Ex Parte Ishikawa et al

Board of Patent Appeals and Interferences

Aug 16, 2012

11897103 (B.P.A.I. Aug. 16, 2012)

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.
11/897,103 08/28/2007 Muriel Y. Ishikawa 1003-002-002H-DIV005 3948
44765 7590 08/16/2012
THE INVENTION SCIENCE FUND
CLARENCE T. TEGREENE
11235 SE 6TH STREET
SUITE 200
BELLEVUE, WA 98004
EXAMINER
RIGGS II, LARRY D
ART UNIT PAPER NUMBER
1631
MAIL DATE DELIVERY MODE
08/16/2012 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 MURIEL Y. ISHIKAWA, EDWARD K.Y. JUNG,
NATHAN P. MYHRVOLD,
RICHA WILSON, and LOWELL L. WOOD, JR.
__________

Appeal 2011-013299
Application 11/897,103
Technology Center 1600
__________

Before DONALD E. ADAMS, LORA M. GREEN, and
STEPHEN WALSH, Administrative Patent Judges.

GREEN, Administrative Patent Judge.

DECISION ON APPEAL
This is a decision on appeal under 35 U.S.C. § 134 from the
Examiner‟s rejection of claims 54, 56, 58, 61-63, 66, 67, 70-76, 78-80, 83,
84, and 87-91. We have jurisdiction under 35 U.S.C. § 6(b).
Appeal 2011-013299
Application 11/897,103

2
STATEMENT OF THE CASE
Claim 54 is representative of the claims on appeal, and reads as
follows:
54. A system, comprising:
circuitry for associating at least one computable antigen of one or
more agents with at least a part of an immune response;
circuitry for identifying, in a computing device, information relating
to a computable pattern of past variations of the at least one computable
antigen;
circuitry for extrapolating a pattern of one or more predicted changes
determined by analysis of the computable pattern of past variations of the at
least one computable antigen;
circuitry for selecting, in response to said circuitry for extrapolating,
one or more immune response components; and
circuitry for communicating to at least one system user the selected
one or more immune response components.

The following grounds of rejection are before us for review:
1

I. Claims 54, 56, 58, 61-63, 66, 67, 70-76, 78-80, 83, 84, and 87-91
stand rejected under 35 U.S.C. § 102(b) as being anticipated by
Chirino
2
(Ans. 5).
II. Claims 54, 56, and 58 stand provisionally rejected on the ground of
nonstatutory obviousness-type double patenting as being
unpatentable over claim 9 of USSN 10/925,905 (Ans. 9-10).

1
The obviousness-type double patenting rejections over USSNs 10/925,904
(Ans. 9), 11/001,259 (Ans. 10-11), 11/044,656 (Ans. 11-12), 11/724,580
(Ans. 13), 11/891,871 (Ans. 19-20), 11/897,574 (Ans. 22), 11/899,550 (Ans.
22-23) are moot in view of the abandonment of those applications.
2
Chirino et al., US 2003/0022285 A1, published Jan. 30, 2003.
Appeal 2011-013299
Application 11/897,103

3
III. Claims 54, 56, and 58 stand provisionally rejected on the ground of
nonstatutory obviousness-type double patenting as being
unpatentable over claim 81 of USSN 11/900,442 (Ans. 11).
IV. Claims 54, 56, and 58 stand provisionally rejected on the ground of
nonstatutory obviousness-type double patenting as being
unpatentable over claims 51 and 56 of USSN 11/046,658 (Ans. 12-
13).
V. Claims 54, 56, and 58 stand provisionally rejected on the ground of
nonstatutory obviousness-type double patenting as being
unpatentable over claim 12 of USSN 11/724,593 (Ans. 14).
VI. Claims 54, 56, and 58 stand provisionally rejected on the ground of
nonstatutory obviousness-type double patenting as being
unpatentable over claims 1 and 40 of USSN 11/728,950 (Ans. 14-
15).
VII. Claims 54, 56, and 58 stand provisionally rejected on the ground of
nonstatutory obviousness-type double patenting as being
unpatentable over claim 15 of USSN 11/729,958 (Ans. 15-16).
VIII. Claims 54, 56, and 58 stand provisionally rejected on the ground of
nonstatutory obviousness-type double patenting as being
unpatentable over claims 25 and 50 of USSN 11/731,001 (Ans.
16).
IX. Claims 54, 56, and 58 stand provisionally rejected on the ground of
nonstatutory obviousness-type double patenting as being
unpatentable over claims 2 and 18 of USSN 11/807,335 (Ans. 16-
17).
Appeal 2011-013299
Application 11/897,103

