Veracyte’s Whole-Genome Sequencing-Based MRD Test Shows High Accuracy for Muscle-Invasive Bladder Cancer Detection
Veracyte, Inc., a leader in cancer diagnostics, has announced groundbreaking new data demonstrating the accuracy and effectiveness of its whole-genome sequencing (WGS)-based minimal residual disease (MRD) testing platform for detecting cancer in patients treated for muscle-invasive bladder cancer (MIBC). The results, which show superior accuracy compared to digital droplet PCR (ddPCR)-based blood testing and earlier detection than standard imaging techniques, were presented at the 40th Annual European Association of Urology Congress (EAU25) in Madrid. The findings, derived from the independent, multicenter, interventional TOMBOLA trial (NCT04138628), were highlighted in an oral presentation by Dr. Iver Nordentoft of Aarhus University (Abstract A0162: “Comparison of ctDNA detection methods for monitoring minimal residual disease in patients with bladder cancer: Insights from the TOMBOLA Trial”).
Study Overview and Key Findings
The study examined 100 patients enrolled in the TOMBOLA trial who had been diagnosed with MIBC and were undergoing standard-of-care treatment, including neoadjuvant chemotherapy (NAC) followed by radical cystectomy (RC). Blood samples collected from these patients were analyzed using both ddPCR-based and Veracyte’s WGS-based MRD testing platform to detect circulating tumor DNA (ctDNA), a biomarker for disease recurrence. Patients were also monitored through imaging techniques as part of the study’s standard protocol.
The results demonstrated that at the 6-month follow-up point, Veracyte’s MRD testing platform showed a comparable negative predictive value (95.9%) to ddPCR-based testing (96.2%), meaning that both methods were equally effective at confirming the absence of recurrence. However, Veracyte’s MRD testing platform outperformed ddPCR in specificity (88% vs. 62%), indicating that it produced fewer false positives and was more reliable in correctly identifying true negative cases. Additionally, Veracyte’s platform detected cancer recurrence a median of 93 days earlier than imaging techniques, providing a crucial advantage in early intervention and treatment adjustments.
Further long-term follow-up is needed to fully understand the clinical impact of these results. However, the early findings indicate that Veracyte’s WGS-based MRD test could play a pivotal role in improving cancer detection and patient outcomes. In the ongoing TOMBOLA trial, patients identified as ctDNA-positive receive immunotherapy and are closely monitored for clinical response, which could further validate the utility of this approach.
Importance of Early Detection in Muscle-Invasive Bladder Cancer
Bladder cancer remains a significant global health concern, with muscle-invasive bladder cancer being one of its most aggressive forms. Approximately 50% of patients with MIBC experience disease recurrence within two years of their initial treatment, making early and accurate detection of residual disease critical to improving long-term survival rates.
Currently, standard surveillance methods include imaging techniques such as CT scans, which, while valuable, have limitations in detecting microscopic levels of residual disease. Liquid biopsy approaches using ctDNA analysis offer a promising alternative, but ddPCR-based methods have certain limitations, including lower specificity and challenges with large-scale clinical implementation. Veracyte’s whole-genome sequencing approach seeks to address these shortcomings by offering a more precise and scalable solution for MRD detection.
Dr. Lars Dyrskjøt Andersen, professor at Aarhus University and principal investigator of the TOMBOLA trial, emphasized the potential impact of this advancement, stating, “Up to half of patients with muscle-invasive bladder cancer experience recurrence within two years of initial treatment, and using ctDNA status to guide oncological treatment would spare some patients from unnecessary treatments. ctDNA testing using ddPCR has demonstrated promise for MRD detection, but it has inherent limitations that may impede its clinical use, particularly on a large scale. Our findings show that Veracyte’s whole-genome sequencing approach to MRD testing demonstrates high accuracy and may improve overall clinical utility compared to ddPCR.”
How Veracyte’s MRD Testing Platform Works
Veracyte’s MRD testing platform combines whole-genome sequencing with artificial intelligence (AI) to provide a comprehensive and highly accurate assessment of residual cancer presence in a patient’s blood sample. Unlike traditional ctDNA testing methods that rely on predefined panels of mutations, Veracyte’s approach analyzes the complete set of cancer-related genetic alterations present in the tumor tissue and blood. This enables a more personalized and sensitive detection process.
Key advantages of Veracyte’s MRD testing platform include:
- Higher Accuracy: The whole-genome sequencing method reduces false positives and improves specificity compared to ddPCR-based testing.
- Faster Results: AI-driven analysis speeds up the detection process, enabling earlier intervention for patients at risk of recurrence.
- Less Blood Required: The test requires a smaller blood sample compared to traditional ctDNA testing methods, making it more convenient for patients.
- Personalized Monitoring: By characterizing the complete genomic landscape of a patient’s tumor, the test can provide tailored insights into disease progression and treatment response.
Veracyte plans to launch its first MRD test for muscle-invasive bladder cancer in the first half of 2026, with future expansion into other cancer indications.
Broader Implications for Cancer Diagnostics
The promising results from the TOMBOLA trial reinforce Veracyte’s broader mission to revolutionize cancer diagnostics through innovative genomic solutions. The Veracyte Diagnostics Platform, which underpins all of the company’s tests, is now expanding into MRD testing, building on the success of its existing products in the urology space.
Philip Febbo, M.D., Veracyte’s chief scientific officer and chief medical officer, highlighted the significance of this development, stating, “The new data presented at EAU25 reinforce the power of the Veracyte Diagnostics Platform, which is at the core of all of our tests and will now enable us to expand into MRD testing in a clinically meaningful way. With our first MRD test in muscle-invasive bladder cancer, we are excited to expand our test offerings along the care continuum in urologic cancers, where our Decipher tests are widely used and trusted by clinicians to help guide prognosis and treatment decisions.”
Additional Research and Future Prospects
Beyond MRD testing, Veracyte continues to make strides in the field of genomic diagnostics. At EAU25, the company presented seven additional abstracts focused on its Decipher Prostate and Decipher Bladder tests, which are widely used for cancer risk assessment and treatment guidance. These studies further underscore the company’s commitment to advancing precision medicine and improving patient outcomes across various cancer types.
