Ex Parte Bangera et al

Patent Trial and Appeal Board

Feb 24, 2017

11728950 (P.T.A.B. Feb. 24, 2017)

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.
11/728,950 03/26/2007 Mahalaxmi Gita Bangera 1003-002-002G-CIP001 3403
44765 7590 02/28/2017
INTELLECTUAL VENTURES - ISF
ATTN: DOCKETING, ISF
3150- 139th Ave SE
Bldg. 4
Bellevue, WA 98005
EXAMINER
LIN, JERRY
ART UNIT PAPER NUMBER
1631
NOTIFICATION DATE DELIVERY MODE
02/28/2017 ELECTRONIC
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.
Notice of the Office communication was sent electronically on above-indicated "Notification Date" to the
following e-mail address(es):
ISFDocketInbox@intven.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte MAHAL AXMI GITA BANGERA, MURIEL Y. ISHIKAWA,
EDWARD K.Y. JUNG, NATHAN P. MYHRVOLD,
ELIZABETH A. SWEENEY, RICHA WILSON, and
LOWELL L. WOOD JR.,
Appeal 2014-0029571
Application 11/728,9502
Technology Center 1600
Before LORA M. GREEN, RICHARD M. LEBOVITZ, and
ULRIKH W. JENKS, Administrative Patent Judges.
LEBOVITZ, Administrative Patent Judge.
DECISION ON APPEAL
This appeal involves claims directed to computer-implemented
methods comprising identifying, with reference to a computer database, a
predicted past epidemiological variation of the computable epitope of a
virus; and identifying antibodies predicted to bind to future changes in the
1 The Appeal Brief (“Appeal Br.”) 4 lists Searete, LLC, in Bellevue, WA, an
affiliate of Intellectual Ventures Management, LLC, as the real-party-in-
interest.
2 “The ’950 Application.”
Appeal 2014-002957
Application 11/728,950
computable epitope. The Examiner rejected the claims as obvious under 35
U.S.C. § 103(a) and under non-statutory obviousness-type double-patenting.
We have jurisdiction under 35 U.S.C. § 134. The obviousness rejections are
affirmed-in-part. The non-statutory obviousness-type double-patenting is
affirmed. A new ground of rejection under 35 U.S.C. § 112, first paragraph,
is set forth pursuant to 37 C.F.R. § 41.50(b). The application in this appeal
is related to numerous related applications. Appeal Br. 4—6.
STATEMENT OF CASE
Appellants appeal from the rejection by the Examiner of claims 1, 2,
4, 9-18, and 40-67. Final Rej. Summary. The claims stand rejected by the
Examiner as follows:
1. Claims 1, 2, 4, 9-15, 18, 40-A4, and 47 under 35 U.S.C. § 103(a)
as obvious in view of Chirino3 and Soudeyns.4 Final Rej. 3.
2. Claims 15, 17, 45, and 46 under 35 U.S.C. § 103(a) as obvious in
view of Chirino, Soudeyns, and Hertz.5 Final Rej. 8.
3. Claims 1 and 40 on the ground of non-statutory obviousness
double-patenting over claims 1, 25, and 50 of Application 11/731,001 and
claims 1, 19, and 37 of Application 11/807,336. Final Rej. 10.
3 Chirino et al., US 2003/0022285 Al, published Jan. 30, 2003 (“Chirino”).
Also referred to as “the Chirino Application.” During the prosecution of the
Chirino Application, a Final Rejection was issued by the USPTO. This
Final Rejection is cited in this Decision.
4 Soudeyns et al., Selective pressure exerted by immunodominant HIV-1-
specific cytotoxic T lymphocyte responses during primary infection drives
genetic variation restricted to the cognate epitope, 29 Eur. J. Immunol.
3629-35 (1999)(“Soudeyns”).
5 Hertz et al., US 2006/0281697 Al, published Dec. 14, 2006 (“Hertz”).
2
Appeal 2014-002957
Application 11/728,950
Claim 1, reproduced below, is representative (for reference, bracketed
numbers have been added to the claim to number the clauses; this numbering
system was utilized by Appellants in their discussion of the claim):
A computer-implemented method, comprising:
[1] accepting, in a computing device, nucleic acid
sequence information identifying a virus present in a location at
a first time;
[2] designating, in the computing device, a computable
epitope in the nucleic acid sequence information identifying the
virus present in the location at the first time;
[3] identifying, with reference to a computer database, a
predicted past epidemiological variation of the computable
epitope of the virus prior to the first time;
[4] extrapolating, in the computing device, from the
predicted past epidemiological variation of the computable
epitope of the virus, a predicted future change in the
computable epitope at a second time in the future;
[5] identifying, with reference to a computer database, an
antibody predicted to bind to the predicted future change in the
computable epitope at the second time in the future; and
[6] communicating, by the computing device, the
identified antibody to at least one system user.
Appeal Br. 70 (Claims Appendix).
THE PERSON OF ORDINARY SKILL IN THE ART
When making a patentability determination under 35 U.S.C., we
consider the claims and the scope and content of the prior art to be directed
to one of ordinary skill in the art. Thus, a determination as to whether the
claims conform to the patentability requirements of 35 U.S.C., including the
requirements of 35 U.S.C. §§ 103 and 112, is made from the perspective of
one of ordinary skill in the art. In this case, the claimed subject matter
involves a computer implemented method for performing bioinformatics on
3
Appeal 2014-002957
Application 11/728,950
the components (proteins, antibodies, epitopes) of an antibody response.
The cited prior art includes a published patent application and peer-reviewed
scientific journal publications. The latter is the forum for scientists who
typically have a Ph.D. or are working towards a Ph.D. or master’s degree in
the pertinent field. Here, the pertinent fields are molecular biology,
immunology, and bioinformatics as evidenced by the subject matter of the
cited prior art publications. Accordingly, the person of ordinary skill in the
art is a scientist, who publishes work in peer-reviewed scientific
publications, and has at least a post-graduate level understanding of
molecular biology, immunology, and bioinformatics, and is able to perform
bioinformatics analysis on proteins.
