PTO Hearings On Patenting Of Nucleic Acid Sequences

During hearings in April on issues associated with protecting nucleic acid sequences, the U.S. Patent and Trademark Office (PTO) signaled its intention to exact a premium for examining patent applications with claims that cover large or very numerous sequences. Apparently bowing to the inevitable, the PTO thus focused on the practical logistics of such examination, and did not pursue concerns expressed previously over whether the patenting of complete genomes or human genome fragments would inhibit the advancement of biotechnology.

The hearings, conducted on April 16 in La Jolla, CA, and on April 23 in Arlington, VA, had been held over from late last year, when the PTO postponed scheduled meetings to provide more time for submission of comments. See 1184 Official Gazette 110 (March 26, 1996). As a prelude to the hearings, the PTO had hosted an open house on April 3, to demonstrate the time and cost involved with searching very large sequences.

At the hearings the PTO explained that there are roughly 70 applications now pending that fall into the "mega sequence" category. PTO officials stated their expectation that this number would increase, given the level of current research involving genomic sequencing.

The PTO estimated that 90 senior examiners will require at least 9 months, at a cost of $12 million, to scrutinize the 70 mega-sequence applications with respect to prior art alone. The PTO therefore concluded that some manner of fee increase is justified to underwrite the significantly higher cost of examining these cases.

Opposition to a fee increase was a theme voiced widely by participants at the hearings. But there also were several suggestions made on how the PTO could ease implementation of a policy for handling mega-sequence applications. Among the proposals floated in this regard were:

• upgrading the PTO's computer software for searching these mega sequences;
• establishing a working panel of PTO, biotech, and computer personnel to collaborate continuously on this problem;
• employing genus/species classification to narrow the original search, for example, to avoid "meaningless" homology matches;
• amending the sequence rules, 37 CFR §§1.821-1.825, to eliminate the present duty of applicants to include non-claimed sequences (comparison sequences, primers, linkers, probes, etc.) in sequence listings; and
• adapting, as a model for searching large DNA molecules, the techniques used in the chemical-polymer arts, where claimed compounds and working examples may encompass millions of "actual" compounds by virtue of (R)-group permutations.

The PTO stated that it would review the testimony marshaled from the hearings and then would formulate a policy which would appear in a forthcoming issue of the Official Gazette. In the meantime, written transcripts of oral testimony will be available for purchase around the first week of May from Miller Reporting Service (202-546-6666).