4
X. Claims 54, 56, and 58 stand provisionally rejected on the ground of
nonstatutory obviousness-type double patenting as being
unpatentable over claims 1 and 19 of USSN 11/807,336 (Ans. 17-
18).
XI. Claims 54, 56, and 58 stand provisionally rejected on the ground of
nonstatutory obviousness-type double patenting as being
unpatentable over claims 1 and 13 of USSN 11/807,337 (Ans. 18).
XII. Claims 54, 56, and 58 stand provisionally rejected on the ground of
nonstatutory obviousness-type double patenting as being
unpatentable over claim 17 of USSN 11/891,331 (Ans. 18-19).
XIII. Claims 54, 56, and 58 stand provisionally rejected on the ground of
nonstatutory obviousness-type double patenting as being
unpatentable over claim 1 of USSN 11/895,989 (Ans. 20-21).
XIV. Claims 54, 56, and 58 stand provisionally rejected on the ground of
nonstatutory obviousness-type double patenting as being
unpatentable over claims 1, 79, and 85 of USSN 11/895,341 (Ans.
21).
XV. Claims 54, 56, and 58 stand provisionally rejected on the ground of
nonstatutory obviousness-type double patenting as being
unpatentable over claims 174 and 202 of USSN 11/899,592 (Ans.
23-24).
XVI. Claims 54, 56, and 58 stand provisionally rejected on the ground of
nonstatutory obviousness-type double patenting as being
unpatentable over claim 75 of USSN 11/213,325 (Ans. 24-25).
Appeal 2011-013299
Application 11/897,103

5
XVII. Claims 54, 56, and 58 stand provisionally rejected on the ground of
nonstatutory obviousness-type double patenting as being
unpatentable over claim 19 of USSN 11/904,636 (Ans. 25).

We affirm rejections I-XVII.

ISSUE
Has the Examiner established by a preponderance of the evidence that
Chirino anticipates the claimed system?

FINDINGS OF FACT
FF1. The Specification teaches that the “application relates, in general, to
detection and/or treatment” (Spec. 3).
FF2. As to “system,” the Specification teaches:
[O]ne aspect of a system that may serve as an illustrative
environment of and/or for subject matter technologies, for
example, a computer-based method for designating an immune
response component for modulating an epitope and/or a
computable epitope displayed by an agent.

(Id. at 12.)
FF3. As to “immune response component,” the Specification teaches that it
may include, but is not limited to, at least a part of a
macrophage, a neutrophil, a cytotoxic cell, a lymphocyte, a T-
lymphocyte, a killer T-lymphocyte, an immune response
modulator, a helper T-lymphocyte, an antigen receptor, an
antigen presenting cell, a dendritic cell, a cytotoxic T-
lymphocyte, a T-8 lymphocyte, a cluster differentiation (CD)
molecule, a CD3 molecule, a CD1 molecule, a B lymphocyte,
an antibody, a recombinant antibody, a genetically engineered
Appeal 2011-013299
Application 11/897,103

6
antibody, a chimeric antibody, a monospecific antibody, a
bispecific antibody, a multispecific antibody, a diabody, a
chimeric antibody, a humanized antibody, a human antibody, a
heteroantibody, a monoclonal antibody, a polyclonal antibody,
a camelized antibody, a deimmunized antibody, an anti-
idiotypic antibody, an antibody fragment, and/or a synthetic
antibody and/or any component of the immune system that may
bind to an antigen and/or an epitope thereof in a specific and/or
a useful manner.

