Ex Parte Kirovski et al

Patent Trial and Appeal Board

Oct 23, 2012

11764402 (P.T.A.B. Oct. 23, 2012)

UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
__________

Ex parte DARKO KIROVSKI, DAVID E. HECKERMAN,
and NEBOJSA JOJIC
__________

Appeal 2011-013069
Application 11/764,402
Technology Center 1600
__________

Before TONI R. SCHEINER, JEFFREY N. FREDMAN, and
STEPHEN WALSH, Administrative Patent Judges.

WALSH, Administrative Patent Judge.

DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134(a) from the rejection of
claims directed to a system for designing a vaccine, a computer-
implemented method of efficient vaccine design, and a system that facilitates
efficient vaccine design. The Patent Examiner rejected the claims for
obviousness. We have jurisdiction under 35 U.S.C. § 6(b). We reverse.
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STATEMENT OF THE CASE
Claims 1-8, 10-16, and 18-20 are on appeal. Claim 1 is illustrative
and reads as follows:
1. A system for designing a vaccine for a pathogen population,
comprising:
a processor;
a computer memory having stored thereon the following components
executable by the processor:
a graphing component that receives a set of epitopes present in
the pathogen population and a set of weighting factors and constructs a
graph at least in part by generating vertices corresponding to respective
epitopes, weighting respective vertices based on one or more of the
weighting factors, and generating respective directed edges between a first
vertex corresponding to a first epitope and a second vertex corresponding to
a second epitope that the first epitope overlaps; and
a design component that designs a candidate vaccine sequence
for the pathogen population based at least in part on a combinatorial
algorithm, the candidate vaccine sequence includes overlapping epitopes
corresponding to a maximum-weight length-constrained path (MLP) through
the graph.

The Examiner rejected the claims as follows:
 claims 1-4, 6-8, 10, 11, 14, and 18-20 under 35 U.S.C. § 103(a) as
unpatentable over Boecker,
1
Hanke,
2
Tong,
3
and Wu;
4

1
Sebastian Boecker et al., US 2005/0009053 A1, published Jan. 13, 2005.
2
Tomas Hanke et al., Design and construction of an experimental HIV-1
vaccine for a year-2000 clinical trial in Kenya, 6 NATURE MEDICINE 951-
955 (2000).
3
Joo Chuan Tong et al., Methods and protocols for prediction of
immunogenic epitopes, 8 BRIEFINGS IN BIOINFORMATICS 96-108 (2006).
4
Bang Ye Wu et al., An efficient algorithm for the length-constrained
heaviest path problem on a tree, 69 INFORMATION PROCESSING LETTERS 63-
67 (1999).
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 claims 5 and 13 under 35 U.S.C. § 103(a) as unpatentable over
Boecker, Hanke, Tong, Wu, and Vanetik;
5

 claims 15 and 16 under 35 U.S.C. § 103(a) as unpatentable over
Boecker, Hanke, Tong, Wu, and Govindan;
6
and
 claim 12 under 35 U.S.C. § 103(a) as unpatentable over Boecker,
Hanke, Tong, Wu, and Pai.
7

OBVIOUSNESS
The Issues
Appellants present three arguments for reversal:
(A) the cited references are not analogous art (App. Br. 9-15);
(B) the rationale for combining the cited references is legally insufficient
(id. at 15-27); and
(C) the combination of cited references fails to teach or suggest every
limitation of Appellants‟ claims (id. at 27-45).

Discussion
(A) Each reference discloses its pertinence to at least one other reference,
and taken together, the references are analogous art.

