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

PathogenDx is expanding into the clinical labs, providing low-cost multiplex testing with the D3 Array™

From the advent of microscopes to quantitative polymerase chain reaction (qPCR) and next-generation sequencing (NGS), clinical labs are more capable than ever to run effective diagnostic tests. However, even today’s powerful diagnostic tools can’t do it all—there remains a need for new advances to expedite and improve clinical testing.

Where qPCR and NGS fall short, PathogenDx seeks to pick up the slack by addressing challenges in performance, throughput, and cost with regards to multiplex testing with the expansion of their D3 Array™ platform.

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 set their sights on the clinical industry. 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 ideal for variant testing—something that wasn’t previously seen as necessary.

“Government and doctors would say there's no clinical utility in variant testing,” says Milan Patel, CEO and co-founder of PathogenDx, who recently spoke with Lab Manager. 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. “The next natural progression with the use of our technology is in the area of infectious disease,” he says.

Patel and the developers of the D3 Array™ also realized that this form of testing wasn’t exclusively of value to human diagnostics 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 assesses 13 different subspecies of Salmonella in the same test.

The ability to quickly move 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,” says Patel. “That's the beauty of the technology.”

Fast, affordable, and precise

While qPCR and NGS are both powerful and useful tools, there remain gaps in the diagnostic testing market. Most notably for qPCR, multiplexing testing often has a limited throughput, while NGS, which has an even lower throughput, takes a 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.

“The best things about the [D3 Array™] are that it's a fraction of the cost of next-gen sequencing, it provides the same level of multiplexing capability as next-gen sequencing, and it supersedes anything that qPCR can do,” says Patel. Where NGS 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, he says.

UTIs and beyond

PathogenDx intends to continue expanding the use of the D3 Array™ in other clinical areas that use multiplex testing, such as UTI (urinary tract infection) diagnosis and antibiotic resistance to infection-causing pathogens, with potential applications in women’s health and cancer diagnostics. The D3 Array™ may also have potential applications in telehealth and 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 lead the charge to better diagnostics to provide clinicians with more actionable information for diagnoses and treatment, as well as better, more cost-effective multiplex testing. “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,” says Patel, “whether it's infectious disease in the area of molecular diagnostics or other multiplexing applications.”


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