OFFICIAL GAZETTE NOTICE
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.l42(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 International 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.
Date: October 17, 1996
Bruce A. Lehman
Assistant Secretary of Commerce and
Commissioner of Patents and Trademarks