(Id. at 15-16.)
FF4. As to “agent,” the Specification teaches:
The term “agent”, as used herein, . . . may include, for example,
but is not limited to, an organism, a virus, a dependent virus, an
associated virus, a bacterium, a yeast, a mold, a fungus, a
protoctist, an archaea, a mycoplasma, a phage, a
mycobacterium, an ureaplasma, a chlamydia, a rickettsia, a
nanobacterium, a prion, an agent responsible for a transmissible
spongiform encephalopathy (TSE), a multicellular parasite, a
protein, an infectious protein, a polypeptide, a
polyribonucleotide, a polydeoxyribonucleotide, a
polyglycopeptide, a polysaccharide, a nucleic acid, an
infectious nucleic acid, a polymeric nucleic acid, a metabolic
byproduct, a cellular byproduct, and/or a toxin. The term
“agent” . . . may include, but is not limited to, a putative
causative agent of a disease or disorder, or a cell or component
thereof that is deemed, for example, a target for therapy, a
target for neutralization, and/or or a cell whose apoptosis,
phagocytic envelopment, removal, lysis or functional
degradation may prove beneficial to the host. The term “agent”
. . . may also include, but is not limited to, a byproduct or
output of a cell that may be neutralized and/or whose removal
or functional neutralization may prove beneficial to the host.
Furthermore, the term “agent”. . . may include an agent
belonging to the same family or group as the agent of primary

Appeal 2011-013299
Application 11/897,103

7
interest, or an agent exhibiting a common and/or a biological
function relative to the agent of primary interest.

(Id. at 16.)
FF5. The Specification teaches further:
The term “epitope” . . ., as used herein, may include, but is not
limited to, a sequence of at least 3 amino acids, a sequence of at
least nine nucleotides, an amino acid, a nucleotide, a
carbohydrate, a protein, a lipid, a capsid protein, a coat protein,
a polysaccharide, a sugar, a lipopolysaccharide, a glycolipid, a
glycoprotein, and/or at least a part of a cell. As used herein, the
term “epitope”. . . may, if appropriate to context, be used
interchangeably with antigen, paratope binding site, antigenic
determinant, and/or determinant. As used herein, the term
“determinant” can include an influencing element, determining
element, and/or factor, unless context indicates otherwise. In
one aspect, the term “epitope” . . . includes, but is not limited
to, a peptide-binding site. As used herein, the term “epitope”
. . . may include structural and/or functionally similar sequences
found in the agent . . . . The term “epitope”. . . includes, but is
not limited to, similar sequences observed in orthologs,
paralogs, homologs, isofunctional homologs, heterofunctional
homologs, heterospecific homologs, and/or pseudogenes of the
agent. . . . The epitope. . . may include any portion of the agent.
In one aspect, the epitope. . . may include at least a portion of a
gene or gene-expression product. In another aspect, the epitope
may include at least a part of a non-coding region.

(Id. at 19).
FF6. As to the term “computable epitope,” the Specification teaches:
The term “computable epitope” as used herein, includes, but is
not limited to, an epitope . . . whose likely future mutable forms
may be predicted by using, for example, including, but not
limited to, practicable computer-based predictive methodology
and/or practicable evolutionary methods and/or practicable
probabilistic evolutionary models and/or practicable
Appeal 2011-013299
Application 11/897,103

8
probabilistic defect models and/or practicable probabilistic
mutation models.

(Id. at 19-20.)
FF7. The Examiner‟s statement of the rejection may be found at pages 5-8
of the Answer. We also highlight the following facts from Chirino.
FF8. Chirino teaches that it relates
to the use of a variety of computational methods for modulating
the immunogenicity of proteins by identifying and then altering
potential amino acid sequences that elicit an immune response
in a host organism. In particular, proteins will be screened for
MHC binding motifs [MHC], T cell receptor [TCR], and B cell
receptor [BCR] binding sequences.

