Ex Parte 8012690 et al

Patent Trial and Appeal Board

May 26, 2015

95001765 (P.T.A.B. May. 26, 2015)

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
322164-2196
9678
58249 7590 05/27/2015
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
05/27/2015 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
____________

LIFE TECHNOLOGIES CORPORATION
Requester, Cross-Appellant and Respondent

v.

454 LIFE SCIENCES CORPORATION
Patent Owner, Appellant, and Cross-Respondent

____________

Appeal 2015-000178
Reexamination Control 95/001,765
Patent 8,012,690 B2
1
Technology Center 3900
____________

Before RICHARD M. LEBOVITZ, JEFFREY N. FREDMAN, and
RAE LYNN P. GUEST, Administrative Patent Judges.

Opinion for the Board filed by Administrative Patent Judge LEBOVITZ.

Opinion Concurring filed by Administrative Patent Judge GUEST.

LEBOVITZ, Administrative Patent Judge.

DECISION ON APPEAL AND CROSS-APPEAL

1
US Patent 8,012,690 B2 is hereinafter referred to as “the ’690 patent.”
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This is a decision on the appeal by the Patent Owner from Patent Examiner’s
decision to reject claims 1–9, 20–28, 39–47, and 57–65 in the above-identified
inter partes reexamination of United States Patent 8,012,690 B2. This is also a
decision in a cross-appeal by the Third Party Requester of the Patent Examiner’s
decision finding claims 10–14 and 16–19 patentable and not adopting certain
rejections of claims 1-9 as obvious under 35 U.S.C. § 103 in view different
combinations of the prior art. The Board’s jurisdiction for this appeal is under 35
U.S.C. §§ 6(b), 134, and 315 (pre-AIA). We affirm and set forth new grounds of
rejection over claims 1–14 and 16–19.

I. BACKGROUND
The patent in dispute in this appeal is United States Patent 8,012,690 B2
which issued Sep. 6, 2011. The patent is subject to a terminal disclaimer. The real
party in interest and owner of the ’690 patent is 454 Life Sciences Corporation, a
Roche Company (“Patent Owner”). Owner Appeal Br. 1. The Third Party
Requester is Life Technologies Corporation (“Requester”). Requester Resp’t Br. 1
A request for inter partes reexamination of the ’690 patent was filed Sept.
15, 2011. Request under 35 U.S.C. §§ 311–318 (pre-AIA) and 37 C.F.R. §§
1.902–1.997 (pre-AIA) (“Request”).
The Examiner determined that claims 1–9, 20–28, 39–47, and 57–65 are
unpatentable. Right of Appeal Notice (“RAN”). Patent Owner appeals from this
determination. Owner Appeal Br. The Examiner determined that claims 10–14
and 16–19 are patentable. Id. Requester cross–appeals from this determination.
Requester Appeal Br.
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An oral hearing was held March 18, 2015. A transcript of the hearing has
been entered into the record (“Hearing Tr.”).
The claimed subject matter of the ’690 patent involves methods for
enriching for sequestered populations of amplified nucleic acid molecules. The
claims involve amplifying a template nucleic acid in an aqueous emulsion, where
the template is immobilized to beads. The amplification beads are referred to as
“A–beads” by Requester. After amplification, the beads carrying the amplified
nucleic acid are isolated using enrichment beads to which a capture primer is
attached. The enrichment beads are referred to as “E-beads” by Requester.
Claims 1 and 10 are representative and read as follows (underlining showing
language added relative to the original claims):
1. A method of enriching for sequestered populations of
amplified nucleic acid molecules, comprising:
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;
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; breaking the aqueous emulsion droplets to
release the beads of the first and second subsets; and
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
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portion of one or more of the immobilized complementary nucleic
acid molecules and the capture primer is coupled to the enrichment
beads;
isolating the one or more enrichment beads away from the
beads of the second subset; and separating the enrichment beads from
the beads of the first subset by separating the capture primers from the
immobilized complementary nucleic acid molecules.

10. A method of enriching for sequestered populations of amplified
nucleic acid molecules, comprising:
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 at least one of
the beads and one or more species of the template nucleic acid
molecules compartmentalized therein, and a
second subset of the droplets comprise at least one of the beads
without any of the species of template nucleic acid molecules
compartmentalized therein;
amplifying the species of template nucleic acid molecules
within the first subset of the droplets, wherein during the
amplification a plurality of copies of the species of template nucleic
acid molecule hybridize to a plurality of first primers immobilized on
the one or more beads and a plurality of complementary nucleic acid
molecules are extended therefrom;
breaking the aqueous emulsion droplets to release the beads of
the first and second subsets;
disassociating the hybridized copies of the species of the
template nucleic acid molecules from the first primers and extended
complementary nucleic acid molecules immobilized on the beads of
the first subset;
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 disposed on one or more enrichment
beads enabled for isolation under a selective condition thereby linking
the enrichment beads to one or more of the beads of the first subset;
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extending the second primer hybridized to the 3’ end of the one
or 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
applying the selective condition to isolate the one or more
enrichment beads from the beads of the second subset; and
separating the enrichment beads from the beads of the first
subset by separating the second primers from the immobilized
complementary nucleic acid molecules.

A. Appeal
Patent Owner appeals from the Examiner’s decision to reject claims
1–9, 20–28, 39–47, and 57–65 as follows (Owner Appeal Br. 5):
1. Claims 1–8 under 35 U.S.C. § 103(a) (pre–AIA) as obvious in
view of Dressman
2
and O’Neill.
3

2. Claims 1–9 under 35 U.S.C. § 103(a) (pre–AIA) as obvious in
view of Dressman and Lundeberg.
4

3. Claims 1–8 under 35 U.S.C. § 103(a) (pre–AIA) as obvious in
view of Dressman and Vann.
5

4. Claims 1–8 under 35 U.S.C. § 103(a) (pre–AIA) as obvious in
view of Dressman and Oliphant.
6

5. Claims 1–8 under 35 U.S.C. § 103(a) (pre–AIA) as obvious in
view of Dressman, O’Neill, and Vann.

2
Devin Dressman et al., Transforming Single DNA Molecules into Fluorescent
Magnetic Particles for Detection and Enumeration of Genetic Variations, 100(15)
Proceedings of the National Academy of Sciences 8817 (July 22, 2013).
3
Roger A. O’Neill et al., US 6,124,092 (September 26, 2000).
4
Joakim Lundeberg et al., WO 00/15842 (Pub. March 23, 2000).
5
Charles Vann et al., WO 03/045310 (Pub. June 5, 2003).
6
Arnold Oliphant et al., US 2003/0108900 A1 (Pub. June 12, 2003),
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6. Claims 20–28, 39–47, and 57–65 under 35 U.S.C. §314(a) as
enlarging the scope of the patent.

