LONDON – DNA Electronics Ltd. (DNAe) won a U.S. FDA breakthrough device designation for its semiconductor-based DNA sequencing technology Lidia-seq and for the first assay based on the platform, which will detect bloodstream infections and antimicrobial resistance (AMR) genes at point of care.

The designation paves the way for clinical trials and will bolster work the company is doing to adapt the technology for the diagnosis of COVID-19 infections.

Meanwhile, DNAnudge Ltd., another company set up by DNAe’s founder Chris Toumazou, reported it has repurposed its consumer DNA device to detect COVID-19. The U.K. government has ordered 10,000 of its testing cartridges, which use optical technology to identify the coronavirus.

DNAe says Lidia-seq will bring genomic analysis into use at point of need. The entire process is automated, with all processing taking place in a single, hands-free cartridge. The compact device can be used by non-specialists.

“We can now go from raw specimen directly to actionable result, and have automated the entire process,” said Samuel Reed, president of DNAe. “Apart from [increased] accuracy, we can go rapidly from a sample and we can do it in a diversity of environments,” he told BioWorld.

The prototype assay considered by the FDA consists of more than 1,000 bacterial, 150 fungi and yeast and 35 AMR markers. London-based DNAe is developing as a test for suspected sepsis, where it will avoid the current delay of 12 to 36 hours it currently takes to culture samples.

Lidia-seq can identify pathogens and AMR markers in under three hours, allowing patients to receive targeted, rather than broad spectrum anti-infectives.

DNAe’s sequencing technology uses standard silicon chips to detect the hydrogen ions that are released when DNA or RNA bases pair with their opposite number. The signal registers as an electrical impulse. If there is no match, no hydrogen ions are released, and no signal is detected.

The technology has been validated commercially, for research use only, by DNAe licensee Thermo Fisher, in its Ion Torrent next generation sequencing machines.

In November 2018, DNAe was the first to demonstrate it is possible to sequence the DNA of bacteria directly from an unprocessed blood sample. That completed the initial phase of a US$51.9 million contract with the Biomedical Advanced Research and Development Authority and released $10.9 million for the development of the prototype device.

Now the FDA breakthrough designation provides recognition that Lidia-seq and the associated assay has the potential to enable faster and more meaningful DNA-specific diagnosis of life-threatening sepsis.

DNAe will benefit from the extra FDA input, Reed said. “We can have frequent and informal interactions, whereas the [conventional] process is more formal. It will help smooth the path,” he said.

Although it is yet to be tested in clinical trials, Reed said the company has assessed Lidia-seq on patient samples. Following behind the sepsis assay, a pipeline of tests are in development for viruses and for cancer testing and monitoring.

In the face of the current pandemic, DNAe has been working to apply the technology to detecting SARS-CoV-19. “We are doing testing in-house with [Lidia-seq] with the coronavirus sequence, to show it could be directly applied,” Reed said.

There could be advantages over standard polymerase chain reaction tests, including greater accuracy and the fact that Lidia-seq generates more information, said Reed. “We are doing everything we can do expedite [this test].”

Repurposing

At Imperial College London, a second DNA detection technology invented by Toumazou is being repurposed to fight COVID-19. The DNAnudge in-store testing device, launched in November 2019, matches individual users’ genetic profiles to nutrition related traits. The data is used to help people make the correct choices when they are food shopping.

The test, which uses a cheek swab, has now been converted to detect the RNA of SARS-CoV-19. The repurposed test, which delivers results in just over an hour, has been clinically validated in an initial trial in COVID-19 patients.

It is now being assessed in a bigger group of patients, with a view to a national rollout in the U.K.

The Department of Health has procured 10,000 DNAnudge COVID-19 test cartridges. The test requires no sample handling, with swabs being placed directly into the cartridge, and no need to send samples to a central laboratory.

Toumazou, professor of engineering and founder of the Institute of Biomedical Engineering at Imperial College, said the early results have been excellent. “The test was developed as a lab-free, on-the-spot consumer service that can be delivered at scale, so we clearly believe it offers very significant potential in terms of mass population testing during the COVID-19 pandemic,” he said.

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