Ex Parte 7449289 et al

Patent Trials and Appeals Board

Aug 27, 2014

95001599 - (R) (P.T.A.B. Aug. 27, 2014)

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.
95/001,599 04/08/2011 7449289 GENOM.051X(P-7330 RX) 7698
95896 7590 05/26/2015
David W. Highet, VP and Chief IP Counsel
Becton, Dickinson and Company
(Knobbe Martens)
1 Becton Drive, MC-110
Franklin Lakes, NJ 07417
EXAMINER
TURNER, SHARON L
ART UNIT PAPER NUMBER
3991
MAIL DATE DELIVERY MODE
05/26/2015 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
____________

BECKMAN COULTER, INC.
Requester and Respondent

v.

GENEOHM SCIENCES CANADA, INC.
Patent Owner and Appellant
____________

Appeal 2014-002900
Reexamination Control 95/001,599
Patent 7,449,289
Technology Center 3900
____________

Before RICHARD M. LEBOVITZ, JEFFREY N. FREDMAN, and
JEFFREY B. ROBERTSON, Administrative Patent Judges.

LEBOVITZ, Administrative Patent Judge.

DECISION ON REQUEST FOR HEARING
This is decision on Requests for Rehearing under 37 C.F.R. § 41.79 by
Patent Owner (“PO Req. Reh’g” dated Sept. 26, 2014) and Third Party Requester
(“TPR Req. Reh’g” dated Sept. 29, 2014) of the Patent Trial and Appeal Board
Decision on Appeal of Aug. 28, 2014 (“Dec. App.”).

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I. PATENT OWNER’S REQUEST FOR REHEARING
1. Anticipation of claim 1 by Oliveira 2000
Patent Owner contends that the Board’s decision to affirm the rejection of
claim 1 as anticipated by Oliveira 2000 is not supported by substantial evidence.
PO Req. Reh’g 2. It was stated in the Board’s decision that, as “shown in Figure 1
[of Oliveira 2000], IS P4 in combination with a reverse MDV primer would
amplify a region comprising IS431 which contains SEQ ID NO: 42.” Dec. App.
24. This statement about IS431 containing SEQ ID NO: 42 was based on
disclosure in the ’289 patent.
According to the ’289 patent, SEQ ID NO: 42 “exhibited nearly 100%
identity with IS431.” ’289 patent, col. 17, ll. 45-46. The patent
discloses that the inventors’ “sequence data revealed for the first time
the location of this IS431 sequence at the right extremity of SCCmec
adjacent to the integration site.” Id. at col. 17, ll. 47-49. IS431
encodes a transposase and had been described previously “within the
right segment of SCCmec.[”] Id. at col. 13, ll. 64-67.
Id. at 9,
However, as pointed out by Patent Owner, Attachment 1 shows that only 61
nucleotides of SEQ ID NO: 42 are within the actual IS431 element. PO Req.
Reh’g 3. Thus, the statement in the Decision that “IS431 . . . contains SEQ ID NO:
42” was an error.
We have not been pointed to evidence that any other part of SEQ ID NO: 42
is present in Oliveira 2000. As discussed in the Decision, strain 85/2082 said to
contain SEQ ID NO: 42 at the MREJ (MRSA polymorphic right extremity
junction) region, is not disclosed in Oliveira 2000. Dec. App. 23. The issue is
therefore whether amplification of a part of IS431 in the MREJ region is sufficient
to meet the claim limitation.
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We have interpreted the claim to cover amplifying only a part of SEQ ID
NO: 42, as long as that part is indicative of a MREJ type iv MRSA strain. Dec.
App. 8. As discussed on page 24 of the Decision on Appeal, the IS431 element is
a part of the right extremity MREJ region. Patent Owner’s statement that it is not
the rightmost region is not persuasive since the claim does not specify that the
amplified region must be the rightmost. PO Req. Reh’g 3-4. In addition, because
the claim does not require the complete SEQ ID NO: 42 to be amplified as
acknowledged by Patent Owner (see PO Req Reh’g 4 “It is not necessary to decide
whether all or only some of the sequence of SEQ ID NO: 42 constitutes ‘the MREJ
region sequence’”), we conclude that amplification of a part of IS431 which is
present in the right extremity region (see Oliveira 2000, Fig. 1) is sufficient to
anticipate the claim 1. Consequently, while we agree the Decision on Appeal
contained an error, this error does not change the determination that the claim 1 is
anticipated by Oliveira 2000.

