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API Closes on $28M Round Supporting Development of Colorectal Test, Biomarker Discovery Efforts

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Applied Proteomics said this week that it has closed a $28 million Series C financing round.

The company plans to use the funds to support development and commercialization of its first proteomic diagnostic, a mass spectrometry-based blood test to aid in the early detection of colorectal cancer, as well as to launch discovery efforts in several new indications, API President and CEO Peter Klemm told ProteoMonitor.

In part, the funds will go toward the construction of a high-capacity CLIA laboratory out of which API will perform the test, which uses multiple-reaction monitoring mass spec. The company inked an agreement with Agilent in March to collaborate on clinical MRM mass spec assays and workflows for its colorectal cancer test (PM 3/29/2013).

That test identifies patients likely to have colon polyps or adenomas with the idea being that such molecular evidence will encourage them to undergo recommended colonoscopies. In a 100-patient, 10-fold cross-validation study presented at the Mass Spectrometry's Applications to the Clinical Lab annual meeting in February, the test identified patients with colon polyps or adenomas with an area under the curve of 0.92.

API is in ongoing validation studies for the test, Klemm said. He declined to provide an exact timeline for its launch, but said that the company plans to test it in at least 5,000 patient samples spanning a variety of geographies and ethnicities before taking it to market. John Blume, API's chief science officer, told ProteoMonitor that the company currently has "a couple thousand" patient samples in hand.

API has broken ground on its planned CLIA laboratory, Klemm said, and it expects to complete construction in the first half of 2014.

Upon completion, the CLIA facility will be capable of running around 1,000 samples per day, Blume said.

One area of focus for API's collaboration with Agilent has been integrating Agilent's RapidFire separation device into its mass spec workflow – a move that could significantly up that throughput figure. In particular, the companies are working on upping the multiplexing capabilities of the RapidFire system to allow for the processing of API's colorectal panel, which could include as many as 20 proteins.

As Can Ozbal, director of Agilent's RapidFire business, told ProteoMonitor in February, Agilent researchers have managed to perform as many as 20 MRM assays in a single RapidFire injection and believe that they could theoretically perform close to 30 MRMs in one injection. However, measuring a 20-protein panel using the RapidFire will almost certainly require two separate injections.

Work on this multiplexing issue is ongoing, Blume said. He added that API plans to launch the colorectal cancer panel using a standard UHPLC system upfront of the mass spec, noting such a workflow would be sufficient to meet the expected initial demand.

"A single mass spec can process up to around 300 samples per day with a six-minute cycle time on UHPLC," he said. "So, then, with multiple mass spec lines you can basically scale to whatever throughput you like."

The RapidFire system – which brings cycle times down from the six-minute range to the six-second range – would likely come into play later in the commercialization process, Blume said.

"When you start thinking about the 44 million people [comprising the test's potential market] and wanting to get to big numbers in that market, that is when you start thinking about the next level up [in throughput]," he said. "The work on the RapidFire is to think about the next phase [of commercialization] where you want to go from hundreds of thousands of tests a year to 10 [times] that."

In addition to continuing development of the colorectal cancer test, API is moving ahead with biomarker discovery efforts in conditions including cardiovascular disease, pancreatic cancer, Alzheimer's, and appendicitis, Klemm said.

While API has declined to provide much detail on its discovery platform, it has traditionally highlighted it as its key differentiating technology. 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, the company has credited Hillis' and Applied Minds' technical expertise, in particular, with facilitating highly reproducible mass spec-based biomarker discovery.

"The differentiating factor for us is that we've got the thing humming so well that we've effectively dialed the noise component way down, and that gives us tremendous reproducibility, and that translates into very practically sized studies," Klemm told ProteoMonitor in a 2012 interview (PM 2/10/2012).

Klemm said this week that API would be using its discovery platform over the next two quarters for a series of pilot studies in the aforementioned indications, "and then from a signal strength point of view decide on the next downstream project." He noted that the company had obtained "excellent plasma samples" for these diseases.

According to Blume, the company's discovery system primarily uses Agilent Q-TOF mass specs with some work done on Thermo Fisher Scientific's Orbitrap instruments, as well.

The Series C round was led by Malaysian investment firm Genting Berhad, with existing investors Domain Associates and Vulcan Capital also participating in the financing. Upon completion of the round, Genting Berhad Chairman and CEO Tan Sri Lim Kok Thay was appointed to the API board of directors.

The funding follows a $22.5 million Series B round the company completed in February 2012 and a $4 million Series A round it closed in 2007.

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