DECLARATION
Appellants provided declarations by Wayne Kindsvogel, Ph.D. Dr.
Kindsvogel holds a Ph.D. in molecular biology and was employed as a
scientist at a biotechnology company. Kindsvogel March 2012 Decl. 1
and 3. We therefore consider him one of ordinary skill in the art. Dr.
Kindsvogel is currently employed by the real-party-in-interest. Id., 12.
OBVIOUSNESS BASED ON CHIRINO AND SOUDEYNS
Chirino “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.” Chirino, Abstract. Chirino teaches that the protein modified by
the computational method can be used in the development of vaccines and
immunotherapeutics. Id.,^ 255.
4
Appeal 2014-002957
Application 11/728,950
The Examiner found that Chirino teaches the steps of the claimed
computer implemented method, but not “predicted past epidemiological
variation of the computable epitope of the virus prior to the first time.” Final
Rej. 3^4 (see steps [3] and [4]). For this aspect, the Examiner cited
teachings in Soudeyns of identifying changes in the HIV envelope protein
during infection (“predicted past epidemiological variation of the
computable epitope”) and using that information to make future vaccines
and immune-based interventions (“extrapolating . . . from the predicted past
epidemiological variation of the computable epitope of the virus, a predicted
future change in the computable epitope at a second time”). Id., 4.
Appellants contend that the Examiner did not establish prima facie
obviousness of the claims because the specific recitations in the claims were
not addressed. Appeal Br. 16 and 19-20. We address Appellants’
arguments for each of the clauses of claim 1 below.
[1] accepting, in a computing device, nucleic acid sequence
information identifying a virus present in a location at a first time;
[2] designating, in the computing device, a computable epitope in the
nucleic acid sequence information identifying the virus present in the
location at the first time;
The Examiner cited the Abstract and paragraph 17 of Chirino for
designating epitopes. Final Rej. 3^4. The Chirino Abstract describes
“modulating the immunogenicity of proteins by identifying and then altering
potential amino acid sequences that elicit an immune response in a host
organism.” Chirino, Abstract. An epitope can be a protein sequence which
is antigenic or immunogenic, i.e., capable of eliciting an immune response,
such as antibodies. ’950 Application 12 and 21—22 (paragraph spanning
5
Appeal 2014-002957
Application 11/728,950
pages). Thus, because the Chirino Abstract describes identifying amino acid
sequences that elicit immune responses, and because an epitope is an amino
acid sequences that elicits immune response, the Abstract teaches identifying
epitopes of any protein, including a virus. Chirino also teaches that the
proteins altered by its methods can be used to make a vaccine against a
virus, which necessarily constitutes an immune response. Chirino 255
and 261.
Clauses 1 and 2 of the claim require starting from a nucleic acid
sequence and then identifying (“designating”) the coding sequence within
the nucleic acid sequence. Chirino teaches that “source of the sequences can
vary widely, and include taking sequences from one or more of the known
databases, including” protein and nucleic acid databases. Chirino 177.
Chirino further teaches that the sequences can be subjected to analysis of
gene prediction {id., 178), providing a reason to have “designat[ed], in the
computing device, a computable epitope in the nucleic acid sequence
information” (predicting a gene or region of a gene, namely, an epitope) as
recited in clause 2 of claim 1. Chirino also teaches that “Candidate variant
proteins may also be identified as being encoded by candidate variant
nucleic acids” {id., 1179), providing additional reason to enter “nucleic acid
sequence information identifying a virus” in a computing device as in clause
1 of claim 1 and then designate a computable epitope (“candidate variant
protein”) in the nucleic acid sequence information for the virus.
Dr. Kindsvogel testified in his declaration that Chirino does not teach
“computable epitopes.” Kindsvogel March 2012 Deck Tflf 5—6. A
“computable epitope” is “an epitope that can be utilized within a computing-
device system or method.” See Appeal Brief, filed in Application
6
Appeal 2014-002957
Application 11/728,950
11/807,336, page 4. The Examiner cited various disclosures in Chirino for
teaching such an epitope. For example, the Chirino Abstract cited by the
Examiner (Final Rej. 3) states: “The present invention 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.” Chirino Abstract. We
already addressed how such disclosure of an immunogenic region constitutes
an epitope. Chirino teaches that the epitope is modified in the computational
method, and therefore is utilized within a “computing-device system or
method,” meeting the Appellants’ definition of a “computable epitope”.
Accordingly, we find Dr. KindsvogeTs testimony to be unsupported by a
preponderance of the evidence.
Dr. Kindsvogel characterizes Chirino’s teachings, stating that such
teachings are not a teaching of “epitopes specifically based upon a pattern of
past epidemiological variations.” Kindsvogel March 2012 Decl. Tflf 5—6.
However, the Examiner specifically relied on Soudeyns for teaching “past
epidemiological variations.” Moreover, while Dr. Kindsvogel denied that
Chirino describes a computable epitope, he provided no explanation of how
Chirino’s computational method performed in a computing device could be
carried out on anything other than a computable epitope.
[3] identifying, with reference to a computer database, a predicted
past epidemiological variation of the computable epitope of the virus
prior to the first time
The Examiner found that Soudeyns teaches “longitudinal analysis of
sequence variation in the envelope (env) gene of HIV in two human subjects
during primary HIV infection.” Final Rej. 4. The Examiner identified
7
Appeal 2014-002957
Application 11/728,950
disclosure in Soudeyns which showed the accumulation of mutations in the
HIV envelope protein over time. Id. Based on this teaching, the Examiner
cited Soudeyns’ conclusion that:
It is conceivable that an immunodominant HIV-specific CTL
response directed against a single epitope may favor the
emergence of virus mutants that escape the immune response.
The latter issue should be taken into consideration in the design
of strategies aimed at the development of candidate HIV
vaccines and immune-based interventions.
