with an overall sensitivity of 80.4%, specificity of 94.9%, and AUC of 0.91. Meanwhile, UroCAD assay outperformed cytology tests with significantly improved sensitivity (80.4% vs. 33.9%; P < 0.001) and comparable specificity (94.9% vs. 100%; P ¼ 0.49).Conclusions: UroCAD could be a robust urothelial carcinoma diagnostic method with improved sensitivity and similar specificity as compared with cytology tests. It may be used as a noninvasive approach for diagnosis and recurrence surveillance in urothelial carcinoma prior to the use of cystoscopy, which would largely reduce the burden on patients.

Low-Coverage Sequencing of Urine Sediment DNA for Detection of Copy Number Aberrations in Bladder Cancer

“…It believes that the | Z| is related to tumor grade. 33 This result is similar to some of ours. However, the calculation of change in genome requires a large number of urine genome samples from normal people as a negative control.…”

Bacillus Calmette–Guérin Treatment Changes the Tumor Microenvironment of Non-Muscle-Invasive Bladder Cancer

“…We compared the chromosome instability (CIN) score between different groups ( Figure S5 ). Relapsed tumors had a significantly higher CIN score than primary tumors (Wilcoxon signed-rank test, p = 0.0078) when we calculated the CIN score according to a recent study ( 14 ).…”

Novel Non-Invasive Diagnosis of Bladder Cancer in Urine Based on Multifunctional Nanoparticles

“…None of these markers have been accepted for diagnosis or follow-up in daily practice or clinical guidelines (Babjuk et al, 2022). More recently, several detection platforms based on high-throughput sequencing have been developed, such as CxBladder (Kavalieris et al, 2016) and Xpert (Valenberg et al, 2019) (multigene expression markers); Bladder EpiCheck (Mancini et al, 2020), UriFind (Ruan et al, 2021), and utMeMA (Chen et al, 2020) (DNA methylation markers); and UroCAD (Chromosomal instability) (Zeng et al, 2020). These novel markers were reported to have both high sensitivity and specificity and NPV.…”