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USPTO Says Illumina IP Application Predates Existing Affy IP; Illumina Is Senior Party

The US Patent and Trademark Office has decided that a patent tied to a technology sold by Affymetrix interferes with an Illumina patent application because Illumina’s application was filed ahead of Affy’s, Illumina said last week.
The decision, which gives Illumina an advantage in the case by naming it the senior party, comes one week before Affymetrix and Illumina are scheduled to appear in court as part of a July 2004 suit launched by Affy that claims Illumina infringes five patented DNA microarray and related technologies (see BAN 2/9/2007).
According to Illumina, the interference relates to Affymetrix’s molecular inversion probe genotyping technology, which is protected by US Patent No. 6,858,412, “Direct multiplex characterization of genomic DNA.“
The patent was filed in 2001 by Stanford University inventors and later used by ParAllele BioScience to protect its flagship molecular inversion probe technology.
Affymetrix acquired the technology through its purchase of ParAllele BioScience in October 2005, and Illumina asked the USPTO the very same day to investigate the IP for a possible interference (see BAN 10/26/2005).
According to the patent’s abstract, it claims “methods of multiplexing nucleic acid reactions, including amplification, detection and genotyping” that “rely on the use of pre-circle probes that are circularized in the presence of the corresponding target nucleic acids, cleaved, and then amplified.”
Illumina last week said the USPTO named it the senior party because its “original patent filing predates that of the ‘412 patent.” It is unclear which of its earlier patent applications contain claims similar to the ‘412 patent.
Illumina declined comment beyond the statement this week.

When it alerted the USPTO of a possible interference in 2005, Illumina said that the technology was invented by Illumina scientists "during the course of early research and development at the company," although it is "not currently in use" at Illumina.

"The earlier filing date is expected to establish Illumina as the 'senior party' in the interference proceeding, placing on the '412 patent inventors the burden of proof to establish an earlier date of invention," Illumina had said in the statement.
Illumina’s senior party designation could put Affymetrix at a big disadvantage. According to a patent attorney with experience in the interference review process, statistics show that companies named a junior party have a miniscule chance of winning the US patent office’s designation as original inventor.
In such cases, the patent office designates a senior party — the party that filed first — and a junior party. “My understanding is that the senior party wins 97 percent of the time,” Richard Warburg, an intellectual property attorney with Foley and Lardner, told BioArray News sister publication BioCommerce Week last fall in relation to a separate interference case.
“It’s a huge disadvantage to be the junior party … because you have the burden to prove you had the invention beforehand. You have to prove you actually made the invention, or that you had a full concept of the invention prior to the other person,” he said.
Now, according to Illumina, the interference proceeding will try to sort out which company first invented the technology that is protected by US Patent No. 6,858,412. Affymetrix last week declined to comment on the interference case.
Affymetrix has yet to widely commercialize the MIP technology since it acquired it in 2005. Last month, during Affymetrix’s fourth-quarter earnings call, CEO Steve Fodor said that it expects to start recording revenue from its acquisition of ParAllele by the end of the year (see BAN 2/20/2007).
Fodor hinted that the firm’s manufacturing issues in 2006 had distracted the company from launching MIP-based products. “It's always a little bit bigger of a job to get things out into the marketplace than when you first assume, when you sort of purchase a new technology,” Fodor said. “But, even though we were distracted from quite a bit last year, we have been working constantly on it.”

“It’s a huge disadvantage to be the junior party... because you have the burden to prove you had the invention beforehand. You have to prove you actually made the invention, or that you had a full concept of the invention prior to the other person.”

Trial Opens this Week

Separate from the patent interference case is Affy’s suit against Illumina, which opens this week in the US District Court for the District of Delaware.
In its suit, Affy is demanding lost profits, royalties, and damages for willful infringement, and a permanent injunction prohibiting Illumina from using the technology claimed in five Affy patents.
In September 2006, the judge in the case issued a Markman order to interpret 15 key terms of the case (see BAN 9/5/2006).
Both parties interpreted the announcement as a small victory: Affymetrix said the court found that the patents go beyond in situ synthesis, probes linked to a single surface, or to the placement of probes at predetermined locations.
Meantime, Illumina held that the ruling supported its position as the “proper interpretation,” although the judge in the case denied Illumina’s motion to dismiss the case.
Illumina CEO Jay Flatley has maintained that Affymetrix’s allegations are “without merit” as Illumina believes the patents are “invalid and unenforceable.”

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