Ex Parte Wagner et al

Board of Patent Appeals and Interferences

Sep 21, 2010

10107122 (B.P.A.I. Sep. 21, 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.
10/107,122 03/26/2002 Peter Wagner 0002.P2.C1D1.USN 5292
20350 7590 09/22/2010
TOWNSEND AND TOWNSEND AND CREW, LLP
TWO EMBARCADERO CENTER
EIGHTH FLOOR
SAN FRANCISCO, CA 94111-3834
EXAMINER
YANG, NELSON C
ART UNIT PAPER NUMBER
1641
MAIL DATE DELIVERY MODE
09/22/2010 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 PETER WAGNER, STEFFEN NOCK, DANA AULT-RICHE and
CHRISTIAN ITIN
____________

Appeal 2009-013022
Application 10/107,122
Technology Center 1600
____________

Before RICHARD E. SCHAFER, ROMULO H. DELMENDO, and
RICHARD M. LEBOVITZ, Administrative Patent Judges.

LEBOVITZ, Administrative Patent Judge.

DECISION ON APPEAL1
This is a decision on the appeal under 35 U.S.C. § 134 by the Patent
Applicant from the Patent Examiner’s rejection of claims 46, 49-54, 56, 57,

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 2009-013022
Application 10/107,122

2
60, 64, 69-75, and 77. The Board’s jurisdiction for this appeal is under 35
U.S.C. §§ 6(b). We affirm.

STATEMENT OF THE CASE
There is one rejection at issue in this appeal: the rejection of clams 46,
49-54, 56, 57, 60, 64, 69-75, and 77 under 35 U.S.C. § 103(a) as obvious
over Sparks, 2 Felder, 3 and Eggers4 (Ans. 3). Claims 46 is representative.
Claims 49-54, 56, 57, 60, 64, 69-75, and 77 fall with claims 46 (App. Br. 4).
Claim 46 reads as follows:
Claim 46. A method for screening a plurality of proteins for
their ability to interact with a component of a fluid sample,
comprising delivering the fluid sample to a protein array
comprising the plurality of proteins comprising at least 100
different proteins, and simultaneously detecting for the presence
of an interaction of the component with each protein of the
plurality of proteins, wherein the protein array comprises the
plurality of proteins each immobilized site-specifically on
different discrete, known regions of a substrate, wherein the
discrete, known regions are present at a density of at least 100
per cm2, thereby detecting an interaction of a protein of the
plurality of proteins and the component of the fluid sample,
wherein each of the proteins in the plurality of proteins is
a different purified recombinant fusion protein, and the proteins
in the plurality of proteins are structurally related, functionally
related, suspected of being functionally related, suspected of
being structurally related, or are members of the same family.

2 U.S. Patent 6,309,820 B1, issued Oct. 30, 2001.
3 U.S. Patent 6,232,066 B1, issued May 15, 2001.
4 U.S. Patent 5,532,128, issued Jul 2, 1996.
Appeal 2009-013022
Application 10/107,122

3
ISSUE
Does the combination of Sparks, Felder, and Eggers suggest a
screening method using a protein array of at least 100 different proteins at a
density of at least 100 per cm2, where the proteins “are structurally related,
functionally related, suspected of being functionally related, suspected of
being structurally related, or are members of the same family”?
Was there a reasonable expectation of success of arriving at the
claimed method based on the teachings of Sparks, Felder, and Eggers ?

FINDINGS OF FACT (FF)
Sparks
1. Sparks describes a kit that may be used to identify new drug candidates,
where the kit comprises a “a plurality of purified polypeptides, . . . each
polypeptide containing a function domain of interest” (Sparks, col. 25, ll. 51-
55; col. 26, ll. 17-19).
2. The polypeptides can be immobilized on a solid support, such as on a
microtiter well (id. at col. 25, ll. 9-11; col. 29, ll. 30-35).
3. “Using the methods of the present invention, it is possible to identify and
isolate large numbers of polypeptides containing functional domains . . .
Using these polypeptides, one can construct a matrix relating the
polypeptides to an array of candidate drug compounds.” (Id. at col. 31, ll. 1-
6).
Felder
4. Felder discloses an apparatus and methods for high throughput screening
of potential drugs (Felder, col. 1, ll. 31-34; col. 2, ll. 11-13).
Appeal 2009-013022
Application 10/107,122

