Ex Parte Cole et al

Board of Patent Appeals and Interferences

Sep 2, 2010

10802796 (B.P.A.I. Sep. 2, 2010)

UNITED STATES PATENT AND TRADEMARK OFFICE
UNITED STATES DEPARTMENT OF COMMERCE
United States Patent and Trademark Office
Address: COMMISSIONER FOR PATENTS
P.O. Box 1450
Alexandria, Virginia 22313-1450
www.uspto.gov
APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO.
10/802,796 03/18/2004 Stewart Cole 03495.0320-01000 6307
22852 7590 09/02/2010
FINNEGAN, HENDERSON, FARABOW, GARRETT & DUNNER
LLP
901 NEW YORK AVENUE, NW
WASHINGTON, DC 20001-4413
EXAMINER
HA, JULIE
ART UNIT PAPER NUMBER
1654
MAIL DATE DELIVERY MODE
09/02/2010 PAPER
Please find below and/or attached an Office communication concerning this application or proceeding.
The time period for reply, if any, is set in the attached communication.
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
__________

Ex parte STEWART COLE,
ROLAND BUCHRIESER-BROSCH, STEPHEN GORDON, and
ALAIN BILLAULT
__________

Appeal 2009-013916
Application 10/802,796
Technology Center 1600
__________

Before ERIC GRIMES, FRANCISCO C. PRATS, and
JEFFREY N. FREDMAN, Administrative Patent Judges.

PRATS, Administrative Patent Judge.

DECISION ON APPEAL1
This appeal under 35 U.S.C. § 134 involves claims to polypeptides.
The Examiner rejected the claims as lacking utility and enablement.

1 The two-month time period for filing an appeal or commencing a civil
action, as recited in 37 C.F.R. § 1.304, or for filing a request for rehearing,
as recited in 37 C.F.R. § 41.52, begins to run from the “MAIL DATE”
(paper delivery mode) or the “NOTIFICATION DATE” (electronic delivery
mode) shown on the PTOL-90A cover letter attached to this decision.
Appeal 2009-013916
Application 10/802,796

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We have jurisdiction under 35 U.S.C. § 6(b). We reverse.
STATEMENT OF THE CASE
Claims 51-54 and 57 are pending and on appeal (App. Br. 1). Claim
51 is representative and reads as follows:
51. A purified polypeptide, encoded by a polynucleotide
comprising an Open Reading Frame contained within SEQ ID
NO: 1, wherein the polynucleotide is selected from:
(a) nucleotide 1,696,019 through nucleotide 1,697,420 of
the Mycobacterium tuberculosis chromosome;
(b) nucleotide 1,696,019 through nucleotide 1,699,892 of
the Mycobacterium tuberculosis chromosome;
(c) nucleotide 1,696,019 through nucleotide 1,701,088 of
the Mycobacterium tuberculosis chromosome;
(d) nucleotide 1,696,019 through nucleotide 1,702,588 of
the Mycobacterium tuberculosis chromosome;
(e) nucleotide 1,696,019 through nucleotide 1,704,091 of
the Mycobacterium tuberculosis chromosome;
(f) nucleotide 1,696,019 through nucleotide 1,705,056 of
the Mycobacterium tuberculosis chromosome;
(g) nucleotide 1,696,019 through nucleotide 1,705,784 of
the Mycobacterium tuberculosis chromosome;
(h) nucleotide 1,696,019 through nucleotide 1,706,593 of
the Mycobacterium tuberculosis chromosome;
(i) nucleotide 1,696,019 through nucleotide 1,707,524 of
the Mycobacterium tuberculosis chromosome; or
(j) nucleotide 1,696,019 through nucleotide 1,708,648 of
the Mycobacterium tuberculosis chromosome.

The following rejections are before us for review:
(1) Claims 51-54 and 57, rejected under 35 U.S.C. § 101 as being
unsupported by a substantial asserted utility or a well established utility
(Ans. 3); and
(2) Claims 51-54 and 57, under 35 U.S.C. § 112, first paragraph, as
failing to comply with the enablement requirement (Ans. 3-4).
Appeal 2009-013916
Application 10/802,796

3
DISCUSSION
In finding that the claimed polypeptides lack utility, the Examiner
reasons that the Specification “suggests but does not demonstrate that the
claimed polypeptides have GDP-D-mannose dehydratase activity based on a
51% homology with a GDP-D-mannose dehydratase from another organism.
Neither the specification nor the art describe the significance of this activity
or a real world use for a protein with this activity” (Ans. 3).
Appellants argue that the polypeptides’ utility is independent of “any
homology to GDP-D-mannose dehydratases. This utility derives from the
selective presence of one or more claimed polypeptides in one strain of
Mycobacterium compared to another strain, and the ability of a conventional
assay to distinguish the two strains by the mere presence (or absence) of the
polypeptide” (App. Br. 15).
The Examiner responds that, rather than providing a specific benefit
available to the public on the application’s filing date, the Specification uses
“speculative language to describe the utility of the claimed polypeptides.
Throughout the specification, Appellant uses the words, ‘could be’, ‘can be’,
‘may be’ to establish utility for the claimed polypeptides” (Ans. 7).
Moreover, the Examiner argues, the Specification “does not disclose
the actual function of the [claimed] purified polypeptides” (id. at 8). Thus,
the Examiner urges, “without [the] function of the polypeptide, there is no
utility” (id. at 9).
As stated in In re Oetiker, 977 F.2d 1443, 1445 (Fed. Cir. 1992):
[T]he examiner bears the initial burden . . . of presenting a
prima facie case of unpatentability. . . .
After evidence or argument is submitted by the applicant
in response, patentability is determined on the totality of the
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Application 10/802,796

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record, by a preponderance of evidence with due consideration
to persuasiveness of argument.

