Biotech Startups: Utah-Based Biotech Startup IDbyDNA Launches New Metagenomics Testing Platform To Aid In COVID-19 Management
: Utah based biotech startup; IDbyDNA’s explify platform for metagenomics analysis is transforming highly sophisticated research-only laboratory tools into practical diagnostics tools for easy routine hospital use.
With the new platform, doctors can now determine not just whether a patient has COVID-19, but also in the same test whether that patient has other respiratory pathogens that are exacerbating the illness.
Basically metagenomics can look across the entire genomic sequence of more than 50,000 species of organisms that may be present in a patient sample and compare millions of sequences from a patient with millions of reference sequences. Having a diagnostic profile of possibly causative pathogens in a given sample helps physicians determine whether there is a genetic basis for the phenotype.
Dr Robert Schlaberg, MD, PhD, MPH - IDbyDNA co-founder and CMO told Thailand Medical News, “That’s the broadest way you can test. But, if you have a hypothesis, you can use targeted metagenomics panels that address certain categories of disease.”
The biotech startup is developing a targeted respiratory pathogen panel to identify the presence of the SARS-CoV-2 virus and approximately 250 additional pathogens that can be tested in parallel.
Dr Schlaberg added, “Individuals are concerned about the flu season coinciding with the COVID-19 pandemic, so we expect to launch the platform before October.”
Dr Schlaberg further added, ”For metagenomics, that’s a huge leap forward. A few years ago, metagenomics was technically challenging, even for researchers. Compute times were long and biologists needed expertise across the whole tree of life.”
As a result, metagenomics analysis was usually performed by only the most sophisticated labs, such as those at the Centers for Disease Control & Prevention (CDC). Therefore, it was used to analyze unexplained disease outbreaks rather than routine diagnostics.
The new IDbyDNA’s Explify platform simplifies the process. It turns diagnosis into a computational problem rather than a lab testing exercise. It also starts by digitizing the sample.
Dr Schlaberg explained, “It takes all the RNA from the patient and from other bacteria in the sample, so it’s a mix that represents all the living things in that sample. We generate DNA sequences for that whole mix, then the application scans the sample for known pathogens or closely related sequences. From sample to report takes less than 24 hours while from detailed sequencing to report takes less than one hour.
He developed the basis of this platform during his work at the University of Utah. He said, “I had been a medical director at a large, national reference lab and was responsible for molecular testing. I knew the limitations of the current tests.”
As a result of his time in research labs, he also knew what was possible, based on the technology. “The gap was apparent.”
His research team launched a retrospective research project that looked at child pneumonia patients who had tested negative for othe
r pathogens. In a high percentage, “We found infections that traditional testing methods had missed. Sometimes they were things no one would have thought to have looked for.”
The platform was also used in a recent research reported at the 2017 Annual Meeting of the American Thoracic Society, where the usage of metagenomics to detect pathogens in children with respiratory disease proved beneficial. Metagenomics confirmed the results of standard tests, but also identified undetected pathogens in 44% of the children who had negative microbiology test results. That study helped underscore the validity of metagenomics as a diagnostic tool and has been followed by other studies with similar findings. https://www.idbydna.com/wp-content/uploads/2017/07/Detection-of-Previously-Missed-Pathogens_ATS-2017.pdf
In late 2014 Dr Schlaberg incorporated IDbyNDA and continued developing the Explify platform. Now that’s it’s in commercial use, he aims to democratize metagenomics testing, bringing it to as many labs and as many patients as possible. The focused pathogen panels IDbyDNA is developing will help tremendously, by bringing a practical, cost-effective element to metagenomics that so far has been lacking. The benefits extend beyond just diagnosis.
The accurate and rapid ability to detect 50,000 organisms, including 6,000 known pathogens, based on the entire genome. “…helps you identify transmission throughout the community and to characterize the virus, determining, for instance, whether it is evolving, becoming more pathogenic, or becoming resistant to treatment,” he said. For perspective, “Existing diagnostic tests, like PRC, look for a single short piece of the genome , often shorter than 100 nucleotides of a particular pathogen, such as the SARS-CoV-2 virus. Then you infer whether this is the virus.”
He understands that for the purposes of diagnosis, having a catalog of every pathogen in a sample could be overwhelming and counterproductive. The analysis interprets the findings, finding and prioritizing variants.
Hence labs can access the Explify metagenomics platform in either of two ways. They can send samples to IDbyDNA’s CLIA-certified lab in Salt Lake City for analysis, or they can install the testing solution developed jointly by Illumina and IdbyDNA and thus create their own lab-developed tests.
Dr Schlaberg added, “Illumina provides the next gen sequencing instruments and reagents. We offer the application-specific pieces, the materials and protocols to digitize the sample and the software to turn the data into a diagnostic report.”
A key benefit of the in-house solution developed with Illumina is the elimination of shipping time.
Dr Schlaberg commented, “We partner with the labs, working with them throughout the development of their test and its validation, suggesting quality control processes, qualified reagents or optimized protocols, for example.”
“Post-launch, the company can help labs with data analysis. The Explify platform can run on premises or in the cloud. Either way, it uses machine learning to continuously improve,” he added.
The metagenomics approach enables physicians to learn about the pathogen in context, putting them in a better diagnostic position, he said, “but learning still needs to occur,” Dr Schlaberg said.
The metagenomic platform is involved in clinical trials to correlate findings from samples to patients’ conditions. “We can provide a lot of actionable information today, and also generate information we can use to become better at interpreting results,” he added.
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