B. Cross-Appeal
Requester cross-appeals the Examiner’s determination favorable to
the patentability of claims 10–14 and 16–19. Requester also cross-appeals
the Examiner’s determination not to adopt additional proposed rejections of
claims 1–8. Requester proposed 42 different grounds of rejection.
Requester Appeal Br. 7–9. We have considered only Rejections 5–12
because these address all of the appealed claims. The rejections are as
follows (renumbered 7–14):
7. Claims 1–14 and 16–19 under 35 U.S.C. § 103(a) (pre–AIA) as
obvious in view of Holliger
7
and O’Neill.
8. Claims 1–14 and 16–19 under 35 U.S.C. § 103(a) (pre–AIA) as
obvious in view of Holliger and Lundeberg.
9. Claims 1–14 and 16–19 under 35 U.S.C. § 103(a) (pre–AIA) as
obvious in view of Holliger and Vann.
10. Claims 1–14 and 16–19 under 35 U.S.C. § 103(a) (pre–AIA) as
obvious in view of Holliger and Oliphant.
11. Claims 1–8 and 10–14, and 16–18 under 35 U.S.C. § 103(a) (pre–
AIA) as obvious in view of Drmanac
8
and Oliphant.
12. Claims 1–8 and 10–14, and 16–18 under 35 U.S.C. § 103(a) (pre–
AIA) as obvious in view of Drmanac and O’Neill.

7
Philipp Hollinger et al., WO 02/22869 A2 (Pub. March 21, 2002).
8
Radoje Drmanac et al., EP 0 392 546 A2 (Pub. October 17, 1990).
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13. Claims 1–8 and 10–14, and 16–18 under 35 U.S.C. § 103(a) (pre–
AIA) as obvious in view of Drmanac and Lundeberg.
14. Claims 1–8 and 10–14, and 16–18 under 35 U.S.C. § 103(a) (pre–
AIA) as obvious in view of Drmanac and Vann.

I. CLAIM INTERPRETATION
The dispute in this appeal involves the interpretation of the phrase “capture
primer is coupled to the enrichment beads.” This phrase appears in the fourth step
of claim 1 which reads as follows:
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
In the attaching step, beads containing the immobilized complementary
nucleic acid are attached to enrichment beads by hybridizing them to a capture
primer. The Examiner interpreted the disputed phrase to mean that the capture
primer is already coupled to the enrichment beads when the “hybridizing a capture
primer to a portion of one or more of the immobilized complementary nucleic acid
molecules” is carried out. RAN 6. Patent Owner contends that the broadest
reasonable construction of the disputed phrase “permits the enrichment capture
primer to be coupled to or disposed on the enrichment bead either before or after
the act of hybridization of the enrichment primer to the amplified nucleic acid
templates.” Owner Appeal Br. 8.
First, we begin with the language of the claim. The disputed phrase involves
the step of “attaching” beads “comprising the immobilized complementary copies
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to one or more enrichment beads.” The “wherein” clause of the step specifies that
“the beads” comprising the immobilized complementary nucleic acid molecules
“are attached to the one or more enrichment beads by hybridizing a capture primer
to a portion of . . . the immobilized complementary nucleic acid molecules. The
“attaching” step is accomplished “by hybridizing a capture primer” to the
immobilized nucleic acid.
It is clear from the claim language that the “attaching” of the capture primer
to the immobilized nucleic acid is accomplished by a “hybridizing” step in which
the capture primer is hybridized to the nucleic acid. It is also explicit that the
capture primer is coupled to an enrichment bead at the end of the process.
However, unlike the positive recitation of “attaching” and “hybridizing,” the claim
does not recite an active step describing how the capture primer “is coupled to the
enrichment beads.” Rather, the claim recites that the capture primer “is coupled”
to the enrichment bead, indicating that the primer is attached to the enrichment
bead when the primer is “hybridizing . . . to a portion of one or more of the
immobilized complementary nucleic acid molecules.” In other words, the capture
primer is pre-coupled to the enrichment bead or coupled to the enrichment bead
before carrying out the “hybridizing” step.
Patent Owner contends that the claim also covers “hybridizing” the “capture
primer to a portion of one or more of the immobilized complementary nucleic acid
molecules” when the primer is not already coupled to the enrichment bead, but
instead coupling the primer to the bead after the primer has hybridized to the
immobilized nucleic acid. Patent Owner’s construction of the claim requires
reading “the capture primer is coupled to the enrichment beads” as not being
“coupled to the enrichment bead” until after “hybridizing a capture primer to . . .
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the immobilized complementary nucleic acid molecules.” In our opinion, the
claim is not open to this interpretation because the claim language explicitly states
that “the capture primer is coupled to the enrichment beads,” expressly requiring it
to be coupled to the bead during the “attaching” step. This is the broadest
reasonable interpretation
9
of the claim because the “wherein” clause of the step
further limits the attachment to occur by “hybridizing” the capture primer to the
nucleic acid, where the “capture primer is coupled to the enrichment beads” –
representing the status of the capture primer during the “attaching” step.
In asserting its interpretation, Patent Owner argues that provisional
application No. 60/476,504, filed on Jun. 6, 2003 (“the ’504 provisional
application”) and parent Application No. 10/767,899, filed on Jan. 28, 2004 (“the
’899 Application”) describe “the enrichment capture primer being hybridized to
the immobilized amplified nucleic acid templates on the beads of the first subset
(see step 2 of Fig 3) and thereafter those enrichment capture primers become
coupled to or disposed on the enrichment bead (see step 3 of Figure 3).”
(Emphasis added.) Owner Appeal Br. 8. This embodiment is the only disclosed
embodiment in the ’504 provisional application, and the parent ’899 application in
which the capture primer is used to capture nucleic acid immobilized on beads.
’504 provisional application 16:25–17:8; 28–29 (example 6); ’899 application 18:
14–26; 32–33 (example 6); Fig. 3. Patent Owner contends it is error to exclude a
preferred embodiment from the claims. Id. at 9.

