Clinical proteomics firm Somalogic announced last week that it has partnered with IT and communications giant NEC to explore business opportunities related to its Somamer protein detection technology.
Somalogic's agreement with NEC, which has purchased an equity stake in the company, is part of its plan to expand beyond its traditional focus on biomarker discovery and diagnostics development to become a "health information company" that can "provide actionable medical information to patients, physicians, and researchers," director of corporate strategy Mark Messenbaugh told ProteoMonitor.
The collaboration will employ NEC's SVM+ machine learning data-analysis technique as well as its BioPrism proteomics software, which provides researchers simultaneous access to multiple analytical data and information stored in public databases. The goal, Messenbaugh said, is to build a cloud-based informatics platform capable of integrating a wide range of 'omics data from a variety of sources.
"The future of biological research, the future of medicine, is going to [involve] the integration of multiple sources of information — that's molecular, proteomics, genetics, imaging, as well as clinical information. There are going to be a host of different inputs that [will] come together to make sense of what's happening in a person at a given point in time and what should be done next to best maintain their health. So this kind of integration is very important to optimize health management," he said.
Messenbaugh added that Somalogic envisions its Somamer technology as the potential anchor of this platform.
"Somalogic has always thought that some dataset is going to be at the center of this. [We have] a uniquely powerful proteomics tool. So the bet here that we're mutually making is to say, 'Let's build a tool based on multiplexed proteomics which integrates these other sources of information in a way that leverages knowledge beyond what proteomics alone can deliver but with proteomic data as the centerpiece of the analysis," he said.
The Somamer technology uses a modified form of aptamers – single-stranded nucleic acids capable of binding target molecules – for the detection of proteins. The molecules represent an alternative to antibodies for protein discovery and identification, offering a high level of specificity that allows for multiplex arrays significantly larger than is possible using traditional ELISA platforms.
"There's an upper limit of multiplexing [with] ELISAs of around 25 analytes," Messenbaugh said. Somalogic, on the other hand, has been running aptamer-based arrays capable of multiplexing 850 analytes and, he noted, plans this November to "unveil the next version of our multiplex assay where we're measuring over 1,000 proteins simultaneously in 15 microliters of blood."
The company has used the technology to develop a series of protein biomarker-based diagnostics including tests for the detection of lung cancer, pancreatic cancer, breast cancer, and chronic kidney disease. It has partnered with Quest Diagnostics to commercialize the pancreatic and lung cancer tests, with a laboratory-developed version of the lung cancer diagnostic slated for launch next year and a US Food and Drug Administration-approved version planned for 2012. It is also currently "looking at strategies to commercialize" a mesothelioma diagnostic, Messenbaugh said.
The NEC partnership will focus on more than just facilitating these biomarker development efforts, however.
"This is not just Somalogic outsourcing bioinformatics to NEC," he said. "[NEC has] been experimenting with aptamers and they have had an interest in the power and flexibility of our technology platform for years. Through several years of contact we got to know one another and where each of us think we're headed in the health and life sciences research space."
The two companies decided that they "shared a vision of being a health information powerhouse," Messenbaugh said, with Somalogic bringing its Somamer technology and NEC offering "the sophistication, the heft, the programming capacity, and an infrastructure to develop an innovative set of tools which can support our assay and increase the value of the information that's coming off of it."
In an e-mail, NEC spokesperson Chris Shimizu told ProteoMonitor that NEC will be using BioPrism's "existing data administration and storage functions as well as its security algorithms," while adding "new functionality such as a suite of data analytics algorithms for testing of samples and the development of biomarkers," to take advantage of Somalogic's aptamer technology.
Somalogic continues to add to its Somamer library and aims to have assays capable of measuring 5,000 proteins simultaneously within the next several years. It uses microarrays from Agilent for internal work, although company researchers "think that there are a lot of options" with regard to array platforms, Messenbaugh said, citing as particularly promising arrays from Roche Nimblegen.
Key to increasing its multiplexing capabilities is the continued improvement of its Somamers' specificity. According to Messenbaugh, the company has thus far been able to reduce noise even as it adds additional molecules to its assay.
"We're very confident about the specificity of our aptamers," he said.
The company's collaboration with Emerald BioStructures, also announced last week, is, in part, an effort to continue to improve on this specificity, Nebojsa Janjic, Somalogic's chief science officer, told ProteoMonitor.
The multi-year agreement expands on the two companies' 2009 collaboration, which led to the first X-ray structure of a Somamer bound to its protein target. Under the new agreement, Emerald will investigate the structural features of several other molecules from Somalogic's Somamer library.
"We want to learn through the Emerald collaboration what are the structural features of Somamers. That's the first basic and important question," Janjic said. "Once we begin to understand those rules, we will be able to optimize the properties of Somamers to not only improve the existing menu of about 1,000, but to learn how to more efficiently expand the menu."
Ultimately, he said, Somalogic hopes to develop a multiplex assay covering the entire human proteome.