Uses proven Cell3™ Target error suppression technology allowing confident and accurate calling of somatic mutations down to 0.1% VAF

Developed for and validated on genomic DNA from urinary cell-pellet (cpDNA) and ctDNA from urine.

Provides clinical and translational researchers with a viable non-invasive alternative to cystoscopy for profiling 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)

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.

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

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.

References

1. Kelly JD, Fawcett DP, Goldberg LC (2009). Assessment and management of non-visible haematuria in primary care. BMJ2009; 338
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.
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.
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.
    

* Cell3™ Target panels are available in the following 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)