2. Obviousness of claim 5 in view of Oliveira 2000
In the Decision, the Board entered a new ground of rejection of claim 5 in
view of Oliveira 2000 combined with the ’507 patent or Hiramatsu 1996. Dec.
App. 40. Claim 5 depends from claim 1 and specifies which sequence identifiers
are indicative of which MREJ type. Patent Owner contends we erred in affirming
the rejection of this claim for the same reasons as for claim 1. PO Req. Reh’g 8.
Since we have found that the portion of IS431 present in the right extremity of
Fig. 1 of Oliveira 2000 would be indicative of a MREJ type iv (’289 patent,
col. 13, ll. 64–67), we decline to modify our Decision with respect to this claim.

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Summary
Patent Owner’s Request for Rehearing is DENIED.

II. REQUESTER’S REQUEST FOR REHEARING
1. Claim Interpretation
Requester contends that the Board’s interpretation of claim 1 improperly
imports a limitation from the specification of the ’289 patent into the claim. TPR
Req. Reh’g 3. Specifically, Requester argues that the Board’s “definition of MREJ
imported a limitation from the specification that the MREJ region sequences are
only sequences ‘adjacent’ to the junction site and therefore excludes some but not
all DNA sequences that are found farther upstream from integration site but are
still downstream of mecA.” Id. at 3–4. In support of this position, Requester
contends that “MREJ region” as used in the claim and the ’289 patent uses the term
“includes” which is open-ended. Id. at 5. This argument is insufficient to show
error in the Board’s interpretation.
The claim recites that the MREJ region “includes sequence from both the
SCCmec insert right extremity and chromosomal DNA adjoining that right
extremity.” First, while it is true that “includes” is open-ended and could include
additional sequence, the term “MREJ” itself would limit it to sequences of the right
extremity. Second, the claim requires amplification of a MREJ region selected
from a specific group of recited sequences, including SEQ ID NO: 42. The recited
sequences correspond to a “MREJ region, which term is used in the ’289 patent
and the prior art to mean sequences bracketing the right SCCmec-chromosome
junction point. Dec. App. 6–8.
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Claims must be interpreted in the context of the specification. In re Morris,
127 F.3d 1048, 1054 (Fed. Cir. 1997). It is clear from reading the ’289 patent that
the invention is based on the discovery of MREJ sequences which are located in
the right extremity region of the MRSA chromosome (Dec. App. 3–4), and not
sequences in the entire right downstream region as argued by Requester.