4
5. Felder describes a “combination [which] comprises a surface comprising
a plurality of spatially discrete regions, which can be termed test regions and
which can be wells, at least two which are substantially identical.” (Id. at
col. 1, ll. 51-55).
6. “This invention relates e.g. to compositions, apparatus and methods
useful for concurrently performing multiple biological or chemical assays,
using repeated arrays of probes. A plurality of regions each contains an array
of generic anchor molecules.” (Id. at col. 1, ll. 8-12.)
7. Felder discloses:
In one embodiment, for example, using 96-well . . .
[microplates], 36 different oligonucleotides can be spotted onto
the surface of every well of every plate to serve as anchors. The
. . . same 36 anchors can be used for all screening assays. For
any particular assay, a given set of linkers can be used to
program the surface of each well to be specific for as many as
36 different targets or assay types of interest, and different test
samples can be applied to each of the 96 wells in each plate.
(Id. at col. 2, ll. 34-46).
8. “Substantially identical region . . . refers to regions which contain
identical or substantially identical arrays of anchors and/or anchor/linker
complexes.” (Id. at col. 5, l, 66 to col. 6, l. 1).
9. Felder discloses:
The number of anchors in a test region can be at least two,
preferably between about 8 and about 900 (more or less being
included), more preferably between about 8 and about 300, and
most preferably between about 30 and about 100 (e.g. about
64). In a most preferred embodiment, each anchor in a test
region has a different specificity from every other anchor in the
array.
(Id. at col. 7, 42-48).
Appeal 2009-013022
Application 10/107,122

5
10. Felder also discloses that probes can be proteins, such as enzymes
(proteases or kinases) and antibodies (id. at col. 4, ll. 34 & 49).
Eggers
11. Eggers describes arrays of probes which utilize electrical signals to
detect whether a probe has bound a target (Eggers, col. 3, ll. 4-10 & 63-67;
col. 4, ll. 1-7).
12. Peptide antigens can be used in the arrays (id. at col. 10, 55-65).
13. The “presence of hundreds or thousands of different antibodies or other
proteins” can be detected by the arrays (id. at col. 11, 11-14).
14. Eggers describes various ways of producing arrays with probes,
including utilizing prior art methods for large scale peptide synthesis (id.
beginning at col. 7, l. 60 & col. 8, l. 12-col. 9, l. 2).

ANALYSIS
Claim 46 is directed to a “method for screening a plurality of proteins
for their ability to interact with a component of a fluid sample.” The method
involves delivering a sample to “a protein array comprising at least 100
different proteins” where each protein is immobilized in a discrete region of
a substrate “at a density of at least 100 per cm2.” Each of the proteins is
“structurally related, functionally related, suspected of being functionally
related, suspected of being structurally related, or are members of the same
family.”
The Examiner found that Sparks described a screening method that
involved screening drug candidates that interacted with polypeptides having
functional domains, where the proteins were immobilized on a substrate, as
in claims 46 (Ans. 3). The Examiner found that Sparks did not describe the
Appeal 2009-013022
Application 10/107,122

6
claimed number of proteins (“at least 100 different”) arranged in the claimed
density, but found these elements described in the Felder and Eggers patents
(id. at 3-5), and determined it would have been obvious to modify Sparks
with these teachings “to achieve a better and more thorough screening
process” (id. at 5).
Appellants contend that the claimed plurality of 100 different proteins
is not taught or suggested in the prior art (App. Br. 6).
As found by the Examiner, Sparks describes utilizing a plurality of
proteins in its screening method (FF1 & FF3), but does not disclose the
recited number of 100 “different” polypeptides. However, Sparks’
disclosure of using large numbers of proteins in assays reasonably suggests
numbers such as 100, as this number is large. Consequently, we do not find
Appellants’ argument about lack of a reason to modify Sparks with the
teachings of Felder and Eggers persuasive (App. Br. 9).
Moreover, as found by the Examiner, both Felder and Eggers suggest
the claimed limitation. Felder describes a surface with regions, which each
region can have from 8-900, preferably 30-100 anchors in each regions,
where each anchor has a different specificity (FF7 & FF9). Thus, persons of
ordinary skill in the art would have recognized that the anchors could be
associated with as many as 100 different proteins, where the different anchor
specificities would permit different proteins to be attached. Eggers also
describes detecting “hundreds or thousands of different antibodies or other
proteins” (FF13), reasonably suggesting corresponding numbers of different
peptide antigens (FF12 & 13).
Appellants contend that Felder does not state that anchors within a test
region had different specificities (Reply Br. 3). We do not agree with
Appeal 2009-013022
Application 10/107,122

