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Applied Proteomics Releasing Second-Gen Colon Cancer Test; Exploring Dried Blood Spots


NEW YORK (GenomeWeb) – Diagnostics company Applied Proteomics plans to release a second-generation version of its SimpliPro Colon proteomic colon cancer test within the next several months.

Like the original test, the new version is intended for increasing patient compliance with recommended colonoscopies in patients with elevated risk of colon cancer.

It improves upon the first-generation test primarily by offering higher specificity. Additionally, the new test will run on a multiplex platform from Meso Scale Discovery, which will lower costs, said API CEO Premal Shah.

The company is also developing a blood-based proteomic test for assessing risk of colon cancer in asymptomatic patients, Shah said. He added that API planned to offer this and other future tests in a mass spec format using dried blood spots as a sample source.

Dried blood spots are an emerging area of interest in clinical work due to their ease of collection, shipping, and storage, but their use for clinical proteomics assays has been limited to date. Were API to bring such a test to market, it could provide an early test case for the format's utility in clinical proteomic applications.

Launched in 2007 by David Agus, director of the University of Southern California's Center for Applied Molecular Medicine, and Danny Hillis, chairman and co-founder of technology firm Applied Minds, API has made much of Hillis' and Applied Minds' technical expertise and the role it has played in aiding development of a high-performing, highly reproducible mass spec-based biomarker discovery system.

After initially planning to transfer its markers from mass spec to an immunoassay format for commercialization, API changed course, announcing in 2013 that it would instead use multiple-reaction monitoring mass spec for its assays. With the launch of SimpliPro, though, it went back to its original plan, a decision that the company said stemmed from a desire to go to market as early as possible and the fact that the test's 11-protein panel was smaller than they expected, thus reducing the anticipated multiplexing benefits of mass spec.

API markets the SimpliPro colon test as a tool for encouraging symptomatic patients to undergo a colonoscopy. The test is aimed not so much at changing physician decisions as at providing doctors with another piece of evidence they can use to convince patients hesitant about having the procedure.

According to company data, the original test detects advanced adenoma with 45 percent sensitivity and 80 percent specificity; stage I and II CRC with 75 percent sensitivity and 78 percent specificity; and stage III and IV CRC with 88 percent sensitivity and 78 percent specificity.

Shah said that the second version of the test detects advanced adenoma with the same levels of accuracy and early- and late-stage colon cancer with the same levels of sensitivity but with specificity of 83 percent. This performance data was determined in studies looking at around 4,400 patients, he said.

Shah noted that API's SimpliPro Colon commercialization efforts are currently focused on establishing clinical utility for the test and preparing a submission to MolDx, a program run by Medicare contractor Palmetto GBA that evaluates the clinical utility of molecular tests and determines coverage. He declined to give sales figures for the test but said revenues had grown sequentially over the four quarters of 2016.

API is also working to develop a test for assessing colon cancer risk and encouraging compliance with colonoscopy guidelines in the general asymptomatic population. This, in fact, was the company's original goal before it shifted to assessing the symptomatic population with SimpliPro Colon.

The company has obtained for this development effort two prospectively collected sample sets totaling more than 7,000 patients, Shah said, adding that early data indicates they may be able to identify a protein signature that addresses asymptomatic patients.

If API was to bring such a test to market it would face competition from existing US Food and Drug Administration-cleared tests including Exact Sciences' Cologuard and Epigenomics Epi proColon. As a blood-based test, the API test would arguably have an advantage in terms of convenience over Cologuard, which is stool-based, though Epi proColon also is blood-based.

Test performance will obviously be a key point of competition for API as it tries to move into this space, but Shah also suggested the company hopes its anticipated dried blood spot-mass spec format will provide advantages in terms of speed and cost.

Running the Mesoscale-based second generation of the SimpliPro test will cost less than $150, Shah said, and, he added, by combining dried blood spots with mass spec, API believes it can launch future tests at a cost of $50 or less.

Typically consisting of microliter volumes of blood spotted and dried on filter paper, dried blood spots can be stored and shipped without refrigeration, meaning they can be sent through standard mail. Conventional blood draws, on the other hand, require rapid, cold shipping via services like FedEx, which are significantly more expensive.

And while dried blood spots' limited sample volume makes them poorly suited to panels of immunoassays, mass spec can measure relatively large multiplexes of proteins in such samples.

In a poster presented at the Association of Biomolecular Resource Facilities annual meeting in March, 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.

A clinical assay would likely measure much smaller panels of proteins, and Shah said that API believed that "from a technical standpoint we are right there." He declined to provide a specific timeline for when the company might launch a mass spec-based dried blood spot test but said that he did not see it as "a multi-year exercise. It is much more in the near term."

Leigh Anderson, CEO of SISCAPA Assay Technologies and a proponent of dried blood spot sampling, agreed that mass spec-based dried blood spot assays are now "clinically workable" for proteomic assays. Anderson, who is not affiliated with API but has collaborated with the company in the past on mass spec workflow development, said he thought API's exploration of dried blood spot samples "makes a lot of sense."

He said that at SISCAPA, he and his colleagues have built five- to 20-plex proteins panels that they analyze in dried blood spots with coefficients of variation in the range of 5 percent or less.

He noted that, in addition to refinement of mass spec techniques, significant progress is being made on the collection side of the equation, with a number of companies putting out dried blood spot collection cards that provide improved standardization of things like blood volume and hematocrit than do traditional cards.

"There are 15 or 16 companies out there with dried blood spot [collection devices]," he said. "Which is great because improvements in collection of the samples are going to be really important."

In the work presented at ABRF, API used Noviplex Cards, a device offered by mass spec vendor Shimadzu and developed by sample prep firm Novilytic Laboratories that use a series of filters to standardize and extract proteins in dried blood spot samples.

A key issue now facing clinical implementation of such assays is integrating these new blood spot card formats into existing automation systems, Anderson said. Automation for standard dried blood spots already exists, because such samples are widely used for neonatal screening assays, but additional automation development is needed to incorporate the new devices.

"It's important but totally tractable," he said.

Another potential issue with dried blood spots is sensitivity, as in some cases assays are less sensitive in these samples than in traditional blood draws.

Bruce Wilcox, API's head scientist and lead of research and development, said the company was currently working to benchmark how sensitivities differed between the two formats across various proteins, though he said it wasn't yet able to discuss the results of this work.

To support its various efforts, API closed a financing round in March. Shah declined to say how much the company raised but said he expected it would "get us through some of our key milestones over the next year, year and a half."

Prior to its most recent cash infusion, API had raised $54.5 million in three funding rounds, the last being a $28 million Series C round in August 2013.