Ex Parte Apffel

Board of Patent Appeals and Interferences

Feb 19, 2010

10405438 (B.P.A.I. Feb. 19, 2010)

UNITED STATES PATENT AND TRADEMARK OFFICE
____________

BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
____________

Ex parte JAMES ALEXANDER APFFEL, JR.
____________

Appeal 2009-003727
Application 10/405,438
Technology Center 1600
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Decided: February 22, 2010
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Before DONALD E. ADAMS, DEMETRA J. MILLS, and
STEPHEN WALSH, Administrative Patent Judges.

ADAMS, Administrative Patent Judge.

DECISION ON APPEAL
This appeal under 35 U.S.C. § 134 involves claims 1-22 and 32-41.
We have jurisdiction under 35 U.S.C. § 6(b).

Appeal 2009-003727
Application 10/405,438

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STATEMENT OF THE CASE
The claims are directed to a method for detecting one or more target
proteins in a sample suspected of containing a plurality of target proteins
(claims 1-12 and 33-41) and a method for determining one or more different
target proteins in a sample suspected of containing a plurality of target
proteins (claims 13-32). Claims 13, 32, and 33 are illustrative:
13. A method for determining one or more different target proteins in
a sample suspected of containing a plurality of said target proteins, said
method comprising:
(a) incubating an assay medium comprising said sample with a surface
of a substrate comprising an array of capture agents bound thereto, wherein a
set of capture agents specific for different binding sites on each of said
different target proteins suspected of being in said sample is employed and
wherein said capture agents of said set are disposed on said surface in a
spatial relationship such that said capture agents of said set bind to a single
molecule of said target protein and wherein said capture agents of said set
comprise different types of entities that belong to different families of
capture agents, said assay medium being incubated under conditions for
binding of said capture agents to said target proteins, and
(b) examining said substrate surface for the presence of said target
proteins.
32. A method according to Claim 13 wherein said capture agents of
said set are linked together to form a conjugate capture agent wherein the
capture agents of said set bind to said single molecule of said target protein.
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33. A method for detecting one or more target proteins in a sample
suspected of containing a plurality of said target proteins, said method
comprising:
(a) incubating an assay medium comprising said sample with a
surface of a substrate comprising multiple pairs of capture agents bound
thereto in a predetermined pattern as an array , wherein for each target
protein suspected of being in said sample a pair of capture agents is
employed wherein capture agents of said pair are spatially disposed on the
surface in such a manner that the capture agents of the pair bind to a single
molecule of the target protein and wherein capture agents of said pair
comprise different types of entities that belong to different families of
capture agents, said assay medium being incubated under conditions for
binding of said capture agents to said target proteins, and
(b) examining said substrate surface for the presence of said target
proteins.

The Examiner relies on the following evidence:
Bellet et al. US 5,011,771 Apr. 30, 1991
Wagner et al. US 6,329,209 B1 Dec. 11, 2001
Campbell et al. US 2004/0018577 A1 Jan. 29, 2004

The rejections presented by the Examiner are as follows:
1. Claims 1-22, 33, 35-41 stand rejected under 35 U.S.C. § 103(a) as
unpatentable over the combination of Bellet and Wagner.
2. Claims 32 and 34 stand rejected under 35 U.S.C. § 103(a) as unpatentable
over the combination of Bellet, Wagner, and Campbell.
We affirm.
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PRINCIPLES OF LAW
In proceedings before the Patent and Trademark Office, the Examiner
bears the burden of establishing a prima facie case of obviousness based
upon the prior art. In re Fritch, 972 F.2d 1260, 1265 (Fed. Cir. 1992). On
appeal to this Board, Appellants must show that the Examiner has not
sustained the required burden. See Ex parte Yamaguchi, 88 USPQ2d 1606,
1608 and 1614 (BPAI 2008) (precedential); Ex parte Fu, 89 USPQ2d 1115,
1118 and 1123 (BPAI 2008) (precedential).
“The combination of familiar elements according to known methods
is likely to be obvious when it does no more than yield predictable results.”
KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 416 (2007).
When there is a design need or market pressure to solve a
problem and there are a finite number of identified, predictable
solutions, a person of ordinary skill has good reason to pursue
the known options within his or her technical grasp. If this
leads to the anticipated success, it is likely the product not of
innovation but of ordinary skill and common sense. In that
instance the fact that a combination was obvious to try might
show that is was obvious under § 103.

