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Agilent Develops a Protein Array Platform, But Commercialization Plans Still Unclear


SAN FRANCISCO — Agilent Technologies has developed a protein array platform that it is providing to a small group of academic partners to facilitate research in such areas as liver cancer, cardiovascular disease, rheumatoid arthritis, and lupus, according to a scientist at the company's R&D lab.

However, the company has not yet decided if, when, or how it will commercialize the platform, which could be the first entrance of a major microarray manufacturer into the emerging protein array market.

Dorothy Yang, a member of the protein array team at Agilent's Palo Alto, Calif.-based laboratories, told attendees at the Beyond Genome conference held here last week that the company has produced a prototype protein array with its proprietary ink-jet method, and that the array can be read and analyzed using equipment that is normally used in DNA microarray experiments.

While "it was a huge undertaking" to create the protein array platform, Yang said that the company was able to "limit its investment" by using existing tools and informatics.

Yang said the arrays are printed on a 1- by 3- inch slide, with eight arrays per slide, using Agilent's ink-jet technology, which can print the antibodies without contact or surface tension between the print head and the substrate. "[Agilent's] ink-jetting technology [was] very helpful in making the protein arrays," said Yang.

As is the case with the company's DNA microarray assays, Yang added that Agilent's protein array assays are "fluorescence-based experiments."

Asian Liver Cancer

"We can put as many proteins on as we want," Yang said.

One of the first research labs to get a crack at the new protein array platform has been the Asian Liver Center, a 9-year-old non-profit at nearby Stanford University. The center was founded, in the words of director Samuel So, "to address the disproportionately high incidence of chronic hepatitis B and liver cancer in Asians and Asian and Pacific Islander Americans."

According to So, his team at the Asian Liver Center has been combating these diseases by engaging in "translational research that focuses on liver cancer genomics and proteomics to find novel diagnostic and prognostic and treatment targets."

"Early diagnosis is the best way to improve one's chances of surviving liver cancer, but the current blood screening test can miss 50 percent of the cancers," explained So.

As Yang detailed at Beyond Genome, one problem the ALC has faced is discovering biomarkers that could be targeted for possible diagnostics, and the center turned to Agilent to help them in this process.

Yang said that So's lab had provided Agilent with a list of 65 proteins of interest to print based on prior research. She stressed that the number was only relevant to So's research, and that Agilent had no technical limitations in printing protein arrays. "We are not limited by the number of proteins we can put on a substrate. We can put as many proteins on as we want," Yang said.

The experiments were run by a joint team of researchers from Agilent and the ALC at Agilent Labs, and samples from 13 liver cancer patients and 10 controls, with two replicates per sample, were run to establish a list of possible biomarkers, Yang said.

Yang called the array results "highly reproducible," and said that they correlated well with data from enzyme-linked immunosorbent assays.

"The next step is to validate the biomarkers with a larger sample set, either with ELISA or other technologies," Yang said.

So called the preliminary study with Agilent "quite promising," and said that the team plans to embark on a much larger-scale research study.

'Very Much a Prototype'

Brian Peter, another member of Agilent's protein array team, told ProteoMonitor's sister publication BioArray News at Beyond Genome that the company has made protein arrays for several other labs, including Thomas Quertermous' lab at Stanford, which studies the genetic basis of cardiovascular development, function, and disease, as well as a team led by William Robinson that is investigating the genetic basis of rheumatoid arthritis and lupus at Stanford University School of Medicine.

"These collaborations are multi-month, multi-sample things that are very likely to lead to publication," said Peter. However, he said that the new platform is "still very much a prototype."

That means Agilent Labs will have to transfer the technology to Agilent's commercial arm before other researchers can access them as a product or service.

Yang hinted during her talk that it was inevitable that the labs will move the arrays out of R&D to be fully commercialized. "We will eventually put them to the marketing department," she said.

However, Willie McAllister, who is heading the protein array team, told BioArray News this week that the array had yet to be transferred to Agilent's commercial arm, and that it was "hard for [him] to speculate" on whether Agilent would join a developing protein array marketplace that includes companies like Invitrogen and Procognia.

"Basically we are doing long-term investigations of possible market areas that the company could participate in," McAllister said. "It's a technology research investigation, and the company has not transferred it [to business development] yet."

Though Agilent is working as a custom protein array supplier to several academic labs, McAllister said that it would be unlikely that other labs could work out similar partnerships with his team.

"We have a history of working with academic collaborators in many of our research projects. Right now we are just proceeding with a selected group with whom we have already established our relationship," McAllister said.

— Justin Petrone ([email protected])

This article originally appeared in BioArray News, ProteoMonitor's sister publication.

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