7
Appellants’ position. Felder stated that “each anchor in a test region has a
different specificity from every other anchor in the array.” Felder described
each “region” as containing an “array.” (F6 & F8). Therefore, describing
“each anchor in a test region” as having “a different specificity from every
other anchor in the array” is a reference to the anchors in a single array of a
test region.
Appellants also argue that the Examiner mischaracterized Sparks by
relying on the matrix of table 1 as describing an array of 10 different
proteins (App. Br. 8). However, while it may be correct that the matrix is
not explicitly described as an array, Sparks described immobilizing proteins
on solid supports, such as microtiter wells (FF2), reasonably suggesting
arrays of a plurality of different proteins as recited in claim 46. Arrays of
proteins as established by each of Felder and Eggers were known in the art.
Appellants argue that Felder’s teaching of “’substantially identical’”
regions” teaches away from the claimed invention (Reply Br. 5). While we
agree that Felder does describe that certain embodiments have substantially
identical regions, such regions are also characterized as arrays having as
many as 900 anchors with different specificities (FF9). Thus, each identical
region is an array that suggests the claimed limitation of at least 100
different proteins.
Appellants also contend that the claim limitation that proteins be
related or members of the same family is not met by the prior art (App. Br.
7). To the contrary, Felder describes that the arrays proteins can be
proteases or kinases (FF10), which would have been considered to be
“members of the same family” as required by claim 46.
Appeal 2009-013022
Application 10/107,122

8
Appellants assert that obviousness has not been established because
“none” of Sparks, Eggers, or Felder “successfully demonstrates a method to
immobilize at least 100 purified recombinant fusion proteins on a substrate”
with the density as claimed (App. Br. 10). We do not agree. As argued by
the Examiner, there is no evidence that the methods disclosed in Felder and
Sparks would not work for arrays of large numbers of proteins (Ans. 11-12).
Eggers disclosed specific methods for making arrays of peptides (F14).
Thus, the evidence of record supports the Examiner’s determination that
peptide arrays were enabled by the prior art.

SUMMARY
The combination of Sparks, Felder, and Eggerss suggests a screening
method with a protein array of at least 100 different proteins at a density of
at least 100 per cm2, where they “are structurally related, functionally
related, suspected of being functionally related, suspected of being
structurally related, or are members of the same family.” There was a
reasonable expectation of success that the claimed method would be arrived
at based on the teachings of Sparks, Felder, and Eggers. The rejection of
claim 46 is affirmed. Claims 49-54, 56, 57, 60, 64, 69-75, and 77 fall with
claim 46.

Appeal 2009-013022
Application 10/107,122

9
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

cu

Townsend and Townsend and Crew, LLP
Two Embarcadero Center, Eighth Floor
San Francisco, CA 94111-3834

UNITED STATES PATENT AND TRADEMARK OFFICE
____________

BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
____________

Ex parte PETER WAGNER, STEFFEN NOCK, DANA AULT-RICHE and
CHRISTIAN ITIN
____________

Appeal 2009-013022
Application 10/107,122
Technology Center 1600
____________

Before RICHARD E. SCHAFER, ROMULO H. DELMENDO, and
RICHARD M. LEBOVITZ, Administrative Patent Judges.

LEBOVITZ, Administrative Patent Judge.

DECISION ON APPEAL1
This is a decision on the appeal under 35 U.S.C. § 134 by the Patent
Applicant from the Patent Examiner’s rejection of claims 46, 49-54, 56, 57,

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 2009-013022
Application 10/107,122

2
60, 64, 69-75, and 77. The Board’s jurisdiction for this appeal is under 35
U.S.C. §§ 6(b). We affirm.

STATEMENT OF THE CASE
There is one rejection at issue in this appeal: the rejection of clams 46,
49-54, 56, 57, 60, 64, 69-75, and 77 under 35 U.S.C. § 103(a) as obvious
over Sparks, 2 Felder, 3 and Eggers4 (Ans. 3). Claims 46 is representative.
Claims 49-54, 56, 57, 60, 64, 69-75, and 77 fall with claims 46 (App. Br. 4).
Claim 46 reads as follows:
Claim 46. A method for screening a plurality of proteins for
their ability to interact with a component of a fluid sample,
comprising delivering the fluid sample to a protein array
comprising the plurality of proteins comprising at least 100
different proteins, and simultaneously detecting for the presence
of an interaction of the component with each protein of the
plurality of proteins, wherein the protein array comprises the
plurality of proteins each immobilized site-specifically on
different discrete, known regions of a substrate, wherein the
discrete, known regions are present at a density of at least 100
per cm2, thereby detecting an interaction of a protein of the
plurality of proteins and the component of the fluid sample,
wherein each of the proteins in the plurality of proteins is
a different purified recombinant fusion protein, and the proteins
in the plurality of proteins are structurally related, functionally
related, suspected of being functionally related, suspected of
being structurally related, or are members of the same family.