(Chirino, p. 1, ¶2.)
FF9. Chirino teaches further:
[T]he present invention provides methods for generating
polypeptides exhibiting enhanced immunogenicity comprising
the steps of inputting a target protein backbone structure with
variable residue positions into a computer, applying at least one
computational immunogenicity filter to generate a set of
primary variant amino acid sequences, computationally
analyzing said set of primary variant amino acid sequences
using at least one protein design algorithm and identifying at
least one variant protein with enhanced immunogenicity. This
same method may be used to generate polypeptides exhibiting
reduced immunogenicity.

(Id. at p. 2, ¶18.)
FF10. According to Chirino, “the methods of the invention involve starting
with a target protein and using computational analysis to generate a set of
primary sequences” (id. at pp. 7-8, ¶69), and “sequence and/or structural
Appeal 2011-013299
Application 11/897,103

9
alignment programs can be used to generate primary libraries” (id. at p. 8,
¶76).
FF11. Chirino teaches that “sequence homology based alignment methods
can be used to create sequence alignments of proteins related to the target
structure,” which are “then examined to determine the observed sequence
variations,” which are tabulated to define a primary library (Id. at p. 8, ¶79.)
FF12. According to Chirino:
Sequence based alignments can be used in a variety of ways.
For example, a number of related proteins can be aligned, as is
known in the art, and the “variable” and “conserved” residues
defined; that is, the residues that vary or remain identical
between the family members can be defined. These results can
be used to generate a probability table, as outlined below.
Similarly, these sequence variations can be tabulated and a
secondary library defined from them as defined below.
Alternatively, the allowed sequence variations can be used to
define the amino acids considered at each position during the
computational screening. Another variation is to bias the score
for amino acids that occur in the sequence alignment, thereby
increasing the likelihood that they are found during
computational screening but still allowing consideration of
other amino acids. This bias would result in a focused primary
library but would not eliminate from consideration amino acids
not found in the alignment. . . .

(Id. at p. 8, ¶80.)
FF13. Chirino teaches that the computational processing results in a set of
optimized variant candidate sequences, which are different from the target
protein sequence in regions critical for MHC, TCR, or BCR binding (id. at p.
14, ¶124.)

Appeal 2011-013299
Application 11/897,103

10
FF14. Chirino teaches further:
In an additional aspect, the present invention provides methods
for eliciting an enhanced immune response in a patient
comprising the steps of inputting a target protein backbone
structure with variable residue positions into a computer,
applying in any order at least one computational protein design
algorithm and at least one computational immunogenicity filter,
identifying at least one variant protein with enhanced
immunogenicity, and administering said variant protein to a
patient.

(Id. at p. 2, ¶21.)

PRINCIPLES OF LAW
In order for a prior art reference to serve as an anticipatory reference,
it must disclose every limitation of the claimed invention, either explicitly or
inherently. In re Schreiber, 128 F.3d 1473, 1477 (Fed. Cir. 1997).
Moreover, our mandate is to give claims their broadest reasonable
interpretation. In re American Academy of Science Tech Center, 367 F.3d
1359, 1364 (Fed. Cir. 2004). “An essential purpose of patent examination is
to fashion claims that are precise, clear, correct, and unambiguous. Only in
this way can uncertainties of claim scope be removed, as much as possible,
during the administrative process.” In re Zletz, 893 F.2d 319, 322 (Fed. Cir.
1989).

