The Patent Office is considering whether or not to appeal a recent ruling by a U.S. District Court in Virginia, which voided the new rules limiting how many times companies could submit patent applications, according to a report by the San Francisco Business Journal.

The ruling was viewed as a victory for the biotech industry, since the industry had opposed the new rule changes. 

The San Francisco Business Journal explained the industry’s position as follows:

The problem is that, for competitive reasons, the biotech industry often has to submit patent applications before it has completed clinical trials. New drug technology only gets patent approval if it has been proven to help cure disease, but as clinical trials take years, companies might loose out if they wait to file until the benefits have been demonstrated in humans. Instead, applications are usually based on lab data that show a drug is likely to impact the molecular processes involved in disease. Sometimes patent reviewers find this data to be insufficient, especially if a new, little-understood class of therapies are featured in the application.

This is why the biotech industry disliked the changes. They only allowed companies two chances to resubmit if the patent reviewer rejected an initial application. The patent applications would also have to be more narrowly focused, forcing companies to limit the scope of their drug therapies early on.

In contrast, the opposing view by patent rule change supporters was that the "changes would help prevent abuses of the system," and that the biotech industry had been guilty of those abuses.  The San Francisco Business Journal reported on the position of supporters as follows:

[Many biotech companies submit patent] applications before new drug candidates have been thoroughly investigated. In these cases the patent application is used to curtail competitors while the research process continues. This goes against the fundamental nature of the patent process, which has never allowed a patent application to serve as a "hunting license."

The new rules were scheduled to go into effect on November 1, 2007, according to The Recorder.  However, Triantafyllos Tafas, founder of Ikonisys, and GlaxoSmithKline filed suit against the Patent and Trademark Office and its director Jon Dudas, to block this from happening.  Eastern Virginia U.S. District Judge James Cacheris granted a preliminary injunction on Oct. 31, 2007 and GlaxoSmithKline and Tafas filed for summary judgment on Dec. 20, 2007.

According to The Recorder, Cacheris granted summary judgment to the plantiffs earlier this month, ruling that the patent office can’t make "substantive" changes to the rules, only "procedural" ones. 

Ultimately, the Patent and Trademark Office’s decision on whether or not to appeal this ruling could be irrelevant.  The San Francisco Business Journal reported:

If a patent reform act passes over the next few years, the debate may become a mute point. A patent reform bill was proposed in early 2007 that would grant the USPTO more rule making autonomy.

Of course, patent reform legislation has not to date been passed, and so life sciences companies, including biotech companies, are likely to continue their challenge of this exercise of Patent and Trademark Office rulemaking.