Ex Parte 8012690 et al

Patent Trial and Appeal Board

Jul 21, 2017

95001765 (P.T.A.B. Jul. 21, 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.
95/001,765 09/15/2011 8012690 454L-008002US 9678
322164-2196
58249 7590
COOLEY LLP
ATTN: Patent Group
1299 Pennsylvania Avenue, NW
Suite 700
Washington, DC 20004
EXAMINER
CAMPELL, BRUCE R
ART UNIT PAPER NUMBER
3991
MAIL DATE DELIVERY MODE
07/21/2017 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
LIFE TECHNOLOGIES CORPORATION
Requester, Cross-Appellant and Respondent
v.
454 LIFE SCIENCES CORPORATION
Patent Owner, Appellant, and Cross-Respondent
Appeal 2017-006630
Reexamination Control 95/001,765
Patent 8,012,690 B21
Technology Center 3900
Before RICHARD M. LEBOVITZ, JEFFREY N. FREDMAN, and
RAE LYNN P. GUEST, Administrative Patent Judges.
LEBOVITZ, Administrative Patent Judge.
37 C.F.R. § 41.77(f) DECISION
This is a final decision under 37 C.F.R. § 41.77(f).
The above-identified inter partes reexamination of U.S. Patent No.
8,012,690 B2 was decided by the Patent Trial and Appeal Board Decision on
1 US Patent 8,012,690 B2 is hereinafter referred to as “the ’690 patent.”
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Patent 8,012,690 B2
May 27, 2015 (“Decision on Appeal” or “DOA”). In the Decision, the
Examiner’s determination not to adopt the following rejections was
reversed:
1. Claims 1—9 under 35 U.S.C. § 103(a) as obvious in view Holliger2
and one of O’Neill,3 Lundeberg,4 Oliphant,5 and Vann.6
2. Claims 10-14 and 16—19 under 35 U.S.C. § 103(a) as obvious in
view Holliger and Vann.
3. Claims 1—8 under 35U.S.C. § 103(a) as obvious in view Drmanac7
and one of O’Neill, Lundeberg, Oliphant, and Vann.
4. Claims 10-14 and 16—19 under 35 U.S.C. § 103(a) as Drmanac
obvious in view Vann.
A reversal of a determination by the Examiner to not adopt a rejection
is treated as a new ground of rejection under 37 C.F.R. § 41.77(b). Pursuant
to § 41.77(b)(1), Patent Owner requested that prosecution be re-opened and
filed concurrent claim amendments to claims 1 and 10. The proposed
amendment to claim 1 was not entered; however, the amendment to claim 10
was entered. Order Remanding Inter Partes Reexamination under 37 C.F.R.
§ 41.77(d) to the Examiner (June 17, 2016).
Requester filed comments under § 41.77(c) on Patent Owner’s
request. Requester also provided a declaration by Kyusung S. Park, Ph.D.
2 Holliger et al., WO 02/22869 A2, published March 21, 2002 (“Holliger”).
3 O’Neill et al., US 6,124,092, issued Sept. 26, 2000 (“O’Neill”).
4 Lundeberg et al., WO 00/15842, published March 23, 2000 (“Lundeberg”)
5 Oliphant et al., US 2003/0108900 Al, issued June 12, 2003 (“Oliphant”).
6 Vann et al., WO 03/045310 A2, published June 5, 2003 (“Vann”).
7 Drmanac et al., EP 0 392 546, published Oct. 17, 1990 (“Drmanac”).
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dated July 28, 2015 (“Park Deck”), in support of the rejections based on
Drmanac. The declaration was entered. Id., 5.
Upon remand to the Examiner, the Examiner issued a determination
under 37 C.F.R. § 41.77(d) (“41.77d Determination”; entered Oct. 17, 2016)
maintaining all four rejections. 41,77d Determination 2—6. The Examiner
also rejected claims 11—14 and 16—19 under 35 U.S.C. § 314(a) as enlarging
the scope of the original claims of the patent. Id. at 2. Comments following
the Examiner’s Determination under § 41.77d were filed by Patent Owner
(“PO 41.77e Comments”; filed Nov. 17, 2016) and by Requester (Reqf r
41.77e Comments; filed Dec. 19, 2016). The appeal has now been returned
to the Board for a final decision under 37 C.F.R. § 41.77(f).