ANALYSIS
Initially, we note that Appellants only appear to bring separate
arguments as to independent claim 54 (see, e.g., App. Br. 37). We thus treat
independent claims 54, 56, and 58 as a group, with claim 54 representative,
Appeal 2011-013299
Application 11/897,103

11
and claims 56 and 58 stand or fall with claim 29. 37 C.F.R.
§ 41.37(c)(1)(vii). Moreover, Appellants also do not appear to present
separate arguments as to dependent claims 73 and 90, and thus those claims
also stand or fall with claim 54.
Claim 54 is drawn to a system that includes: 1)circuitry for
associating at least one computable antigen of one or more agents with at
least a part of an immune response; 2) circuitry for identifying, in a
computing device, information relating to a computable pattern of past
variations of the at least one computable antigen; 3) circuitry for
extrapolating a pattern of one or more predicted changes determined by
analysis of the computable pattern of past variations of the at least one
computable antigen; 4)circuitry for selecting, in response to said circuitry for
extrapolating, one or more immune response components; and 5)
circuitry for communicating to at least one system user the selected one or
more immune response components.
Thus, the claim is very broad, and written at a very general, high
level, and covers a multitude of systems. Moreover, the Specification is
written very broadly, and there is nothing in the Specification that would
preclude interpreting claim 29 from reading on a system as taught by
Chirino.
Specifically, Chirino teaches computer methods, and thus teaches
circuitry (see Spec. 47 (noting that circuitry includes electrical circuitry
forming a general purpose computer)), for identifying MHC binding motifs,
T cell receptors, and B cell receptor binding sequences on a protein (see,
e.g., FF8). The MHC binding motifs, T cell receptors, and B cell receptor
Appeal 2011-013299
Application 11/897,103

12
binding sequences read on the computable antigen (see FFs 5 and 6) and the
protein reads on an agent (see FF4). Thus, Chirino teaches element 1) of the
system of claim 54.
Chirino also teaches that sequence alignment may be used to identify
sequence variations in the protein (FFs 10-12). Thus, Chirino teaches
element 2) of the system of claim 54, wherein the identified sequence
variations read on “a computable pattern of past variation,” that is, a pattern
of changes determined using sequence alignment.
Next, Chirino teaches that using the sequence alignment one can
identify variable and conserved residues, and the allowed sequence
variations to define the amino acids considered at each position during the
computational screening (FF12). Thus, by identifying variable residues and
looking at allowed sequence variation, Chirino teaches circuitry “circuitry
for extrapolating a pattern of one or more predicted changes determined by
analysis of the computable pattern of past variations of the at least one
computable antigen.” Thus, Chirino teaches element 3) of the system of
claim 54.
Chirino then teaches an immunogenicity filter is used to identify those
variants that have enhanced immunogenicity with respect to MHC, TCR, or
BCR binding (which read on the immune response components). Thus,
Chirino teaches element 4) of the system of claim 54, that is “circuitry for
selecting, in response to said circuitry for extrapolating, one or more
immune response components.” That is, Chirino teaches computational
methods for identifying variants of the target protein that have increased
binding affinity to MHC, TCR, or BCR.
Appeal 2011-013299
Application 11/897,103

13
Finally, Chirino teaches that the variant may be administered to a
patient. Thus, the computational system must necessarily have circuitry for
“communicating to at least one system user the selected one or more
immune response components.” That is, as Chirino teaches target protein
variants having increased affinity to MHC, TCR, or BCR, which are then
tested and can be used therapeutically, Chirino must necessarily
communicate the results, that is the variants and the immune response
component to which it has increased affinity, and thus enhanced
immunogenicity, to a user. Thus, Chirino teaches component 5) of the
system of claim 54.
We thus agree with the Examiner that Chirino anticipates the system
of claim 54.
Appellants assert that the Examiner misconstrued Appellants‟ claims
(App. Br. 28-30). Appellants assert further that the Examiner misconstrued
the teachings of Chirino (id. at 30-37). Appellants also argue that the
Examiner‟s allegations regarding the appealed claims and Chirino are
insufficient to support a finding of anticipation, and also failed to provide
objective evidence or reasoning to support the rejection (id. at 50-59
The Examiner did rely on objective evidence, that is Chirino, and
Appellants‟ attention is directed to an analysis of the claim and the analysis
of Chirino, and how it is applied to claim 54 above. In this regard, we agree
with the Examiner (Ans. 26) that Appellants are in large part arguing that
since there is not ipsis verbis support for the subject matter of the claims in
Chirino, Chirino cannot serve as an anticipatory reference. But as discussed
Appeal 2011-013299
Application 11/897,103

