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Celera Gets Value from Proteomics Via Partnerships and Improved Data Analysis

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Celera Genomics still hopes to get value out of its proteomics effort by trying to turn proteins into drug targets or diagnostics. Last month, Abbott became the first company to begin validating Celera's cell-surface antigens with two proteins from the company's proteomics program.

Almost a year after Celera signed its first partnerships with Abbott, GE (see PM 7/16/04), and later, Seattle Genetics and Genentech, the company is still validating targets it discovered internally.

Celera has chosen 128 of its cell surface antigens for internal validation, of which 23 have been through the validation process and are now ready for collaborations, according to Steven Ruben, Celera's vice president for protein therapeutics.

Apart from Abbott, each of the other firms is still evaluating Celera's data. Abbott is the first to choose two targets for further experimental studies.

Most of its partners want to focus on developing antibody therapeutics against Celera's antigens. Celera is also evaluating new antigens internally as potential targets for small molecules, and — in collaboration with Celera Diagnostics — for diagnostic opportunities.

Over the last year, Celera has also added two new cancers types — breast and renal — to its program, which so far had focused on pancreatic, colon, and lung cancer. It is also currently looking into new disease areas, including diabetes and obesity.

In addition, Celera has started using its platform to study not only differentially expressed cell-surface proteins, but also proteins that are shed from or secreted by tumor cells. So far, the group has identified approximately 80, according to Ruben, and is investigating which of those may be valuable as diagnostic markers or targets.

The group has also improved the analysis of its proteomics data by linking patient and sample data with mass spec data in a searchable database. "That has allowed us to see relationships for most of the targets that may not be obvious otherwise," especially across different diseases, said Ruben.

The improved data analysis has also enabled the researchers to use mass spectrometry as a validation tool, Ruben said. "Whereas before, we counted on having sequenced an ion to allow us to move forward, now … we don't necessarily have to go through that sequencing to help us in the validation," he added.

Further, the improved informatics capabilities are helping the company to evaluate the novelty of its targets. "That helps shape our decisions in terms of where the program is, when we should wind a program down … and where to direct sequencing efforts based on the novelty of the targets coming out," Ruben said.

Celera's proteomics group, based in Rockville, Md., has grown since last year from its headcount of 35 and has acquired new mass spectrometry instrumentation, but would not disclose any details.

— JK

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