Last year, the U.S. Patent and Trademark Office (PTO) routinely assigned patent applications for bioinformatics inventions to examiners in diverse departments. Then the office made a projection, based on input from companies, that it would receive more than 300 such applications in the fiscal year that ended Sept. 30. To ensure consistent treatment for the predicted flood of filings, PTO created Art Unit 1631 (AU1631) last December. This unit now consists of 10 examiners holding degrees, sometimes joint ones, in disciplines ranging from biology to physics to electrical engineering.
The deluge, however, never materialized. As of Oct. 1, there were about 110 pending applications in AU1631, most of which claim diagnostic methods based on analysis of gene arrays, according to Jasemine C. Chambers, a director of PTO's Technology Center 1600, which oversees the unit. Uncertain as to why the shortfall occurred, she suggests that some inventors may have merely filed provisional applications to establish priority of invention. Such applications, which PTO doesn't examine, expire after a year. If inventors decide to turn them into full applications, however, they are assigned to AU1631.
Adriane M. Antler, a partner at the New York law firm Pennie & Edmonds, says that the creation of AU1631 has made PTO's processing of bioinformatics applications more efficient. "There tends to be a shorter time period from filing until [patent] issuance," observes Antler, who has prosecuted more than 30 such applications. She adds, "It's a great aid to have examiners in the Patent Office who have the technical background to understand these applications," which requires knowledge of biology and computational skills.
AU1631's caseload may now be light, but bioinformatics patent work is likely to grow. "The genome projects have developed a huge amount of data," notes James E. Austin, a partner at Beyer Weaver & Thomas, a law firm based in Mountain View, Calif., that has handled bioinformatics patent work for nearby Incyte Genomics Inc. "And one of the biggest problems is going to be trying to sort through that data to get some useful medical and biochemical information."
Two years ago, bioinformatics patents received a boost when a federal appeals court ruled that a data-processing system designed for making financial calculations was not an unpatentable abstract idea; it was useful and patentable.1 Chambers views this decision and a later one2 as relevant to patents that claim computer programs for analyzing or predicting biological functions or structures. But business-method patents remain controversial, so she cautions that Congress might eventually forbid them.
PTO advises bioinformatics applicants to follow the computer-programming guidelines set forth in sections 2106.01 and 2106.02 of the manual used by patent examiners.3 Inventors should also take note of a recent change in the rules that should slim down their bulky applications. As of September, applicants may file nucleotide and amino acid sequences and annotation tables on CD-ROM, instead of on paper.
One problem with applications, according to Chambers, is that "the claims are very broadly written with respect to both the biological and computer aspects, frequently to the point of incomprehensibility." She says that bioinformatics has also challenged PTO to develop new systems to classify inventions; new ways to handle the sometimes voluminous data sets; and new approaches to searching for and applying "prior art" (which prevents inventions from receiving patent protection). The office has established three groups to look into these issues. In a pilot project, PTO recently began to outsource sequence searches.
Douglas Steinberg is a freelance writer in New York.
1. State Street Bank & Trust Co. v. Signature Financial Group Inc., 149 F.3d 1368 (Fed.Cir. 1998).
2. AT&T Corp. v. Excel Communications Inc., 172 F.3d 1352 (Fed.Cir. 1999).
3. The Manual of Patent Examining Procedure is available at www.uspto.gov.