Soudeyns 3633. Thus, the cited disclosure from Soudeyns shows “predicted
past epidemiological variation of’ a viral epitope as in clause 3. The
Examiner found that one of ordinary skill in the art would have had reason
to apply this teaching to Chirino:
It would have been further obvious to analyze epitopes of a
human host infected with HIV at a first time point and a second
time point in the future because Soudeyns et al. shows that
epitopes encoded by the HIV env gene mutate during infection,
and that eight variable regions in the env gene are sites of
variation, and that the variant epitopes escape host cytotoxic T
lymphocytes. Soudeyns et al. provides guidance that future
variation in the env gene that escape preexisting host CTL
specificities should be considered in HIV vaccines.
Final Rej 6.
Appellants attempt to distinguish the claims by stating that Soudeyns
does not teach performing clause 3 “prior to the first time” as recited in the
claim. Appeal Br. 24. This argument does not persuade us that the
Examiner erred. The claim requires the virus to be “present in a location at a
first time.” The analysis is performed on the virus sequence present in this
location at a first time and then an antibody is identified which is predicted
to bind to the virus at a future time. For example, the analysis could be
performed in a patient infected with the virus for the first time, where the
8
Appeal 2014-002957
Application 11/728,950
purpose of the analysis is to predict an antibody to treat the vims. Soudeyns
expressly teaches this purpose by stating that epitope changes should be
taken into consideration when designing immune-based intervention.
Soudeyns 3633. Consequently, Appellants’ argument is not supported by
evidence.
Appellants also attempt to distinguish Soudeyns by arguing Soudeyns
is “a RNA and cDNA based clinical study. No epitope, and more
specifically, no ‘computable epitope’ as recited in the third clause of claim 1
is shown or described by Soudeyns.” Appeal Br. 25 (emphasis added).
This argument does not accurately reflect the disclosure in Soudeyns.
Soudeyns studied changes in protein epitopes of the HIV envelope protein
that occur during HIV infection. Soudeyns states that their results “provide
compelling evidence that the CTL epitope mutations directly resulted from
the selective pressure exerted by the vims-specific cytotoxic response.”
Soudeyns Abstract. The protein epitope mutations were detected by DNA
sequencing (“Here we report detailed longitudinal analysis of DNA
sequence variation performed over the entire HIV-1 envelope in two
subjects during primary HIV infection.”). Id. For example, Soudeyns
teaches:
Thus, the progressive accumulation of dN nucleotide
substitutions within the DNA sequence of the IPRRIRQGL
epitope resulted in the emergence of vims variants that were no
longer recognized by the HIV-specific CTL.
Soudeyns 3632. In view of this disclosure, we find that Appellants’
argument that no epitope is shown or described by Soudeyns to be
misleading.
9
Appeal 2014-002957
Application 11/728,950
Dr. Kindsvogel stated in his declaration that “epitope variations
known to occur in nature (epidemiological variations) are excluded from the
invention of Chirino.” Kindsvogel March 2012 Deck 4. However, the
rejection is based on the combination of Chirino and Soudeyns, not Chirino
alone. Chirino is cited for its teachings on how to modify proteins using
computing devices and Soudeyns is cited for directing the skilled worker
where to modify the protein when using the computing device described in
Chirino. Consequently, while Chirino may describe modifying natural-
occurring sequences to make them more immunogenic, Dr. Kindsvogel did
not direct our attention to anything in the publication that would restrict the
computational method from being used to modify epitopes based on past
epidemiological changes.
[4] extrapolating, in the computing device, from the predicted past
epidemiological variation of the computable epitope of the virus, a
predicted future change in the computable epitope at a second time in
the future
As found by the Examiner, Soudeyns teaches taking into account the
“predicted past epidemiological variation of the computable epitope of the
virus” by taking “into consideration” the “progressive accumulation of
mutations” (the “variations” in claim 1) observed in the HIV envelope
protein during infection. Final Rej. 4—5. Thus, Soudeyns teaches predicting
future changes in the HIV envelope protein based on past changes in the
viral envelope protein. While Soudeyns does not expressly teach making
this extrapolation in a “computing device,” the sequencing analysis is
performed in an automatic sequencer (Soudeyns 3634). Chirino, as found by
the Examiner, describes predicting changes in a protein using computational
10
Appeal 2014-002957
Application 11/728,950
methods (Final Rej. 3), thus the Examiner’s determination that it would have
been obvious to have performed Soudeyns’ prediction steps in Chirino’s
computing device is supported by the evidence. Id., 5—6. Indeed, as shown
by Chirino, bioinformatics analysis is typically carried out by a computer so
it would have been within the skill of the ordinary skilled worker to create a
program to perform such an analysis. See section titled “The person of
ordinary skill in the art.”
We have considered Appellants’ contention that the Examiner did not
establish that clause 4 is described by Chirino or Soudeyns. Appeal Br. 26—
27. However, the Examiner specifically cited Chirino as “predicting one or
more changes in the epitopes” (Final Rej. 3) and Soudeyns as taking past
changes in the HIV envelope protein into account when designing vaccines
and immunotherapeutics {id., 4—5). For this reason, we find Appellants’
arguments that the Examiner has made conclusory statements “devoid of any
factual support in evidence” (Appeal Br. 27) to be inconsistent with the
record before us. Appellants did not provide an adequate explanation as to
why the facts relied on by the Examiner (cited and explained above) do not
render clause 4 obvious to one of ordinary skill in the art.
[5] identifying, with reference to a computer database, an antibody
predicted to bind to the predicted future change in the computable
epitope at the second time in the future
The Examiner cited Soudeyns’ disclosure showing changing
variations in the HIV envelope protein and statements that such changes
should be taken into account when designing vaccines and immune-based
interventions as making obvious clause 5 of claim 1. Final Rej. 4.
11
Appeal 2014-002957
Application 11/728,950
Appellants contend that Soudeyns does not teach such predicted changes and
not with reference to a database. Appeal Br. 27.
This argument is not persuasive. Appellants did not address the
express disclosure in Soudeyns cited by the Examiner regarding taking into
account variations in the HIV envelope protein. Soudeyns 3633. In
addition, the Examiner did not rely on Soudeyns for teaching a database and
computational aspects, but rather cited Chirino for these teachings. Thus,
Appellants’ argument does not address the basis of the rejection, but rather
attacks the teachings of only one of the cited prior art publications.