2. Anticipation by the ’507 patent
The Decision on Appeal reversed the anticipation rejection of claims 1, 2,
and 5 for two reasons. First, the Decision concluded that the Examiner had not
provided sufficient evidence that SEQ ID NO: 42, present in bacterial strain
85/2082, is situated in the mecA “right extremity” junction. Dec. App. 12-13.
Rather, it was found that the sequence is “located 31 kb from the integration
junction” in a “downstream region, but not in the right extremity as required by the
claim. Id. at 13. Second, it was concluded in the Decision that the Examiner did
not establish by a preponderance of the evidence that primers were described in the
’507 patent that would amplify SEQ ID NO: 42. Id.
Requester contends that “the PTAB’s requirement for the prior art to
disclose a specific primer pair is improper as the PTAB itself recognizes that
claim 1 does not require a specific primer pair.” TPR Req. Reh’g 8. This
argument is not persuasive. The Decision did not require disclosure of a “specific
primer pair,” but rather only a primer pair enabling for the amplification of an
MREJ region. Dec. App. 13.
The Decision found that the Examiner did not establish that primers were
present in the ’507 patent that would amplify SEQ ID NO: 42. Id. Requester
argues that there are examples in the ’507 patent that combine a mec side primer
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with a junction side primer which “would allow one of skill in the art to envisage
using the primers to amplify IS431.” Id. at 9 (emphasis added). It is unclear to
what “the primers” Requester is referring. Requester mentions Nmec5 and Gmec
1045 in the Requester for Rehearing (id.), but it does not appear that these primers
were said to be anticipatory in the Request for Reexamination. At the very least,
Requester has not identified how this primer pair meets the claimed step of
“contacting the sample with at least two primers” to amplify a sequence of SEQ ID
NO: 42.
With respect to the idea of envisaging choosing mecA and junction side
primers (id.) to amplify an MREJ region, this alleged disclosure in the ’507 patent
is not specific enough to anticipate the claimed subject matter because it requires a
choice of primers from numerous sequences disclosed in the ’507 patent. Atofina
v. Great Lakes Chem. Corp, 441 F.3d 991, 999 (Fed. Cir. 2006). Consequently, we
find Requester’s arguments unavailing.

