Clinically relevant content for bladder cancer
Detects 451 clinically relevant somatic mutations found in 96% of bladder cancer cases
Ultra-sensitive mutation detection
Uses proven Cell3™ Target error suppression technology allowing confident and accurate calling of somatic mutations down to 0.1% VAF
Validated on cpDNA and ctDNA from urine
Developed for and validated on genomic DNA from urinary cell-pellet (cpDNA) and ctDNA from urine.
A non-invasive alternative to cystoscopy
Provides clinical and translational researchers with a viable non-invasive alternative to cystoscopy for profiling bladder cancer.
Non-invasive urine assay for profiling bladder cancer
Currently the main method for the detection of bladder cancer tumors is flexible cystoscopy, an invasive procedure that requires the insertion of a camera into the bladder. In the UK alone over 110,000 flexible cystoscopies are carried out each year at a cost of £55M to the NHS and significant discomfort to patients1. 88% of these cystoscopies turn out to be unnecessary as the patient has no abnormality or malignancy.
The Cell3™ Target Bladder Cancer panel, developed in partnership with researchers at the University of Birmingham, is a targeted NGS panel that covers the vast majority of somatic mutations found in bladder cancer.
Based on the ultra sensitive Cell3™ Target chemistry developed by Nonacus, this sequencing panel enables researchers to sequence the tumor DNA found in the urine of bladder cancer patients to raw read depths in excess of 20,000x. This depth of coverage provides the sensitivity and accuracy needed to offer a viable genomic alternative to flexible cystoscopy for the profiling of bladder cancer.
Comprehensive coverage of clinically relevant somatic mutations associated with bladder cancer
The Cell3™ Target Bladder Cancer panel is an NGS sequencing panel that targets promoter and exonic regions of 23 of the most relevant genes associated with bladder cancer.
Identified by a combination of publicly available data and deep exome sequencing the 451 somatic mutations present in the panel have been shown to detect 96% of bladder cancers in over 1,000 clinical samples2.
Table 1. Bladder Cancer Panel gene content.
Figure 1. Correlation between MAFs in cfDNA and cpDNA determined by capture-based urine DNA analysis using Nonacus Bladder Cancer Panel in paired samples from 45 patients. (Ward et al 2019)
Validated on urinary cpDNA and cfDNA samples
The Bladder Cancer Panel has been validated on both gDNA from urinary cell-pellet as well as cell-free DNA. MAF’s in cfDNA and cpDNA are highly correlated but the higher, more reliable yields of cpDNA make it more suited to clinical research.
- Optimised for 20ng of cell-pellet genomic DNA and 10ng cfDNA
- Quick and easy workflow < 10 hours, with < 2 hours hands-on time
- Supports manual or automated preparation of 1 – 96 samples in a single batch
- 384 patient/sample indexes ensure that customer can use the Cell3™ Target Bladder Cancer panel on the smallest to the largest output sequencers.
Ultra-sensitive mutation detection
Flexible cystoscopy has a sensitivity and specificity of around 85-90% for identifying tumors in the bladder3,4. To provide a viable alternative, a DNA-based assay must be close to or even match this.
Cell3™ Target enrichments incorporate error suppression technology including unique molecular indexes (UMIs) and unique dual indexes (UDI’s) which remove both PCR and sequencing errors and index hopping events. This allows confident and accurate calling of mutations down to 0.1% VAF from as little as 20ng of cell-pellet genomic DNA or 10ng cfDNA input. Recent data has shown that the Cell3™ Target Bladder Cancer panel provides a much more sensitive test than previous methods and would get very close to matching the sensitivity and specificity of flexible cystoscopy2.
We provide advice and provision of ready to go analysis scripts for error removal using UMI’s.
Figure 2. Using UMI’s to identify and quantify individual DNA molecules during library preparation increases sensitivity
Optimised sequencing performance
The baits used in Cell3™ Target Bladder Cancer panel are designed to deliver excellent uniformity of coverage. By improving uniformity of coverage and reducing the number of low coverage exons, this panel optimises sequencing efficiency and sample capacity per sequencing run.
- Kelly JD, Fawcett DP, Goldberg LC (2009). Assessment and management of non-visible haematuria in primary care. BMJ2009; 338
- Ward DG, Gordon NS, Boucher RH, et al (2019). Targeted deep sequencing of urothelial bladder cancers and associated urinary DNA: a 23-gene panel with utility for non-invasive diagnosis and risk stratification. BJU Int. Sep; 124(3):532-544.
- Zheng C, Lv Y, Zhong Q, Wang R, Jiang Q (2012) Narrow band imaging diagnosis of bladder cancer: systematic review and meta-analysis. BJU Int. 2012 Dec;110 (11 Pt B):E680-7.
Svatek RS, Hollenbeck BK, Holmäng S, Lee R, Kim SP, Stenzl A, Lotan Y (2014). The economics of bladder cancer: costs and considerations of caring for this disease. Eur Urol. 2014 Aug;66(2):253-62.
Cell3 Target panels are available with one of two versions of our library preparation kits:
-Fragmentation: for use with gDNA (FF or FFPE)
-Non-Fragmentation: for use with cell free DNA
|Cell3™ Target: Bladder Cancer Panel, Frag 16 samples
|Cell3™ Target: Bladder Cancer Panel, Frag 96 samples
|Cell3™ Target: Bladder Cancer Panel, Non Frag 16 samples
|Cell3™ Target: Bladder Cancer Panel, Non Frag 96 samples
* To provide flexibility in multiplexing samples, our 96-sample kits offer a choice in adapter plate:
A = Adapter plate with indexes 1-96
B = Adapter plate with indexes 97-192
C = Adapter plate with indexes 193-288
D = Adapter plate with indexes 289-384
Detailed product information available to download.
For Research Use Only. Not for use in diagnostic procedures.
If you have any questions about any of our products, including access to the BED files and example data sets, please fill in the support request form here and we will get back to you as soon as possible.
Learn more about our products for oncology
Cell3™ Target: Hereditary Cancer Panel
A comprehensive NGS sequencing panel for analysing germline mutations associated with hereditary cancers
Cell3™ Target: Pan Cancer TMB/MSI (524) Panel
A comprehensive panel of 524 oncogenes that allows you to accurately profile and stratify all common cancers and predict response to immunotherapy.
Cell3™ Target: Tumor Exome
Whole exome capture with improved, clinically relevant content for comprehensive tumor sequencing
Cell3™ Target: Custom NGS Panels
Target the genes and variants important to you by creating your own NGS panel using our ultra-sensitive Cell3™ Target technology