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SomaLogic Publishes Details of Upcoming Lung Cancer Test, New Proteomics Discovery Platform

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By Justin Petrone

Proteomics technology firm SomaLogic this week published two papers describing the use of its platform in lung cancer and in chronic kidney disease biomarker-discovery programs.

The studies, published in Nature Precedings, an online resource of papers submitted to Nature that are still under review, are part of an effort by SomaLogic to learn more about the role its technology platform can play in the development of diagnostics.

"We have a big push right now to develop our clinical studies and push diagnostic products," Jeff Walker, a medical scientist at Boulder, Colo.-based SomaLogic, said this week. "It is important for us as a timely way to get this information out to people so that they can learn about our technology, especially for our partners. This was a good way to make [this information] publicly available."

Both studies used custom-designed microarrays manufactured by Agilent Technologies.

In the first study, SomaLogic and partners at the University of Colorado, Boulder, and in New York University, the Roswell Park Cancer Institute, and the University of Pittsburgh used the company's aptamer-based approach to survey 1,326 archived blood samples in long-term tobacco-exposed patients to identify markers linked to non-small cell lung cancer.

The study led the firm to develop a 12-protein panel that can be used to determine if an at-risk, tobacco-exposed individual has lung cancer.

In the second study, SomaLogic and partners at CU Boulder, the Sally Jobe Breast Center in Denver, and the Rogosin Institute in New York used the firm's approach to study chronic kidney disease and identified two well-known CKD biomarkers and 58 potential new ones.

Walker said that of the two studies published this week, the one describing the lung cancer protein panel is closest to being developed into a commercial test. He told BioArray News that SomaLogic has partnered with Quest Diagnostics to bring it to market, which aims to debut a laboratory-developed test next year and a US Food and Drug Administration-cleared version in 2012.

"Quest will take the technology and they will develop a test that they will offer," said Walker. "They will do the next steps that include more clinical study and validation. It's in the hands of Quest at this point."

Walker said the CKD project has farther to go before yielding a test, and praised the market in which it could play. "CKD is a growing problem and another area where early detection might help," he said. "That is an early-stage project and we will continue to work on that with our partners from Rogosin and potentially other places."

Lung cancer and CKD represent just two areas of diagnostic interest for SomaLogic, which continues to transform itself into a test-development partner. It was founded in 2000 to sell a technology developed at NeXstar Pharmaceuticals, which was acquired by Gilead Sciences the prior year.

The platform is designed to quantify the presence of proteins in blood by using Somamers, chemically modified nucleic acid aptamers made via a process called systematic ligand evolution by exponential enrichment. Specifically, the assay converts target protein concentration to specific Somamer concentration, which is then quantified with readily available DNA technologies, including microarrays.

"The goal is to measure proteins in blood and there is no real easy way to do that," said Walker. "One way is using mass [spectrometry, though] we know that that doesn't work so well."

Walker compared SomaLogic's methodology to antibody-based approaches, but with two important distinctions: Somamers are believed to be more sensitive and more specific than antibodies, and they can be synthesized more readily.

"The assay we have developed uses a molecule that's targeted to a specific protein," Walker said. "We mix it and at the end we recapture the molecule and then that molecule is in the same concentration as the protein was present in the sample."

SomaLogic can uses any of a number of techniques to measure the resulting molecules — in the past it has used quantitative PCR, Luminex xMAP technology, and Illumina BeadChips — but in the two recent studies it used custom Agilent arrays.

'Clinical Research as Principle'

Walker said the 10-year-old company began to intensify its focus on diagnostic development in early 2008, when it began an ongoing quest for partners who can bring new protein-based tests to market.

"SomaLogic was founded with clinical research as a principle, and from the beginning we have had a medical group who basically identifies diseases using criteria, including scientific rationale and medical need, and then looks for the best partners to develop the program," Walker said.

"We definitely have a focus in oncology, but that's because of the unmet need for detection," he said. "There was a large effort in the beginning of the company to map out [clinical need], and it continues to be iterative as we go."

