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MIT and Spinout E8 Pharmaceuticals Sue Affymetrix for Alleged Patent Infringement

The Massachusetts Institute of Technology and spinout company E8 Pharmaceuticals have sued Affymetrix alleging that the company’s GeneChip technology infringes on a patent owned by MIT and licensed to E8.
The suit, which was filed last week in the US District Court for the District of Massachusetts, claims that Affymetrix’s use, manufacture, and sale of its GeneChip products for certain applications infringes US Patent No. 6,703,228.
The ‘228 patent, entitled “Methods and products related to genotyping and DNA analysis,” was issued to MIT in March 2004. It has been licensed to E8, a Cambridge, Mass.-based company co-founded by David Housman, a professor of biology at MIT and one of the inventors named on the patent.
According to court documents, the ‘228 patent covers technology that “enables users to perform accurate, reproducible, and cost-effective genetic analysis using minute amounts of sample DNA and a small number of reactants to generate results that were previously impossible, even in specialized high-throughput centers using many thousands of different reactants.”
The dispute between Affymetrix and MIT over the patent has been ongoing since 2005. Six months after MIT was granted the ‘228 patent, Affymetrix filed a US patent application, serial no. 10/942,479, with the US Patent and Trademark Office claiming priority to an earlier 1994 application, according to court documents.
MIT and E8 allege that in March 2005 Affymetrix filed new claims with the USPTO corresponding to the claims of the ‘228 patent, “thereby assert[ing] the patentability of and ownership of the methods claimed” in the ‘228 patent.
As a result of MIT and Affymetrix claiming the same methods and claiming that each was first to develop them, the USPTO instituted a patent interference in April 2006.
Following a year of patent interference proceedings, the USPTO on May 2, 2007, ruled that Housman’s group at MIT “was the first to invent the claimed methods and was therefore entitled to the patent,” according to court documents.

“E8 is the licensee of the patent at this point, and is the prime mover here in the litigation.”

At this point E8 had not yet been founded. According to documents from the state of Delaware division of corporations, E8 was incorporated in the state on Jan. 17, 2008.
Founded by Housman and Harvard genetics professor Richard Mulligan, E8 has licensed the ‘228 patent from MIT and has the exclusive right to grant sublicenses to the patent.
“E8 is the licensee of the patent at this point, and is the prime mover here in the litigation.” Housman told BTW this week. “The company is recent and relevant to the litigation.”
Housman, who is also a faculty member in the Harvard-MIT Division of Health Sciences and Technology, declined to provide additional details about E8’s business plan. According to the Harvard-MIT HST website, Housman is “interested in developing a system that includes cell-based screening of compounds using cells derived from different backgrounds, combined with rapid genotyping, to identify genetic markers linked to drug response and toxicity.”
It is unclear why MIT did not file suit as a lone plaintiff last year after the USPTO ruled that it was the first to invent the methods covered by the ‘228 patent, instead waiting until after E8 was founded and joining the fledgling company as a co-plaintiff. A spokesperson for MIT said that the university would not comment on the litigation.
In any event, according to court documents, MIT and E8 have asked the court to enter a judgment that Affymetrix is infringing the ‘228 patent by “making, having made, using, offering to sell, and/or selling GeneChip products and directing its customers to use them according to the methods of the ‘228 patent.”
Further, the co-plaintiffs allege that Affymetrix’s customers are directly infringing the ‘228 patent by practicing the patented method in accordance with Affymetrix’s guidance. E8 and MIT are seeking triple damages because they believe that alleged infringement has been willful, according to the complaint; and have asked the court to award them ongoing royalties or issue a permanent injunction prohibiting Affymetrix from “continued unlicensed infringement.”
According to the complaint, Affymetrix has “significant contacts” within the US District Court for the District of Massachusetts venue because, for example, it manufactured GeneChip instrumentation products at a manufacturing facility in Bedford, Mass.; and the company’s wholly owned subsidiary, Genetic Microsystems, “is or has been incorporated in Massachusetts, and is or has been a manufacturer of instruments for fabricating and an analyzing DNA arrays used in life sciences R&D applications.”
It is unclear how important the ‘228 patent is to Affymetrix’s core business. An Affymetrix spokesperson told BTW that the company does not comment on ongoing litigation as a matter of policy.
However, in a filing with the US Securities and Exchange Commission last week, Affymetrix said that it believes the plaintiffs' claims “are without merit and we will vigorously defend against the claims advanced in the complaint."

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