Ex Parte Warnes et al

Board of Patent Appeals and Interferences

Aug 14, 2008

10253147 - (D) (B.P.A.I. Aug. 14, 2008)

UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
__________

Ex parte
DANIEL JOSEPH O’MAHONY, VERNON L. ALVAREZ,
and MICHELA SEVESO
__________

Appeal 2008-2117
Application 10/104,603
Technology Center 1600
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Decided: August 14, 2008
__________

Before DONALD E. ADAMS, ERIC GRIMES, and MELANIE L.
McCOLLUM, Administrative Patent Judges.

McCOLLUM, Administrative Patent Judge.

DECISION ON APPEAL

This is an appeal under 35 U.S.C. § 134 involving claims to a peptide.
The Examiner has rejected the claims as not being supported by an adequate
written description. We have jurisdiction under 35 U.S.C. § 6(b). We
affirm.
Appeal 2008-2117
Application 10/104,603

STATEMENT OF THE CASE
Claims 14-16, 19-25, 36 and 37 are on appeal. Claims 38-45 are also
pending but have been indicated to be allowable.
The claims on appeal have not been argued separately1 and therefore
stand or fall together. 37 C.F.R. § 41.37(c)(1)(vii). We will focus on
claim 14, the broadest claim on appeal, which reads as follows:
14. A peptide which permits or facilitates the transport of an active
agent through an epithelial cell layer lining a lumenal side of a human or
animal gastro-intestinal track,2 the peptide being identified by a method
comprising the steps of:
(a) administering in vivo or in situ to the lumenal side of the gastro-
intestinal track in an animal a predetermined amount of phage from a
random phage library or a preselected phage library;
(b) at a predetermined time harvesting phage from the animal to select
transported phage, wherein the harvesting site is separated from the lumenal
side of the gastro-intestinal track by an epithelial cell layer;
(c) amplifying the transported phage in a host;
(d) repeating in order step (a) using the transported phage obtained in
step (b) and amplified in step (c) and steps (b) and (c) a predetermined
number of times to obtain a selected phage library containing phage which

1 With regard to claims 15, 16, 19-25, 36 and 37, which depend from
claim 14, Appellants argue that the Specification provides written
description for the additional features recited in these claims (App. Br. 14-
17). However, Appellants have not provided arguments that any of these
claims would be patentable even if claim 14 is not patentable. Thus,
Appellants have not provided arguments that these claims are separately
patentable.
2 As amended on February 26, 2007, claim 14 recites a “gastro-intestinal
track.” However, the Claims Appendix included with the Appeal Brief
indicates that claim 14 recites a “gastro-intestinal tract.”
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Application 10/104,603

can be transported from the lumenal side of the human or animal gastro-
intestinal track to the site of harvesting; and
(e) determining the identity of at least one peptide coded by phage in
the selected phage library to identify a peptide which permits or facilitates
the transport of an active agent through an epithelial cell layer lining the
lumenal side of the human or animal gastro-intestinal track.
Claims 14-16, 19-25, 36, and 37 stand rejected under 35 U.S.C. § 112,
first paragraph, as failing to comply with the written description requirement
(Ans. 3). The Examiner finds that the “claims contain subject matter which
was not described in the specification in such a way as to reasonably convey
to one skilled in the relevant art that the inventors, at the time the application
was filed, had possession of the claimed invention” (id.). In particular, the
Examiner finds that “the claims are drawn to a huge genus of peptides with
only a common function, and not common structure, wherein said peptides
are identified and claimed via a product-by-process approach” (id.). The
Examiner also finds that, although Appellants describe eight species, these
“disclosed peptides do not share a common structure that contribute to the
common desired activity of the peptides” (id. at 4-5). Therefore, the
Examiner concludes that “the other species within the diverse genus also
would be expected to have diverse structures” and “the only means of
identifying them is by a common function” (id. at 5).
Appellants contend that, based on the large amount of information
provided in the Specification, “one of ordinary skill would recognize that
Applicants were in possession of the claimed invention at the time of filing
the application” (App. Br. 12). In particular, Appellants argue that, “[g]iven
that phage display technology was routine at the time Applicants filed the
instant application, and the specification provided a clear-cut method by
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Application 10/104,603

