United States Patent and Trademark Office OG Notices: 27 March 2007

                      Examination of Patent Applications
                       Containing Nucleotide Sequences

I. Summary

The United States Patent and Trademark Office (Office) published
an Official Gazette notice in November of 1996 providing a
partial waiver of the requirements for restriction pursuant to 37 CFR
1.141 et seq. and for unity of invention determinations
pursuant to 37 CFR 1.475 et seq. See Examination of Patent
Applications Containing Nucleotide Sequences, 1192 Off. Gaz.
Pat. Office 68 (Nov. 19, 1996) (1996 Notice). The 1996 Notice
permitted examination of a reasonable number, normally up to ten,
independent and distinct molecules described by their nucleotide
sequence in a single patent application. The Office has reconsidered
the policy set forth in the 1996 Notice in view of changes in the
complexity of applications filed, the types of inventions claimed and
the state of the prior art in this technology since that time. Because
of these changes, the search and examination of up to ten molecules
described by their nucleotide sequence often consumes a
disproportionate amount of Office resources over that expended in 1996.
Consequently, with this Notice the Office rescinds the partial waiver
of 37 CFR 1.141 et seq. for restriction practice in national
applications filed under 35 U.S.C. 111(a), and 37 CFR 1.475 et
seq. for unity of invention determinations in both PCT
international applications and the resulting national stage
applications under 35 U.S.C. 371. This Notice is effective immediately
and is applicable to all pending applications. Note, however, that
supplemental restriction requirements will not be advanced in
applications that have already received an action on their merits in
the absence of extenuating circumstances.

II. Background

In 1996, the Office held public hearings to address concerns
relating to patent protection of nucleic acids described by their
nucleotide sequences. The ease of using automated techniques for
sequencing large numbers of nucleotides resulted in the filing of a
growing number of patent applications, many of which recited thousands
of individual nucleotide sequences. After the public hearings, the
Office modified its restriction and unity of invention practice for the
examination of patent applications that claim large numbers of
polynucleotide molecules described by their nucleotide sequences in an
effort to encourage and promote growth in this technology while taking
into account the unprecedented search and examination challenges that
such applications pose.

In the 1996 Notice, the Office partially waived the requirements
of 37 CFR 1.141(a) and permitted applicant to claim and have examined
in a single application a reasonable number, normally up to ten,
independent and distinct inventions described by their nucleotide
sequences. At that time, the Office determined that such a practice
would not create an undue burden on the Office and would promote
efficient, cost effective examination of these types of applications.
The Office made a similar revision to practice for search and
examination of applications filed under the PCT. Pursuant to the
partial waiver of 37 CFR 1.475 et seq., up to ten nucleotide
sequences would be searched and/or examined in international
applications or national stage applications filed under 35 U.S.C. 371;
where applicants paid a fee for search and/or examination of at least
one additional group (see 37 CFR 1.476(b)), up to four additional
sequences would be searched and/or examined per group.

Patent applications that prompted the public hearings and the
1996 Notice often disclosed multiple partially characterized
complementary DNA (cDNA) molecules, discovered by expressed sequence
tag (EST) techniques, that were claimed and described by simple
reference to a nucleotide sequence. At that time, and in many of those
applications, little information was provided relating to function of
the nucleic acid, nor was there significant description of the function
or the information content (e.g., protein coding capacity)
of the nucleic acid claimed. Consequently such claims were, in many
instances, simple in format and narrow in scope. Often, the examination
of narrowly drawn claims to EST-type nucleic acid molecules required
little more than automated database searches. Further, the review and
analysis of sequence search results could be accomplished within
examination time constraints.

Since 1996, the technology has evolved and the types of nucleic
acid sequence-based claims have become more diverse and complex. In
1996, polynucleotide molecules were often claimed by simple reference
to a nucleotide sequence. Polynucleotide molecules are now often
claimed in a single application in a variety of complex formats, some
of which may embrace multiple inventions, such as by reference to: the
amino acid sequence of the protein encoded; the ATCC number of a
deposited plasmid containing the polynucleotide molecule; arbitrary
laboratory designations; function of the nucleic acid alone or in
combination with a partial linear nucleotide sequence; a genus
described in terms of homology, percent identity, or hybridization; a
genus (or subgenus) described by nucleic acid sequence with variable
positions specified within the sequence listing; single nucleotide
polymorphisms (SNPs); antisense; or interfering RNA.

Advances over the past ten years in automated sequencing and
polynucleotide characterization techniques have made such activities
routine. The entire genome of several organisms, including humans, has
been determined and deposited into nucleotide sequence databases.
Consequently, patent applications claiming large numbers of lengthy
polynucleotides, such as full-length open reading frames and entire
genomes, have become more the norm rather than the exception. The
advances in nucleic acid sequencing techniques have also lead to the
exponential growth in the size of nucleic acid sequence databases and
an increase in the number and complexity of such databases.

The GenBank(R) database in 1996 contained 651,972,984 nucleotides
in 1,021,211 sequences. In 2000 the database contained 11,101,066,288
nucleotides in 10,106,023 sequences, about a seventeen-fold increase in
the number of nucleotides and about a ten-fold increase in the number
of sequences. In February 2006, the GenBank database contained
59,750,386,305 bases in 54,584,635 sequence records or about a
ninty-one-fold increase in the number of nucleotides and about a
fifty-four-fold increase in the number of sequences.

These factors are responsible for exacerbating the search and
examination burden faced by the Office with respect to polynucleotide
inventions claimed and described in currently filed applications. It
now requires significantly more computational time to run individual
nucleotide sequence searches for examination purposes than in 1996, and
there is significantly more pertinent prior art to consider. In
addition, it currently takes more Office resources to correlate the
claimed polynucleotide with the polynucleotide as defined in the prior
art because it is increasingly common for both patent applicants and
prior art references to describe a polynucleotide molecule in different

The foregoing illustrate that the evolution of the technology and
current claim drafting practices are placing an ever-growing resource
burden on the Office to search and examine patent applications
disclosing and claiming nucleotide sequences. Rescission of the 1996
Notice is intended to enhance the Office's ability to provide a
focused, thorough and quality examination of polynucleotide inventions,
and to lead to consistency in the examination of polynucleotide
molecules, regardless of the manner in which they are claimed, and
equitable use of Office computational and examination resources.

III. Examination Guidelines

For National applications filed under 35 U.S.C. 111(a),
polynucleotide inventions will be considered for restriction, rejoinder
and examination practice in accordance with the standards set forth in
MPEP Chapter 800 (except for MPEP 803.04 which is superceded by this
Notice). Claims to polynucleotide molecules will be considered for
independence, relatedness, distinction and burden as for claims to any
other type of molecule.

For International applications and national stage filings of international
applications under 35 U.S.C. 371, unity of invention determination will be
made in view of PCT Rule 13.2, 37 CFR 1.475 and Chapter 10 of the ISPE
Guidelines. Unity of invention will exist when the polynucleotide
molecules, as claimed, share a general inventive concept, i.e., share a
technical feature which makes a contribution over the prior art.

February 22, 2007                                                 JOHN DOLL
                                                   Commissioner for Patents