Informed Genomics Bladder Service

The following information is designed to provide the key features and performance characteristics of the Informed Genomics (IGL) bladder service using Nonacus GALEAS® Bladder.

This document is designed to support the delivery of key information regarding this test to understand the scope and limitations of the test enabling an
informed decision regarding bladder cancer testing to be made.

How does it work
IGL bladder cancer service uses the Nonacus GALEAS® Bladder test. The test was developed by Nonacus in partnership with University of Birmingham and designed as a molecular triage for haematuria patients, to support clinical management decisions.
The test screens selected regions from 23 genes for the presence of somatic variants (changes in DNA that occur in tumours, tumour DNA) that have been shown to be present in bladder cancer patients 1,2,3 . The presence of one or more of these somatic variants has been linked to a higher likelihood of bladder cancer being present. In total the somatic variants across the 23 genes are
found in over 96% of bladder cancers.

Who is this test for
This test is for patients with haematuria. The presence of blood in the urine (micro or macro) provides a biological indicator that somatic variation maybe detectable.

The technology
The test utilises urine as the primary sample source. This non-invasive sample collection is one of the benefits of this test and the use of urine can enable the direct assessment of DNA released from urological cancers.
Sample collection kits are provided, with full instructions. It is important these instructions are followed to reduce the risk of sample failure and to optimise test results.The collected urine sample is spun down creating a cell pellet containing a mixture of non-cancerous cells and cancer cells shed from bladder tumours (if present).The DNA extracted from the cell pellet is analysed for somatic variation using ultra deep sequencing.Ultra deep sequencing refers to sequencing a genomic region hundred or even thousands of times allowing variants to be detected at very low levels. The ability to detect low level variants is important as the number of cancer cells and thus proportion of tumour DNA can be very low
compared to background genomic DNA from normal cells.

Limitations
The test has a has reported positive predictive value (PPV) of 87%.
Currently it is not possible to determine the proportion of tumour DNA to genomic DNA. In a small percentage of cases somatic variants may be present but at a level beyond the detection limit of the test. In these cases, a negative result would be returned.Secondly there may be somatic variants present in alternative genes or within the 23 genes that are not part of the panel of variants detectable by this test. It is estimated the somatic variants across the 23 genes on the panel are found in over 96% of bladder cancers. As the test is looking for very low levels of variants, a small proportion of cases testing positive for somatic variants will not have cancer as these represent technical artefacts generated through the testing process.
The test has a has reported negative predicative value (NPV) of 89%. This data was derived from a clinical cohort enriched for cancer patients and when prevalence correction is considered, the NPV is estimated to be 99%.

Clinical Utility
GALEAS bladder has been developed to support the triage of haematuria patients. The clinical sensitivity and specificity of this test was determined in haematuria patients using urine as the primary sample. The testing of non-haematuria patients is not supported.This test has been validated as triage tool to determine cancer risk and the results should not be used as predictive markers for targeted treatment decisions.

Clinical Validity
GALEAS bladder targets selected variants in 23 genes linked to bladder cancer where tumour derived variants have been shown present and clinically correlated with known bladder cancer patients. The GALEAS Bladder clinical sensitivity and specificity for this test was determined in over 770 haematuria urine samples from patients with haematuria and compared favourably to cystoscopy 4
and has reported PPV of 87%, NPV of 89% (prevalence correction 99%) and sensitivity of 89% for the detection of all stages of bladder cancer 1,2,3

Data Analysis
Results are analysed on a secure cloud-based clinical software portal GALEAS. This generates a clinical report that is reviewed by HCPC registered Clinical Scientists prior to release.

DNA storage
DNA is stored for a minimum of 6 months. It is not stored indefinitely and will be discarded after 6 months. This period allows the laboratory to troubleshoot any queries regarding test results. DNA maybe used internally for quality assurance and service improvements for bladder testing service. DNA is not shared with 3 rd parties.

Data Storage
The laboratory will retain a copy of the clinical report for its records.
Sequencing data (FASTQ) will be stored for a minimum of 12 months.

Key Information
The following summary information represents the key information for informed consent
1. This test has been validated as a molecular triage for haematuria (blood in the urine) for
determining the likelihood of bladder cancer only. The results of this test must be
considered in relation to other clinical investigations. It cannot be used for any other
indications.
2. The test will require the collection of a urine sample. Failure to collect urine as per
instructions may result in a failed test and impact the accuracy of the results.
3. This test has a NPV of 89% (prevalence correction 99%). A negative test result indicates that, at the time of GALEAS Bladder testing, cancer associated variants were not detected,suggesting the presence of bladder cancer is unlikely but does not completely exclude the presence of bladder cancer.
4. This test has a PPV of 87%. A positive test result indicates that, at the time of GALEAS Bladder testing, cancer associated variants were detected and there is a high likelihood that bladder cancer is present.
5. This is not a diagnostic test, if a high likelihood of bladder cancer is indicated, this must be confirmed by alternative methods (e.g. cystoscopy).
6. Routine laboratory practice is to store the genetic material extracted from my sample even after the current testing is complete. This is not stored indefinitely and will be discarded after a defined period of time.
7. Stored samples may be used internally by IGL for quality control purposes and bladder cancer service improvements.



References
1. Ward DG, Baxter L, Ott S, et al. Highly Sensitive and Specific Detection of Bladder Cancer via
Targeted Ultra-deep Sequencing of Urinary DNA. Eur Urol Oncol. 2023;6(1):67-75.
doi:10.1016/j.euo.2022.03.005
2. Ward DG, Gordon NS, Boucher RH, et al. Targeted deep sequencing of urothelial bladder cancers
and associated urinary DNA: a 23-gene panel with utility for noninvasive diagnosis and risk
stratification. BJU Int. 2019;124(3):532-544. doi:10.1111/bju.14808
3. Feber A, et al. GALEAS Bladder - A non-invasive biomarker for the detection of bladder cancer.
White paper 2023
4. Cha0-Zhe Zhu et al J cancer 2019 A review on the accuracy of bladder detection methods.