Id. at 421. It is proper to “take account of the inferences and creative steps
that a person of ordinary skill in the art would employ.” Id. at 418. See also
id. at 421 (“A person of ordinary skill is also a person of ordinary creativity,
not an automaton.”). In sum, the “suggestion test is in actuality quite
flexible and not only permits, but requires, consideration of common
knowledge and common sense.” DyStar Textilfarben GmbH & Co.
Deutschland KG v. C.H. Patrick Co., 464 F.3d 1356, 1367 (Fed. Cir. 2006).
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The combination of Bellet and Wagner:
ISSUE
Has Appellant established error in the Examiner’s prima facie case of
obviousness?

FINDINGS OF FACT
FF 1. Bellet “teaches a method for detecting one or more target proteins in
a sample suspected of containing [a] plurality of target proteins . . .
comprising”, inter alia, “wherein for each target protein at least two capture
agents specific for different binding sites . . . on said target protein are
employed” (Ans. 4).
FF 2. The Examiner finds that Bellet “fails to teach a method, wherein the
substrate surface comprises an array of the capture agents” (Ans. 6).
FF 3. Wagner “teaches an array of protein capture agents useful for
simultaneous detection of a plurality of proteins” (id.).
FF 4. Wagner teaches that “[t]he protein capture agent can include
antibodies, antibody fragments or synthetic biomolecules (column 4, lines
48-67) including aptamers (column 12, lines 45-64)” (id.).
FF 5. Wagner teaches
Typically, only one type of protein-capture agent is
present on a single patch of the array. If more than one type of
protein-capture agent is present on a single patch, all of the
protein-capture agents of that patch must share a common
binding partner. For instance, a patch may comprise a variety
of polyclonal antibodies to the same antigen (although,
potentially, the antibodies may bind different epitopes on that
same antigen).

(Wagner, col. 10, ll. 60-67; see also Ans. 11.)
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ANALYSIS
Based on the foregoing findings of fact (FF 1-5) the Examiner
concludes that
[I]t would have been obvious to one of ordinary skill in the art
at the time of the invention to use a protein microarray format
of Wagner et al., which include capture molecules including
antibodies and aptamers . . . in the method of Bellet et al. in
order to perform high throughput analysis of proteins in [a]
variety of different samples.

(Ans. 6-7.)
Appellant presents arguments with respect to the following three
groups of claims: “(1) claims 1-22, 33, and 35-41; (2) claims 13-22 and 32;
and (3) claims 33 and 35-381” (App. Br. 5). As claims 13-22 are included in
both groups (1) and (2), and claims 33 and 35-38 are included in both groups
(1) and (3), we designate claims 13 and 33 as representative. See 37 C.F.R.
§ 41.37(c)(1)(vii).

Claim 13:
We are not persuaded by Appellant’s contentions regarding Bellet’s
failure to teach two capture agents that belong to different families of
capture agents or an array of capture agents bound to a surface of a substrate
(App. Br. 7; Reply Br. 2). The Examiner relies on Wagner to teach these
elements of Appellant’s claimed invention.
We are not persuaded by Appellant’s contention that Wagner fails to
teach “at least two capture agents [that] comprise different types of entities

