Cell3™ Target: Bladder Cancer

A comprehensive NGS panel for translational and clinical research into urothelial bladder cancer (UBC)

Targeting 451 somatic mutations found in 96% of bladder cancer cases, this panel has the potential to offer a non-invasive alternative to cystoscopy via urinary DNA analysis

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.

cpDNA-MAF-graph

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.

Umi diagram

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.

Customise content for profiling bladder cancer

Designed to be flexible, the Cell3™ Target enrichments allow you to add extra content specific to your project. Whether this is additional content or increased coverage of existing content, our Probe Design Tool makes this a simple and easy process to implement. Our rapid production turnaround means you will receive a fully NGS-validated custom product within 4 weeks.

  • Additional content with high enrichment uniformity
  • Increased coverage of specific genes covered by Cell3™ Target Bladder Cancer panel
  • Optimization of spike-in ratio

Log into the Probe Design Tool at My Nonacus  to start the design process and get a quote or drop us an email at info@nonacus.com

References

  1. Kelly JD, Fawcett DP, Goldberg LC (2009). Assessment and management of non-visible haematuria in primary care. BMJ2009; 338 https://doi.org/10.1136/bmj.a3021
  2. 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. https://doi.org/10.1111/bju.14808.
  3. 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. http://doi: 10.1111/j.1464-410X.2012.11500.x.
  4. 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. doi: 10.1016/j.eururo.2014.01.006.

Ordering Information

Product: Cell3™ Target Bladder Cancer,  (16 samples)
Catalogue No.: C3222BC (options A/B/C*)

Product: Cell3™ Target Bladder Cancer, (96 samples)
Catalogue No.: C3223BC (options A/B/C*)

*All Cell3™ Target panels are available with three fragmentation options:

A = non-fragmentation e.g. cffDNA/ctDNA,
B = fragmentation e.g. gDNA (cell-pellet DNA) or FFPE,
C = Both Fragmentation and Non-Fragmentation (half of each)

Product Support

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.

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