New Nanopore-Based Method Speeds Up Brain Tumor Diagnosis During Surgery

TAIPEI, TAIWAN, May. 29th, 2025- A team of researchers from the University of Nottingham has developed a fast and practical method to classify brain tumors during surgery using nanopore sequencing. This new approach could dramatically reduce the time it takes to diagnose brain cancers—from several weeks down to just a couple of hours—enabling quicker treatment decisions and improved outcomes for patients.

When patients undergo surgery to remove a brain tumor, the standard process for identifying the exact type of tumor typically involves sending tissue samples for lab-based testing, including genetic and epigenetic profiling. These tests, while accurate, often take weeks. During this waiting period, patients may not receive targeted treatments, and surgeons don’t have immediate data to guide surgical decisions.

To solve this problem, the research team created a new diagnostic pipeline called ROBIN—short for Rapid Onsite DNA-Based Intraoperative Nanopore Sequencing. ROBIN combines real-time nanopore sequencing with a machine learning model that analyzes DNA methylation patterns, allowing clinicians to classify tumors quickly while the patient is still in surgery.

This method is built on a streamlined lab and computational workflow. After a tumor sample is collected during surgery, DNA is extracted and sequenced using a portable nanopore device. The sequencing data is then compared against a reference database to identify the tumor type based on its methylation profile.

In a clinical study involving 50 patients, ROBIN was able to classify 90% of tumors within 24 hours and 76% in under an hour. The classification results closely matched those from traditional methods, showing that the rapid approach doesn’t sacrifice accuracy for speed.

The method was tested on a range of brain tumors. In many cases, the sequencing and analysis were completed while the surgery was still ongoing, giving neurosurgeons potentially actionable insights in real time.

The implications are significant. Surgeons could adapt their surgical approach based on the tumor type immediately, which is especially useful for cases where aggressive or conservative resection strategies depend on the diagnosis. Additionally, patients can begin personalized treatment plans, such as chemotherapy or radiation, much sooner.

Another major advantage is cost. The team estimates that each test costs around £450, which is substantially cheaper than the combination of histology, immunohistochemistry, and DNA methylation profiling typically used today. The researchers hope to roll out ROBIN across hospitals in the UK’s National Health Service within the next year. They are also working on expanding the reference database to improve classification accuracy and include rarer tumor types.

This new approach offers a promising step forward in making precision cancer diagnostics faster, more accessible, and more useful during critical surgical moments.

Reference:

[1] New Nanopore Method Enables Intraoperative Classification, Rapid Molecular Profiling of Brain Tumors

[2] ROBIN - revolutionising brain tumour classification with real-time Oxford Nanopore sequencing and adaptive sampling

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