Appellants did not identify a specific defect in the Examiner’s findings nor
conclusion. Id., 26—27.
[6] communicating, by the computing device, the identified antibody
to at least one system user
The Examiner found that Chirino reasonably suggested
communicating the identified antibody to a user (“Chirino et al. teach
making the computationally designed protein, which would require ... an
output to a user of the Chirino et al.’s method.”) Final Rej. 4. Appellants
assert that the Examiner did not establish the obviousness of this clause, but
did not address the Examiner’s specific reasons in the Final Rejection for
finding clause 6 obvious. Appeal Br. 29.
CLAIMS 2, 4, 9, 10 and 11
The Examiner cited specific disclosure in Chirino where the
limitations recited in claims 2, 4, 9, 10, and 11 are found. Final Rej. 5.
Appellants contend that the Examiner erred in finding the limitations
12
Appeal 2014-002957
Application 11/728,950
described in Chirino. Appeal Br. 30. As evidence, Appellants cited Dr.
Kindsvogel’s March 2012 declaration.
Dr. Kindsvogel attests that “it is well known that peptides (i.e.
epitopes) bind to MHC class I and class II molecules in an extended
conformation which is substantially linear,” and thus not “a computable
epitope of a substantially non-linear form” as recited in claim 4. Kindsvogel
March 20012 Deck 6 (first full paragraph).
This argument is not persuasive. Chirino teaches “conformation
epitopes” (Chirino 132 and 257) which were well known at the time of
the invention to include non-linear epitopes. See Decision on Appeal in
Application 11/807,336 (Appeal No. 2014-004154) mailed concurrent to this
decision, pages 10-13.
Dr. Kindsvogel also denied that Chirino teaches epitopes having “a
substantially similar functional sequence match or structural sequence match
with at least one host” as recited in claims 9 and 10. Kindsvogel March
2012 Deck 6. However, Chirino discloses that “candidate variant proteins
that are more immunogenetic [sic, immunogenic] than the target protein are
used in the development of vaccines and immunotherapeutics for
autoimmune disease and cancer.” Chirino 1255. Such proteins involved in
cancer and autoimmune disease are host proteins having epitopes that have a
functional and structural match with a host as required by the claims.
Dr. Kindsvogel also challenged the Examiner’s finding that the cited
publications described the limitation of claim 11 of “predicted courses of an
immune response in a host and wherein the one or more predicted courses
are responsive to one or more interventions that include the antibody.”
Kindsvogel March 2012 Deck 7. However, the cited Soudeyns publication
13
Appeal 2014-002957
Application 11/728,950
teaches mutations in the HIV envelope that occur in a host during the course
of the immune response, and state that such mutations, which may escape
the host immune response, “should be taken into consideration in the design
of strategies aimed at the development of candidate HIV vaccines and
immune-based interventions”. Soudeyns 3633. Thus, whatever
shortcomings are present in Chirino, they are made up for by the express
teaching in Soudeyns of designing interventions based on the predicted
course of the immune response in which the envelope protein may mutate
and evade the immune response during the infection.
Appellants’ argue that claims 2, 4, 9, 10, and 11 are not obvious over
Chirino and Soudeyns because of the failure to describe a virus present in
the location at the first time and past epidemiological variations. Appeal Br.
31—32. These limitations appear in the independent claims and are
addressed above. The relevance of these limitations to the rejection of the
dependent claim has not been articulated by Appellants.
CLAIMS 12-15 and 18
The Examiner cited to disclosure in Chirino for teaching the
limitations recited in claims 12—15 and 18. Final Rej. 5.
Claims 12, 13, and 15 recite “an antibody that is at least part of ’ a T-
lymphocyte, B-lymphocyte, and CD molecules.” We note that the ’950
Application describes selecting parts of the recited lymphocytes and
molecules, not antibodies that are part of such cells and proteins. ’950
Application 40. The Examiner cited disclosure in Chirino of selecting T-cell
and B-cell epitopes. Final Rej. 5 citing Abstract, lines 5—6; page 4,
paragraph 0035; page 4, paragraph 0040-page 5, paragraph 0044). In
14
Appeal 2014-002957
Application 11/728,950
attempting to distinguish the claimed subject matter, Dr. Kindsvogel states
that “there is no ‘aiding the identification’ of B cells and T cells.”
Kindsvogel March 2012 Decl. 8. However, the phrase referred to by Dr.
Kindsvogel does not appear in the claims reproduced in the claims appendix
nor the amendment filed Oct. 17, 2017, which appears to the last amendment
entered in this application. Consequently, Dr. Kindsvogel’s declaration is
ineffective.
Claim 18 depends from claim 1 and further recites “an antibody that is
directed to at least one of a glycoprotein, and/or a receptor ligand.” Chirino
expressly teaches glycoproteins and proteins that are glycosylated. 25, 97,
191,274. Thus, the limitation of claim 18 is met by Chirino. Dr.
Kindsvogel’s declaration refers to the claim as reciting “aiding in the
identification of a receptor ligands,” but such language does not appear in
the claim. Kindsvogel March 2012 Decl. 8. Accordingly, we again find the
declaration ineffective.
Appellants correctly quote the language of these claims in their brief
(Appeal Br. 34), but do not explain why the Examiner’s findings regarding
T-cell and B-cell epitopes are factually incorrect and do not render obvious
the claimed subject matter. See Appeal Br. 35—36 where Appellants make
general denials about the lack teachings in Chiron with respect to claims 13—
15, but do not address the interpretation of the claims nor the Examiner’s
findings.
CLAIM 40
Appellants contend that the Examiner ignored the distinct recitations
in claims 1 and 40. Appeal Br. 16—19. While we agree with Appellants that
15
Appeal 2014-002957
Application 11/728,950
there are different recitations between claims 1 and 40, we do not agree that
such differences necessitated that the Examiner apply different prior art.
We address the differences between claims 1 and 40 below.
