(99) Examination of Patent Applications
Containing Nucleotide Sequences
I. Introduction
Biotechnology is expected to be an important growth industry from now
until well into the twenty-first century, particularly in the United
States, one which will produce new therapeutics for the benefit of
mankind. The Patent and Trademark Office (PTO) has taken a very active
role in working together with its customers to simplify and standardize
PTO policies and procedures and to encourage and promote the growth of
this industry for the benefit of humanity.
For at least a decade, researchers in the biotechnology industry have
been filing patent applications claiming isolated DNA or RNA sequences
of nucleotides, referred to as nucleotide or nucleic acid sequences.
Scientific and technological advances now permit researchers to identify
large numbers of gene sequences rapidly. The ease of using automated
techniques for sequencing large numbers of nucleotides in a nucleic acid
has resulted in the filing of a growing number of patent applications,
many of which recite thousands of individual nucleotide sequences with
each sequence reciting at least several hundred nucleotides. The
examination of these applications presents unprecedented search and
examination challenges, even with the most modern, up-to-date equipment.
Faced with these challenges, the PTO held public hearings on issues
relating to patent protection of nucleotide sequences on April 16, 1996,
in San Diego, California and on April 23, 1996, in Arlington, Virginia.
At those hearings, the PTO received several recommendations that
restriction practice pursuant to 35 U.S.C. 121 should be applied to
patent applications claiming nucleotide sequences.
This Notice responds to comments received during the hearings. This
Notice clarifies PTO's policy for examination of patent applications
that claim large numbers of nucleotide sequences.
II. The PTO Will Permit Applicants to Claim Up to Ten
Independent and Distinct Nucleotide Sequences In One
National Application
By statute, "[i]f two or more independent and distinct inventions are
claimed in one application, the Commissioner may require the application
to be restricted to one of the inventions." 35 U.S.C. 121. Pursuant
to this statute, the Rules of Practice in Patent Cases provide that
"[i]f two or more independent and distinct inventions are claimed in a
single application, the examiner in his action shall require the
applicant . . . to elect that invention to which his claim shall be
restricted." 37 CFR 1.142(a). See also 37 CFR 1.141(a).
Nucleotide sequences encoding different proteins are structurally
distinct chemical compounds and are unrelated to one another. These
sequences are thus deemed to normally constitute independent and
distinct inventions within the meaning of 35 U.S.C. 121. Absent
evidence to the contrary, each such nucleotide sequence is presumed to
represent an independent and distinct invention, subject to a
restriction requirement pursuant to 35 U.S.C. 121 and 37 CFR 1.141 et
seq. Nevertheless, to further aid the biotechnology industry in
protecting its intellectual property without creating an undue burden on
the Office, the Commissioner has decided sua sponte to partially waive
the requirements of 37 CFR 1.141 et seq. and permit a reasonable number
of such nucleotide sequences to be claimed in a single application.
Accordingly, in most cases, up to ten (10) independent and distinct
nucleotide sequences will be examined in a single application without
restriction. It has been determined that normally ten sequences
constitute a reasonable number for examination purposes. The PTO
believes that allowing applicants to claim up to ten (10) independent
and distinct nucleotide sequences in a single application will promote
efficient, cost-effective examination of these types of applications. In
addition to the specifically selected sequences, those sequences which
are patentably indistinct from the selected sequences will also be
examined. Furthermore, nucleotide sequences encoding the same protein
are not considered to be independent and distinct inventions and will
continue to be examined together.
In some exceptional cases, the complex nature of the claimed
material, for example a protein amino acid sequence reciting three
dimensional folds, may necessitate that the reasonable number of
sequences to be selected be less than ten (10). In other cases,
applicants may petition pursuant to 37 CFR 1.181 for examination of
additional nucleotide sequences by providing evidence that the different
nucleotide sequences do not cover independent and distinct inventions.
III. Under the Unity of Invention Standard in an Interna-
tional Application or National Stage Application Filed
Under 35 U.S.C. 371, Up to Ten Nucleotide Sequences
Will Be Searched and/or Examined Without Payment of
An Additional Fee
International applications filed under the Patent Cooperation Treaty
(PCT) and national stage applications filed under 35 U.S.C. 371 will
be treated in a similar manner. Under 37 CFR 1.475 and 1.499 et seq.,
when claims do not comply with the requirement of unity of invention,
i.e., when the claimed subject matter does not involve "one or more of
the same or corresponding special technical features," 37 CFR 1.475(a),
an additional fee is required to maintain the claims in the same
application. 37 CFR 1.476(b).