CLAIM 1
Claim 1 is reproduced below. The steps of the claim have been
numbered [1]—[6] for reference.
1. A method of enriching for sequestered populations of
amplified nucleic acid molecules, comprising:
[1] distributing a solution comprising a plurality of beads
and a plurality of species of template nucleic acid molecules
into a plurality of aqueous emulsion droplets in a continuous oil
phase, wherein a first subset of the droplets comprise one or
more of the beads and one or more of the species of template
nucleic acid molecule compartmentalized therein, and a second
subset of the droplets comprise one or more of the beads
without any of the species of template nucleic acid molecules
compartmentalized therein;
[2] amplifying the species of template nucleic acid
molecules within the first subset of the droplets, wherein a
plurality of nucleic acid molecules complementary to the
species of template nucleic acid molecules are immobilized to
the one or more beads within the first subset of the droplets;
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[3] breaking the aqueous emulsion droplets to release the
beads of the first and second subsets; and
[4] attaching one or more of the beads of the first subset
comprising the immobilized complementary copies to one or
more enrichment beads, wherein the beads of the first subset are
attached to the one or more enrichment beads by hybridizing a
capture primer to a portion of one or more of the immobilized
complementary nucleic acid molecules and the capture primer
is coupled to the enrichment beads;
[5] isolating the one or more enrichment beads away
from the beads of the second subset; and
[6] separating the enrichment beads from the beads of the
first subset by separating the capture primers from the
immobilized complementary nucleic acid molecules.
CLAIM INTERPRETATION
The phrase “capture primer is coupled to the enrichment beads” was
interpreted in the Decision on Appeal to “require that the [capture] primer is
coupled to the enrichment beads when the primer is hybridized to the nucleic
acid.” DOA 14. Patent Owner had argued for a broader interpretation in
which the capture primer is coupled to the beads either before or after
hybridization. DOA 7. Even if the narrower interpretation applied in the
Decision on Appeal is not correct, it does not change the outcome of the §
103 rejections because the narrower interpretation is encompassed by the
broader one urged by Patent Owner.
35 U.S.C. § 314(a) REJECTION
Claim 10 was amended to recite that the primers are hybridized to the
nucleic acid on the beads and then “disposed” on the enrichment beads. In
contrast, original claim 1 was interpreted to require that the primers were
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already disposed on the enrichments beads when hybridized to the nucleic
acid. DO A 14. Thus, claim 10, as amended, is broader than original claim
1. Under (pre-AIA) 35 U.S.C. § 314(a), “no proposed amended or new
claim enlarging the scope of the claims of the patent shall be permitted” in
an inter partes reexamination proceeding. The amendment to claim 10
enlarges the scope of original claims 1 and 10 because it is directed to an
embodiment that is not included in the subject matter of the original claim.
Consequently, we affirm the Examiner’s determination that claim 10
impermissibly broadened the scope of the original claims.
REJECTION BASED ON HOLLINGER
Hollinger was published March 21, 2002, O’Neill on September 26,
2000, Lundeberg on March 23, 2000, and Vann on June 5, 2003. The
earliest priority date asserted by Patent Owner is June 6, 2003. PO
Respondent Br. 4 (“Priority Issue”) (Jan. 9, 2014). This priority date is after
the publication date of each of the cited publications. Thus, even if the ’690
patent has the benefit of the asserted date, neither Hollinger, O’Neill,
Lundeberg, nor Vann is eliminated as prior art. Oliphant has a later
publication date of June 12, 2003, but priority dates reaching back to 2001.
Claims 1—9
The rejection of claim 1 is based on findings that Holliger describes
bead-based emulsion amplification of nucleic acid that includes the steps of
[1] “distributing,” [2] “amplifying,” and [3] “breaking.” DOA21. The
Decision on Appeal found that the use of enrichment beads in step [4] and
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the subsequent [5] “isolating” and [6] “separating” steps are not described in
Holliger. Id. However, the Decision on Appeal found that each of O’Neill
{id., 22), Lundeberg {id., 23—24), and Vann {id., 24—25) describe using
enrichment beads to separate amplification products. The Decision on
Appeal concluded:
[E]ach of O’Neill, Lundeberg, Vann, and Oliphant provide
evidence of the known function of enrichment beads to purity
nucleic acids, including nucleic acids which are amplification
products. It would have been obvious to one of ordinary skill in
the art to have utilized the enrichment beads for their known and
expected function to enrich for the amplification products of
Holliger. One of ordinary skill in the art would have been
motivated to do so in order to increase the amounts of nucleic
acid available for sequencing to improve sequencing efficiency
and accuracy.