With respect to the rejection presently at issue,
the PTO has the initial burden of challenging a presumptively
correct assertion of utility in the disclosure. Only after the PTO
provides evidence showing that one of ordinary skill in the art
would reasonably doubt the asserted utility does the burden
shift to the applicant to provide rebuttal evidence sufficient to
convince such a person of the invention’s asserted utility.

In re Brana, 51 F.3d 1560, 1566 (Fed. Cir. 1995) (citation omitted).
We have carefully considered both Appellants’ and the Examiner’s
respective positions. While we understand the Examiner’s concerns, in the
instant case a preponderance of the evidence supports Appellants’ position
that an ordinary artisan viewing the Specification would have recognized
that the claimed polypeptides were useful for distinguishing between M.
tuberculosis and M. bovis.
The Specification discloses “a method for isolating a polynucleotide
of interest that is present in the genome of a mycobacterium strain and/or is
expressed by said mycobacterium strain and that is absent or altered in the
genome of a different mycobacterium strain” (Spec. 1). Thus, “a
polynucleotide of approximately 12.7 kilobases has been isolated that is
present in the genome of M. tuberculosis but is absent of the genome of M.
bovis BCG” (id. at 9).
The Specification further discloses:
For diagnostic purposes, this 12.7 kb deletion should
allow a rapid PCR screening of tubercle isolates to identify
whether they are bovine or human strains. . . . More
importantly, assuming that some of the gene products from this
region represent proteins with antigenic properties, it could be
Appeal 2009-013916
Application 10/802,796

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possible to develop a test that can reliably distinguish between
the immune response induced by vaccination with M. bovis
BCG vaccine strains and infection with M. tuberculosis or that
the products (e.g. polysaccharides) are specific immunogens.

(Id. at 11.)
It is undisputed that the polypeptides recited in the claims are encoded
by (sub)sequences of the nucleotide sequence described in the Specification
as being present in M. tuberculosis, but not in M. bovis. We therefore agree
with Appellants that an ordinary artisan would have recognized that, because
a sample containing M. tuberculosis also contained the claimed
polypeptides, whereas a sample containing M. bovis did not, a skilled
practitioner would be able to distinguish between samples containing M.
tuberculosis and M. bovis in an immunoassay specific for the claimed
polypeptides.
The Examiner points to no specific evidence suggesting that an
ordinary artisan would have failed to recognize that the claimed
polypeptides would have been useful for distinguishing between M.
tuberculosis and M. bovis. Thus, a preponderance of the evidence supports
Appellants’ position that an ordinary artisan viewing the Specification would
have understood, at the time the application was filed, that the claimed
polypeptides were useful as immunogenic markers allowing a practitioner to
distinguish between samples containing M. tuberculosis and M. bovis.
It may be true that the function of the polypeptides was not described
in the Specification. Given the relevant disclosures in the Specification,
however, we agree with Appellants that a skilled artisan would nonetheless
have recognized that the polypeptides were useful in distinguishing M.
tuberculosis from its closely related M. bovis strain.
Appeal 2009-013916
Application 10/802,796

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Accordingly, for the reasons discussed, we reverse the Examiner’s
rejection of claims 51-54 and 57 as lacking utility under 35 U.S.C. § 101.
The Examiner argues that the claimed polypeptides are not enabled,
even if a skilled artisan would have considered them useful (Ans. 13).
Specifically, the Examiner urges that the claimed polypeptides are asserted
as having only 51.9% homology to GDP-D-mannose dehydratase, and that
given the large degree of substitution allowable, and the Specification’s
failure to identify the portion of the molecules critical to enzymatic activity,
it is unpredictable whether the claimed polypeptides would have GDP-D-
mannose dehydratase activity (id. at 14).
We are not persuaded by this argument. As discussed above, we
agree with Appellants that an ordinary artisan would have understood the
claimed polypeptides to be useful in distinguishing between M. tuberculosis
and M. bovis. The Examiner points to no specific evidence suggesting that a
skilled practitioner, given the present Specification’s disclosure, would have
had to experiment unduly to devise an appropriate immunoassay for
distinguishing between the two bacterial strains.
Given this utility, and the absence of specific evidence suggesting that
practicing that use required undue experimentation, we are not persuaded
that the claimed polypeptides fail to meet the how-to-use prong of the
enablement requirement of 35 U.S.C. § 112, first paragraph. We therefore
also reverse the Examiner’s enablement rejection of claims 51-54 and 57.

REVERSED

Appeal 2009-013916
Application 10/802,796

7

cdc

FINNEGAN, HENDERSON, FARABOW, GARRETT & DUNNER
LLP
901 NEW YORK AVENUE, NW
WASHINGTON, DC 20001-4413