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DiscernDx to Use Applied Proteomics Assets to Explore New Dx Approaches

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NEW YORK (GenomeWeb) – Startup DiscernDx plans to use mass spectrometry to explore new and emerging notions around applying proteomic and other molecular data to the clinic.

The company, which launched last year and is backed by venture firm Khosla Ventures, last month purchased the assets of defunct proteomics outfit Applied Proteomics for $1.85 million. According to Khosla principal and DiscernDx board member Alex Morgan, the firm sees the API assets as enabling data-intensive, machine learning-based approaches to healthcare.

Clinical omics efforts have typically revolved around the development of discrete tests focused on specific medical questions, but more recently certain researchers and companies have begun discussing the idea of moving from this classical approach to models in which large-scale omics data is broadly and continually applied to patient management.

For instance, at last month's JP Morgan Healthcare Conference, Sean George, CEO of genetics firm Invitae, declared that "genetic testing is dead," and said his company aims to develop a new business model for genomics in healthcare based on managing genomic data within networks of patients, doctors, and healthcare systems.

Similarly, proteomic firm Somalogic recently announced plans to sell clinical products based on its SomaScan platform not as individual tests but as sets of "insights" derived from data collected on the levels of thousands of proteins in patients that could be offered via, for instance, an enterprise solutions model in which the company sells access to the SomaScan platform to patients and providers.

In academia, researchers like Stanford University Professor Michael Snyder have embarked on large-scale omics projects longitudinally monitoring genomic, transcriptomic, proteomic, metabolomic, and other data from hundreds of patients.

DiscernDx and Khosla are interested in a similar approach to using omics data, Morgan said.

"We view many of the tools in diagnostic space as not necessarily being about a single diagnostic — like, we're going find a biomarker for X and build a diagnostic tool," he said. Rather, such tools are "the sort of sensor arm of a future vision of healthcare where much of the recommendations and decision-making is derived in software. And the [richer] the data that you collect is, the more powerful the outcome you can get."

"Classically in medicine there's this idea that you want to order one test where you know exactly what decision you're going to make when you get the answer back," Morgan added. "But the sort of broader view is that as you go along you want to collect large, multiplex data sets that inform your decision making, maybe not immediately, but as you go forward. Because the things that you measure, oftentimes it may not be the single time point that is interesting, but the evolution of the measurement over time in an individual."

Given this view of where clinical omics is heading, Khosla and DiscernDx were more interested in API's mass spec technology and workflows than its clinical product portfolio, which at the time of the sale consisted of SimpliPro Colon, a blood-based proteomic test to assess the risk of colon cancer in symptomatic patients.

Launched in 2015, SimpliPro Colon was never a commercial success, but Morgan said, in the process of developing that test, API "developed a very robust [mass spec proteomics] pipeline, both in hardware and software."

SimpliPro Colon is interesting," Morgan said "With a little bit more work and critical evidence you may have maybe a product that can exist in the future. It's indeterminate if we'll go down that path. I think it has value, but we need to unlock it. And we have probably a broader vision of what we want to do with the API assets."

Khosla founder and namesake Vinod Khosla was an investor in API in its early days "when they were more of a discovery-oriented company," Morgan said. "And the general idea is that we are returning it to those initial roots as more of a discovery-oriented company."

Bruce Wilcox, formerly API's head scientist and leader of research and development, is CEO of DiscernDx, and the company is in discussions with other API employees about joining the new company, Morgan said.

API was launched in 2007 by David Agus, director of the University of Southern California's Center for Applied Molecular Medicine, and Danny Hillis, chairman and cofounder of technology firm Applied Minds. While the company focused much of its efforts in recent years on commercialization of SimpliPro Colon, it was also involved in biomarker discovery work in diseases including pancreatic cancer.

Mass spec-based proteomics discovery workflows are at this point well-established, implemented in hundreds to thousands of academic and industry labs around the world. However, Morgan noted, getting these systems "productized" to where they can be used reliably and efficiently by a variety of operators is still a significant challenge, which made the API assets attractive.

"Basically all the little things that you need to do to operationalize a business, they've done over years," he said. "It's not a single technology improvement. It's figuring out all the little things you need to do to make something work more efficiently. Reducing the coefficients of variation, getting things down to a per-sample cost basis that is attractive and tenable."

"One of the challenges [to mass spec proteomics] has been in a lot of these operational efficiencies and consistency and getting robust data both out of your physical system and your informatics pipeline," he said. "Those are important [challenges] that the company did a very good job at solving."

API's more recent assay development work using dried blood spot samples could also prove relevant to DiscernDx's vision of ongoing collection of large, multiplex patient data sets. In a poster presented at the Association of Biomolecular Resource Facilities annual meeting last year, API demonstrated a shotgun proteomics-based approach that used dried blood spot samples combined with spiked-in stable isotope-labeled peptide standards to quantify on the order of hundreds of proteins.

"I think in general there's a huge amount of innovation that's gone on in physical sampling technology over the past few years," Morgan said. "We're moving into an age where we will be able to do not just point-of-care collection of bio-tissues, but collection at the point of living, in peoples' homes. We have all kinds of needleless blood draw systems, various kinds of blood spot [systems]… all kinds of technology that is enabling collection of samples in a much more streamlined way. And a variety of these can go into the/a mass spec pipeline."