Id., 25-26.
Holliger
Patent Owner contends that Holliger “fails to teach or suggest any
methods of bead emulsion PCR.” PO 41.77e Comments 12.
The ’690 patent under reexamination describes its invention as “bead
emulsion amplification,” or “bead emulsion PCR” when PCR is used as the
amplification technique. ’690 patent, col. 3,11. 45—50. The ’690 patent
explains:
In one aspect of the invention, bead emulsion amplification is
performed by attaching a template (e.g., DNA template) to be
amplified to a solid support, preferably in the form of a generally
spherical bead. . . . The beads are suspended in aqueous reaction
mixture and then encapsulated in a water-in-oil emulsion.
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Id., col. 3,11. 51-65.
In certain embodiments, the emulsion is composed of
discrete aqueous phase microdroplets .... Each microdroplet
contains, preferably, amplification reaction solution (i.e., the
reagents necessary for nucleic acid amplification). An example
of an amplification reaction solution would be a PCR reaction
mixture (polymerase, salts, dNTPs; see Example 2 for an
example of one embodiment) and a pair of PCR primers (primer
A and primer B). See, FIG. 2 A. In some cases, the template DNA
is included in the reaction mixture. A subset of the microdroplet
population includes the DNA bead and the template. This subset
of microdroplet is the basis for the amplification. The remaining
microcapsules do not contain template DNA and will not
participate in amplification.
Id., col. 4,11. 1-15.
This disclosure in the ’690 patent corresponds to step [1], [2], and [3]
of the claimed method. Patent Owner’s argument that Holliger does not
describe these steps is principally based on the fact that Holliger’s method
has a different purpose than disclosed in the ’690 patent, namely for DNA
sequencing. We are not persuaded the claimed amplification process steps
are limited to this purpose.
Holliger characterizes its method as for “selecting an enzyme having
replicase activity” and, more generally, for enzymes having nucleic acid­
processing (NAP) activity. Holliger, Abstract; 3:14—15. Holliger also
discloses that its method is “for use in in vitro evolution of molecular
libraries,” where the evolution is with respect to NAP. Id., 1:1—2; 32:28—
33:2. See also PO 41.77e Comments 8. However, while Holliger’s method
may have been designed for selecting enzymes with NAP activity, such as
replicases, this stated purpose is not evidence that the claimed steps are not
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carried out by Holliger. To the contrary, while Patent Owner describes the
steps in Holliger’s method (PO 41.77e Comments 9—12), Patent Owner did
not identify a defect in the findings relied upon in the Decision on Appeal to
conclude that bead amplification is carried out by Holliger. To the contrary,
there are apparent admissions by Patent Owner that Hollinger carried out
bead amplification. For example, Patent Owner stated in their Comments:
Holliger states that “different members of the nucleic acid
library or pool are sorted or compartmentalized into many
compartments or microcapsules. In preferred embodiments, each
compartment contains substantially one nucleic acid member of
the pool (in one or several copies).” (Holliger at page 13, line 28
through page 14, line 2.) A skilled artisan, reading this statement
in context with the surrounding text, would interpret this passage
to teach that the “one nucleic acid member of the pool” must
actually encode a replicase or another protein entity that is to be
selected for a unique property.
Id., 10.
Holliger also discloses that instead of an entire E.coli bacterium,
the water-in-oil compartment may contain the mutant
polymerase gene, either as a plasmid or linear fragment, and the
enzymes necessary for in vitro transcription/translation. (See
Holliger at page 17, line 25 through page 18, line 2.)
Id.
More specifically, Holliger describes encapsulating the E. coli
cells being studied in a water-in-oil emulsion, along with the
appropriate polymerase, PCR reagents, and streptavidin-coated
polystyrene beads. (Holliger at page 76, lines 22-26.) Thus as
Example 25 expressly states, multiple, distinct nucleic acids
would be delivered to a single bead in a microreactor.
Id., 12.