which the claimed genus of peptides may be obtained, the claimed genus of
peptides was adequately described by the specification” (id. at 13 (emphasis
omitted)). Appellants also argue that, from their disclosure, “the skilled
artisan could readily identify the genus of peptides capable of transporting
an active agent through an epithelial cell layer lining a lumenal side of a
human or animal gastro-intestinal tract” (id.). Additionally, Appellants
argue that they “have disclosed a representative number (8) of peptides
derived by the method outlined in the Specification, which entitles
Applicants to be able to claim the genus of peptides obtained by the outlined
method” (id.).
ISSUE
The issue is whether the disclosure of a method for identifying a
peptide having a specified function, together with the disclosure of eight
specific peptides having the function, which were identified by the method,
is sufficient to support a generic claim directed to peptides having the
function, which were identified by the method, where neither the Examiner
nor Appellants have identified structural characteristics common to the eight
species.
FINDINGS OF FACT
1. The Specification discloses “a method of identifying a peptide
which permits or facilitates the transport of an active agent through a human
or animal tissue,” specifically epithelial cells lining the lumenal side of a
gastro-intestinal tract (Spec. 4).
2. Claim 14 requires a peptide that “permits or facilitates the
transport of an active agent through an epithelial cell layer lining a lumenal
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Application 10/104,603

side of a human or animal gastro-intestinal track.” It is undisputed that this
function is not correlated to a particular, known structure (Ans. 3-5; App. Br.
passim; Reply Br. passim).
3. Claim 14 also requires that the peptide be identified by a
particular method. This method does not require hybridization of the nucleic
acids encoding the peptides to a common oligonucleotide.
4. In Example 4, the Specification describes the identification of
peptide sequences from transported phage in colon tissue segments
(Spec. 33). The method includes sequencing clones from the sixth cycle of a
screening process (id.). It was determined that:
[a] number of clones/DNA sequences [were] present more than
once. . . .
Based on the recurrent random peptide sequences . . . ,
two synthetic oligonucleotides were constructed and used to
screen phage populations representing colon screening cycles 1-
6 in a series of oligonucleotide hybridization reactions to
determine whether these phage and corresponding peptides
were being selected during the screening process. . . . [I]t
appears that there is a gradual selection of phage which
hybridize to [these] oligonucleotide[s].
(Id. at 34.)
5. In Example 6, the Specification describes the transport of phage
from rat lumen into portal and systemic circulation (id. at 40). “In this
study, phage from random phage display libraries . . . were injected into the
lumen of the rat gastro-intestinal tract[,] . . . [b]lood was collected over time
from either the systemic circulation or portal circulation and the number of
phage which were transported to the circulation was determined” (id.) From
this study, “[e]ight DNA sequences . . . with corresponding peptide
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Application 10/104,603

sequences SEQ. NOS. ID: 19, 21, 23, 25, 27, 29, 31 and 33 were
discovered” (id. at 45). The Specification states that these peptides “are
capable of facilitating the transport of an active agent . . . through a human
or animal tissue” (id.).
6. It is undisputed that the eight peptide sequences identified in
Example 6 have no common structure (Ans. 3-5; App. Br. passim; Reply Br.
passim).
ANALYSIS
The first paragraph of 35 U.S.C. § 112 “requires a ‘written description
of the invention’ which is separate and distinct from the enablement
requirement.” Vas-Cath Inc. v. Mahurkar, 935 F.2d 1555, 1563 (Fed. Cir.
1991). An adequate written description of a chemical invention “requires a
precise definition, such as by structure, formula, chemical name, or physical
properties.” University of Rochester v. G.D. Searle & Co., Inc., 358 F.3d
916, 927 (Fed. Cir. 2004); Regents of the Univ. of Cal. v. Eli Lilly & Co.,
Inc., 119 F.3d 1559, 1566 (Fed. Cir. 1997); Fiers v. Revel, 984 F.2d 1164,
1171 (Fed. Cir. 1993). “A description of what a material does, rather than of
what it is, usually does not suffice.” Rochester, 358 F.3d at 923; Eli Lilly,
119 at 1568. Instead, the “disclosure must allow one skilled in the art to
visualize or recognize the identity of the subject matter purportedly
described.” Id. However, not all functional descriptions “necessarily fail as
a matter of law to meet the written description requirement; rather, the
requirement may be satisfied if in the knowledge of the art the disclosed
function is sufficiently correlated to a particular, known structure.” Amgen
Inc. v. Hoechst Marion Roussel, Inc., 314 F.3d 1313, 1332 (Fed. Cir. 2003).
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Application 10/104,603

