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Biotech Celera partners with area biotechs for online protein database



Biotech: Celera Partners With Local Firms for Online Protein Database

Craig Venter recently said half-jokingly that UCSD’s superb education must be one reason why San Diego’s biotechnology industry continues to thrive.

Half-jokingly, because the president of Celera Genomics in Rockville, Md., the small private company that shared the credit in cracking the human genetic code, is a UCSD graduate.

Venter recently returned to his alma mater to tell alumni, UCSD staff and students about his bold move in going after the human genome at a dizzying speed.

Venter’s epochal achievements in sequencing the human genome years earlier than originally predicted left even his bitterest critics in awe.

“We’re barely 3 years old as an organization and have accomplished more in three years than most people thought would be possible in 20 for whole governments, but the biggest challenge is continuing to understand all the data we generated,” Venter said during a press conference at the La Jolla university’s campus Oct. 29.

The human genome , the genes that spell out the instructions for making proteins which are the building blocks of every cell in the body , still holds many secrets.

But if Venter has his way, Celera will also play a pivotal role in unlocking these secrets, paving the way for novel treatments for cancer and infectious disease.


Partnerships

Celera has partnered with other biotechnology companies to pave the way, including GeneFormatics Inc., Sequenom and Structural GenomiX in San Diego.

When asked about San Diego-based commercial opportunities, Venter remained vague.

“We’re looking for any group that can provide good quality information in areas we haven’t yet developed ourselves,” he said.

Last week, GeneFormatics, which uses software and other technologies to determine the function and structure of proteins, agreed to deliver thousands of proteins to be added to Celera’s Applera Corp. online database.

Financial details of the agreement were not disclosed, but GeneFormatics’ president and chief executive John Chiplin said this contract is only the first phase in an ongoing relationship with Celera.

Venter prides himself in having the largest proteomics database , information on proteins, in the world. But he said, “It’s a very large universe of information, so when other people have data, we will add that to the database as well.”

So far, Celera has signed up 15 companies and 100 academic laboratories which pay an undisclosed amount of money to access the enormous genomics and proteomics database, said Tony Kerlavage, senior director product strategy at Celera’s online business.

Scientists depend on such data in order to discover new drugs.

But Venter and Chiplin admit that sifting through the wealth of information to find drug targets, proteins that cause disease, is onerous.


Potential Targets

So far, only 500 disease-causing proteins have been identified. The human genome yielded about 30,000 genes that code for proteins. GeneFormatics alone has identified the function of 7,000 proteins, said Chiplin, but he couldn’t say how many of them could be drug targets.

“We want to triage the number down after looking at the function of the protein (in the hopes of finding useful targets),” he said.

Meanwhile, pharmaceutical companies are reportedly paying millions of dollars to sift through Celera’s index, which now includes GeneFormatics’ data as well.

Chiplin said GeneFormatics will start marketing its own database during the first quarter of next year, charging subscribers between $500,000 and $1 million for access.

He said potential subscribers, including pharmaceutical companies, food and agricultural businesses, and genomics companies will be able to get a “sneak preview” when the database is finished.

Last month, GeneFormatics raised $22 million from investors, including Massachusetts-based Bruker Daltonics and two affiliated Bruker companies, which will drive the effort.

Chiplin said his strategy is to “grow revenues” and drive towards profitability.

But besides cashing in on genetic information from its own subscribers, GeneFormatics will also continue to feed information to rival databases, including Celera’s, Chiplin said.

“Other discussions are on-going (with Celera) pertaining other annotation opportunities,” he said. It’s likely that their relationship could be extended to other genomes, such as the fruit fly, mouse, rice, corn and bacteria, he added.

The findings of these genomes could also open a whole new frontier for public and private researchers. Chiplin points to the anthrax scare, which has brought an urgency to develop new antibiotics to the forefront.

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