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The ’690 patent similarly characterizes its bead emulsion
amplification method as forming compartments with one nucleic member,
using the same term “microcapsule” to characterize its compartments as
does Holliger. ’690 patent, col. 4,11. 1—15 (“In some cases, the template
DNA is included in the reaction mixture. A subset of the microdroplet
population includes the DNA bead and the template. This subset of
microdroplet is the basis for the amplification. The remaining microcapsules
do not contain template DNA and will not participate in amplification.”).
Compare steps [1] and [2] of rejected claim 1.
Holliger describes its compartments as “consisting] of the
encapsulated aqueous component of a water-in-oil emulsion.” Holliger, col.
6,11. 11—17. See also PO 41.77e Comments 10 (“Here, the entire bacterial
cell is segregated into an aqueous compartment of a heat-stable water-in-oil
emulsion. (See Holliger at page 10, lines 20-22.).” Thus, Holliger teaches
the same compartmentalization step [1] of rejected claim 1 (“distributing a
solution comprising a plurality of beads and a plurality of species of
template nucleic acid molecules into a plurality of aqueous emulsion
droplets in a continuous oil phase.”)
Patent Owner also acknowledges that “Holliger teaches that within
each compartment, there should be an individual intact bacterial cell
containing one mutated polymerase gene.” PO 41.77e Comments 10
(emphasis added). Holliger also discloses that beads can be used in its
methods. Holliger 53:14—17; 76:25. This disclosure meets step [1] of
rejected claim 1 of “a first subset of the droplets comprise one or more of the
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beads and one or more of the species of template nucleic acid molecule
compartmentalized therein.”
Patent Owner attempts to distinguish Holliger on the basis that claim
1 is concerned with amplifying nucleic acids, even if they do not encode a
protein. PO 41.77e Comments 10. This argument is not persuasive because
the claims do not exclude nucleic acids that encode proteins, including
replicases as described in Holliger.
The Decision on Appeal found that Holliger did not describe
enrichment beads, but concluded it would have been obvious to do so based
on the teachings in O’Neill, Lundeberg, Vann, and Oliphant, each which
teach enrichment beads to purify amplification products. DOA 22—36.
Patent Owner contends that the skilled worker would not have been
“motivated ... to modify the teachings of the reference in order to arrive at
the method recited in claim 1.” PO 41.77e Comments 12. Patent Owner
reasoned that “because Holliger is not concerned with bead emulsion PCR at
all, Patent Owner submits that the skilled artisan, looking for ways to
increase the efficiency of bead emulsion PCR methods would not have been
motivated to utilize the Holliger methods (which, as noted above, are not
related to DNA sequencing).” Id.
This argument is not persuasive because Patent Owner’s premise, i.e.,
that Holliger does not teach bead emulsion PCR, is not supported by the
evidence. Beads emulsion amplification is defined in the ’690 patent as
“performed by attaching a template (e.g., DNA template) to be amplified to
a solid support, preferably in the form of a generally spherical bead .... The
beads are suspended in aqueous reaction mixture and then encapsulated in a
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water-in-oil emulsion.” ’690 patent, col. 3,11. 51—65. Holliger includes
Example 25 disclosing emulsion compartments comprising PCR reagents,
polymerase, and PCR fragments. Holliger 76:22—25. The PCR fragments
are transferred to a single bead and labeled with fluorescent probe and then
counted by fluorescence activated cell sorting (“FACS”). Id., 76:25—77:2.
Holliger indicates that the beads are present in the emulsion:
The approach involves compartmentation of the cells in
question in the emulsion (see W09303151) together with PCR
reagents etc. and polymerase. However, instead of linking genes
derived from one cell by PCR assembly, one (or several)
biotinylated primers are used as well as a streptavidin coated
polystyrene beads (or any other suitable means of linking primers
onto beads).
Id., 76:22-26.
The PCR fragments “are immobilized to the one or more beads within
the ... [emulsion] droplets” as required by step [2] of claim 1. Id., 76:22—26.
In order to carry out the FACS steps, it would be necessary to break the
emulsion droplets as step [3] of claim 1. Patent Owner attempts to
distinguish Example 25, stating that “multiple, distinct nucleic acids would
be delivered to a single bead in a microreactor.” PO 41.77e Comments 12.
However, Patent Owner does not identify language in the claim that would
require only one distinct nucleic acid to be present in the microemulsion
droplet.
Holliger does not utilize enrichment beads as recited in the claim.
However, as explained in the Decision on Appeal, O’Neill, Fundeberg,
Vann, and Oliphant provide evidence of the known function of enrichment
beads to purify nucleic acids.