9
During reexamination of an unexpired patent, claims are given their broadest
reasonable interpretation consistent with the patent specification. In re Suitco
Surface, Inc., 603 F.3d 1255, 1259 (Fed. Cir. 2010); In re Abbott Diabetes Care
Inc., 696 F.3d 1142, 1148 (Fed. Cir. 2012).
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We agree with Patent Owner that “a claim interpretation that excludes a
preferred embodiment from the scope of the claim is rarely, if ever, correct.”
On-Line Tech., Inc. v. Bodenseewerk Perkin–Elmer GmbH, 386 F.3d 1133, 1138
(Fed. Cir. 2004). Owner Appeal Br. 10. However, this principle is only applicable
if the language of the claim, itself, does not exclude a preferred embodiment. The
existence of a preferred embodiment, or of any specific example in a patent, is not
license to read it into the claims, when the plain language of the claim does not
permit it. See Phillips v. AWH Corp., 415 F.3d 1303, 1323 (Fed.Cir.2005) (en
banc). (“[A]lthough the specification often describes very specific embodiments of
the invention, we have repeatedly warned against confining the claims to those
embodiments.”). The pertinent inquiry is whether the claims were drafted to
include the preferred embodiment.
Claim 1 was added as new claim 45 on October 31, 2007 when the
application
10
that led to the ’690 patent was filed as a continuation of the ’899
application. Request for Filing a New Nonprovisional (Continuation) Utility
Patent Application. The claim recited “attaching one or more beads of the first
subset comprising the immobilized complementary copies to one or more
enrichment beads enabled for isolation under a selective condition.” The claim
was amended with the addition of the current “wherein” clause in response to 35
U.S.C. §§ 102 and 103 rejections of the claim (Non–Final Office Action dated
March 20, 2009). This amendment introduced for the first time the language “the
capture primer is coupled to the enrichment beads.” Remarks/Amendment in ’095
Application (June 19, 2009). In making the amendment, Patent Owner stated:

10
Serial No. 11/982,095 (“the ’095 application”).
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In the interest of advancing prosecution, Applicants have
amended claim 45 to add the elements of original claim 50 to further
clarify to the scope of the claimed invention, and which the Office
Action concedes is not anticipated by Griffiths.
Remarks/Amendment in ’095 Application (June 19, 2009), p. 10.
Claim 50 read as follows (emphasis added):
The method of claim 45, wherein: the beads of the first subset are
attached to the one or more enrichment beads by hybridizing a capture
primer disposed on the enrichment beads to a portion of one or more
of the immobilized complementary nucleic acid molecules.
Claim 50 required the capture primer to be “disposed” or coupled to the
enrichment beads prior to being hybridized to the complementary nucleic acid on
the amplification beads. The capture primer is pre-coupled to the enrichment
beads.
Despite stating that “the elements” of claim 50 were added to claim 45, the
phrase “by hybridizing a capture primer disposed on the enrichment beads” was
not incorporated into claim 45, but rather claim 45 was amended to recite “the
capture primer is coupled to the enrichment beads.” Nonetheless, to the extent
that we give the prosecution history any weight,
11
we are inclined to consider this
as evidence in support of the Examiner’s construction of the claim to read on the
primer already attached to the enrichment bead in view of Patent Owner’s
statement about adding the elements of claim 50 to claim 45 (subsequently
renumbered as claim 1), which included the primer being disposed on the bead
when hybridized to the immobilized nucleic acid.

11
In Tempo Lighting, Inc. v. Tivoli, LLC, 742 F.3d 973, 977 (Fed. Cir. 2014), the
Federal Circuit stated “the prosecution history, while not literally within the patent
document, serves as intrinsic evidence for purposes of claim construction. This
remains true in construing patent claims before the PTO.”
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In reaching this construction, we emphasize that Patent Owner had the
opportunity to clarify the claim scope during prosecution of the ’899 application,
but only obscured it by stating that “Applicants have amended claim 45 to add the
elements of original claim 50 to further clarify to the scope of the claimed
invention,” but did not add the verbiage of “hybridizing a capture primer disposed
on the enrichment beads to a portion of one or more of the immobilized
complementary nucleic acid molecules.”
“An essential purpose of patent examination is to fashion claims that are
precise, clear, correct, and unambiguous. Only in this way can uncertainties of
claim scope be removed, as much as possible, during the administrative process.”
In re Zletz, 893 F.2d 319, 322 (Fed. Cir. 1989).
[T]he PTO gives a disputed claim term its broadest reasonable
interpretation during patent prosecution. . . . The “broadest reasonable
interpretation” rule recognizes that “before a patent is granted the
claims are readily amended as part of the examination process.”
Burlington Indus. v. Quigg, 822 F.2d 1581, 1583 (Fed. Cir. 1987).
Thus, a patent applicant has the opportunity and responsibility to
remove any ambiguity in claim term meaning by amending the
application.
In re Bigio, 381 F. 3d 1320, 1324 (Fed. Cir. 2004).
Reexamination is no different since a Patent Owner has the opportunity to
amend the claims. In this case, Patent Owner could have amended the claim to
explicitly require the capture primer of claim 1 to be coupled to the enrichment
bead before and after hybridization to the immobilized nucleic acid, but did not do
so. For example, in the Office action dated November 19, 2011, the Examiner –
in distinguishing prior art from claim 1 – stated that the prior art Oliphant
publication did not disclose a method “wherein the capturing oligonucleotides
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[capture primers] are bound to beads before hybridizing with PCR products as
required by the claims.” Non-Final Office Action 7 (Nov. 19, 2011).
Consequently, Patent Owner was aware that Examiner had construed claim 1 to be
limited to the capture primer already attached to the bead when hybridized to the
immobilized nucleic acid.
The construction that “the capture primer is coupled to the enrichment
beads” after the primer is hybridized to the immobilized nucleic acid is not the
broadest reasonable interpretation of claim 1 because the claim recites
“hybridizing a capture primer” to the immobilized nucleic acid and then specifies
that “the capture primer is coupled to the enrichment beads.” The most reasonable
interpretation of the latter limitation, as explained above, is that it reflects the status
of the capture primer when the “attaching” and “hybridizing” steps are carried out.
In the Rebuttal Brief, Patent Owner argued:
There is no requirement for a working example for each and every
specific embodiment in order to meet the written description
requirement. That is especially true where, as here, there are only two
members of the genus - where the capture primer is either pre– or
post–coupled to the enrichment bead. There can be no question that
the written description requirement for the genus of these two
embodiments has been met here, given the extensive disclosure in the
’504 specification on the enrichment process and the description of
how to attach a capture primer to an enrichment bead (whether pre- or
post-coupled in the “attaching” step) – see p. 16, line 25 – p. 17, line
15, Example 6, Figure 3 and claims 24–32).
Owner Rebuttal Br. 4.
Patent Owner’s argument requires that the claim be construed to cover the
genus of methods comprising hybridizing the capture primer (1) before it is
coupled to the enrichment bead; and (2) after it is coupled to the enrichment bead.
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However, as already discussed, the evidence does not support such a broad
construction that would require us to consider whether the disclosure of the single
post–coupling embodiment is sufficient to support even a limited genus of
coupling species.
Patent Owner provided declarations by Yi-Ju Chen, Ph.D., a named inventor
of the ’690 patent. First Chen Decl. ¶ 1 (Jan. 19, 2012); Second Chen Decl. ¶ 1
(Oct. 19, 2012). Dr. Chen was also an employee of Patent Owner when the
declarations were executed. Id. Dr. Chen testified:
In my view, in the “attaching” step of claim 1 of the ’690 patent, the
enrichment capture primer may be coupled to the enrichment bead
either before or after being hybridized to the amplicons immobilized
on the beads of the first subset. What is important in the “attaching”
step of claim 1 is that by the end of that step, the beads (of the first
subset) carrying the amplified nucleic acid templates become attached
to one or more enrichment beads.
Second Chen Decl. ¶ 5. While it is clearly important that the capture primer is
coupled to the enrichment beads in order to achieve separation, the pertinent issue
is whether the claim language permits the reading the claim to cover coupling
before and after hybridizing is performed. Dr. Chen did not explain how the
recitation of “the capture primer is coupled to the enrichment beads” in the
“wherein” clause of the “attaching” step means that the capture primer is coupled
to the bead after hybridization rather than just an express statement of the status of
the capture primer during the “attaching” step.
In sum, we construe the “attaching” step in which the beads carrying the
immobilized nucleic acid are hybridized to the capture primer, where “the capture
primer is coupled to the enrichment beads,” to require that the primer is coupled to
the enrichment beads when the primer is hybridized to the nucleic acid.
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II. APPEAL
DRESSMAN REJECTIONS
Claims 1–9 stand rejected as obvious in view of Dressman and additional
cited prior art. Patent Owner asserts that the rejections should be withdrawn
because Dressman is not prior art to the claims because it was published after their
earliest priority date. This issue is considered below.