2 U.S. Patent 6,309,820 B1, issued Oct. 30, 2001.
3 U.S. Patent 6,232,066 B1, issued May 15, 2001.
4 U.S. Patent 5,532,128, issued Jul 2, 1996.
Appeal 2009-013022
Application 10/107,122

3
ISSUE
Does the combination of Sparks, Felder, and Eggers suggest a
screening method using a protein array of at least 100 different proteins at a
density of at least 100 per cm2, where the proteins “are structurally related,
functionally related, suspected of being functionally related, suspected of
being structurally related, or are members of the same family”?
Was there a reasonable expectation of success of arriving at the
claimed method based on the teachings of Sparks, Felder, and Eggers ?

FINDINGS OF FACT (FF)
Sparks
1. Sparks describes a kit that may be used to identify new drug candidates,
where the kit comprises a “a plurality of purified polypeptides, . . . each
polypeptide containing a function domain of interest” (Sparks, col. 25, ll. 51-
55; col. 26, ll. 17-19).
2. The polypeptides can be immobilized on a solid support, such as on a
microtiter well (id. at col. 25, ll. 9-11; col. 29, ll. 30-35).
3. “Using the methods of the present invention, it is possible to identify and
isolate large numbers of polypeptides containing functional domains . . .
Using these polypeptides, one can construct a matrix relating the
polypeptides to an array of candidate drug compounds.” (Id. at col. 31, ll. 1-
6).
Felder
4. Felder discloses an apparatus and methods for high throughput screening
of potential drugs (Felder, col. 1, ll. 31-34; col. 2, ll. 11-13).
Appeal 2009-013022
Application 10/107,122

4
5. Felder describes a “combination [which] comprises a surface comprising
a plurality of spatially discrete regions, which can be termed test regions and
which can be wells, at least two which are substantially identical.” (Id. at
col. 1, ll. 51-55).
6. “This invention relates e.g. to compositions, apparatus and methods
useful for concurrently performing multiple biological or chemical assays,
using repeated arrays of probes. A plurality of regions each contains an array
of generic anchor molecules.” (Id. at col. 1, ll. 8-12.)
7. Felder discloses:
In one embodiment, for example, using 96-well . . .
[microplates], 36 different oligonucleotides can be spotted onto
the surface of every well of every plate to serve as anchors. The
. . . same 36 anchors can be used for all screening assays. For
any particular assay, a given set of linkers can be used to
program the surface of each well to be specific for as many as
36 different targets or assay types of interest, and different test
samples can be applied to each of the 96 wells in each plate.
(Id. at col. 2, ll. 34-46).
8. “Substantially identical region . . . refers to regions which contain
identical or substantially identical arrays of anchors and/or anchor/linker
complexes.” (Id. at col. 5, l, 66 to col. 6, l. 1).
9. Felder discloses:
The number of anchors in a test region can be at least two,
preferably between about 8 and about 900 (more or less being
included), more preferably between about 8 and about 300, and
most preferably between about 30 and about 100 (e.g. about
64). In a most preferred embodiment, each anchor in a test
region has a different specificity from every other anchor in the
array.
(Id. at col. 7, 42-48).
Appeal 2009-013022
Application 10/107,122

5
10. Felder also discloses that probes can be proteins, such as enzymes
(proteases or kinases) and antibodies (id. at col. 4, ll. 34 & 49).
Eggers
11. Eggers describes arrays of probes which utilize electrical signals to
detect whether a probe has bound a target (Eggers, col. 3, ll. 4-10 & 63-67;
col. 4, ll. 1-7).
12. Peptide antigens can be used in the arrays (id. at col. 10, 55-65).
13. The “presence of hundreds or thousands of different antibodies or other
proteins” can be detected by the arrays (id. at col. 11, 11-14).
14. Eggers describes various ways of producing arrays with probes,
including utilizing prior art methods for large scale peptide synthesis (id.
beginning at col. 7, l. 60 & col. 8, l. 12-col. 9, l. 2).