In the present case, claim 14 is directed to any peptide having a
particular function, which is identified by a particular method (Findings of
Fact (FF) 2-3). It is undisputed that the disclosed function is not correlated
with a known structure (FF 2). Thus, we agree with the Examiner that the
mere recitation of peptides having this function is insufficient to show
possession thereof.
The Specification (and the claims) also provides a method for
identifying peptides having the claimed function (FF 1-3). However,
“[p]ossession may not be shown by merely describing how to obtain
possession of members of the claimed genus.” Ex parte Kubin, 83 USPQ2d
1410, 1417 (BPAI 2007) (citing Rochester, 358 F.3d at 927).
Appellants argue that “the manner in which the peptides were isolated
provides a structural link between the claimed peptides” (Reply Br. 4). In
particular, based on Specification Example 4, Appellants argue:
The isolated peptides share a commonality of structure by
virtue of the homology shared by their underlying nucleotide
sequences. Since the peptides are isolated based on a
commonality of function . . . , as well as commonality of
structure, i.e., ability of the nucleotide sequences that encode
the peptides to hybridize to a common oligonucleotide, they are
encompassed within a defined genus.
(Id.)
We are not persuaded by this argument. In Example 4, the
Specification describes conducting “a series of oligonucleotide hybridization
reactions to determine whether these phage and corresponding peptides were
being selected during the screening process” (FF 4). However, the method
recited in claim 14 does not require hybridization to a common
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oligonucleotide (FF 3). Thus, we do not agree with Appellants that the
method of claim 14 provides a structural link between the claimed peptides.
Instead, we agree with the Examiner that the disclosure of this identification
method is insufficient to show possession of the claimed peptides.
It is also not disputed that the Specification discloses eight peptides
(SEQ ID NOs: 19, 21, 23, 25, 27, 29, 31 and 33) identified by the claimed
method that have the claimed function (FF 5). In addition, possession of a
genus “may be achieved by means of a recitation of a representative number
of [compounds] . . . falling within the scope of the genus.” Eli Lilly, 119 at
1569. However, it is undisputed that there is no structure common to these
eight peptides (FF 6).3 Thus, we agree with the Examiner that “other
species within the diverse genus also would be expected to have diverse
structures” (Ans. 5) and that therefore the disclosed species are not
representative of the broad genus (id. at 9).
CONCLUSION
We conclude that the Examiner has set forth a prima facie case that
claim 14 is not supported by an adequate written description, which
Appellants have not rebutted. We therefore affirm the rejection of claim 14

3 As discussed above, Appellants argue that “the manner in which the
peptides were isolated provides a structural link between the claimed
peptides” (Reply Br. 4). However, based on Appellants’ reliance on
Specification Example 4 rather than Specification Example 6, which
discloses the identification of these eight peptides (FF 5), Appellants do no
appear to be arguing that the nucleic acids encoding these eight peptides
hybridize to a common oligonucleotide. However, even if they did, they
would not be representative of the genus encompassed by claim 14, which
does not require hybridization to a common oligonucleotide (FF 3).
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Application 10/104,603

under 35 U.S.C. § 112, first paragraph. Claims 15, 16, 19-25, 36 and 37 fall
with claim 14.
No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § 1.136(a).

AFFIRMED

cdc

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