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Leo Verpillot was ten years old when he learned he had a brain tumor. To determine the malignancy of the tumor, parts of the tumor had to be removed and analyzed through surgery. Now 19, Mr Verpillot remembers how painful it was to wait three months for a diagnosis. The news was good and today Mr Verpillot is a first year biomedical student at Cardiff University. But the months-long wait after an operation remains difficult for patients. Maybe one day that wait will be a thing of the past.
On 27 June a group of brain surgeons, neuropathologists and computational biologists met at Queen’s Medical Centre in Nottingham where they heard about an ultrafast sequencing project being developed by researchers at the University of Nottingham and a local hospital. Their work will allow brain tumours to be classified from tissue samples in two hours or less. As brain surgery usually takes several hours, this will allow results to be available before the end of surgery and inform the operation.
Different tumors require different treatments. Some can be treated with just radiation therapy or drugs, while others require surgery. But deciding how much of a tumor should be removed in a delicate part of the brain, where removing it could cause lifelong damage to patients, is extremely difficult. And without knowing how dangerous the tumor is, surgeons can’t decide how aggressive they should be.
To help them, the Nottingham team relies on a technique called nanopore sequencing. This sequences molecules of DNA or RNA by passing them through tiny pores made in a membrane. By measuring the changes in the electric current passing through those pores as different parts of the molecule pass through them, DNA can be read in real time. Nanopore sequencers can also speed up analysis by doing something called adaptive sampling. This scans each DNA strand to see if it contains specific mutations that might be of interest. If none are found, the strand is ejected from the pores, leaving them open to sequence another strand.
As the data comes out of the sequencing device, it is processed by algorithms that classify the tumour as malignant or otherwise. Since March last year the team has analysed tumours from 90 patients. Thirty were retrospective samples, to check that their technique matched the answers given by traditional molecular and genomic classification methods. A further 60 were prospective samples taken during surgery. Across all 90 patients, the results matched those obtained by older techniques in more than 90% of cases, says Simon Penn, a consultant neuropathologist at the University of Nottingham and part of the project team.
Stuart Smith, a consultant neurosurgeon at Nottingham University Hospitals Trust and another member of the team, asked his colleagues for data already collected on patients’ tumours. Their results suggest that the new technique may have changed the surgical strategies used between 18% and 50% of the time. In some cases patients will only need one brain surgery instead of two.
The method is attracting a lot of interest. Dr. Penn says several UK neurology centers have approached him about the technique. He thinks the technique could eventually spread to the analysis of other types of tumors, including lymphoma and leukemia, for which several tests already exist. If ultrafast sequencing can be made even faster, drugs capable of blocking genetic changes in brain tumors could one day be delivered during an operation. The team hopes they can get the test validated and approved for use as a diagnostic tool in the coming months.
Neurosurgeons are not the first clinicians to discover the benefits of nanopore sequencing. A recent three-year study at Guy’s and St Thomas’ NHS Foundation Trust used it to sequence pathogens found on patients in intensive care, and found that pathogens responsible for dangerous diseases such as Legionnaires’, as well as dangerous strains of MRSA, were present in 3% of patients. Bringing genetic sequencing into the medical field has ushered in a new era of diagnostic possibilities.
© 2024, The Economist Newspaper Limited. All rights reserved. From The Economist, published under licence. Original content can be found at www.economist.com.
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