Claim 1
designating, in the computing device, a computable epitope in the
nucleic acid sequence information identifying the virus present in the
location at the first time
Claim 40
identifying, in the computing device, an association of a
computable epitope of the identified virus present in a location at
a first time with at least a part of an immune response in a host,
wherein the host is a person requiring management for infection
by the virus
Claim 1 refers to “designating” the computable epitope in the “nucleic
acid sequence information.” Because epitopes are typically protein, one of
ordinary skill in the art would understand a sequence is being identified and
designated in the nucleic acid sequence that codes for a protein epitope of
the virus. In claim 40, “an association of computable epitope of the virus”
with “an immune response of the host” is recited. In other words, an epitope
of the virus must be identified, as in claim 1 and then such epitope must be
associated with an immune response, such as an antibody response. Thus,
claim 40 has the additional requirement of identifying an immune response
to the protein epitope. The Examiner cited Soudeyns for this limitation.
Final Rej. 4. Soudeyns teaches:
We then determined whether the evolution of HIV-1 env in
patients 15 and 23 was correlated with the HIV specific CTL
response. Of note, patient 15 was previously shown to exhibit a
potent immunodominant CTL response directed against a B7-
restricted determinant (IPRRIRQGL) located within the C-
terminal portion of VS . . .
16
Appeal 2014-002957
Application 11/728,950
Soudeyns 3631. Soudeyns describes an epitope (“IPRRIRQGL”) and an
immune response to it (“immunodominant CTL Response”). Thus, the
additional limitation in claim 40 is met by Soudeyns.
Another difference between claims 1 and 40 is as follows (emphasis
added):
Claim 1
identifying, with reference to a computer database, an antibody
predicted to bind to the predicted future change in the computable
epitope at the second time in the future; and communicating, by the
computing device, the identified antibody to at least one system user.
Claim 40
identifying, with reference to a computer database, an antibody
predicted to bind to the predicted future change in the computable
epitope at the second time in the future;
identifying, with reference to a computer database, a prophylactic
treatment for the host, wherein the prophylactic treatment includes the
identified antibody predicted to bind to the predicted future change in
the computable epitope at the second time in the future; and
communicating the identified prophylactic treatment for the host to a
system user.
In both claims, an antibody predicted to bind an epitope is identified.
Claim 40 additionally requires prophylactic treatment for the host,
wherein the prophylactic treatment includes the identified antibody. ”
Chirino describes passive immunotherapy which would constitute a
prophylactic treatment and further teaches the addition of other therapeutics
Chirino, 274 and 276. Consequently, to the extent there is an additional
difference between claim 1 and claim 40, this difference is described in
Chirino.
17
Appeal 2014-002957
Application 11/728,950
Appellants separately argue claim 40, but the arguments are
principally the same as those for claim 1 and thus have already been
addressed. See Appeal Br. 37-42. For the clauses reproduced above,
Appellants simply deny that it is described by Chirino, but failed to address
the entirety of the disclosure which was before them. Appellants had fair
notice that the Examiner considered all the limitations of claim 40 as
rendered obvious by the combination of Chirino and Soudeyns, but did not
fully respond to the thrust of the rejection. See In re Jung, 637 F.3d 1356,
1362-64 (Fed. Cir. 2011).
CLAIMS 41—44
Claims 41—44 recite the same limitations as in claims 12—15 and 18.
Appellants’ specific arguments for these claims (Appeal Br. 44-47) are
identical to the arguments made for the latter claims that have already been
addressed above.
CLAIM 47
Claim 47, depends from claim 40, and further recites “identifying, in
the computing device, an association of the computable epitope of the
identified virus present in a location at a first time with at least one of: a
polyglycopeptide, a polysaccharide, a nucleic acid, or a toxin.” The
Examiner found “that one use of the variant protein produced by the
computer mediated method of Chirino et al. is to generate antibodies or
vaccines for use in immunotherapy.” Final Rej. 6. Chirino also teaches that
the variant proteins (comprising a computable epitope) can be administered
“with other therapeutics,” including a zinc-alpha2-glycoprotein, which meets
the requirements of claim 47 of a “polyglycopeptide.” Chirino 1274. See
18
Appeal 2014-002957
Application 11/728,950
also id., 1272 (“cellulose,” “starch,” which are polysaccharide), 1275.
Consequently, the limitations are met by Chirino.
OBVIOUSNESS BASED ON CHIRINO, SOUDEYNS, AND HERTZ
The Examiner further rejected claims 16, 17, 45, and 46 based on
Hertz. Final Rej. 8. Claims 16 and 45 are directed to a humanized antibody;
claims 17 and 46 are directed to a modulator of a humanized antibody. The
Examiner stated that Hertz teaches a humanized antibody and a modulator of
it. Id. The Examiner determined it would have been obvious to have
utilized the strategies of Hertz in Chirino and Soudeyns “to identify B-cells
for affecting the immune system of a patient.” Id.
Dr. Kindsvogel attests that Chirino does not aid the “identification of
a humanized antibody or a modulator of a humanized antibody” in paragraph
[0253], as stated by the Examiner.” Kindsvogel March 2012 Decl. 8. The
Examiner relied on Hertz for teaching a humanized antibody, not Chirino.
Final Rej. 8. Consequently, while Dr. Kindsvogel’s declaration has been
considered, it doesn’t overcome the rejection.
Appellants contend that Hertz only teaches a specific humanized
antibody, and not humanized antibodies generally. Appeal Br. 51.
Appellants also contend that Hertz does not teach a modulator of it. Id.
Hertz provides a specific reason to have used a humanized antibody:
“because it gives rise to substantially no immunological reactions.” Hertz
2000. This general teaching would have led one of ordinary skill in the art
to utilize a humanized antibody to avoid an immunological reaction.
19
Appeal 2014-002957
Application 11/728,950
Appellants have focused on the specific antibodies described in Hertz, while
overlooking the more general teachings.
With respect to claims 17 and 46, the disclosure in Hertz relied upon
by the Examiner for “a modulator of a humanized antibody” is for
modulating binding of SEQ ID NO:3 to its receptor, not an antibody as
correctly pointed out by Appellants. Consequently, we are compelled to
reverse the rejection of claims 17 and 46.
