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Affy and Ardais Team Up for Tissue Profiling; Will GeneChip Become the De Facto Standard?

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In a move to launch itself further into the clinical research arena, Affymetrix on Monday announced a research agreement to generate gene expression profiles from a tissue library assembled by research tissue supplier Ardais of Lexington, Massachusetts.

Under this collaboration, Affymetrix will have access to more than 120,000 human tissue samples and clinical information that Ardais, a four-year-old startup backed by some $47 million in venture capital, has collected from several thousand patients of surgical units at medical institutions.

Financial terms of the deal were not disclosed.

“This collaboration is part of our overall mission to move into clinical care applications,” said Affymetrix spokeswoman Anne Bowdidge. “We are still a chip manufacturer, but we are trying to push into clinical genomics.”

Affymetrix will exclusively own the commercial rights from data gained from the collaboration, Bowdidge told BioArray News.

The first effort of this union with Ardais will be an examination of tumor tissues of an undisclosed cancer type from approximately 50 patients — to test the compatibility of Affymetrix’s technology and the Ardais samples. The agreement follows on the heels of a similar project, Affymetrix’s announcement last month of a collaboration with Todd Golub of the Whitehead Institute to profile common cancers using Affymetrix chips, concentrating on lymphoma and prostate cancer.

Both the Golub collaboration and this one are designed as a way to standardize gene expression profiling of disease tissues around the Affymetrix GeneChip brand platform. “Affymetrix would love to be the standard for clinical care applications,” Bowdidge said. Collab-orating with Ardais also encourages a standardized approach to tissues collection and sample preparation.

“They might be the standard — for those who have access to it,” said Michael Bittner, associate investigator, cancer genetics, with the National Human Genome Research Institute in Bethesda, Maryland. “To set the standard, you would have to be something that could be widely looked at,” he said. “It’s hard for a small group to decide what is the best way to do something that is very complex.”

Bittner works with the International Genomics Consortium, based in Phoenix, Arizona, which has begun a project, expO (Expression Project in Oncology), that has the goal of collecting 10,000 tumor tissue samples from a large number of cancer types, as well as 1,000 normal tissues, and make the data from gene expression analysis freely available to the public.

The microarray platform to be used for expO’s gene expression analysis has yet to be chosen. Affymetrix is being considered — as well as its chief competitors, Agilent and Amersham. All have donated chips to a pilot project conducted last year.

Still, despite the concern over commercial bars surrounding perhaps critically important human health information, there does appear to be great value in this collaboration, said Bittner.

“100,000 of any gene expression [profiles] would be a very interesting database simply because that would be a larger number than has previously been available,” said Bittner.

The agreement also seems to place Affymetrix into a competitive orbit with a long-time customer, Gene Logic, a Gaithersburg, Maryland-based company that sells gene expression databases derived from its tissue research conducted with Affymetrix’s technology.

A Gene Logic spokesman said his company doesn’t see Affymetrix as a competitor. “This deal is just a business transaction,” said Robert Burrows of Gene Logic. “I don’t believe Affymetrix will be making databases on the backs of tissues using the Affymetrix chip.”

The issue is tissue, he said: “There is a need for gene expression tools for drug discovery development community, and tissues are what’s going to drive the next step in genomics. The tissue business is a competitive one and suddenly a lot of people are trying to acquire samples. Invariably, the quality isn’t there. To do this well takes a lot of time. We have been there for some time.”

Ardais, in the meantime, has set up the National Clinical Genomics Initiative, with partners Beth Israel Deaconess Center of Boston, Duke University Medical Center, Maine Medical Center, and the University of Chicago. The group wants to create standards for processing and storing clinical materials and associated information.

— MOK

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