3. Anticipation by Ito
The anticipation rejection by Ito was reversed because there was insufficient
evidence that a primer pair was disclosed in Ito that amplifies a MREJ region
sequence which includes sequence from SEQ ID NO: 42. Dec. Appeal 20-21. The
Decision identified tetK4 and merA1 primers as amplifying a part of a sequence of
SEQ ID NO: 42, but determined that such sequence was not in the right extremity
as required by the claim. Id. at 21. Requester urges in the Request for Rehearing
that that “[o]ne of skill in the art would understand that primers can be designed”
to unique regions that meet the claimed step of amplifying the MREJ region, but
fails to explain how such “understanding” teaches with sufficient specificity the
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amplification of an MREJ region corresponding to one of the recited sequence
identifiers as required by an anticipation rejection. TPR Req. Reh’g 9. Atofina,
441 F.3d at 999. Consequently, Requester’s arguments do not convince us of
error.
4. Anticipation by Oliveira 2001
Oliveira 2001 is cited as anticipatory under 35 U.S.C. § 102(a) (pre-AIA).
To rebut the rejection, Patent Owner provided a declaration under 37 C.F.R.
§ 1.131 to establish that the inventors reduced to practice as much of the
embodiment of claims 1, 2, and 5 said to be shown in Oliveira 2001. PO Appeal
Br. 24; Declaration of Ann Huletsky, dated July 30, 2011 (“Huletsky Decl.”). The
Decision found the declaration to be effective for the purpose of antedating
Oliveira 2001.
To antedate Oliveira 2001, it must be shown that the declaration shows as
much as the invention which is taught by the publication. In re Stempel, 241 F.2d
755, 760 (CCPA 1957). First, it must be determined what Oliveira 2001 describes.
Oliveira 2001 is said to be anticipatory because it is said to disclose primers which
would yield amplicons within SEQ ID NO: 42-46, and 51. Request 46. Although
SEQ ID NO:42 may not be 100% identical to the sequences in Oliveira 2001, such
identity is not necessary as long as there are amplicons within SEQ ID NO: 42
which share 100% identity within amplicons disclosed in Oliveira 2001.
To show that the inventors reduced to practice as much as shown in Oliveira
2001, i.e., an amplicon within SEQ ID NO: 42, Ms. Huletsky referred to Canadian
Patent Application No. CA 02348042 (“the ’042 Application”) as describing SEQ
ID NO: 42 and primers SEQ ID NOS: 64 and 79, which produced an amplicon
from SEQ ID NO: 42 which is within the scope of claim 1. Huletsky Decl. ¶ 7.
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Neither the Examiner nor Requester provided evidence that such amplicon is not
present in Oliveira 2001.
Requester contends that the Board erred because:
The Huletsky Declaration fails to establish possession of the invention
or something falling within the scope of the claims. The legal standard
requires that the signed Declaration itself must establish possession of
the claimed subject matter and this Declaration fails to do so. This
Declaration does not incorporate the Canadian priority document but
rather selects out certain portions of the priority document, and then
improperly uses those selected portions to conclude that the evidence
is sufficient to support amplification of the MREJ region of at least
one of NOs: 42, 43, 44, 45, 46, and 51. The Huletsky Declaration
cannot establish possession of primers that amplify the MREJ region
sequence of SEQ ID NO: 43-46 and 50 because those sequences in the
Canadian priority document differ from those filed in the PCT
application.
TPR Req. Reh’g 10.
This argument is not persuasive. The Canadian ’042 application contains
the data which Ms. Huletsky relied upon to establish reduction to practice of an
embodiment within the scope of the claim, i.e., SEQ ID NO: 42 and primers 64 and
79. It is common sense that a declaration establishing reduction to practice would
necessarily need to refer to outside documents for such evidence, as is the case
here, to show that what was asserted to have been done by a specific date was
actually done. Requester did not provide sufficient legal basis to exclude the
Huletsky declaration because the declarant required the ’042 application to prove
the existence of an embodiment of the invention prior to the publication of Oliveira
2001. The rule, itself, permits “exhibits of drawings or records” to “accompany
and form part of the affidavit and declaration.” 37 C.F.R. § 1.131(b).
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Requester, as well as the Examiner, further found fault with the declaration
because only one embodiment was shown. TPR Req. Reh’g 10-11. Requester has
ignored In re Spiller, 500 F.2d 1170, 1177 (CCPA 1974) and In re Schreiber, 587
F. 2d 59, 62 (CCPA 1978) which establish that an applicant only has to show as
much as what the reference discloses, or so much to render it obvious. Dec.
App. 25 (fn. 12). In this case, the disclosure of SEQ ID NO: 42 as indicative of
type iv MRSA strain, and primers 64 and 79, would render any sequence amplicon
within SEQ ID NO: 42 obvious because the selection of other amplicons and
oligonucleotides from the larger genus was routine and conventional at the time of
the invention and because such amplicons and oligonucleotides could readily be
envisaged. In re Gleave, 560 F.3d 1331, 1338 (Fed. Cir. 2009) (“a person of
ordinary skill in the art equipped with an IGFBP sequence is admittedly capable of
envisioning how to make any antisense sequence”).
Requester also contends:
. . . alignment of primer SEQ ID NO:79 with SEQ ID NO:42 shows
that this primer will not amplify the entire sequence of SEQ ID
NO:42. The Declaration provides no explanation as to why amplifying
a portion of the sequence of SEQ ID NO:42 is sufficient to establish
possession of the entire sequence or why a single species of primer
was sufficient to antedate a genus of amplicons as disclosed in
Oliveira 2001.
TPR Req. Reh’g 11.
As explained in the claim interpretation section, the claim does not require
that the primers amplify the complete sequence of SEQ ID NO: 42. According to
the ’289 patent, primers 68 and 70 were initially utilized to discover SEQ ID
NO: 42 as residing in the MREJ of certain MRSA strains, leading to the
identification of a marker for the type iv MRSA. ’289 patent, col. 14, ll. 3–9, 38–
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43, 53–59. Subsequently, primers 64 and 79 were used to amplify MRSA DNA
and determine whether the strain is a type IV MRSA. Id. at col. 5, l. 55; col. 7, ll.
21–22. The amplicon produced by these primers appears to be 215 bps (id. at col.
34, l. 12), which is less than the 1045 bp size of SEQ ID NO: 42 (id. at col. 85–
86).
1
The Canadian ’042 application identifies the SEQ ID NO: 42 and primers 64
and 79 within it, which are used to detect the type IV MRSA. Thus, such
disclosure shows possession of embodiment of the claim. This embodiment is
sufficient to antedate Oliveira 2001 because it shows an amplicon indicative of an
MREJ type iv, and renders obvious other amplicons within SEQ ID NO: 42
obvious.
Requester further contends that the Huletsky declaration is defective because
the “sequence of SEQ ID NO: 42 is not the same as HDG2 [of Oliveira 2001] (it
has 99% sequence identity)” and the primer used to amplify the HDG2 sequence
was different in sequence than SEQ ID NO:79. TPR Reh’g Req. 11.
The rejection was based on the following finding: “Oliveira [2001]
reference discloses several species of the claimed invention via disclosure of a
number of different primer sets, and different sample DNAs corresponding to
different sequences from the same (MRSA mecA-ofrX) MREJ regions which
produce an amplicon.” RAN 18. The claim does not require specific primer sets
as long as they amplify an MREJ region of a MREJ type iv. It is not necessary to
find 100% identity to the complete SEQ ID NO: 42 sequence or to the specific
primers disclosed in the ’289 patent because the claims are not limited to SEQ ID

