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MIT filed a lawsuit against biotechnology company Affymetrix last month, alleging the company’s GeneChip technology infringes an existing MIT patent.

The complaint, filed on July 1, accuses Affymetrix for knowingly infringing the patent and involving others to infringe by marketing the technology in the United States. It cites E8 Pharmaceuticals and MIT as plaintiffs. E8 Pharmaceuticals is a company co-founded by MIT Biology Professor David E. Housman, who is also a co-inventor of the patented technology.

On July 3, Affymetrix filed a notice about the lawsuit to the U.S. Securities and Exchange Commission. The notice stated, “We believe that the plaintiffs’ claims are without merit and will vigorously defend against the claims advanced in the complaint.” According to its Web site, Affymetrix invented its GeneChip technology in the late 1980s, with the company now offering “the gold standard tool for analyzing complex genetic information.”

The Affymetrix public relations manager declined to comment, citing pending litigation. The plaintiffs and their attorneys also declined to comment.

MIT and Affymetrix have clashed before, as the MIT complaint reveals. In 2004, the U.S. patent office assigned MIT the patent, naming Housman as co-inventor. A year later, Affymetrix sought a patent for the same technology, therefore provoking the patent office to interfere. In 2007, the patent office determined Housman and his associates as the inventors.

“The fact that the patent interference was decided in MIT’s favor was an important milestone,” Housman said in an e-mail. “The steps which have been taken more recently are also important in resolving this case to reflect the value of the intellectual property which was created at MIT.”

The technology causing the dispute is essentially an efficient DNA microarray. According to the complaint filed by MIT, the technology allows users to cost-effectively analyze genes with minute DNA samples and few reactants, yet yielding results previously considered impossible, even in laboratories employing thousands of different reactants.

DNA microarrays, also known as gene chips, are commonly used in a variety of disciplines such as gene expression analysis, toxicology, and forensic analysis. The chips are single-use, can be customized for a specific organism or to target certain genes, and cost about $200 to $400 dollars each.

Besides supplying products to MIT laboratories, Affymetrix actually has ties to MIT and Harvard’s Broad Institute, collaborating with Broad to develop some of its newest gene chips. How the lawsuit will affect the relationship is unknown.

If MIT wins, up to three times the damages plus interest and attorney’s fees could be awarded, a hefty amount since its claims affect a crucial component of Affymetrix’s business, worth $603 million. Affymetrix faced a similar lawsuit against competitor Illumina four years ago in which the jury awarded Affymetrix $90 million. Patent litigation is not uncommon, especially in the field of biotechnology, with most of the cases settled outside the court.

For court documents related to the suit, see http://www-tech.mit.edu/V128/N30/affymetrix/.