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A computer generated image of the D3 Array probe

The D3 Array™ Is Filling the Gaps Left by NGS and qPCR

The DArray is expanding into the clinical and agricultural spaces, providing low-cost multiplex testing

Ian Black, MSComm, MSc

Ian Black is the assistant editor for LabX. Before joining the team, he obtained a masters in science communication from Laurentian University and an MSc in biology from Brock University....

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The clinical space has progressed tremendously since the early days of diagnostic technology. From the advent of the microscope to quantitative polymerase chain reaction (qPCR) and next-generation sequencing (NGS), labs are more capable than ever to run effective diagnostic tests. Even these powerful tools have gaps, however, and there is always room for new advances to expedite and improve clinical testing. Where qPCR and NGS can fall short, the just-announced expansion of the D3 Array™ from PathogenDx seeks to pick up the slack by addressing challenges in performance, throughput, and cost with regards to multiplex testing.

The newly expanded D3 Array

Originally developed for the cannabis sector, the researchers at PathogenDx knew that their array was capable of much more and had their sights set on the clinical and agricultural spheres. It proved difficult at first to break into these sectors as one of the great strengths of the D3 Array is its ability to test almost 100 targets in triplicate in a relatively short time, making it potentially ideal for variant testing—something that wasn’t seen as necessary at the time. 

“Back then the government and doctors would say there's no clinical utility in variant testing,” says Milan Patel, CEO and co-founder of PathogenDx. However, when the world was struck by COVID-19, the demand for quick variant testing rose dramatically. “We could detect [using the D3 Array] not just SARS-CoV-2, but variants that were important from a clinical perspective.” 

By proving the utility of the D3 Array during the height of the pandemic, PathogenDx had positioned their array to stand with diagnostic tools like qPCR and NGS in the clinical sector. “So, what we said is the next natural progression with the use of our technology is in the area of infectious disease,” says Patel. Patel and the developers of the D3 Array also realized that this form of testing wasn’t just of value to human diagnostics exclusively but could also be used in the food and agriculture sectors. Salmonella, for example, also has variants that cause infections, so PathogenDx built out a salmonella serotyping assay for the D3 Array that can assess the 13 different subspecies of salmonella all in the same test. 

The ability to move so quickly into these other sectors is another strength of the D3 Array, which is highly standardized across different labs. “The array is no different between what you see in a cannabis testing array versus a clinical array versus a food array. It's the same array. If you're looking at E. Coli in cannabis, and you're looking at E. Coli in a GI panel for clinical or E. Coli in food, it's the same exact array, the primers and the probes are all the same,” exclaims Patel. “That's the beauty of the technology.” 

Fast, affordable, and precise

While qPCR and NGS are both powerful and useful tools, they don’t fill all the gaps in the market with regards to testing tools. Most notably for qPCR, throughput is often very limited on multiplexing while NGS, which has very low throughput, can take a very long time to run and is cost prohibitive. Seeking to address these concerns, the D3 Array boasts high throughput and speed as well as being a much more cost-effective option for diagnostic labs. 

“At the end of the day, the best things about this particular product [D3 Array] are it's a fraction of the cost of next gen sequencing, [and] it provides the same level of multiplexing capability as next gen sequencing and supersedes anything that qPCR can do,” says Patel. Additionally, Patel spoke to the incredible turnaround time of the D3 Array in relation to NGS. Where next-generation sequencing can take weeks to deliver results, the D3 Array takes only days, meaning clinicians can develop treatment plans faster and deliver precision medicine at more efficient and cost-effective rates.

UTIs and beyond

PathogenDx has no intention of stopping their expansion of the D3 Array. They see the potential for this array in many other clinical areas, specifically any area that uses multiplex testing. The developers of the array hope to see it applied next in areas such as urinary tract infection diagnosis and antibiotic resistance to infection-causing pathogens, with many possible applications in women’s health as well as cancer diagnostics. Further down the line, the D3 Array may have potential applications in telehealth with respect to at-home diagnostic testing in certain use cases, such as STIs. 

Regardless of what the future holds, the minds at PathogenDx are confident that the D3 Array will be leading the charge to provide better diagnostics to aid physicians with more actionable information for treatment and therapy, and better, more cost-effective multiplex testing. Said Patel: “There are issues with respect to [qPCR and NGS] that this particular D3 Array microarray technology, completely addresses in terms of what the market needs, whether it's infectious disease in the area of molecular diagnostics or other multiplexing applications.”