By Randall Osborne

West Coast Editor

Affymetrix Inc. wrapped up yet another deal, but this package is unlike the others in scope and in the nature of its heavyweight partner, Millennium Pharmaceuticals Inc.

The four-year research and development agreement, plus a volume discount supply contract, is for developing a new generation of Affymetrix¿s Gene Chip, which already has garnered many customers.

¿Millennium is migrating its entire array platform onto ours,¿ said Ann Bowdidge, director of investor and public relations for Santa Clara, Calif.-based Affymetrix, which will develop gene expression arrays with Millennium, of Cambridge, Mass.

In exchange, Affymetrix is giving Millennium ¿preferred access and pricing¿ to the gene expression platform, in return for a ¿volume commitment¿ to GeneChip. Financial details were not disclosed.

Affymetrix¿s high-throughput DNA arrays allow for monitoring tens of thousands of genes in one experiment. Armed with Millennium¿s informatics expertise, the company will use a joint research team to develop sample preparation solutions, along with automated array processing, sample and probe array bar coding, and tracking systems.

The idea is to make GeneChip easier to use for drug development and patient care ¿ which will benefit both companies and eventually their customers and partners, Bowdidge said.

¿People, when they think of Affymetrix¿s technology, traditionally think of research, but this deal pushes it into [applications such as] toxicology and clinical trials,¿ she said. ¿Some of our larger pharmaceutical companies have already looked at it for those applications.¿

Affymetrix has commercialization rights to chip process and application upgrades made through the deal, and is paying technology development fees and royalties to Millennium, which gets the right to use jointly developed technology for itself and with collaborators.

Everybody wins.

¿It¿s all in one standardized platform,¿ Bowdidge said.

At its manufacturing plants in West Sacramento, Calif., and Sunnyvale, Calif., Affymetrix uses photolithography to make arrays in a way similar to the way semiconductors are made. Wafers are cut into chips that can be more carefully quality controlled, Bowdidge said.

The technology, as it¿s improved more and more, can be useful in diagnostics as well as other aspects of patient care and drug development, she added.

¿We already have partnerships with Roche Molecular Systems and bioMerieux,¿ Bowdidge said.

The 1995 deal was made with Roche Molecular Systems Inc., of Branchburg, N.J. (a subsidiary of Roche Holdings Ltd., of Basel, Switzerland), to develop a microfabricated chip to detect mutations in cystic fibrosis patients.

In 1998, bioMerieux Vitek Inc., of Hazelwood, Mo., exercised its option to expand a 1996 bacteriology agreement with Affymetrix to diagnostics for detecting sequence variations in the HIV genome. The agreement also includes genotyping tests to detect microbial contamination of food.

Bowdidge told BioWorld Today the company has deals ¿outside the traditional drug discovery area,¿ too.

¿We have agreements with chocolate companies,¿ she said. ¿Why do you feel the way you do when you eat chocolate. What genes are turned on and off?¿

But the Millennium pact takes aim directly at patients and their health.

Steve Sylven, corporate communications associate with Millennium, said the shift from his firm¿s internally developed, nylon-based transcription profiling system to Affymetrix¿s Gene Chip will take place over the four-year duration of the agreement, which carries an optional one-year renewal.

¿It¿s just another step forward, allowing us to focus more attention downstream,¿ he told BioWorld Today.

Bowdidge said of the GeneChip system: ¿It¿s the gold standard now, and we¿re continuing to push the envelope.¿

Affymetrix¿s (NASDAQ:AFFX) stock closed Wednesday at $21.53, up $1.57. Millennium¿s shares (NASDAQ:MLNM) ended the day at $24.32, up $1.08.