DECLARATIONS
Appellants contend that the Examiner did not address the March 2012
and October 2012 Declarations of Dr. Kindsvogel. Appeal Br. 54.
However, as stated in the Answer, the Examiner considered both
Declarations. Ans. 4. The Examiner stated that upon consideration of the
October 2012 Declaration, “the Examiner withdrew the rejection made
under 35 U.S.C. § 103 based upon Chirino et al. and Florea et al. (Final
Office Action, January 3, 2013, page 2).” Id. With respect to the March
2012 Declaration, for completeness, we have addressed it in the discussion
above.
CHIRINO ENABLEMENT
During the prosecution of the cited Chirino Application, the Examiner
rejected the application claims under 35 U.S.C. § 112, second paragraph,
and under § 112, first paragraph, as lacking a written description of
“immunogenicity filter.” Final Rejection 4 of Chirino Application
(“Chirono Final Rej.”). The Examiner also made an enablement rejection
under § 112, first paragraph, stating that the Chirino Application did not
enable one of ordinary skill in the art to make and use the invention as
20
Appeal 2014-002957
Application 11/728,950
claimed. Id., 7—9. The Examiner found the “immunogenicity filter” recited
in the claims to lack enablement. Id. Second, the Examiner found the effect
of replacing amino acids in the claimed target protein structure to be
unpredictable. Id. Chirino abandoned the application. Notice of Express
Abandonment (May 31, 2005) of Chirino Application.
Appellants point to the statements made by the Examiner in the Final
Rejection of the Chirino Application about the lack of enablement to argue
that Chirino is defective as prior art against the rejected claims in this appeal
and inconsistent with the USPTO’s own interpretation of Chirino. Appeal
Br. 56.
Appellants’ argument does not persuade us that the Examiner erred in
rejecting the claims as obvious in view of Chirino and Soudeyns.
“When the reference relied on expressly anticipates or makes obvious
all of the elements of the claimed invention, the reference is presumed to be
operable. Once such a reference is found, the burden is on applicant to
provide facts rebutting the presumption of operability. In re Sasse, 629 F.2d
675, 207 USPQ 107 (CCPA 1980).” M.P.E.P. § 2121.1. In this case,
Appellants have the burden of demonstrating that Chirino is not enabled.
Appellants’ evidence that Chirino is not enabled is based solely on a
determination by an Examiner in that application to reject its claims for lack
of enablement (and written description) under § 112, first paragraph.
First, we are not bound by the determination of an Examiner in a
different, unrelated case.
Second, and independently, the Examiner’s determination was that the
claims of the Chirino Application were not enabled. This determination
does not necessarily mean that the portions of the Chirino Application
21
Appeal 2014-002957
Application 11/728,950
disclosure relied upon by the Examiner in this present appeal are also non-
enabled. (“[A] prior art reference need not enable its full disclosure; it only
needs to enable the portions of its disclosure alleged to anticipate the
claimed invention.” In re Antor Media Corp., 689 F.3d 1282, 1290 (Fed.
Cir. 2012)). Appellants did not establish that the portions of Chirino’s
specification relied upon and cited by the Examiner did not enable one of
ordinary skill in the art at the time of the invention, when combined with
Soudeyns, to have made the claimed subject matter.
Third, we considered the basis of the enablement rejection in the
Chirino Application and how it relates to the claims in this appeal and find
that it does not undermine the operability of the rejection based on Chirino
in this appeal.
The claims in Chirino had steps of a) inputting three dimensional
coordinates to a target structure and then applying: “i) at least one
computational protein design algorithm using at least two scoring functions;
ii) an immunogenicity filter that modifies at least one T cell epitope of said
target protein by creating a variant of said T cell epitope.” The Examiner’s
rejection in the Chirino Application was based on the lack of written
description and enablement of these steps. Chirino Final Rej. 4, 7, 8.
The rejection in this appeal is based on Chirino and Soudeyns.
Soudeyns is cited by the Examiner for its teaching of epitope variations in
the envelope protein during HIV infection and making changes to the
epitope based on the changes that are predicted to occur during HIV
infection. Final Rej. 4-5. Thus, the starting point for the claim does not
necessarily require inputting three dimensional coordinates and then using a
design algorithm and immunogenicity filter as required by the claims of
22
Appeal 2014-002957
Application 11/728,950
Chirino and determined by the Examiner to lack enablement. Rather,
epitopes and epitopic variations described in Soudeyns can serve as the
starting point. Consequently, we conclude that the description and
enablement of the claimed subject matter of the Chirino Application is not
relevant to whether Chirino makes the rejected claims obvious in
combination with Soudeyns and Hertz.
Appellants also contend that the enablement rejection made in the
Chirino Application provides evidence that Chirino did not describe
“computable epitopes” as required by the rejected claims. Appeal Br. 58.
However, as fully explained above, Chirino expressly teaches manipulating
an epitope in a computing device. Appellants’ discussion of unpredictability
of modifying a target structure relates to the claims of the Chirino
Application {id., 58—59) and neglect the fact that the Examiner cited
Soudeyns as guidance for making changes to an epitope based on the
predicted changes that occur during infection.
In sum, Appellants did not provide persuasive evidence that Chirino
lacks enablement for the specific teachings relied upon by the Examiner.
RATIONALE TO COMBINE THE CITED PRIOR ART REFERENCES
Appellants contend that the Examiner “failed to articulate a
convincing technical rationale to combine Chirino and Soudeyns to result in
the subject matter of independent claims 1 and 40 as well as their respective
dependent claims 2, 4, 9—18, and 41—47, which is fatal to the Examiner’s
obviousness rejection.” Appeal Br. 60. Appellants also contend: “At no
time did the Examiner describe how the teachings of the references could
23
Appeal 2014-002957
Application 11/728,950
allegedly be combined in any way to reach the recitations of the claims.”
Id., 61.
Appellants’ argument is unavailing.