14
above, Appellants‟ claims is very broad, and encompasses the system taught
by Chirino.
As to dependent claims 61 and 78, Appellants argue that the portion
of Chirino relied upon by the Examiner are directed to what vaccines may be
designed against, and not what a target protein may be from (App. Br. 37-
39).
Claims 61 adds the limitation to element 1) of claim 54 as including
“circuitry for identifying an association of at least one computable antigen
with one or more agents wherein at least one of the one or more agents is a
putative causative agent of a disease.” The Examiner finds that Chirino
teaches that the “target protein may be from dengue fever, malaria,
Hepatitis, anthrax, botulism, [and] cancers” (Ans. 6). Specifically, Chirino
teaches that candidate variant proteins that are more immunogenic than the
target protein may be used in the development of vaccines (Chirino, p. 27, ¶
255), and that vaccines may be made against Hepatitis, anthrax, botulism,
etc. (id. at p. 29, ¶¶ 259-264). Thus, the ordinary artisan would understand
that the agent, which includes the computable antigen, is from, for example,
hepatitis, and thus is a putative cause of a disease,
As to claims 62 and 79, Appellants argue that “„[c]andidate variant
proteins‟ that „are more immunogenic toward different cancers‟ is distinct
from „the target protein may be a particular cancer or family of cancers‟
(emphasis added) as alleged by the Examiner” (App. Br. 39-40).
Claim 62 adds the limitation to element 1) as including “circuitry for
identifying an association of at least one computable antigen with one or
more agents wherein at least one of the one or more agents is an agent
Appeal 2011-013299
Application 11/897,103

15
belonging to a same family or group as an agent of primary interest.” The
Examiner finds that Chirino discloses that “the target protein may be a
particular cancer or family of cancers, e.g. sarcoma (angiosarcoma,
fibrosarcoma, rhabdomyosarcoma, liposarcoma)” (Ans. 6). Specifically,
Chirino teaches that sequence based alignments may be used to compare
related proteins, and conserved and variable residues defined (Chirino, p. 8,
¶ 80). As found by the Chirino also teaches that the cancer may be a
sarcoma, which includes related cancers (id. at p. 28, ¶ 264). Thus, Chirino
teaches identifying an association of at least one computable antigen with
one or more agents wherein at least one of the one or more agents is an agent
belonging to a same family or group as an agent of primary interest.
As to claims 63 and 80, Appellants argue that the portion of Chirino
relied upon by the Examiner does not “describe „circuitry where the target
proteins of agents have a common function‟ as alleged by the Examiner”
(App. Br. 41-44).
Claim 63 adds the limitation to element 1) as including “circuitry for
identifying an association of at least one computable antigen with one or
more agents wherein at least one of the one or more agents is an agent
exhibiting a common function relative to an agent of primary interest.” The
Examiner relies on ¶ 97 of Chirino, which teaches in the context of the
reference that residues that may be fixed in computationally determining
variants include functional residues, and include, for example, residues that
form the active site of an enzyme. Thus, Chirino teaches using an agent that
exhibits a common function relative to an agent of primary interest, such as
a family of enzymes.
Appeal 2011-013299
Application 11/897,103