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As held in KSR Inti Co. v. Teleflex Inc., 550 U.S. 398, 417 (2007):
[I]f a technique has been used to improve one device, and a
person of ordinary skill in the art would recognize that it would
improve similar devices in the same way, using the technique is
obvious unless its actual application is beyond his or her skill.
. . . [A] court must ask whether the improvement is more than the
predictable use of prior art elements according to their
established functions.
Patent Owner contends that the cited O’Neill, Lundeberg, Vann, and
Oliphant do not teach bead emulsion PCR. PO 41.77e Comments 12—13.
However, as indicated above, the preponderance of the evidence supports a
finding that Holliger describes PCR amplification in an emulsion that
comprises beads, and therefore Holliger does accomplish bead emulsion
PCR as that term is defined in the ’690 patent. These additional
publications were cited for their teaching of an alternative, but conventional,
technique using enrichment beads for purifying nucleic acids.
Patent Owner contends “none of these secondary references are
concerned with removing ‘zero’ beads from amplicon-bound beads.” Id.,
13.
The so-called “zero” beads repeatedly referred to by Patent Owner are
the beads in the claimed “second subset of the droplets [which] comprise
one or more of the beads without any of the species of template nucleic acid
molecules compartmentalized therein.” After the emulsion droplets are
broken in step [3], step [5] recites “isolating” the enrichment beads “away
from the beads of the second subset” in step [5]. Because the enrichment
beads are attached to the beads containing the amplified nucleic acid,
removing the enrichment beads (“isolating”) leaves the zero beads,
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satisfying the claim limitation. The Decision on Appeal identified disclosure
in each of O’Neill, Lundeberg, Oliphant, and Vann in which beads or solid
support were isolated. DOA 22—25. Patent Owner did not identify a defect
in these findings, but rather stated that the cited publications did not teach
zero bead removal (PO 41.77e Comments 13—14), ignoring the fact that the
claim requires isolating the enrichment beads, and such isolating step is
taught in in each of O’Neill, Lundeberg, Oliphant, and Vann.
Patent Owner argues that Holliger does not describe an enrichment
step of removing amplicon bound beads from zero beads. Id., 12. However,
Hollinger describes “isolating” steps:
The terms “isolating”, “sorting” and “selecting”, as well
as variations thereof, are used herein. Isolation, according to the
present invention, refers to the process of separating an entity
from a heterogeneous population, for example a mixture, such
that it is free of at least one substance with which it is associated
before the isolation process. . . . The method of the present
invention permits the sorting of desired nucleic acids from pools
(libraries or repertoires) of nucleic acids which contain the
desired nucleic acid.
Holliger 53:21—54:2. Thus while the “Emulsification . . . Amplification
Reactions” of Holliger (e.g., id., 59, 63, 75) may not describe bead
enrichment as claimed, the disclosure in Holliger is clearly not restricted to
the examples and even has broad disclosure concerning isolating steps (see
also id., 76—77).
Claims 10—14 and 16—19
Claim 10 is directed to a method similar to claim 1, but further
requires “extending the second primer hybridized to the 3' end of the one or
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more complementary nucleic acid molecules, wherein the extension
enhances bonding between the second primer and the complementary
nucleic acid molecules immobilized on the beads of the first subset.” The
Decision on Appeal concluded that the recited step is described in Vann.
DO A 29. Patent Owner reiterates arguments that Hollinger does not
describe separating “amplicon-bound beads from ‘zero’ beads.” PO 41.77e
Comments 14. This argument is not persuasive for the reasons stated above,
i.e., the recited step is described in Vann and there is adequate reason to
apply its teachings to Holliger. DOA 24—26.
Patent Owner states that “both Holliger and Vann fail to teach or
suggest any methods of bead emulsion PCR.” PO 41.77e Comments 15.
However, as discussed above, the preponderance of the evidence supports a
finding that Holliger describes PCR amplification in an emulsion that
comprises beads, and therefore Holliger does accomplish bead emulsion
PCR as that term is defined in the ’690 patent. Patent Owner did not
identity a defect in the teachings of Vann.
Summary
For the foregoing reasons, the Examiner’s determination that
Rejections 1 and 2 based on Holliger have not been overcome is affirmed.