ANALYSIS
Claim 46 is directed to a “method for screening a plurality of proteins
for their ability to interact with a component of a fluid sample.” The method
involves delivering a sample to “a protein array comprising at least 100
different proteins” where each protein is immobilized in a discrete region of
a substrate “at a density of at least 100 per cm2.” Each of the proteins is
“structurally related, functionally related, suspected of being functionally
related, suspected of being structurally related, or are members of the same
family.”
The Examiner found that Sparks described a screening method that
involved screening drug candidates that interacted with polypeptides having
functional domains, where the proteins were immobilized on a substrate, as
in claims 46 (Ans. 3). The Examiner found that Sparks did not describe the
Appeal 2009-013022
Application 10/107,122

6
claimed number of proteins (“at least 100 different”) arranged in the claimed
density, but found these elements described in the Felder and Eggers patents
(id. at 3-5), and determined it would have been obvious to modify Sparks
with these teachings “to achieve a better and more thorough screening
process” (id. at 5).
Appellants contend that the claimed plurality of 100 different proteins
is not taught or suggested in the prior art (App. Br. 6).
As found by the Examiner, Sparks describes utilizing a plurality of
proteins in its screening method (FF1 & FF3), but does not disclose the
recited number of 100 “different” polypeptides. However, Sparks’
disclosure of using large numbers of proteins in assays reasonably suggests
numbers such as 100, as this number is large. Consequently, we do not find
Appellants’ argument about lack of a reason to modify Sparks with the
teachings of Felder and Eggers persuasive (App. Br. 9).
Moreover, as found by the Examiner, both Felder and Eggers suggest
the claimed limitation. Felder describes a surface with regions, which each
region can have from 8-900, preferably 30-100 anchors in each regions,
where each anchor has a different specificity (FF7 & FF9). Thus, persons of
ordinary skill in the art would have recognized that the anchors could be
associated with as many as 100 different proteins, where the different anchor
specificities would permit different proteins to be attached. Eggers also
describes detecting “hundreds or thousands of different antibodies or other
proteins” (FF13), reasonably suggesting corresponding numbers of different
peptide antigens (FF12 & 13).
Appellants contend that Felder does not state that anchors within a test
region had different specificities (Reply Br. 3). We do not agree with
Appeal 2009-013022
Application 10/107,122

7
Appellants’ position. Felder stated that “each anchor in a test region has a
different specificity from every other anchor in the array.” Felder described
each “region” as containing an “array.” (F6 & F8). Therefore, describing
“each anchor in a test region” as having “a different specificity from every
other anchor in the array” is a reference to the anchors in a single array of a
test region.
Appellants also argue that the Examiner mischaracterized Sparks by
relying on the matrix of table 1 as describing an array of 10 different
proteins (App. Br. 8). However, while it may be correct that the matrix is
not explicitly described as an array, Sparks described immobilizing proteins
on solid supports, such as microtiter wells (FF2), reasonably suggesting
arrays of a plurality of different proteins as recited in claim 46. Arrays of
proteins as established by each of Felder and Eggers were known in the art.
Appellants argue that Felder’s teaching of “’substantially identical’”
regions” teaches away from the claimed invention (Reply Br. 5). While we
agree that Felder does describe that certain embodiments have substantially
identical regions, such regions are also characterized as arrays having as
many as 900 anchors with different specificities (FF9). Thus, each identical
region is an array that suggests the claimed limitation of at least 100
different proteins.
Appellants also contend that the claim limitation that proteins be
related or members of the same family is not met by the prior art (App. Br.
7). To the contrary, Felder describes that the arrays proteins can be
proteases or kinases (FF10), which would have been considered to be
“members of the same family” as required by claim 46.
Appeal 2009-013022
Application 10/107,122

8
Appellants assert that obviousness has not been established because
“none” of Sparks, Eggers, or Felder “successfully demonstrates a method to
immobilize at least 100 purified recombinant fusion proteins on a substrate”
with the density as claimed (App. Br. 10). We do not agree. As argued by
the Examiner, there is no evidence that the methods disclosed in Felder and
Sparks would not work for arrays of large numbers of proteins (Ans. 11-12).
Eggers disclosed specific methods for making arrays of peptides (F14).
Thus, the evidence of record supports the Examiner’s determination that
peptide arrays were enabled by the prior art.

SUMMARY
The combination of Sparks, Felder, and Eggerss suggests a screening
method with a protein array of at least 100 different proteins at a density of
at least 100 per cm2, where they “are structurally related, functionally
related, suspected of being functionally related, suspected of being
structurally related, or are members of the same family.” There was a
reasonable expectation of success that the claimed method would be arrived
at based on the teachings of Sparks, Felder, and Eggers. The rejection of
claim 46 is affirmed. Claims 49-54, 56, 57, 60, 64, 69-75, and 77 fall with
claim 46.

Appeal 2009-013022
Application 10/107,122

9
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

cu

Townsend and Townsend and Crew, LLP
Two Embarcadero Center, Eighth Floor
San Francisco, CA 94111-3834