1 While Appellant includes claim 34 in their claim grouping (see App. Br.
11), claim 34 was not rejected over the combination of Bellet and Wagner.
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that belong to different families of capture agents” (App. Br. 8; Reply Br. 2-
3). To the contrary, Wagner teaches capture agents that belong to different
families and the use of capture agents that bind to different sites on a target
protein (FF 4-5).
We are not persuaded by Appellant’s contention that “substituting
Bellet’s antibodies with Wagner’s capture agents would change Bellet’s
principle of operation because Bellet’s multiple monoclonal antibodies bind
to the same molecule while Wagner’s bind to different molecules” (App. Br.
8; Reply Br. 3-4). In contrast, Wagner teaches that “[i]f more than one type
of protein-capture agent is present on a single patch, all of the protein-
capture agents of that patch must share a common binding partner” (FF 5).
Stated differently, while different types of protein capture agents may be
present in a particular location on the array, all the capture agents in this
location must bind the same molecule, albeit they may bind different
epitopes of this same molecule (FF 5 (“For instance, a patch may comprise a
variety of polyclonal antibodies to the same antigen (although, potentially,
the antibodies may bind different epitopes on that same antigen”)).
We recognize Appellant’s contention that “Wagner suggests that
polyclonal antibodies may bind to different epitopes but is silent in using
capture agents from different families to bind to the same molecule” (App.
Br. 9). From this, Appellant contends that Wagner is limited to the use of
capture agents from the same family, when multiple capture agents are
present on the same patch of an array (id.). We are not persuaded. Wagner
teaches that “[f]or instance, a patch may comprise a variety of polyclonal
antibodies to the same antigen (although, potentially, the antibodies may
bind different epitopes on that same antigen)” (FF 5). We do not read
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Wagner’s exemplary (e.g., “for instance”) statement as limiting the general
teaching in Wagner of the use of capture agents from the same or different
families. It is proper to “take account of the inferences and creative steps
that a person of ordinary skill in the art would employ.” KSR, 550 U.S. at
418. See also id. at 421 (“A person of ordinary skill is also a person of
ordinary creativity, not an automaton.”).

Claim 33:
Appellant contends that “Bellet neither deals with ‘a sample suspected
of containing a plurality of target proteins,’ nor employs an array on which
‘a set of capture agents [bound thereto is] specific for different binding sites
on each of said different target proteins” (App. Br. 11). Appellant contends
that Wagner fails to make up for this deficiency in Bellet because “it does
not teach or suggest ‘a set of capture agents specific for different binding
sites on each of different target proteins’ because each of the plurality of
Wagner’s capture agents bind to a different expression product” (id.). We
are not persuaded for the reasons set forth above.
As to Appellant’s contentions regarding a set, Wagner teaches that a
defined location, e.g., patch, on an array contains capture agents that bind to
different epitopes on the same target protein (FF 4-5). These capture agents
that are located together in a “patch” and bind to different epitopes on the
same target protein represent a “set of capture agents” as required by
Appellant’s claimed invention. Accordingly, we are not persuaded by
Appellant’s contention to the contrary.

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CONCLUSION OF LAW
Appellant failed to establish error in the Examiner’s prima facie case
of obviousness.
The rejection of claims 13 and 33 under 35 U.S.C. § 103(a) as
unpatentable over the combination of Bellet and Wagner is affirmed.
Claims 1-12, 14-22, 32, and 39-41 fall together with claim 13. Claims 35-38
fall together with claim 33.

The combination of Bellet, Wagner, and Campbell:
ISSUE
Has Appellant established error in the Examiner’s prima facie case of
obviousness?

FINDINGS OF FACT
FF 6. The Examiner relies on the combination of Bellet and Wagner as set
forth above (Ans. 7).
FF 7. The Examiner finds that the combination of Bellet and Wagner “fails
to teach a method, wherein the capture agents of the set are linked together
to form a conjugate capture agent” (id.).
FF 8. The Examiner finds that Campbell “teaches that a variety of different
forms of capture antibodies can be used in the detection assay including
individual antibodies and antibodies, which are conjugated to a common
member using conjugation methods known in the art” (Ans. 8).

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ANALYSIS
Appellant contends that Campbell fails to “remedy the deficiencies of
Bellet and Wagner discussed in the previous sections” (App. Br. 13).
Having found no deficiency in the combination of Bellet and Wagner, we
are not persuaded by Appellant’s contention to the contrary. Further, for the
reasons set forth above, we are not persuaded by Appellant’s contention that
the combination of “Bellet and Wagner . . . do not provide ‘a pair of capture
agents’ as recited in Claim 33” (App. Br. 14).

CONCLUSION OF LAW
Appellant failed to establish error in the Examiner’s prima facie case
of obviousness.
The rejection of claims 32 and 34 under 35 U.S.C. § 103(a) as
unpatentable over the combination of Bellet, Wagner, and Campbell is
affirmed.

Appeal 2009-003727
Application 10/405,438

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TIME PERIOD FOR RESPONSE
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

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