A. Priority and written description
Dressman was published on Jul. 22, 2003. The ’690 patent was filed Oct.
31, 2007 and is a continuation of Application No. 10/767,899, filed on Jan. 28,
2004 (“the ’899 Application”). The ’690 patent further claims benefit to
provisional application No. 60/476,504, filed on Jun. 6, 2003 (“the ’504
provisional application”). (Additional provisional applications are listed in the
related U.S. Application Data of the ’690 patent but these are not asserted to
support priority of claim 1.) The publication date of Dressman is before the filing
dates of the ’899 Application and ’690 patent, but after the Jun. 6, 2003 filing date
of the ’504 provisional application. Accordingly, if the later-filed ’690 patent is
entitled to the priority date of the ’504 provisional Application, Dressman is not
prior art.
Entitlement to the provisional filing date requires that the later-filed claims
of the ’690 patent be described in the provisional application in such a way that the
written description requirements of 35 U.S.C. § 112 are met. See 35 U.S.C.
§§ 119(e); 37 C.F.R. § 1.78(a). See Tronzo v. Biomet, Inc., 156 F.3d 1154, 1158
(Fed. Cir. 1998) (discussing requirements of claiming benefit of priority date of
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earlier application under 35 U.S.C. § 120). This requires the disclosure in the
earlier provisional application to reasonably convey to one of ordinary skill in the
art that the inventors possessed the later-claimed subject matter when they filed the
earlier application. Id.
In this case, the later-claimed subject matter recites that “the capture primer
is coupled to the enrichment beads,” a phrase we have interpreted to mean that the
primer is coupled to the enrichment beads before it is hybridized to the
immobilized nucleic acid. The only example in the provisional application is of
hybridizing a capture primer to the immobilized nucleic acid and then after
attaching the primer to the enrichment bead. ’504 provisional application 16:25 to
17:8; 28:6 to 29:15 (Example 6); claim 24. Patent Owner has not identified a
description in the ’504 provisional application that would establish possession of
an enrichment bead pre-coupled to a capture primer and hybridizing the bead-
coupled capture primer to the immobilized nucleic acid.
Dr. Chen testified that in “the Berka ’504 provisional and the ’690 patent,
we described a preferred embodiment where the enrichment capture primer is
coupled to the enrichment bead after being hybridized to the amplicons
immobilized on the beads of the first subset.” Second Chen Decl. ¶ 6. Dr. Chen
further testified that “[w]e subsequently published the above described ‘after
hybridization’ embodiment (i.e., where the enrichment capture primer is coupled to
the enrichment bead after being hybridized to the amplicons immobilized on the
beads of the first subset) in Nature, 437, pp. 376–380 (2005).” Id. at ¶ 7. Neither
of these statements explains how the ’504 provisional application describes the
coupling to enrichments beads “after hybridization.”
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In sum, there is insufficient evidence to accord claim 1 benefit of the filing
date of the ’504 provisional application.
We shall also not accord claim 1 benefit of the filing date of the ’899
Application.
The ’899 application has the same disclosure as the ’690 patent, but our
attention was directed by Patent Owner directed to claims 24 and 25. Claims 24
and 25 read as follow:
24. The method of claim 1 or claim 22 further comprising the step of
enriching for beads which bind amplified copies of the nucleic acid
away from beads to which no nucleic acid is bound, the enrichment
step selected from the group consisting of affinity purification,
electrophoresis and cell sorting.
25. The method of claim 24 wherein the enrichment step is performed
by affinity purification with magnetic beads that bind nucleic acid.
Claims 24 and 25 of the ’899 application broadly recites an enriching step
for beads which bind amplified copies of nucleic acid. While the “enriching” step
is a genus which arguably covers both before and after attachment of the capture
primer to an enrichment bead, this is not the end of the analysis. If the claim is to
serve as written descriptive support for the species of hybridizing the capture
primer already coupled to the enrichment bead, it must convey possession of this
species to one of ordinary skill in the art. A genus is not necessarily a disclosure of
every species in it, even if the genus is ultimately determined to be small. In this
case, the claim is unrestricted in how the enrichment beads bind the amplified
nucleic acid. Patent Owner has not presented evidence of the size of the genus, let
alone that one of ordinary skill in the art would have recognized that the inventors
possessed the single species that Patent Owner is now claiming. Dr. Chen’s
testimony (Second Chen Decl. ¶¶ 5–6) appears to be more concerned with the
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obviousness of using both configurations, rather than the issue of written
descriptive support.
it is the specification itself that must demonstrate possession. And
while the description requirement does not demand any particular
form of disclosure, Carnegie Mellon Univ. v. Hoffmann–La Roche
Inc., 541 F.3d 1115, 1122 (Fed. Cir. 2008), or that the specification
recite the claimed invention in haec verba, a description that merely
renders the invention obvious does not satisfy the requirement,
Lockwood v. Am. Airlines, 107 F.3d 1565, 1571–72 (Fed. Cir. 1997).
Ariad Pharmaceuticals, Inc. v. Eli Lilly and Company, 598 F.3d 1336, 1352 (Fed.
Cir. 2010).