1
This disclosure of primers 64 and 79 to produce an amplicon less than full-length
SEQ ID NO: 42 is further evidence of the correctness of the construction of
claim 1 to read on amplification of portions of SEQ ID NO: 42 to determine
whether a strain is a type iv MRSA.
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NO: 42 in its entirety nor to a specific primer set. Ms. Huletsky provided adequate
evidence that a sample was contacted with two primers which were capable of
amplifying a sequence of SEQ ID NO: 42 as required by the claim. This
embodiment is the same as the teaching in Oliveira 2001. Requester’s further
requirement that amplicon be the same and the primers be the same is unwarranted
since the claims are not limited to a specific amplicon or primer set, and the
specific showing of primer set 64 and 79, and SEQ ID NO: 42, renders the full
scope of the claim obvious under the Spiller doctrine.

5. Obviousness over Oliveira 2000 in view of the ’507 patent or Hiramatsu 1996
The Board reversed the Examiner’s determination not to reject 5 as obvious
over Oliveira 2000 in view of the ’507 patent or Hiramatsu 1996, but not with
respect to the proposed rejections of claims 2-4. Dec. App. 38-40

Claim 2
Claim 2 depends from claim 1, and further recites “wherein said at least two
primers further include at least two primers that amplify the MREJ region
sequence of anyone of SEQ ID NOs: 1, 20, 21, 22, 23, 24, 25, 41, 199, 2, 17, 18,
19, 26, 40, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 185, 186, 197, 4,
5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 104, 184, and 198 under conditions of 50
mM KCl, 10 mM Tris-HC1 (pH 9.0), 0.1% Triton X-100, 2.5 mM MgCl2, at
55°C.”
Requester contends that we overlooked the teaching in the ’507 patent of
primers that would amplify one of the recited MREJ sequences recited in claim 2.
TPR Req. Reh’g 13. Requester cited previous arguments during the reexamination
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proceeding that the primers utilized to identify the recited sequences are the same
as those in the ’507 patent. Id. We have not been pointed to evidence to the
contrary. Thus, we agree with Requester that it would have been obvious to
combine the primers for a type i MREP sequence of Hiramatsu ’507 with primers
to detect a type iv MREP sequence using the primers of Oliveira 2000. Id.
Consequently, we REVERSE the Examiner’s decision not to adopt the obviousness
rejection of claim 2.

Claim 3
Claim 3 depends from claim 1, and further recites “wherein said at least two
primers include SEQ ID NO: 64 and at least one of the following primers: SEQ ID
NO: 79 for the detection of MREJ type iv; SEQ ID NO: 80 for the detection of
MREJ type v; SEQ ID NO: 204 for the detection of MREJ type vi; SEQ ID
NO: 112 for the detection of MREJ type vii; SEQ ID NO: 113 for the detection of
MREJ type vii; SEQ ID NO: 115 for the detection of MREJ type viii; SEQ ID
NO: 116 for the detection of MREJ type viii; and SEQ ID NO: 109 for the
detection of MREJ type ix.”
Requester contends that the Board erred in not reversing the Examiner’s
determination not to adopt the obviousness rejection. However, Requester has not
provided evidence that the claimed sequences are present in either Oliveira 2000 or
the ’507 patent. TRP Req. Reh’g 13-14. Consequently, absent such evidence, we
maintain our decision to affirm the Examiner’s decision not to adopt the rejection.

