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Alnylam Sues USPTO Over Alleged Patent Term Adjustment Shortfall

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By Doug Macron

This story has been updated to include comment from Roche.

As litigation over its rights to technology within the Tuschl-I and -II patent estates continues (see RNAi News, 7/16/2009), Alnylam Pharmaceuticals has opened a new front in the war to defend its intellectual property, suing the acting director of the US Patent and Trademark Office earlier this month over the term of a patent filed by the company's one-time German subsidiary.

In a suit filed on July 2 by Alnylam Europe against the USPTO's John Doll, who also serves as the agency's deputy under secretary of commerce for intellectual property, the company alleges that the adjusted term of one of its patents was inappropriately cut short by roughly a year and a half.

The IP at issue, US Patent No. 7,473,525, is entitled "Compositions and Methods for Inhibiting Expression of Anti-Apoptotic Genes.” Filed in 2003 and granted earlier this year, the patent claims a dsRNA less than 25 nucleotides long that can inhibit the expression of an anti-apoptotic gene such as a Bcl-2.

"The invention also relates to a pharmaceutical composition comprising the dsRNA together with a pharmaceutically acceptable carrier; methods for treating diseases caused by the expression of an anti-apoptotic gene using the pharmaceutical composition; and methods for inhibiting the expression of an anti-apoptotic gene in a cell," the patent's abstract states.

Pursuant to USPTO procedure, the patent office provides patent term adjustments, or day-by-day extensions to the standard term of a patent, in order to compensate for delays, such as ones resulting from the failure of the agency to prosecute the patent in a timely manner.

For example, the failure of the USPTO to issue a patent within three years of the actual filing date of the application can result in the adjustment of a patent's term.

Instituted as part of the Patent Term Guarantee Act of 1999, patent term adjustments are the result of the change in patent terms to 20 years from the filing of a patent application from the previous term of 17 years beginning with the issuance of the patent, according to the USPTO.

In its suit, Alnylam charges that Doll determined that the '525 patent should be adjusted by 768 days. Disagreeing with that ruling, Alnylam said it filed earlier this year a request for reconsideration of the patent term adjustment, asking that the patent be given an added 1,334 days of exclusivity.

"The determination of this 768-day patent term adjustment is in error because the [US]PTO failed to properly account for the delays that occurred before the date that was three years after the actual filing date of [the patent's] application," the company stated.

As a result, Alnylam argued that the patent is entitled to an adjustment of 1,036 days to reflect the number of days the patent's issue date exceeded three years from the application's filing date. In addition, the patent office experienced an 805-day delay in examining the patent application.

Since a patent term adjustment is not to exceed the actual number of days the issuance of the patent was delayed, and the overlap between the aforementioned delays is 248 days, "the total period of [US]PTO delay is 1,593 days," Alnylam contends in its suit.

While the total period of the patent office's delay is reduced by the period of delay attributable to the patent application's filer, the company alleges, the USPTO incorrectly determined this to be 268 days. In actuality, Alnylam's delay in filing the application was 259 days, it added.

Arguing that the '525 patent is not subject to patent adjustment term limitations, Alnylam said in its suit that the proper term adjustment for its patent is 1,334 days. This represents the sum of the patent office's delay in examining the patent, 805 days, and the number of days the patent's issuance exceeded the three-year term after it was submitted as an application, or 1,036 days, minus the 248-day overlap between the two delays and the 259-day delay attributable to the company.

Doll "arrived at the incorrect 768-day patent term adjustment by miscalculating the overlap between the [two USPTO delays] … in addition to miscalculating the period of [patent] applicant delay," Alnylam contended in the suit.

"The director's determination that the '525 patent is entitled to only 768 days of patent term adjustment is arbitrary, capricious, an abuse of discretion, or otherwise not in accordance with law and in excess of statutory jurisdiction, authority, or limitation," the company added.

As such, Alnylam is seeking a court-ordered change in the patent term adjustment of the '525 patent to 1,334 days.

About two years ago, Roche acquired Alnylam Europe as part of a broad RNAi drug-discovery and IP-licensing deal with Alnylam (see RNAi News, 7/20/2007). Now called Roche Kulmbach, the former Alnylam subsidiary has become Roche's Center of Excellence for RNA Therapeutics.

While Alnylam Europe is listed as the plaintiff in the suit, Alnylam is the '525 patent's assignee and the law firm handling the suit against Doll has performed patent prosecution work for the Cambridge, Mass.-based company before.

A Roche spokeswoman confirmed that Roche is not involved in the suit. Roche Kulmbach, she noted, was split off from Alnylam Europe at the time of the company's deal with Alnylam.

"Only the former was acquired by Roche," she noted.

Alnylam did not return a request for comment.

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