Nanopore sequencing
Credit: Oxford Nanopore Technologies

Researchers at Imperial College London (ICL) working with commercial partner Oxford Nanopore Technologies have developed a method for DNA barcoding that allow nanopore sequencing to identify dozens of biomarkers in one test. The new method, reported today in Nature Nanotechnology, shows promise to identify specific biomarkers of diseases such as heart disease and cancer more accurately allowing for more precise treatment of each patient.

To highlight the power of the new method, the investigators noted that current methods of testing for heart failure typically focus detecting a couple of common proteins to diagnose the condition. In their testing, however, the team demonstrated that combining DNA barcoding and nanopore sequencing detected an additional 40 different types of miRNA molecules which could be potentially used as biomarkers of the condition. The method can also detects proteins, small molecules and miRNA from one sample, and allow for a more complete picture of any one individual’s disease.

“There are many different ways you can arrive at heart failure, but our test will hopefully provide a low-cost and rapid way to find this out and help guide treatment options,” said Caroline Koch, from the Department of Chemistry at ICL and co-first author of the study. “This kind of result is possible with less than a milliliter of blood. It’s also a very adaptable method, so that by changing the target biomarkers it could be used to detect the characteristics of diseases including cancer and neurodegenerative conditions.”

As detailed in their paper, the test works by mixing a patient’s blood sample with small DNA barcodes, which are tags made of short DNA sequences each designed with a unique probe that attaches to a specific biomarker. After mixing the blood sample with the DNA tags, the solution is then injected into the Oxford Nanopore MinION, a portable nanopore sequencing device that allows for remote sequencing, including at the source of the samples.

The DNA barcodes used can be customized depending on the type of test, allowing the new method to used to analyze and characterize the molecular markers of a variety of diseases including cancer. “In principle, we are close to enabling a technology being suitable for clinics, where, in the long run, we hope it could provide a wealth of individualized information for patients with a range of conditions,” said Alex Ivanov, PhD, co-lead researcher on the project, also of the department of chemistry at ICL.

Using the information from their work to identify 40 miRNA molecules from the samples of health blood, the team are now turning to clinical samples of patients with heart failure to validate their results. While there are only a handful of biomarkers currently validated for the diagnosis of heart disease, the researchers believe that measuring these biomarkers simultaneously can help reveal new potential biomarkers.

The hope is that eventually clinicians can use the results from this detection method to determine individual baselines for common blood biomarkers.

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