Ex Parte Mullins et al

Patent Trial and Appeal Board

Sep 18, 2012

11713474 (P.T.A.B. Sep. 18, 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.
11/713,474 03/02/2007 James Mullins 4075-INV-0002P.1US 8386
92855 7590 09/19/2012
McDonnell Boehnen Hubert & Berghoff LLP/UW
300 S. Wacker Drive
Suite 3100
Chicago, IL 60606
EXAMINER
JANSSEN, SHANNON L
ART UNIT PAPER NUMBER
1653
MAIL DATE DELIVERY MODE
09/19/2012 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 PATENT TRIAL and APPEAL BOARD
____________

Ex parte JAMES MULLINS, DAVID NICKLE,
and MORGANE ROLLAND
____________

Appeal 2011-009552
Application 11/713,474
Technology Center 1600
____________

Before TONI R. SCHEINER, DONALD E. ADAMS, and
STEPHEN WALSH, Administrative Patent Judges.

ADAMS, Administrative Patent Judge.

DECISION ON APPEAL
This appeal under 35 U.S.C. § 134 involves claims 1-10 (App. Br. 2;
Ans. 2). We have jurisdiction under 35 U.S.C. § 6(b).
STATEMENT OF THE CASE
The claims are directed to a computational method for identifying
conserved elements in a set of biopolymer sequences for incorporation into a
vaccine. Claim 1 is representative and is reproduced in the Claims
Appendix of Appellants’ Brief.

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Application 11/713,474

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Claims 1-5 and 7-10 stand rejected under 35 U.S.C. § 102(b) as being
anticipated by Baker.
1

Claims 1-10 stand rejected under 35 U.S.C. § 103(a) as unpatentable
over the combination of Baker and De Groot.
2

We reverse.

Anticipation:
ISSUE
Does the preponderance of evidence on this record support
Examiner’s finding that Baker teaches Appellants’ claimed invention?

FACTUAL FINDINGS (FF)
FF 1. Examiner finds, inter alia, that Baker teaches a method wherein
“each position within the biopolymer sequence [(i.e. candidate peptide
epitope) is classified via a computer program] as conserved, semi-conserved
(i.e.: variable), or non-conserved (i.e.: unconserved) ([00112], Table 5
3
)”
(Ans. 4).
FF 2. Baker teaches “a method for identifying a candidate peptide epitope
which induces a HLA class I CTL response against variants of … [the]
peptide epitope” (Baker 31: ¶ [0112]).

1
Baker et al., WO 2005/012502 A2, published February 10, 2005.
2
De Groot et. al., From genome to vaccine – new immunoinformatics tools
for vaccine design, 34 Methods 425-428 (2004).

3
Examiner finds that Baker’s “Table 5 is merely a representation of what the
different classifications are, not a description of the step of classifying”
(Ans. 13).

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FF 3. Baker’s method comprises:
a) identifying, from a particular antigen of an infectious agent,
variants of a peptide epitope 8-11 amino acids in length,
each variant comprising primary anchor residues of the same
HLA class I binding motif;
b) determining whether each of said variants comprises
conserved, semi-conserved or non-conserved non-anchor
residues in comparison to each of the remaining variants;
and
c) identifying a variant which comprises only conserved non-
anchor residues in comparison to at least one remaining
variant.

(Id.)
FF 4. Baker teaches that the “primary anchor residues” may be, for
example, preferred for the “motif and which occur[] with high frequency
within … [a] population” or different as illustrated in Baker’s Tables 1-2
(Baker 33: ¶ [00122]; id. at 34: ¶ [00133]).
FF 5. Baker’s Table 1 is reproduced below for clarity:

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Table 1 summarizes some of Baker’s “primary anchor residues of the HLA
class I peptide epitope supermotifs and motifs…. Preferred primary anchors
are shown in bold, while tolerated primary anchors are shown in italics”
(Baker 35: ¶ [00143]).
FF 6. Examiner finds that Baker’s “anchor positions are the same binding
motif (i.e.: conserved)” (Ans. 12).

