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DNA Test Detects Early Bladder Cancer in Urine

DNA illustration

(DennisM2, Flickr.

2 May 2023. A genomic analysis of urine samples is shown to diagnose the most common form of bladder cancer years before symptoms appear. A team from the test’s developer, Convergent Genomics in South San Francisco, and academic labs presented the data on 28 April at the annual meeting of American Urological Association in Chicago.

Nearly all cancers in the bladder occur in the urothelial cells that line the urethra, bladder, and other organs, called urothelial carcinoma. Cigarette smoking is considered a major risk factor for bladder cancer. In addition, bladder cancer occurs more often in older than younger people and men more than women. According to American Cancer Society, about 82,300 cases of bladder cancer are expected in the U.S. this year, leading to some 16,700 deaths.

Convergent Genomics is developer of the UroAmp test for bladder cancer evaluated in the study. The company was founded in 2015, spun-off from labs at Oregon Health and Science University, and incubated at Illumina Inc., a provider of genomic analytics. A year later, Convergent Genomics received its first of several small business awards from National Cancer Institute, part of National Institutes of Health, funding research for development of the UroAmp test, including the data reported last week.

The UroAmp test assesses ordinary urine samples with a full genomic analysis, which the company says makes 15 billion measurements on 250,000 genomic locations, to quantify the status of 60 target genes, seeking to identify six types of mutations. Convergent says its technology uses machine learning algorithms to analyze the samples and report insights from the data. The company conducts the analysis at its own labs, with samples sent from participating clinics.

Two methods for validating the model

The AUA paper reports on a study led by Yair Lotan, professor of urology at University of Texas Southwest Medical Center in Dallas and a consultant to Convergent Genomics, who presented the findings. The team developed a screening model for the UroAmp test based on urine samples from 96 individuals with urothelial carcinoma and 70 matching healthy participants, then validated the model in two stages.

The first stage independently assessed samples in a clinical trial of the UroAmp test among 70 people with urothelial carcinoma and 96 healthy individuals for comparison. From this first validation, the UroAmp test achieved a true-positive of sensitivity of 71 percent for all cancer cases, with an 86 percent sensitivity for new detected cancers, and a true-negative specificity of 94 percent.

The second validation analyzed specimen samples and data collected and maintained in a biobank from some 50,000 individuals in Golestan Province, Iran in 2004 to 2008, in a partnership with the International Agency for Research on Cancer and National Cancer Institute. (Several Iranian researchers are listed as co-authors of the paper.) From that population, the researchers identified 29 individuals who developed bladder cancer and matched the data to 98 healthy individuals in the group. An analysis of urine samples show the UroAmp test has a 66 percent true-positive sensitivity for detecting bladder cancer as far as 12 years in advance, with a 94 percent true-negative specificity. When limited to a five-year forecast, the sensitivity rate rises to 90 percent.

“This is the first study,” says Lotan in a Convergent Genomics statement, “to show comprehensive genomic profiling of somatic mutations can detect preclinical urothelial cancer more than a decade ahead of a natural diagnosis.” Trevor Levin, the company’s founder and CEO adds, “By leveraging the latest machine learning and next-generation DNA sequencing, we can non-invasively measure with exceptional accuracy the mutations acquired in bladder cells over our lifetimes.”

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