5
N. Vanetik et al., Computing Frequent Graph Patterns from
Semistructured Data, SECOND IEEE INT‟L CONF. ON DATA MINING 458-465
(2002).
6
Ramesh Govindan, Heuristics for Internet Map Discovery, 3 PROC. IEEE
INFOCOM 1371-1380 (2000).
7
Tun-Wen Pai et al., REMUS: a tool for identification of unique
peptide segments as epitopes, 34 NUCLEIC ACIDS RES. W198-W201 (2006).
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“A reference is reasonably pertinent if, even though it may be in a
different field from that of the inventor‟s endeavor, it is one which, because
of the matter with which it deals, logically would have commended itself to
an inventor‟s attention in considering his problem.” In re Clay, 966 F.2d
656, 659 (Fed. Cir. 1992). “[F]amiliar items may have obvious uses beyond
their primary purposes.” KSR Int’l Co. v. Teleflex, Inc., 550 U.S. 398, 402
(2007). “A reference may be read for all that it teaches, including uses
beyond its primary purpose.” In re Mouttet, 686 F.3d 1322, 1331 (Fed. Cir.
2012). “Non-obviousness cannot be established by attacking references
individually where the rejection is based upon the teachings of a
combination of references. Thus, [each reference] must be read, not in
isolation, but for what it fairly teaches in combination with the prior art as a
whole.” In re Merck & Co., Inc., 800 F.2d 1091, 1097 (Fed. Cir. 1986)
(citation omitted).
The first rejection is based on the combined teachings of Boecker,
Hanke, Tong, and Wu. The three subsequent rejections are each based on
these four references plus one more reference said to teach or suggest a
feature of the particular claim(s) addressed in that rejection.
Appellants contend that the subject matter of the Boecker and Wu
references is remote. This reasoning is unpersuasive for two reasons. First,
each reference must be assessed for what it teaches in combination with the
applied art as a whole. Contrasting only two references with the claimed
subject matter ignores how the other two or three applied references may
have informed a person of ordinary skill in the art how the two allegedly
remote references may nevertheless have had relevant uses beyond their
primary purposes. Second, as a matter of substance, the rejections
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established subject matter linkages between all the references showing that
each reference, when taken with the others, would have logically
commended itself to a person designing multiepitope vaccines. Hanke
described the design of a multiepitope vaccine for a pathogen population,
which may also be seen as concatenation of epitope sequences. Tong
disclosed the application of graphical analysis to predicting antigenic
peptides. The Examiner found that a person of ordinary skill in the vaccine
design art would have found Boecker‟s approach to concatenating sequences
to have application to concatenating epitope sequences like Hanke‟s. Tong‟s
explicit disclosure of graphical analysis applied to antigenic peptides would
have been sufficient to suggest the pertinence of other graphical analysis
references, including Wu. Wu demonstrated the application of a well-
known graphing principle to a different practical use, but the application to
graphing in Boecker or Tong would have been recognized as a similar
mathematical procedure, even if the various graphs concern differing subject
matter. In our view, the Examiner‟s findings were prima facie reasonable,
and Appellants‟ attempt to show remoteness without considering what the
references fairly teach in combination is unpersuasive.
(B) The rejections stated a sufficient rationale for combining the
references.
“[R]ejections on obviousness grounds cannot be sustained by mere
conclusory statements; instead, there must be some articulated reasoning
with some rational underpinning to support the legal conclusion of
obviousness.” In re Kahn, 441 F.3d 977, 988 (Fed. Cir. 2006), cited with
approval in KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 417-18 (2007).
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Appellants contend that the rejection provided no rationale as to why
a person of ordinary skill in the art would have seen Hanks‟ epitopes as
analogous to Boecker‟s peptide fragments. (App. Br. 17.) We disagree. It
is undisputed that Boecker disclosed the applicability of its method to
sequence fragments from proteins. (Ans. 6.) We agree with the Examiner
that “[e]ach of the overlapping CTL epitopes of Hanke et al. can be viewed
as a sequence fragment analogous to the peptide fragments generated during
mass spectroscopy induced fragmentation of proteins in Boecker et al.”
(Ans. 9.) Hanke described a vaccine “as a string of partially overlapping
epitopes.” (Hanke 951.) Hanke illustrated an immunogen as an assembly of
peptides and listed the amino acids corresponding to the epitopes (Hanke
952, Figure 1.) Although Hanke constructed its multiepitope vaccine by
recombinant means rather than ligating peptide fragments, Appellants‟
contention that the peptide fragments are not analogous is a form over
substance argument.
Appellants contend that “[t]he only evidence in the record that
suggests such a combination [Boecker and Henke] is Appellant‟s own
disclosure.” (App. Br. 18.) We disagree because Tong also disclosed using
graphical methods for epitope selection. This was a sufficient rational
underpinning for combining the references.
(C) The rejection provides insufficient evidence that the references taught
or suggested every limitation of the appealed claims.
When determining whether a claim is obvious, an Examiner must
make “a searching comparison of the claimed invention – including all its
limitations – with the teachings of the prior art.” In re Ochiai, 71 F.3d 1565,
1572 (Fed. Cir. 1995).
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Appellants contend that the “references of record fail to teach or
suggest „weighting respective vertices based on one or more of the
weighting factors,‟ as recited in Appellant‟s independent claim 1.” (App.
Br. 29.) We find this issue dispositive of error.
The rejection cited Boecker‟s paragraph 307 as evidence that Boecker
taught weighting vertices. (Ans. 7.) Boecker‟s paragraph 307 reads:
The sequencing technique is then modified as follows. A
second threshold t2 is chosen so that t2 is in general larger than t1. For
the constant weighting derived from p=1, this threshold t2 represents a
number of compomers (peaks) that are accepted as missing. A sum of
the weights (denoted as w
*
, and initialized to zero) is then tracked
along with the sequence candidate generated by the recursion. That is,
a character xεΣ is designated as being “admissible” if the admissibility
tests pass and if the following condition holds. Let vx=(v1, ... ,vk)
denote an active vertex in Gk(Cx,x). Then, the (k+1)-tuple (v1, ...
,vk,cx) must be an edge of the sequencing graph, and the total weight
w
*
+wx(v1, ... ,vk,cx) must not exceed the threshold t2. Therefore, when
the sequence candidate is generated by replacing s with the
concatenation sx, the sum of the weights w is also replaced with
w
*
+wx(v1, ... ,vk,cx).

