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Comments on the Proposed Rule Changes

Dear Sir:

This letter is in response to the Patent and Trademark OfficeÂ’s request for written comments on the proposed rule changes set forth at 63 Fed. Reg. 53497-53530. In particular, the following comments concern topic number "8" (Permitting Electronic Submission of Voluminous Material) as it pertains to nucleotide and amino acid sequences.

I am a patent attorney for Novartis Corporation, the United States holding company for Novartis AG, Basel, Switzerland, which was created in December, 1996, by the merger of Sandoz AG and Ciba-Geigy AG. Novartis is one of the worldÂ’s largest life science companies with significant interests in biotechnology. As a result, Novartis files numerous patent applications that include nucleotide and/or amino acid sequence listings. My primary responsibilities for Novartis are preparing and prosecuting such patent applications. I am particularly qualified to address this proposed rule change because I have prepared and filed a number of patent applications containing voluminous sequence listings. The views expressed in these comments are therefore my personal views, as well as those of many of my colleagues.

I wholeheartedly endorse the overall concept of permitting the submission of nucleotide and amino acid sequence listings in only an electronic form. The problems the PTO has set forth in its background of this proposed rule change are also pertinent to patent applicants. We too do not have unlimited file space in which to store paper copies of voluminous sequence listings. Furthermore, I have calculated that one of the greatest out-of-pocket expenses incurred with the filing of applications with voluminous sequence listings is the cost of having the sequence listings printed on paper. The cost of "Express Mail" filing of such applications is not insignificant either. Implementation of this proposed rule change will reduce applicantsÂ’ costs and will greatly simplify applicantsÂ’ storage and management of applications containing voluminous sequence listings.

I further endorse the application of this proposed rule change to provisional applications. Because many biotech patent applications containing nucleotide and/or amino acid sequence listings are filed initially as provisional applications, it would make little sense to require that the sequences contained in provisional applications be submitted in paper form while allowing those contained in non-provisional applications to be submitted in electronic form only. The PTOÂ’s mention of possibly changing the rules of practice to permit provisional applications to be submitted in toto in electronic form would certainly address this issue. However, even if the PTO ultimately decides to still require the rest of the specification of a provisional application to be submitted on paper in the conventional manner, the electronic-only submission of nucleotide and/or amino acid sequences contained in provisional applications should be permitted.

Despite all the enumerated benefits of this proposed rule change, several important issues were not mentioned in the PTOÂ’s notice. For example, what effect (if any) will such a rule change have on the publication of patents upon issuance? Will patents continue to be issued with the entire sequence listing printed on paper, regardless of the format (paper or electronic-only) in which the sequence listing is submitted? Or will the sequence listing only be available on some type of associated electronic database (such as genbank or the PTOÂ’s website) with perhaps a reference to the database in the printed patent (i.e., in a manner similar to references to deposited biological materials)? I note that it is electronic sequences available on searchable databases, not printed sequences, that are actually useful to the public, serving for example as the bases for prior art searches of issued patents. In general, the larger the sequence listing, the more useless the printed version. I assume from the absence of any mention of this issue in the proposed rule change that no change in the printing of patents is contemplated, although this would result in many exceedingly thick printed patents. However, if the entire sequence listing does not become part of the printed patent, additional issues arise. The absence of printed sequences in an issued patent would raise major questions as to whether the nucleotide and/or amino acid sequences not appearing in the printed patent would constitute prior art as of the filing date of the patent application under § 102(e), and possibly even as of the issue date of the patent for purposes of § 102(b). An amendment to 35 U.S.C. § 102 would possibly be necessary to clarify the prior art effect of sequences not appearing in the printed patent, but instead appearing on an associated electronic database.

In addition, what effect (if any) will this proposed rule change have on the use of U.S. patent applications (provisional or non-provisional) as priority documents for foreign filing? Will foreign countries accord priority to U.S. applications that contain only electronic sequence listings? Will applicants (or the PTO) be required to print out the sequence listing to generate the certified copy necessary for foreign filing? Inquiries need to be made with the appropriate foreign entities to ensure that the proposed rule change will not compromise applicantsÂ’ ability to obtain foreign patent protection.

Still another issue that comes to mind is the possibility that an electronic sequence listing submitted with a patent application could become corrupted or otherwise lost before being entered into the PTOÂ’s computer database. Presently, the paper and electronic versions serve as backups for each other; if one version is corrupted or lost, applicants can submit a replacement copy without raising new matter issues by simply referring to the other version. I suggest that applicants be required to submit two identical copies of the sequence listing in electronic form to help avoid this potential pitfall.

Thank you for your consideration of these comments. If you wish to discuss, or would like me to elaborate on, anything set forth herein, please feel free to contact me by telephone (919-541-8587), fax (919-541-8689), or e-mail ( .

Respectfully submitted,

J. Timothy Meigs

United States Patent and Trademark Office
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Last Modified: 7/16/2009 11:23:24 AM