B. Dressman
Since we have determined that claim 1 is not entitled to the filing dates of
the ‘504 provision application or the ’899 application, Dressman is available as
prior art. The Examiner found that Dressman teaches emulsion PCR with primers
bound to beads. RAN 14. This disclosure meets the “distributing” and
“amplifying” steps of the claimed method. Id. As to the claimed “attaching” and
“isolating” steps, the Examiner found that Dressman specifically suggested an
enrichment step:
Another way to increase throughput would be to physically separate
the beads that contained PCR products before flow cytometry, which
could be accomplished with antibodies to modified nucleotides
incorporated into the PCR product during BEAMing.
Dressman 8822 (2
nd
column, first full paragraph).
O’Neill, Oliphant, Lundeberg, and Vann were additionally cited by the
Examiner as teaching enrichment of nucleic acids using enrichment beads. RAN
15–19. In view of Dressman’s explicit suggestion to utilize enrichment, it would
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have been obvious to one of ordinary skill in the art to use the enrichment beads in
each of O’Neill, Oliphant, Lundeberg, and Vann as the specific way to perform the
enrichment step. It is obvious to use a prior art element for its known and
predictable function. KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 417 (2007).
Patent Owner argues that Dressman “teaches away from use of a two bead
enrichment process” because Dressman teaches using antibodies in the enrichment
scheme. Owner Appeal Br. 16. Patent Owner did not explain why the disclosure a
specific enrichment approach constitutes a “teaching away” from a two bead
system.
With respect to the further argument that combining Dressman with O’Neill,
Oliphant, Lundeberg, and Vann would not work because both beads would be
magnetic and therefore would not achieve separation of the so–called empty beads
(id.), we note that the skilled worker is not an “automaton” but is “person of
ordinary creativity” (KSR 550 U.S. at 421) who would know how to adapt the
procedure, e.g. by using only one magnetic bead, in order to achieve separation as
described in each of O’Neill, Oliphant, Lundeberg, and Vann.
For the foregoing reasons, we affirm Rejections 1–5 of claim 1. Patent
Owner did not provide separate arguments regarding the patentability of dependent
claims 2-9. We affirm the rejection of these claims for the reason given by the
Examiner and as summarized in claim charts CC-1 (Dressman), CC-2 (O’Neill),
CC-3 (Oliphant), CC-4 (Lundeberg), and CC-5 (Vann) which were appended to the
original Request for Reexamination.

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REJECTION UNDER 35 U.S.C. 314(a)
The Examiner rejected claims 20–28, 39–47, and 57–65 under 35 U.S.C.
§ 314(a). RAN 26. Under 35 U.S.C. § 314(a)(pre-AIA), “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 Examiner found that new claims 20–
28, 39–47, and 57–65, which were added during the inter partes proceeding,
enlarged the scope of the patent because they change the method from one limited
to the capture primer attached to the enrichment beads prior to hybridization with
the immobilized nucleic acid to a method where the capture primer is attached to
the enrichment beads after hybridization. Id.
The Examiner’s determination is factually supported. The broadest
reasonable interpretation of original claim 1 requires the capture primer to be pre-
coupled to the enrichment bead when hybridized to the nucleic acid. This is also
required by claim 10. Claims 1 and 10 are the only original independent claims
and thus represent the broadest subject matter which is claimed. New independent
claims 20, 39, and 57, however, require that the capture primer is first hybridized
to the nucleic acid and “the capture primer is thereafter coupled to the enrichment
beads.” These claims enlarge the scope of original claims 1 and 10 because they
are directed to an embodiment that is not included in the subject matter of the
original claims. Consequently, we affirm the rejection.

III. CROSS-APPEAL
Requester cross-appeals the Examiner’s decision favorable to the
patentability of claims 10–14 and 16–19, and the Examiner’s decision not to adopt
certain rejections of claims 1–9. Requester Appeal Br. 7–9.
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A. OBVIOUSNESS REJECTIONS OVER HOLLIGER
Requester proposed rejections of claims 1–14 and 16–19 under 35 U.S.C. §
103(a) as obvious in view Holliger and one of O’Neill, Lundeberg, Oliphant, and
Vann. Requester provided evidence that Holliger describes bead-based emulsion
amplification of nucleic acids, meeting the “distributing,” “amplifying,”
“breaking,” and “attaching” capture primer steps of claim 1. Request 97–102;
Steps A–D in the claim chart of Appendix CC-6 appended to the Request.
Requester also provided evidence that the narrower steps of claim 10, describing a
similar method to claim 1, is described in the same manner in Holliger. Request
102–103.
Requester acknowledged that Holliger does not described utilizing
enrichment beads, but cited evidence that enrichment was suggested by Holliger.
Id. at 97, 101–102. With respect to the enrichment steps involving a capture
primer and enrichment bead (“attaching” step) and the subsequent “isolating” and
“separating” steps, Requester cited to O’Neill, Lundeberg, Oliphant, and Vann,
each of which were said by Requester to describe methods which overlap with
Holliger and enrichment steps. Id. at 106–118; claim charts CC-2 (O’Neill), CC-4
(Lundeberg), CC-3 (Oliphant), and CC-5 (Vann).
Requester stated that Holliger describes separating beads with amplification
products (“immobilized nucleic acid” as in claim 1) from beads with no
amplification products. Request 107. Based on this teaching, Requester stated that
it would have been obvious to one of ordinary skill in the art to have applied the
enrichments steps described in one of O’Neill, Lundeberg, Oliphant, and Vann to
Holliger. Id. at 107–118.
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The Examiner decided not to adopt the rejections. Specifically, the
Examiner found:
Holliger does not suggest that “empty” beads should be separated
from beads bearing amplification products. Absent recognition that
this would be advantageous, there was no motivation to use the
methods of O’Neill, Oliphant, Lundeberg or Vann to modify the
method of Holliger.
RAN 20.
Claims 1–9
O’Neill
Requester stated that O’Neill “teach[es] the general desirability of using E-
Beads to remove unextended primers from amplification products in general, in
terms of improved downstream utilization and analysis of extended primers (e.g.,
for DNA sequencing).” Requester Appeal Br. 16. Such disclosure, Requester
argues, provides the reason to have combined O’Neill with Holliger. Requester’s
argument is factually supported. For example, we find the following passage in
O’Neill which teaches the desirability of separating amplification products:
Another aspect of the invention is to provide methods and
compositions for separating a plurality of simultaneously generated
polynucleotide amplification products, such as the amplification
products produced by multiplex PCR. In the subject methods of
separating a plurality of simultaneously generated polynucleotide
amplification products, each amplification product is formed from at
least one recoverable primer having a unique recovery tag (or the
functional equivalent of a recovery tag). In other embodiments of the
invention, the same recovery tag may be present on the different
amplification products so as to provide for the purification of distinct
sets of amplification products.
O’Neill, col. 3, ll. 36–48.
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The above-quoted passage expressly teaches separating amplification
products using recovery tags to enrich for the desired amplification product.
O’Neill further teaches that recovery tags can be immobilized to solid supports,
such as beads. Id. at col. 4, ll. 40–50. It would have been obvious to one of
ordinary skill in the art to have separated the desired amplification products
obtained in Holliger in order to purify them as described by O’Neill. Contrary to
the Examiner’s statement, separating a desired amplification product from
unwanted products would separate empty beads from beads carrying the
amplification product of interest.