ANALYSIS
Appellants contend that Baker’s method identifies “variants of a
particular epitope … in a particular antigen of an infectious agent. Within
these variants … only the non-anchor residues of the variant are determined
to be conserved, semi-conserved, or non-conserved” (App. Br. 9 (emphasis
added)). We agree (FF 1-3). Appellants contend that Baker fails to teach
Appellants’ claimed invention because Baker teaches that “only a portion of
the residues of the identified variants … are subjected to the determination
step (b) in paragraph [00112]” (App. Br. 9). We agree (FF 3 (Baker’s step
“b) determin[es] whether each of said variants comprises conserved, semi-
conserved or non-conserved non-anchor residues”) (emphasis added)).
Examiner asserts that Baker’s “anchor positions are the same binding
motif (i.e.: conserved)” (FF 6). Examiner’s position appears to be that Baker
implicitly determines the identity of the anchor points because they are
conserved residues. Examiner does not, however, identify a portion of
Baker that supports this assertion. In contrast, Baker teaches that the anchor
positions may be variable (FF 4-5). In the absence of an evidentiary basis on
this record to support a finding that Baker teaches the classification of “each
position within the biopolymer sequences as conserved, variable, or
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Application 11/713,474

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unconserved,” are required by Appellants’ claim 1, we are compelled to find
that Examiner failed to establish an evidentiary basis on this record to
support a prima facie case of anticipation (see Claim 1; Cf. FF 3).

CONCLUSION OF LAW
The preponderance of evidence on this record fails to support
Examiner’s finding that Baker teaches Appellants’ claimed invention. The
rejection of claims 1-5 and 7-10 under 35 U.S.C. § 102(b) as being
anticipated by Baker is reversed.

Obviousness:
ISSUE
Does the preponderance of evidence on this record support a
conclusion of obviousness?
FACTUAL FINDINGS (FF)
FF 7. Examiner relies on Baker as set forth above.
FF 8. Examiner finds that De Groot teaches a method “comprising
classifying potential peptide epitopes relative to known epitopes, ranking
binding probability, and selecting epitopes with highest conservation and
binding potential” (Ans. 8). In this regard, Examiner directs attention to the
“entire document, particular pp 4388-4389” and page “4393, col 1, para 2”
of De Groot (Ans. 8 and 15, respectively).

ANALYSIS
Initially, we note that the De Groot reference cited in the “Evidence
Relied Upon” section of Examiner’s Answer contains pages 425-428.
Accordingly, it is unclear if Examiner’s citation of pages 4388-4389 and
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4393 represent a typographical error or whether Examiner intended to rely
on a different De Groot reference. Nevertheless, based on the combination
of Baker and De Groot, Examiner finds that, at the time of Appellants’
claimed invention, it would have been prima facie obvious to a person of
ordinary skill in this art
[T]o avoid sequences with similarity to self as taught by De
Groot et al. in the vaccine design taught by Baker et al. because
all the claimed elements were known in the prior art and one
skilled in the art could have combined the elements as claimed
by known methods (such as the methods taught by Baker et al.
or De Groot et al. regarding computer algorithms to select or
eliminate sequences) with no change in their respective
functions, and the combination would have yielded predictable
results (sequences that do not cross-react with self) to one of
ordinary skill in the art at the time of the invention.

(Ans. 8-9.)
Having reviewed the evidence relied upon by Examiner, we find that
Examiner failed to establish that De Groot makes up for the deficiencies in
Baker (see generally App. Br. 11-12).

CONCLUSION OF LAW
The preponderance of evidence on this record fails to support a
conclusion of obviousness. The rejection of claims 1-10 under 35 U.S.C.
§ 103(a) as unpatentable over the combination of Baker and De Groot is
reversed.

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REVERSED

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