(Boecker 26, [0307].) We have reviewed this paragraph carefully, but are
unable to agree with the Examiner that it describes weighting vertices.
While the Examiner flatly states that the paragraph describes weighting
vertices, the Examiner does not explain how, in the complicated technique
described by Boecker, the vertices are used in a weighting procedure based
on a set of weighting factors that would address the limitation of claim 1.
We therefore agree with Appellants that the rejection of claim 1 must be
reversed because it did not account for this limitation. A similarly worded
limitation appears in independent claims 11 and 19, and the rejection of
those claims must be reversed for the same reason. As the dependent claims
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necessarily incorporate the same limitation, the rejections of the dependent
claims must be reversed.

CONCLUSIONS OF LAW
(A) The references disclose their pertinence to each other and are
therefore analogous art.
(B) Appellants‟ contention that only hindsight motivated the combination
of references is unpersuasive.
(C) Appellants‟ contention that the references did not teach or suggest the
step of weighting vertices is persuasive of error.

SUMMARY
We reverse the rejection of claims 1-4, 6-8, 10, 11, 14, and 18-20
under 35 U.S.C. § 103(a) as unpatentable over Boecker, Hanke, Tong, and
Wu.
We reverse the rejection of claims 5 and 13 under 35 U.S.C. § 103(a)
as unpatentable over Boecker, Hanke, Tong, Wu, and Vanetik.
We reverse the rejection of claims 15 and 16 under 35 U.S.C. § 103(a)
as unpatentable over Boecker, Hanke, Tong, Wu, and Govindan.
We reverse the rejection of claim 12 under 35 U.S.C. § 103(a) as
unpatentable over Boecker, Hanke, Tong, Wu, and Pai.

REVERSED

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