Lundeberg
Requester made the same argument for Lundeberg that it made for O’Neill.
The teachings in Lundeberg are consistent with Requester’s argument about the
obviousness of combining its disclosure with Holliger. The following passages
(underlining added) from Lundeberg were quoted in claim chart CC-4 which was a
part of the Request for Reexamination.
[A] method of isolating primer extension products, produced from a
template vector, said products containing sequences corresponding or
complementary to i) a primer binding region, ii) an insert and iii)
vector derived sequence(s), wherein said method comprises at least
the step or steps of binding a modular oligonucleotide of at least two
parts (modules) to adjacent stretches on said primer extension
products, wherein said modular oligonucleotide is complementary to
and capable of binding to said vector-derived sequences of said primer
extension products, wherein at least one module (capture module) is
immobilized or has means for immobilization.
Lundeberg, page 5, lines 21–34.
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It will be appreciated that in appropriate circumstances modular
oligonucleotides may serve both of the aforementioned functions, e.g.
by serving both as a primer and also as a capture/detection probe for
the nucleic acid products e.g. amplified DNA, thus produced.
Lundeberg, pages 3–4 (emphasis added).
The invention in WO98/13522 therefore describes applications in
which the modular oligonucleotide ... serves as a probe for detection
and/or capture or isolation of target nucleic acid molecules.
Lundeberg, page 3, lines 30–37.
Numerous suitable supports for immobilization of
oligonucleotides, and methods of attaching nucleotides to them, are
well known in the art . . . Particulate materials, especially beads, are
generally preferred. For example, sepharose or polystyrene beads
may be used. Advantageously, the support may comprise magnetic
particles . . ..
Lundeberg, page 17, lines 15–19.
In preferred aspects of the present invention, in contrast, the
sequencing products may be separated from the rest of the sample,
e.g. by the use of magnetic beads to which the capture module is, or
may be, bound.
Lundeberg, page 8, lines 23–27.
The passages reproduced above support the obviousness of using enrichment
beads to purify target amplified nucleic acids from Holliger. See generally claim
chart CC-4, pp. 315–318.

Vann
Vann has similar disclosure about separating amplification products by
“hybridization of nucleic acids” [probes] to a complementary nucleic acid to be
detected. Vann, p. 34, fifth paragraph; p. 35, second paragraph. The probes can
be attached to beads to form “enrichment beads” which fall within the scope of the
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claim. Id. at p. 2–3, 26. Vann’s teachings, as summarized in claim chart CC–5,
support Requester’s contention that it would have been obvious to used Vann’s
enrichment beads to purify the amplification products of Holliger.

Oliphant
Oliphant, as with O’Neill, Lundeberg, and Vann, utilizes probes that “can be
attached to a solid support to allow separation of extended and non-extended
primers.” Oliphant, ¶ 339. See generally claim chart CC-3. Thus, empty beads
(unextended) would be separated from beads carrying the desired product.
Oliphant’s disclosure, as summarized in claim chart CC-3, supports Requester’s
contention that it would have been obvious to used Oliphant’s enrichment beads to
purify the amplification products of Holliger.

Reason to combine
In assessing a claim’s obviousness, we “must ask whether the improvement
is more than the predictable use of prior art elements according to their established
functions.” KSR, 550 U.S. at 417. “The combination of familiar elements
according to known methods is likely to be obvious when it does no more than
yield predictable results.” Id. at 416. In this case, each of O’Neill, Lundeberg,
Vann, and Oliphant provide evidence of the known function of enrichment beads
to purify 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
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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. Requester Appeal
Br. 18, ll. 1–13.
In challenging Requester’s contention about the obviousness of the claims,
Patent Owner argues that there is no teaching about removing “zero beads” and
“detachment of the enrichments beads from the immobilized nucleic acid.” Owner
Resp’t Br. 8. This argument is not persuasive. As discussed above, each of the
enrichment bead prior art describes purifying beads carrying target nucleic acids
from other beads in the mixture, necessarily separating them from beads which do
not carry the target, including from beads which are “empty” and thus which have
zero nucleic acid bound to them.
Oliphant specifically describes separating extended primers from non-
extended primers (at ¶ 339), and thus teaches removing zero beads, where the zero
beads constitute the non-extended primers. Moreover, by enriching for an
amplicon or group of amplicons, such a step would separate the amplicons from
unextended primers (“zero beads”), which Patent Owner admitted was carried out
in the prior art. Owner Resp’t Br. 8. Patent Owner’s arguments are therefore not
factually supported.
With regard to the teaching in paragraph 171 of Oliphant that unreacted
primer can be removed from the mixture, it is true that Oliphant describes
accomplishing this by one method of binding the unreacted and unextended primer
to a solid support. However, Oliphant does not limit its method to this step.
Oliphant ¶ 171. Moreover, Oliphant clearly discloses “Amplicon Enrichment,”
beginning at paragraph 331, which retains only the desired PCR products and
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separates unextended primers from the PCR products. “In a preferred
embodiment, the binding partner can be attached to a solid support to allow
separation of extended and non-extended primers.” Id. at ¶ 339. The binding
partner with an attached label can be used to capture sequences on a second
support surface (id. at ¶ 343), and thus teaches capturing immobilized nucleic acid
as recited in instant claim 1.
Patent Owner also challenges the reason to combine the prior art, arguing
that enrichment prior art utilize “target specific oligonucleotides [which] are
required to separate or detect specific amplicons or groups of amplicons from a
complex mixture of templates and unextended primers in solution (which solution
contains all the reagents for further amplification).” Owner Resp’t Br. 8. Thus,
while Patent Owner acknowledges that it was known to separate amplicons and
groups of amplicons from templates and unextended primers with a capture primer
as required by claims 1 and 10, Patent Owner distinguishes the claims on the basis
that the capture primer in the prior art is target sequence specific. Id. Claim 1,
however, does not limit the sequence of the capture primer. Rather, the only
requirement in the claim is that the primer attaches to the immobilized nucleic acid
“by hybridizing . . . to a portion of one or more of the immobilized complementary
nucleic acid molecules.” Thus, Patent Owner attempts to distinguish the claim
from the cited prior art on the basis of a limitation that does not appear in the
claim.

