UroMark—a urinary biomarker assay for the detection of bladder cancer

Abstract

BackgroundBladder cancer (BC) is one of the most common cancers in the western world and ranks as the most expensive to manage, due to the need for cystoscopic examination. BC shows frequent changes in DNA methylation, and several studies have shown the potential utility of urinary biomarkers by detecting epigenetic alterations in voided urine. The aim of this study is to develop a targeted bisulfite next-generation sequencing assay to diagnose BC from urine with high sensitivity and specificity.ResultsWe defined a 150 CpG loci biomarker panel from a cohort of 86 muscle-invasive bladder cancers and 30 normal urothelium. Based on this panel, we developed the UroMark assay, a next-generation bisulphite sequencing assay and analysis pipeline for the detection of bladder cancer from urinary sediment DNA. The 150 loci UroMark assay was validated in an independent cohort (n = 274, non-cancer (n = 167) and bladder cancer (n = 107)) voided urine samples with an AUC of 97%. The UroMark classifier sensitivity of 98%, specificity of 97% and NPV of 97% for the detection of primary BC was compared to non-BC urine.ConclusionsEpigenetic urinary biomarkers for detection of BC have the potential to revolutionise the management of this disease. In this proof of concept study, we show the development and utility of a novel high-throughput, next-generation sequencing-based biomarker for the detection of BC-specific epigenetic alterations in urine.Electronic supplementary materialThe online version of this article (doi:10.1186/s13148-016-0303-5) contains supplementary material, which is available to authorized users.

Noninvasive diagnosis of urothelial cancer in urine using DNA hypermethylation signatures—Gender matters

“…When using LASSO for parameter shrinkage, we aimed to create a more stable model by restricting the number of model coefficients and feature selections and reducing unwanted effects due to overfitting . In line with previous studies, the combination of individual CpGs appeared to improve the diagnostic reliability for UCa. However, the calculated sets were dependent on the type of control group, and only one CpG (35 CpG 7) was part of the LASSO‐derived CpG sets that could distinguish between both UCa and UCt, and UCa and PCt.…”

“…Therefore, alternative noninvasive molecular approaches have been developed to identify UCa using urine samples with hypermethylation signatures as the most promising candidates. DNA methylation arrays with increasing genome coverage have identified numerous biomarker candidates of UCa, and high specificities and sensitivities have been reported when these biomarkers were applied individually or as a panel . In our study, we aimed to identify urinary UCa methylation biomarkers that can be used to accurately diagnose UCa.…”

Urinary cell‐free microRNA biomarker could discriminate bladder cancer from benign hematuria

“…A study proposed measuring the expression of IGFBP5, HOXA13, MDK, CDK1 and CXCR2 in a voided urine sample (genotypic), and used age, gender, frequency of gross hematuria and smoking history (phenotypic) data from 587 patients with gross hematuria to develop predictive models for BC . Another study investigated a high‐throughput target bisulfite sequencing assay, UroMark, to probe cancer epigenetic alterations in urinary sediments . They designed a 150 loci panel using a genome‐wide DNA methylation profiling assay for the detection of BC in urinary sediment cells.…”

“…Although the data showed high sensitivity and specificity, there were too many variables, which resulted in a complicated and costly assay. compared to previously reported assays, the test proposed in our study is unique for several reasons . Our urinary miRNA biomarker could discriminate BC in patients with hematuria by estimating the expression levels of only two miRNAs in a large number of multicenter clinical samples (326 BC samples, 174 hematuria and 43 pyuria).…”

“…26 Another study investigated a highthroughput target bisulfite sequencing assay, UroMark, to probe cancer epigenetic alterations in urinary sediments. 27 They designed a 150 loci panel using a genome-wide DNA methylation profiling assay for the detection of BC in urinary sediment cells. And CxBladder as well as ASSUREMDx test were evaluated as available test to aid in the decision for cystoscopy.…”