While SomaLogic is oriented toward clinical development — it does not make its platform available as a catalog product — its main strategy calls for partnerships when possible.

"We are not necessarily seeking to be a diagnostics company," Walker said.

The lung cancer panel is the first potential diagnostic fruit of its efforts. The company believes it can be used for early detection of lung cancer in long-term smokers when surgery may offer a successful treatment. In the paper, the authors argue that the panel could enable physicians to test individuals with increased risk of developing lung cancer. As is currently envisioned, a positive result would be followed by a computed tomography screen.

The authors said the protocol could also run in reverse, with the panel used to diagnose lung cancer in individuals with "suspicious lung nodules identified by CT." Such an indication "could help mitigate the problem of morbidity and cost associated with surgical interventions," they said.

Lung cancer is the leading cause of all cancer deaths in the US. In 2009, an estimated 159,390 men and women in the US died from the disease and 219,440 new cases were diagnosed, according to the National Cancer Institute.

Beyond lung cancer, SomaLogic has ongoing programs in chronic kidney disease, pancreatic cancer, mesothelioma, and breast cancer. In the second Nature Precedings paper, SomaLogic analyzed plasma samples from 42 subjects with CKD and identified 60 biomarkers with differences in concentration between early- and late-stage disease.

In April, BioArray News sister publication ProteoMonitor reported that SomaLogic is also developing a test for pancreatic cancer, which consists of 11 proteins, and one for mesothelioma, which will comprise six or fewer proteins. The firm has not determined target launch dates for either panel.

As with the lung cancer panel, Quest has the option on partnering with SomaLogic on any diagnostics developed from those panels.

SomaLogic acknowledged in the second paper that it has been involved in a prospective multicenter breast cancer study designed to compare plasma proteomic-signature proteins of 336 women with suspicious mammogram findings.

Specifically, 32 women surveyed had ductal carcinoma in situ, 57 had invasive breast cancer, and 247 had benign disease. Still, SomaLogic found there were "no statistically significant differences in the proteomic profile among these three groups."

While it said the outcome of the study was "disappointing," SomaLogic said in the paper that it is possible that "with a larger array, new biomarkers of breast cancer will emerge."

CEO Larry Gold told BioArray News last week that SomaLogic will rely on its partnership with Quest to market the first diagnostic products created with its platform, but that the firm in the future hopes to make in vitro diagnostic kits available to clinical labs. The firm is confident that its approach will win adoption because of the ability of protein-based assays to identify disease.

"When you measure genomics, you measure the risk of disease, [and] when you measure proteins, you measure the existence of disease," said Gold. "We measure existing disease. What you need is not risk: To be a good doctor is to know about existing disease when there are actionable steps that make a difference."

'A Larger Array'

In the lung cancer, CKD, and breast cancer studies, SomaLogic measured on average 800 proteins in each sample. According to Gold, the company this year became capable of measuring 1,000 proteins simultaneously, and in the next few years it plans to increase that number to 5,000.

"In our present platform, we measure 1,000 human proteins from concentrations as low as 50 centomolar to even nanomolar," Gold said. "This is the sensitivity of an enzyme-linked immunosorbant assay with huge content, and we only use 15 microliters of plasma."

Gold said that SomaLogic is now increasing the numbers of proteins it can profile simultaneously at the "sensible rate" of between 1,000 and 1,500 proteins per year. "We have built a discovery-sized multiplexed proteomics assay," Gold said. "As soon as we build the content, we'll make it available to pharma and academic collaborators."

Walker said that SomaLogic could hypothetically go beyond profiling 5,000 proteins in the future, potentially surveying all 20,000 known human proteins in one assay. Still, he said, for now, achieving the ability to survey 5,000 proteins in a single assay is the firm's main objective.

"Right now, our focus is the proteins that are present in blood; we think they will be most useful in diagnostics," Walker said. "It's just a measure of time and money."

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