Now FDA officials are talking about patent extensions for companies that develop personalized drugs based on pharmacogenomic research. An FDA working group is preparing a document on how existing incentive programs, such as those for orphan drugs, could be adapted to pharmacogenomic products. Felix Frueh, associate director for genomics at the Center for Drug Evaluation and Research (CDER), is heading this effort, which will include a final guidance on how to submit pharmacogenomic data to FDA. It will discuss how companies might qualify for three-year market exclusivity based on orphan drug status or a new indication by using pharmacogenomic data to stratify patient populations.

Patent Office in Trouble

Of course, in order to protect or extend patents, one has to apply for one from the US Patent and Trademark Office (USPTO), a process that is getting longer and more expensive. USPTO has been overwhelmed by patent applications for increasingly complex technologies. It currently has more than a half-million unexamined applications, and the backlog is projected to hit one million by 2010. Reform is in the air, but the debate is pitting biotechnology and pharmaceutical companies against other high-tech sectors over policy changes that will inevitably create winners and losers.

Probably the most significant change would shift the United States from a first-to-invent to a first-to-file patent award process. This would harmonize the US patent system with the rest of the world, a move welcomed by global pharma companies despite the high cost and turmoil guaranteed to accompany such a significant reform.

The legislation also contains a number of controversial provisions that aim to simplify patent legal challenges and reduce the overall cost of protecting intellectual property rights, but not always in ways that pharma companies support:

Curbs on injunctive relief The bill would make it harder for patent holders to gain injunctive relief against patent infringers pending legal resolution of a patent case. High-tech computer companies with hundreds of patented products back the change as a way to gain relief from frivolous patent challengers. Pharma companies, however, tend to have fewer but higher-value products, and they rely on injunctive relief to protect intellectual property rights.

Streamlined patent challenge process The legislation proposes a nine-month period for challenging newly issued patents through a faster administrative process. The aim is to resolve many early disputes quickly, which pharma and biotech companies generally support. Industry opposes a related proposal that would permit a second window for post-grant opposition review which could make initial patents less secure.

Eliminating the "best mode" requirement Inventors no longer would have to disclose the best mode for producing an invention, a change opposed by generic drug manufacturers.

Jill Wechsler is Pharmaceutical Executive's Washington correspondent.