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Claim 4
Claim 4 depends from claim 1, and further recites “comprising detecting the
presence of SEQ ID NO: 172 as indicative of the presence of MREJ type x.”
Requester contends that one of ordinary skill in the art “using the same strategy
and methods as explicitly disclosed in any of the cited references would detect a
sequence of SEQ ID NO: 172 if it was present in a strain using primers in accord
with the disclosure of the '507 patent, or Oliveira 2000.” TPR Req. Reh’g 14.
Requester has not presented evidence that SEQ ID NO 172 is present in any of the
MRSA strains in the cited publications. Consequently, there is insufficient
evidence that the Board misapprehended or overlooked any points in affirming the
Examiner’s decision not to adopt the rejection of claim 4.

6. Obviousness over the ’507 patent or Ito in view of Hiramatsu 1996, Cheng
(Grounds 11 and 12)
The Board concluded that the Examiner correctly did not adopt the
rejections of independent claim 1, and dependent claims 2-5, as obvious in view of
the ’507 patent, Hiramatsu 1996, and Cheng (Rejection 11); and Ito, Hiramatsu
1996, and Cheng (Rejection 12). The Board found that Requester did not show the
presence of SEQ ID NO: 42 in the right extremity in the only two strains for which
public availably had been established. Dec. App. 33.
Citing In re Kubin, 561 F.3d 1351 (Fed. Cir. 2009), Requester contends that
the Board applied the wrong standard. TPR Req. Reh’g 15. Requester states:
Many of the bacterial strains recited in the ’289 specification and used
to identify the listed sequences of claim 1 were in the public domain
and were known naturally occurring MRSA strains. One of ordinary
skill in the art would have become aware that the Hiramatsu primers
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were not working, but aware of the genetic variations, would have
easily used Hiramatsu’s sequencing strategy, or at the least would
have used a commercially available sequencer to sequence the DNA
genes downstream of mecA as taught by the prior art and then do a
simple comparison to determine the differences between sequences of
all of the known MRSA strains.
Id. at 15-16.
Requester has not provided evidence that “the listed sequences of claim 1
were in the public domain and were known naturally occurring MRSA strains.” Id.
In Kubin, claims to the DNA sequence encoding a NAIL protein were found to be
obvious because the evidence showed the NAIL protein was known and a cDNA
library from which to clone the cDNA encoding NAIL was also known. Kubin at
1354. Thus, the source from which to obtain a NAIL cDNA had been established
in Kubin. In this case, Requester contends strains from which to obtain SEQ ID
NO: 42 were publically available, but did not provide evidence of it. Accordingly,
this case is readily distinguishable from Kubin.

Summary
We decline to modify the Decision on Appeal with respect to 1) claim
interpretation, 2) anticipation by the ’507 patent, 3) anticipation by Ito, 4) Huletsky
declaration antedating Oliveira 2001, and 5) obviousness of claims 3 and 4 over
Oliveira 2000 in view of the 507 patent or Hiramatsu 1996; and 6) obviousness
over the ’507 patent or Ito in view of Hiramatsu 1996, and Cheng.
We modify the Decision on Appeal with respect the proposed obviousness
rejection over Oliveira 2000 in view of the ’507 patent or Hiramatsu 1996 by
reversing the Examiner’s determination not to adopt the rejection of claim 2.
Requester’s Request for Rehearing is GRANTED-IN-PART.
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Patent Owner:

Ned A. Israelsen
KNOBBE, MARTENS, OLSON & BEAR LLP
12790 El Camino Real
San Diego, CA 92130

Third Party Requester:

Katherine M. Kowalchyk
MERCHANT & GOULD, P.C.
Representative for Beckman Coulter, Inc.
P.O. Box 2903
Minneapolis, MN 55402-0903