The Commissioner has decided sua sponte to partially waive 37 CFR
1.475 and 1.499 et seq. to permit applicants to claim up to ten (10)
nucleotide sequences which do not have the same or corresponding special
technical feature, without the payment of an additional fee. The PCT
permits inventions which lack unity of invention to be maintained in the
same international application for the payment of additional fees. Thus,
in international applications, for each group for which applicant has
paid additional international search and/or preliminary examination
fees, the PTO has determined that up to four (4) such additional
sequences per group is a reasonable number for examination. Further,
claims directed to the selected sequences will be examined with claims
drawn to any sequence combinations which have a common technical feature
with the selected sequences. Nucleotide sequences encoding the same
protein are considered to satisfy the unity of invention standard and
will continue to be examined together.
IV. Examples of Nucleotide Sequence Claims That Are the
Subject of this Notice
Examples of typical nucleotide sequence claims impacted by this Notice
include:
(1) an isolated and purified DNA fragment comprising DNA having at least
95% identity to a DNA sequence selected from SEQ ID Nos. 1-1,000;
(2) a combination of DNA fragments comprising SEQ ID Nos. 1-1,000; and
(3) a combination of DNA fragments, said combination containing at least
thirty different DNA fragments selected from SEQ ID Nos. 1-1,000.
Applications claiming more than ten (10) individual independent and
distinct nucleotide sequences in alternative form, such as set forth in
example 1, will be subject to a restriction requirement. Only the ten
(10) nucleotide sequences selected in response to the restriction
requirement and any other claimed sequences which are patentably
indistinct therefrom will be examined.
Applications claiming only a combination of nucleotide sequences,
such as set forth in example 2, will generally not be subject to a
restriction requirement. The presence of one novel and nonobvious
sequence within the combination will render the entire combination
allowable. The combination will be searched until one nucleotide
sequence is found to be allowable. The order of searching will be chosen
by the examiner to maximize the identification of an allowable sequence.
If no individual nucleotide sequence is found to be allowable, the
examiner will consider whether the combination of sequences taken as a
whole renders the claim allowable.
Applications containing only composition claims reciting different
combinations of individual nucleotide sequences, such as set forth in
example 3, will be subject to a restriction requirement. Applicants will
be required to select one combination for examination. If the selected
combination contains ten or fewer sequences, all of the sequences of the
combination will be searched. If the selected combination contains more
than ten sequences, the combination will be examined following the
procedures set forth above for example 2. More specifically, the
combination will be searched until one nucleotide sequence is found to
be allowable with the examiner choosing the order of search to maximize
the identification of an allowable sequence. The identification of any
allowable sequence(s) will cause all combinations containing the allowed
sequence(s) to be allowed.
In applications containing all three claims set forth in examples
1-3, the PTO will require restriction of the application to ten
sequences for initial examination purposes. Based upon the finding of
allowable sequences, claims limited to the allowable sequences as in
example 1, all combinations, such as in examples 2 and 3, containing the
allowable sequences and any patentably indistinct sequences will be
rejoined and allowed.
Rejoinder will be permitted for claims requiring any allowable
sequence(s). Any claims which have been restricted and non-selected and
which are limited to the allowable sequence(s) will be rejoined and
examined.
V. Other Possible Solutions
The PTO is pursuing other possible ways to efficiently examine
applications that claim large numbers of nucleotide sequences, including
the following:
A. Software Development - Using private contractors, the PTO will
attempt to identify, modify or develop software tools to aid in
searching and the analysis of search results.
B. Feedback - The PTO will pursue and evaluate suggestions from
applicants, members of the bar, industry, scientists, government, and
inventors.
C. International Cooperation - The PTO will encourage greater
cooperation between the other patent offices of the world in the area of
biotechnology. The PTO will work with these offices to share resources
thereby minimizing duplication of search and examination.
D. PTO Outside Search Center - The PTO will explore the possibility of
establishing an outside search center which would perform standard
searches for all patent applicants submitting applications containing
nucleotide sequences.
E. Search Standards - The PTO will explore the possibility of
establishing quality and proficiency standards for prior art searches so
that applicants can perform their own pre-examination searches.
Applicants could then submit their searches with their applications, and
the PTO could examine applications based on applicants' searches.
F. Communication - The PTO will communicate its procedures for searching
the prior art and how the current hardware and software have been
optimized for examination needs.
Any questions, comments or suggestions regarding this Notice should be
directed to Esther M. Kepplinger, Supervisory Primary Examiner, Group
Art Unit 1302: by mail to Box Comments-Patents, Assistant Commissioner
for Patents, Washington, DC 20231; by FAX to (703) 305-3601; or by
electronic mail addressed to ekepplin@uspto.gov.
October 17, 1996 BRUCE A. LEHMAN
Assistant Secretary of Commerce and
Commissioner of Patents and Trademarks
[1192 OG 68]