DRMANAC REJECTION
The claims were rejected in the Decision on Appeal based on
Drmanac and one of O’Neill, Lundeberg, Oliphant, and Vann. DOA 30—31.
Patent Owner contends that Drmanac does not teach or suggest “bead
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emulsion PCR” nor separating amplicon-carrying beads away from “zero”
beads. PO 41.77e Comments 16. However, Patent Owner does not identity
a deficiency in the findings adopted in the Decision on Appeal.
As referenced in the Decision on Appeal, Drmanac describes discrete
particles (“DP”), such as beads, which carry copies of the same DNA
fragment. Drmanac 7:11—17. Drmanac further teaches:
It is possible to see the implementation of PCR without the
separation of individual fragments in addressed liquid samples.
The requirement is that micro droplets of an amplification
mixture each containing either a single fragment or none are
enclosed into small spheres (pearls) formed of appropriate
membranes (perhaps the semipermeable ones) together with DP
conglomerates. DP conglomerates are composed of DPs of
similar characteristics and should be easily separable into
individual DP components under mild conditions. The use of
conglomerates provides the way to prepare more DPs with the
same DNA fragments which are required for multiple HA
“replicas”. Microsphere formation should be considered as a
process for formation of fat droplets ....
Id., 12:54—13:11. Such disclosure establishes that Drmanac teaches the
claimed limitation “distributing a solution comprising a plurality of beads
and a plurality of species of template nucleic acid molecules into a plurality
of aqueous emulsion droplets in a continuous oil phase,” where the DP are
the beads and the “pearls” or “fat droplets” or “microsphere[s]” constitute
the “aqueous emulsion droplets in a continuous oil phase.” The declaration
by Dr. Park provides further evidence that Drmanac describes bead emulsion
PCR. Park Decl. §§ 22, 24, 25, 27, 28.
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The step [2] of “amplifying” is also carried out by Drmanac
(“implementation of PCR”) in the emulsion. Subsequently, step [3] of
“breaking the emulsion droplets” is carried out by Drmanac:
After the amplification, the reaction of binding of amplified
fragments to spheres is performed in which suitable reagent for
which membrane is permeable is used. The disruption of
membranes and conglomerates results in a mix of DPs in which
each DNA fragment is represented in a sufficient number of
copies on an adequate number of DPs.
Drmanac 13:15—22.
Consequently, a preponderance of the evidence supports the
determination that Drmanac describes bead emulsion PCR.
With respect to Patent Owner’s contention about separating zero-
beads, we assume that Patent Owner is referring to the step [5] of “isolating
the one or more enrichment beads away from the beads of the second
subset.” As explained in the Decision on Appeal, “Drmanac teaches
‘isolating’ and ‘separating; the DPs by spreading them on a surface as
monolayer. Drmanac, col. 26,11. 9-12.” DOA 31; see also id., 32. Based
on this teaching, the Decision on Appeal determined it would have been
obvious to have utilized the enrichment methods of each of O’Neill,
Lundeberg, Oliphant, and Vann. Id., 31—32. Patent Owner makes the same
unavailing arguments for these publications that were made for the rejection
based on Holliger. PO 41.77e Comments 17.
Claims 10—14 and 16—19
Claim 10 is directed to a method similar to claim 1, but further
requires “extending the second primer hybridized to the 3' end of the one or
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more complementary nucleic acid molecules, wherein the extension
enhances bonding between the second primer and the complementary
nucleic acid molecules immobilized on the beads of the first subset.” The
Decision on Appeal concluded that the recited step is described in Vann.
DOA 29, 34.
Patent Owner contends that “because the oligonucleotide probes
(ONP) are bound to DP prior to hybridization, in Drmanac, the capture
primer is hybridized to the immobilized amplicon prior to being coupled to
the enrichment beads. (See Drmanac at col. 21, lines 28-35).” PO 41.77e
Comments 18. Thus, Patent Owner argues the recited limitation in claim 10
is not taught or suggested by Drmanac. Id.
Patent Owner’s argument fails to identity what steps in the claim are
missing from Drmanac and Vann. Patent Owner makes general statements
without making a connection between what is claimed and what is described
or suggested by the prior art. Id. Absent such explanation, it is difficult to
discern what argument Patent Owner intends to make.