Summary
For the foregoing reasons, we reverse the Examiner’s decision not to adopt
the rejection of claim 1 over Holliger in view of one of O’Neill, Lundeberg, Vann,
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and/or Oliphant (numbered rejections 7–10). While we have considered each one
of O’Neill, Lundeberg, Vann, and Oliphant separately, the four publications
constitute the scope and content of the prior art in which an obviousness
determination is made, Graham v. John Deere Co., 383 US 1, 17–18 (1966), and
thus serve as evidence in each of the separate rejections. We also reverse the
Examiner’s decision not to adopt the rejections of claims 2–9 for the reasons set
forth in the Request for Reexamination.

Claims 10–14 and 16–19
Claim 10 is similar to claim 1, but with several narrowing limitations. For
example, claim 10 recites “extending the second primer hybridized to the 3' end of
the one or 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 Examiner found
claim 10 to be patentable “because none of the cited references suggest extending
bead-bound capture primers by further DNA synthesis.” RAN 27.
Requester argued that each of Vann and Lundeberg teach extension of the
capture primer (“the second primer”).
Vann teaches extension of the E-oligo by polymerization of additional
nucleotides. See, e.g., Vann, p. 35, par. 2 (teaching "[i]n certain
embodiments, a probe comprising a nucleic acid, complementary to a
nucleic acid target sequence [i.e., E-oligo] is attached to a separating
moiety such as a magnetic bead [i.e., E-bead]. In certain
embodiments, the probe is then added to a sample containing the
nucleic acid target sequence [i.e., extended A-primer] ... 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
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nucleotides to the oligonucleotide probe [i.e., extending the
E-oligo]").
Requester Appeal Br. 18–19.
Patent Owner contends that Vann only relates to the addition of a codeable
label to the template nucleic acid. Owner Resp’t Br. 13. However, Vann expressly
teaches that the “codeable labels attached to nucleotides are added to the sample
with a polymerase. . . . 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” Vann 35:7–11. The
addition of nucleotides with a polymerase constitutes primer extension, and
because a polymerase is used, it reasonably suggests that the primer could be
extended using its complement as a template. Thus, the evidence supports
Requester’s contention that the disputed limitation is described in Vann.
With respect to Lundeberg, Requester argues:
Lundeberg teaches extension of the E-oligo by binding additional
oligonucleotides to the extended A-primer. See, e.g., Lundeberg, p. 7,
ln. 20–25 (teaching “modular oligonucleotide” refers to an
oligonucleotide composed of more than one part); p. 20, ln. 3–4
(teaching “[w]hilst the separate modules may be added separately
[i.e., E-oligo], in a preferred embodiment, said primer extension
products are contacted directly with all modules of said modular
oligonucleotide in a single hybridization step [i.e., extending the
E-oligo ]”).
Requester Appeal Br. 20.
We have reviewed the disclosure at pages 19–20 of Lundeberg and agree
with Patent Owner that Lundeberg does not describe or suggest the “extending”
step of claim 10. An immobilized capture oligonucleotide is described in step d)
on page 20, but we cannot identify disclosure of an extending step which produces
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an “extension [that] enhances bonding between the second primer and the
complementary nucleic acid molecules immobilized on the beads of the first
subset.” To the contrary, on page 19, Lundeberg teaches that an extension is made
which is not complementary to the target nucleic acid.
Accordingly, with respect to claim 10, and claims 11–14 and 16–19 which
depend from it, we reverse the Examiner’s decision not to adopt the rejection based
on Holliger and Vann. However, we affirm the Examiner’s decision not to adopt
the obviousness rejection in view Hollinger and Lundeberg, but do not reach the
rejections based on Hollinger and Oliphant or O’Neill of the claims.