The Examiner found that Chirino describes computable epitopes as
recited in the claims. Final Rej. 3 and 5. The Examiner explained that
“Soudeyns et al. provides guidance that future variation in the env gene
should be considered in HIV vaccines. Thus, the combination of the
references teaches considering antibodies that bind to predicted future
changes in the computable epitope.” Final Rej. 7. In other words, the
Examiner determined that it would have been obvious to one of ordinary
skill in the art to apply Soudeyns’ teaching about variations in the HIV
envelope protein to analyze computable epitopes as described in Chirino.
Id., 6.
In addition to this, immediately after discussing Soudeyns, the
Examiner stated it would have been further obvious
to write a computer program to indicate to a user the result of
the computer mediated process of Chirino et al. and to indicate
that a T cell or B cell would recognize and [sic, an] epitope, and
that an antibody could be made for use in immunotherapy that
is directed against the variant protein because Chirino et al.
provides guidance to use the variant protein produced by their
process to raise antibodies for use in immunotherapy.
Id. The mention of an epitope and antibody is a clear reference to Soudeyns’
disclosure. See also Answer 5.
With respect to the rejection based on Hertz, Appellants contend that
the Examiner “does not provide a ‘clear articulation’ of the reason(s) why
the claimed invention would have been obvious.’ Instead, the Examiner
24
Appeal 2014-002957
Application 11/728,950
appears to be directing his allegations to something distinct from Appellant's
actual claims, without further discussion or explanation.” Appeal Br. 61.
While the Examiner made statements about detection strategies, the
Examiner specifically found that Chirino and Soudeyns do not describe
humanized antibodies and that Hertz describes such antibodies. Final Rej. 8.
Because the claimed subject matter is directed to humanized antibodies, it is
apparent that the rejection is based on utilizing a humanized antibody, whose
benefit is taught in Hertz, in the method of Chirino and Soudeyns.
OBVIOUSNESS TYPE DOUBLE-PATENTING REJECTION
Claim 1 and 40 stand rejected by the Examiner on the ground of non-
statutory obviousness type double-patenting over claims 1, 25, and 50 of
Application 11/731,001 and claims 1, 19, and 37 of Application 11/807,336
(“the ’336 Application”). Application 11/731,001 was abandoned May 5,
2016 (“Notice of Abandonment”) and therefore the rejection of it is moot.
Appellants did not address any differences between claims 1,19, and 37 of
the ’336 Application, although they had notice and ample opportunity to do
so. Consequently, we have addressed only claim 1 of the ’336 Application.
The Examiner found that “[ajlthough the conflicting claims are not
identical, they are not patentably distinct from each other because the
differences between the instant claims and the copending claims are minor.”
Final Rej. 10. The Examiner further explained that in regard to “the
program and circuitry claimed in copending Application Nos. . . .
11/807,336, the instantly claimed methods would be obvious because the
computing device of the instant claims would require both a program and
circuitry, as recited in the claims of the copending applications.” Id.
25
Appeal 2014-002957
Application 11/728,950
Appellants contend that the rejection is insufficient as it is conclusory
without evidence or factual basis. Appeal Br. 66—67.
We do not agree. The Examiner stated the statutory basis of the
rejection and provided a concise rationale for the rejection. Final Rej. 10.
Appellants were thus “on notice of the full basis for the examiner’s
rejection.” Jung, 637 F.3d at 1364.
The chart below compares the steps in claims 1 and 40 of the ’950
Application to claim 1 of the ’336 Application. The numbers 1 through 8 in
the left column are referred to “lines” in the discussion below.
11/728,950
(Appeal 2014-002957)
CLAIM 1 CLAIM 40
11/807,336
(Appeal 2014-004154)
CLAIM 1
1 accepting, in a computing
device, nucleic acid sequence
information identifying a
virus present in a location at
a first time
accepting, in a computing
device, nucleic acid
sequence information
identifying a virus present
in a location at a first time
2 identifying, in the
computing device, an
association of a computable
epitope of the identified
virus present in a location at
a first time with at least a
part of an immune response
in a host, wherein the host is
a person requiring
management for infection
by the
virus;
3 designating, in the
computing device, a
instructions for designating
one or more computable
26
Appeal 2014-002957
Application 11/728,950
computable epitope in the
nucleic acid sequence
information identifying the
virus present in the location
at the first time
epitopes of at least one
agent, wherein the one or
more computable epitopes
arise from a substantially
nonlinear form
4 identifying, with reference
to a computer database, a
predicted past
epidemiological variation of
the computable epitope of
the virus prior to the first
time;
identifying, with reference to
a computer database, a
predicted past
epidemiological variation of
the computable epitope of the
virus prior to the first time;
instructions for identifying
a pattern of past
epidemiological variations
of the one or more
computable epitopes of the
at least one agent
5 extrapolating, in the
computing device, from the
predicted past
epidemiological variation of
the computable epitope of
the virus, a predicted future
change in the computable
epitope at a second time in
the future;
extrapolating, in the
computing device, from the
predicted past
epidemiological variation of
the computable epitope of
the virus, a predicted future
change in the computable
epitope at a second time in
the future;
instructions for
extrapolating a pattern of
one or more predicted
future changes in
the one or more
computable epitopes from
the identified pattern of
past epidemiological
variations;
6 identifying, with reference
to a computer database, an
antibody predicted to bind
to the predicted future
change in the computable
epitope at the second time in
the future;
identifying, with reference
to a computer database, an
antibody predicted to bind
to the predicted future
change in the computable
epitope at the second time in
the future;
instructions for aiding
identification of one or
more immune response
components associated
with the pattern of
predicted changes in the
one or more computable
epitopes
of the at least one agent
7 identifying, with reference
to a computer database, a
prophylactic treatment for
the host,
wherein the prophylactic
treatment includes the
identified antibody
predicted to bind to
the predicted future change
in the computable epitope at
the second time in the
future;
8 communicating, by the
computing device, the
communicating the
identified prophylactic
instructions for displaying
the identified one or more
27
Appeal 2014-002957
Application 11/728,950
identified antibody to at treatment for the host to a immune response
least one system user. system user components
As indicated in the chart, claim 1 of the ’336 Application and claim 1
of the ’950 Application designate epitopes (line 3), identify past
epidemiological variations (line 4), extrapolate future changes in the epitope
(line 5), identify immune components (an antibody in the ’950 Application)
associated with the epitope (line 6), and communicate and display the
immune response information (line 8). The ’336 Application requires the
epitope to be non-linear while the ’950 Application does not; however, non­
linear epitopes were known in the art so such a difference is minor. Claim
40 of the ’950 Application has additional steps (lines 2 and 7); however,
such steps were routine in the art and thus would have been obvious to one
of ordinary skill in the art. See above discussion of such limitations.