The “hybridizing” of claim 10 recites “hybridizing a 3' end of one or
more of the complementary nucleic acid molecules immobilized on the
beads of the first subset to one or more second primers that are then disposed
on one or more enrichment beads.” As mentioned, Drmanac teaches DNA
attached to DPs, namely, “nucleic acid molecules immobilized on the beads
of the first subset.” Drmanac 13:19—22. Drmanac also teaches amplification
as in step [2] of claim 10 where the amplified copies are attached to the DPs
(“After the amplification, the reaction of binding of amplified fragments to
spheres is performed.” Id., 13:15—17).
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We agree with Patent Owner that Drmanac does not teach hybridizing
the attached DNA to primers on enrichment beads. However, the Decision
adopted findings in the Request that established Vann describes such a step.
See Request 337 (Chart CC5):
In certain embodiments, a probe comprising a nucleic
acid, complementary to a nucleic acid target sequence, is
attached to a separating moiety such as a magnetic bead. In
certain embodiments, the probe is then added to a sample
containing the nucleic acid target sequence. In certain
embodiments, codeable labels attached to nucleotides are added
to the sample with a polymerase. In certain embodiments, if the
nucleic acid target sequence is present in the sample, the probe
hybridizes to the target, and the polymerase adds the codeable
label-attached nucleotides to the oligonucleotide probe, forming
a detectable complex.
Vann 35.
Patent Owner contends:
Vann does not teach or suggest an enrichment step where one or
more second primers are first hybridized to immobilized
amplicons before to being disposed on one or more enrichment
beads. To the contrary, in Vann, the primer is attached to the bead
before hybridization to the nucleic acid target sequence. (See,
e.g., Vann at page 35, lines 4-14).
PO 41.77e Comments 19.
The Examiner addressed this argument in the Determination, finding
with supporting evidence that the reverse order described in the claim was
conventional, namely, “hybridizing a biotinylated oligonucleotide to
amplified DNA then attaching it to streptavidin coated beads, was known in
the art.” 41,77d Determination 5. Patent Owner does not respond to the
Examiner’s finding in its subsequent Comments.
18
Appeal 2017-006630
Reexamination Control 95/001,765
Patent 8,012,690 B2
Summary
For the foregoing reasons, the Examiner’s determination that
Rejections 3 and 4 based on Drmanac have not been overcome is affirmed.
TIME PERIOD FOR RESPONSE
In accordance with 37 C.F.R. § 41.79(a)(1), the “[pjarties to the
appeal may file a request for rehearing of the decision within one month of
the date of: . . . [t]he original decision of the Board under § 41.77(a).” A
request for rehearing must be in compliance with 37 C.F.R. § 41.79(b).
Comments in opposition to the request and additional requests for rehearing
must be in accordance with 37 C.F.R. § 41.79(c)-(d), respectively. Under
37 C.F.R. § 41.79(e), the times for requesting rehearing under paragraph (a)
of this section, for requesting further rehearing under paragraph (d) of this
section, and for submitting comments under paragraph (c) of this section
may not be extended.
An appeal to the United States Court of Appeals for the Federal
Circuit under 35 U.S.C. §§ 141—44 and 315 and 37 C.F.R. § 1.983 for an
inter partes reexamination proceeding “commenced” on or after November
2, 2002 may not be taken “until all parties’ rights to request rehearing have
been exhausted, at which time the decision of the Board is final and
appealable by any party to the appeal to the Board.” 37 C.F.R. §41.81. See
also Manual of Patent Examining Procedure § 2682 (9th ed., Rev. 07.2015,
Nov. 2015).
19
Appeal 2017-006630
Reexamination Control 95/001,765
Patent 8,012,690 B2
In the event neither party files a request for rehearing within the time
provided in 37 C.F.R. § 41.79, and this decision becomes final and
appealable under 37 C.F.R. § 41.81, a party seeking judicial review must
timely serve notice on the Director of the United States Patent and
Trademark Office. See 37 C.F.R. §§ 90.1 and 1.983.
AFFIRMED; 37 C.F.R, $ 41.77(f)
PATENT OWNER:
COOLEY LLP
ATTN: PATENT GROUP
1299 PENNSYLVANIA AVENUE, NW
SUITE 700
WASHINGTON, DC 2004
THIRD PARTY REQUESTOR:
LIFE TECHNOLOGIES CORPORATION
ATTN: IP DEPARTMENT
5823 NEWTON DRIVE
CARLSBAD, CA 92008
20