16
As to claims 66, 67, 83, and 84, Appellants argue that the section of
Chirino relied upon by the Examiner is in the “Background of Invention”
section, and is thus not part of Chirino‟s invention, and describes general
information regarding the immune system (App. Br. 44). Appellants further
assert that neither ¶ 5 of Chirino, nor ¶24, supports the Examiner‟s position
(id. at 44-45).
Claim 66 adds the limitation to element 4) of claim 54 as including
“circuitry for selecting at least a part of at least one B-lymphocyte.” The
fact that the portion of Chirino relied upon by the Examiner is in the
background section of Chirino is not relevant to the issue, as even though the
portion of the Chirino relied upon by the Examiner is designated as
“Background,” it is still evidence as to what would be understood by the
ordinary artisan. Moreover, even though that disclosure of Chirino may be a
discussion of general immunology, it is still evidence as to what would be
understood by the ordinary artisan.
As found by the Examiner (Ans. 7) Chirino teaches computer
methods, and thus teaches circuitry, for identifying MHC binding motifs, T
cell receptors, and B cell receptor binding sequences on a protein. Chirino
thus teaches that the immune response components may be at least a part of
at least one B-lymphocyte.
As to claims 70 and 87, Appellants argue that the Examiner‟s finding
that Chirino “shows immunogenic sequences may be produced from
sequence encoding at least one conformational three dimensional epitope
that interacts with specific antigens” is not supported by ¶ 257 of Chirino
(App. Br. 45).
Appeal 2011-013299
Application 11/897,103

17
Claim 70 adds the limitation to element 4) of claim 54 as including
“circuitry for selecting one or more immune response components specific
to the conformational state of a protein.” Chirino teaches that one may
insert a sequence encoding at least one conformational three dimensional
epitope that interacts with membrane bound antibodies on naïve B cells
(Chiron, pp. 27-28, ¶257). Thus, Chirino teaches choosing an immune
response component, membrane bound antibodies on naïve B cells, that is
specific to a conformational state of the protein.
As to claims 71 and 88, Appellants argue that the Examiner‟s finding
that “Chirino „shows target proteins that are effector molecules, e.g. proteins
as inhibitors/activators‟” is not supported by the text of Chirino (App. Br.
45-47).
Claim 71 adds the limitation to element 4) of claim 54 as including
“circuitry for selecting one or more immune response components including
one or more effector molecules.” Chirino teaches in the Background section
that T cells are responsible for cellular immunity, and are known to secrete
cytokine, chemokines, and other mediators (Chirino, p. 1 ¶ 5). Thus, by
selecting a T-cell receptor binding sequence as taught by Chirino (see FF8),
one is also selecting for immune response components that include effector
molecules, such as cytokines or chemokines.
As to claims 72 and 89, Appellants argue that the Examiner‟s finding
that Chirino shows “„projecting (predicting) changes relating to the amino
acids within the peptides‟” is not supported by the text of Chirino (App. Br.
47-49).
Appeal 2011-013299
Application 11/897,103

18
Claim 72 adds the limitation to element 4) of claim 54 as including
“circuitry for selecting one or more immune response components with
physico-chemical properties optimized by computer-based screening
methods.” The Examiner finds that Chirino shows “projecting (predicting)
changes relating to the amino acids within the peptides with a computer . . .,
patterns of change in oxidative stability, alkaline stability and thermal
stability can be predicted with the variant proteins” (Ans. 7). Thus, Chirino
teaches changing physic-chemical properties, such as oxidative stability, in
generating variants that have optimized physic-chemical properties for the
desired immune response component.
As to claims 74 and 91, Appellants argue that the Examiner did not
establish the relevance of the teachings of Chirino to the appealed claims
(App. Br. 56-57).
Claim 74 adds the limitation to element 4) of claim 54 as including
“circuitry for selecting one or more immune response components designed
for binding to the smallest effective determinant.” Chirino teaches that
variant sequences will be screened for peptide fragments predicted to bind to
MHC class II ligands, wherein the class two ligands consist of 12 to 25
amino acids (Chirino, p. 16, ¶ 141). Thus, by looking for MHC class II
ligands, one is selecting for an immune response component having a
smallest effective determinant of 12 amino acids.
As to claims 75 and 76, Appellants argue that the Examiner‟s finding
that “Chirino paragraphs [0266] and [0268] „shows, exact dose method of
delivery, degradation, age, body weight, etc. related to the candidate variant
protein administered to a patient in need for treatment will be ascertainable
Appeal 2011-013299
Application 11/897,103

19
by one skilled in the art using known techniques wherein the information
wherein data input would be from a physician utilizing a medical system‟” is
not supported by the text of Chirino (App. Br. 49-50).
Claim 75 adds the limitation to claim 56 as including “circuitry for
accepting input via a medical system.” As Chirino teaches that the variant
may be used in a treatment (FF14), one would have input the sequence of the
desired protein from a medical system that had determined the appropriate
target.