NEW GROUND OF REJECTION UNDER 112, FIRST PARAGRAPH
Claims 17 is directed to a computer-implemented method of claim 1,
further comprising “identifying, with reference to a computer database, an
antibody that is a modulator of a humanized antibody.” Claim 46 is directed
to a computer-implemented method of claim 40, further comprising
“identifying an antibody that is a modulator of a humanized antibody.”
Appellants did not direct our attention to support for claims 17 and 46
in the ’950 Application. We have reviewed the ’950 Application and could
not ascertain disclosure that would enable one of ordinary skill in the art to
identity, in a computer-implemented method, a “modulator of a humanized
antibody” as claimed. Consequently, we enter a new ground of rejection of
claims 17 and 46 as failing to comply with the enablement requirement of 35
28
Appeal 2014-002957
Application 11/728,950
U.S.C. § 112, first paragraph (pre-AIA). A new ground of rejection of
claims 17 and 46 is also entered under of 35 U.S.C. § 112, first paragraph
(pre-AIA) as lacking written description.
Under 35 U.S.C. § 112, first paragraph (pre-AIA), the “specification
shall contain a written description of the invention, and of the manner and
process of making and using it, in such full, clear, concise, and exact terms
as to enable any person skilled in the art to which it pertains, or with which it
is most nearly connected, to make and use the same.” “[T]o be enabling, the
specification of the patent must teach those skilled in the art how to make
and use the full scope of the claimed invention without ‘undue
experimentation.’” In re Wright, 999 F.2d 1557, 1561 (Fed. Cir.1993)
(citing In re Vaeck, 947 F.2d 488, 495 (Fed. Cir. 1991)); In re Wands, 858
F.2d 731, 736-37 (Fed. Cir. 1988); In re Fisher, 57 C.C.P.A. 1099, 427 F.2d
833, 839 (1970).
Since the full scope of the claim must be enabled, we must begin by
determining what subject matter is embraced by the claim. The claims
require “a modulator of a humanized antibody,” but there is no description
or example of such a modulator in the ’950 Application. Thus, while the
claim includes identifying a genus of modulators, there is not even a
description of a single one in the ’950 Application. A fully described genus
must allow one skilled in the art to “visualize or recognize the identity of the
members of the genus” and to “distinguish the claimed genus from others.”
University of California v. Eli Lilly & Co., 119 F.3d 1559, 1568 (Fed. Cir.
1997). “To satisfy the written description requirement in the case of a
chemical or biotechnological genus, more than a statement of the genus is
normally required. One must show that one has possession, as described in
29
Appeal 2014-002957
Application 11/728,950
the application, of sufficient species to show that he or she invented and
disclosed the totality of the genus.” Carnegie Mellon University v.
Hoffmann-La Roche Inc., 541 F3d 1115 (2008). Absent a description of the
genus or even a single exemplary species of a modulator of a humanized
antibody, we conclude that the written description requirement has not been
met.
The Application does not provide guidance as to how one of ordinary
skill in the art would identify a modulator of a humanized antibody, let alone
what constitutes a “modulator.” The Application does not have any
direction or guidance on such a method, there are no working examples, no
evidence that such modulators could be identified predictably, and the
claims are unlimited as to the nature of the modulator. See In re Wands, 858
F.2d 731, 736—37 (Fed. Cir. 1988). Consequently, we concluded that the
’950 Application does not enable claims 17 and 46.
SUMMARY
1. The rejection of claims 1, 2, 4, 9-15, 18, 40-44, and 47 as obvious
in view of Chirino and Soudeyns is affirmed.
2. The rejection of claims 15 and 45 under 35 U.S.C. § 103(a) as
obvious in view of Chirino, Soudeyns, and Hertz is affirmed.
3. The rejection of claims 17 and 46 under 35 U.S.C. § 103(a) as
obvious in view of Chirino, Soudeyns, and Hertz is reversed.
4. New grounds of rejection under 35 U.S.C. § 112, first paragraph,
of claims 17 and 46 are set forth pursuant to 37 C.F.R. § 41.50(b) as lacking
written descriptive support and enablement.
30
Appeal 2014-002957
Application 11/728,950
NEW GROUNDS OF REJECTION
This decision contains new grounds of rejection pursuant to 37
C.F.R. § 41.50(b) (effective September 13, 2004, 69 Fed. Reg. 49960
(August 12, 2004), 1286 Off. Gaz. Pat. Office 21 (September 7,
2004)). 37 C.F.R. § 41.50(b) provides that “[a] new ground of rejection
pursuant to this paragraph shall not be considered final for judicial
review.”
37 C.F.R. § 41.50(b) also provides that the Appellants, WITHIN
TWO MONTHS FROM THE DATE OF THE DECISION, must exercise
one of the following two options with respect to the new ground of rejection
to avoid termination of the appeal as to the rejected claims:
(1) Reopen prosecution. Submit an appropriate amendment of the
claims so rejected or new evidence relating to the claims so rejected,
or both, and have the matter reconsidered by the Examiner, in which
event the proceeding will be remanded to the Examiner. . . .
(2) Request rehearing. Request that the proceeding be reheard under §
41.52 by the Board upon the same record.. .
The amendment and/or new evidence under 37 C.F.R. § 41.50(b)(1),
or the request for rehearing under 37 C.F.R. § 41.50(b)(2), must be filed
within 2 months from the date of the Board’s decision. In accordance with
37 C.F.R. § 41.50(f), this 2-month time period may not be extended by the
filing of a petition and fee under 37 C.F.R. § 1.136(a), but only under the
provisions of 37 C.F.R. § 1.136(b).
AFFRIMED-IN-PART; $ 41.50(b)
31