Conclusion of Law
We conclude that the Examiner has established by a preponderance of
the evidence that Chirino anticipates the claimed system. We thus affirm the
rejection of claims 54, 56, 58, 61-63, 66, 67, 70-76, 78-80, 83, 84, and 87-
91under 35 U.S.C. § 102(b) as being anticipated by Chirino.

ISSUE (Rejections II-XVII)
Has the Examiner established by a preponderance of the evidence that
the claims rejected in each of the provisional obviousness-type double
patenting rejections is rendered obvious by the claims cited in each of the
copending applications?

Findings of Fact
FF15. The Examiner‟s statement of the rejections may be found at pages 8-
25 of the Answer.
FF16. As to Rejection II over USSN 10/925,905, the Examiner concludes:
Appeal 2011-013299
Application 11/897,103

20
Although the conflicting claims are not identical, they are
patentably distinct from each other because the difference
between the instant claims and claim 9 of ‟905 is that claim 9
recites analysis of the pattern of past variations of a computable
epitope whereas the instant claims recite analysis of a pattern of
past variations of a computable antigen. A computable
“epitope” is encompassed by the definition of a computable
“antigen” of the instant claims, (specification, page 41, first
paragraph). Therefore claim 9's recitation of computable
“epitope” make obvious the instantly recited computable
“antigen”.

(Ans. 9-10.)
FF17. Claim 9 of USSN 10/925,905 reads as follows:
A system, comprising:
circuitry configured by a computer program for
identifying an association of at least a portion of one or more
agents with at least a part of an immune response;
circuitry configured by a computer program for
identifying a pattern of past variations of the at least one
computable epitope;
circuitry configured by a computer program for
extrapolating a pattern of one or more predicted changes
determined by analysis of the pattern of past variations of the at
least one computable epitope;
circuitry configured by a computer program for selecting
one or more immune response components responsive to said
circuitry for extrapolating; and
circuitry configured by a computer program for
communicating at least one of the one or more immune
response components to at least one user.

Analysis
Appellants argue that “the Examiner made general assertions
ungrounded in specific facts and unsupported by evidence of record”,
Appeal 2011-013299
Application 11/897,103

21
asserting that “[t]he Examiner did not provide a reasoned, fact-based
explanation for the double patenting allegations, only mere conclusory
statements and assertions” (App. Br. 60).
We disagree, as each rejection explains the Examiner‟s reasoning as
to why the appealed claims are rendered obvious by the claims relied upon
by the Examiner in making the rejection.
Appellants specifically argue two of the rejections as examples: the
rejection over USSN 10/925,904, and the rejection over USSN 10/925,905;
(App. Br. 65-67). As USSNs 10/925,904 has been abandoned, we only
address the arguments as to USSN 10/925,905 (Rejection II).
Appellants assert that the rejection is based on a misconstruction of
appealed claims 54, 56, and 58, as the Examiner has ignored the specific
antecedents in those claims (id. at 66).
Appellants‟ arguments are not convincing. First, it is unclear how the
Examiner has ignored the antecedents, as claim 54 is drawn to a system, as
is claim 9 of USSN 10/925,905, wherein the “computable antigen” of instant
claim 54 read on the “computable epitope” of claim 9 of USSN 10/925,905
(see FF5).
As Appellants did not present separate arguments as to the remaining
rejections, we also affirm Rejections III-XVIII.

Conclusion of Law
We conclude that the Examiner established by a preponderance of the
evidence that the claims rejected in each of the provisional obviousness-type
Appeal 2011-013299
Application 11/897,103

22
double patenting rejections is rendered obvious by the claims cited in each
of the copending applications. We thus affirm Rejections II-XVII.

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
alw