B. OBVIOUSNESS REJECTIONS OVER DRMANAC
Claims 1–8
Requester proposed rejections of claims 1–8, 10–14, and 16–18 under 35
U.S.C. § 103(a) as obvious in view Drmanac and one of O’Neill, Lundeberg,
Oliphant, and Vann. Requester provided evidence that Drmanac describes
emulsion amplification as recited in the “distributing,” “amplifying,” and
“breaking” steps of claim 1. Request 120–121; Claim Chart CC–7 (Drmanac).
The amplified nucleic acid fragments are immobilized on discrete particles (“DP”)
which constitute beads as required by claim 1. Id. Drmanac also describes
attaching two beads together (DP) (the claimed “attaching” step) (“The most
simple application of the first principle is to double DP system in which ONPs
[oligonucleotide probes] are bound to DP which can be mutually discriminated
according to physical characteristics. Positive hybridization would lead to rosette
formation. The target DP would be surrounded with DPs carrying ONPs whose
complementary sequences are present in a given target.” Drmanac, col. 21, ll. 29–
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35; Request 121–122. Drmanac teaches “isolating” and “separating” the DPs by
spreading them on a surface as monolayer. Drmanac, col. 26, ll. 9–12; claim chart
CC–7 (Drmanac).
While Drmanac describes “attaching” beads together, Requester relied on
O’Neill, Lundeberg, Oliphant, and Vann for the steps involving “isolating” and
“separating” the enrichment beads from the beads of the claimed second subset.
Request 125–137. Requester stated that Drmanac teaches bead–liposome–PCR of
templates where the amplicon is bound to beads. Id. at 125. Requester also stated
that Drmanac describes enrichment of the amplicon associated beads. Id.
Requester’s statements are supported a preponderance of the evidence as
summarized above and in claim chart CC–7. Requester stated it would have been
obvious to one of ordinary skill in the art to have applied the enrichment steps
described in O’Neill, Lundeberg, Oliphant, and Vann. Id. at 125–137. The
pertinent disclosure in each of these publications is described above in the rejection
over Holliger.
Because Drmanac describes separation of the sequences attached to beads by
spreading them in a monolayer on solid surface (Drmanac, col. 27, ll. 15–25;
(“after suitable hybridization washing is recognized as a rosette of discrete
particles containing corresponding probe bound to discrete particle or a point on
the solid support where a target containing complementary sequence is placed.”
Id. at col. 28, ll. 19–23)), we agree it would have been obvious to have utilized
enrichment beads to eliminate the DP without the target sequence in order to have
more space on the monolayer surface for visualization and imaging of the DP.
Furthermore, as indicated by Requester each of O’Neill, Lundeberg, Oliphant, and
Vann perform enrichment steps, e.g., to increase the amount of genetic information
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for analysis (Request 130) and with emphasis on the need for purification of
amplification products (id. at 133), and thus it would have been obvious to apply
these techniques as a conventional and known way of achieving such separation.
KSR, 500 U.S. at 417 (“the predictable use of prior art elements according to their
established functions.”)
The Examiner did not adopt the rejections because:
Drmanac does not disclose amplification of DNA in microemulsions.
The detectable discrete particles are used for detection, not
enrichment. There is no suggestion that particles having no bound
DNA should be removed. There is no motivation to combine the
teachings of the references and, even if the references are combined,
the claim limitations are not met. Hence there is no prima facie case of
obviousness.
RAN 21.
The Examiner’s findings are not supported by a preponderance of the
evidence.
Drmanac describes performing the amplification reactions in “small spheres
(pearls) formed of appropriate membranes (perhaps the semipermeable ones)
together with DP conglomerates. . . . Microsphere formation should be considered
as a process for formation of fat droplets.” Since the microspheres are membranes
and considered as a process for fat droplet formation, when present in the aqueous
solution in which amplification is performed, they would constitute emulsions as
claimed.
12
See also Requester Appeal Br. 21 (Section E).

12
To the extent there is any uncertainty about this finding, Holliger and Cohen
establish that emulsion PCR was known in the art, making it obvious to have used
it as the specific type of microspheres described in Drmanac. Requester Appeal
Br. 25
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The Examiner also states that there is no teaching in Drmanac of removing
particles with no bound DNA. Even if this is true, the reason to enrich for the DPs
with target nucleic acid would be to increase the amount of genetic information
available on the solid surface on which the particles are spread as a monolayer.
Finally, with respect to the Examiner’s statement that the particles are used
for detection and not enrichment, we point out that this is not an anticipation
rejection, but one of obviousness. The issue is whether it would have been obvious
to one of ordinary skill in the art to have utilized enrichment beads in Drmanac’s
amplification method. As explained above, Drmanac attaches a second set of
beads to the nucleic acid immobilized on a first set of beads. Patent Owner did not
provide sufficient evidence to rebut this finding. While such beads are used for
detection purposes, based on the teachings in four different publications of the
benefit of enrichment beads (O’Neill, Lundeberg, Vann, and Oliphant), the
ordinary skilled worker would have appreciated that such beads could be used for
enrichment purposes as well.

Summary
For the foregoing reasons, we reverse the Examiner’s decision not to adopt
the rejection of claim 1 over Drmanac in view of one of O’Neill, Lundeberg, Vann,
and/or Oliphant (numbered rejections 11–14). While we have considered each one
of O’Neill, Lundeberg, Vann, and Oliphant separately, the four publications
constitute the scope and content of the prior art in which an obviousness
determination is made, Graham v. John Deere Co., 383 at 17–18, and thus serve as
evidence in each of the separate rejections. We also reverse the Examiner’s
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determination with respect to claims 2–9 for the reasons set forth in the Request for
Reexamination.

Claims 10–14, and 16–18
The same rationale for claims 10–14 and 16–18 discussed in the Holliger
rejection apply to the rejection involving Drmanac. Accordingly, with respect to
claim 10, and claims 11–14 and 16–19 which depend from it, we reverse the
Examiner’s decision not to adopt the rejection based on Drmanac and Vann, but
affirm with regard to Lundeberg, and do not reach with respect to O’Neill and
Oliphant.

SUMMARY
Rejections 1–5 of claims 1–8 are AFFIRMED.
Rejection 6 of claims 20–28, 39–47, and 57–65 is AFFIRMED.
The Examiner’s decision not to adopt Rejections 7–10 (Holliger et al.) of
claims 1–9 is REVERSED.
The Examiner’s decision not to adopt Rejection 8 (Holliger and Lundeberg)
of claims 10–14 and 16–19 is AFFIRMED.
The Examiner’s decision not to adopt Rejection 9 (Holliger and Vann) of
claims 10–14 and 16–19 is REVERSED.
Rejections 7 and 10 of claims 10–14 and 16–19 are not reached.
The Examiner’s decision not to adopt Rejections 11-14 (Drmanac et al.) of
claims 1-8 is REVERSED.
The Examiner’s decision not to adopt Rejection 14 (Drmanac and Vann) of
claims 10-14 and 16-18 is REVERSED.
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The Examiner’s decision not to adopt Rejection 13 (Holliger and
Lundeberg) of claims 10–14 and 16–19 is AFFIRMED.
Rejections 11 and 12 of claims 10–14 and 16–19 are not reached.

NEW GROUND OF REJECTION
This decision contains a new ground of rejection pursuant to 37 C.F.R.
§ 41.77(b) which provides that “[a]ny decision which includes a new ground of
rejection pursuant to this paragraph shall not be considered final for judicial
review.” Correspondingly, no portion of the decision is final for purposes of
judicial review. A requester may also request rehearing under 37 C.F.R. § 41.79, if
appropriate, however, the Board may elect to defer issuing any decision on such
request for rehearing until such time that a final decision on appeal has been issued
by the Board.
For further guidance on new grounds of rejection, see 37 C.F.R. § 41.77(b)–
(g). The decision may become final after it has returned to the Board. 37 C.F.R.
§ 41.77(f).
37 C.F.R. § 41.77(b) also provides that the Patent Owner, WITHIN ONE
MONTH FROM THE DATE OF THE DECISION, must exercise one of the
following two options with respect to the new grounds of rejection to avoid
termination of the appeal as to the rejected claims:
(1) Reopen prosecution. The owner may file a response requesting
reopening of prosecution before the examiner. Such a response must be either an
amendment of the claims so rejected or new evidence relating to the claims so
rejected, or both.
(2) Request rehearing. The owner may request that the proceeding be
reheard under § 41.79 by the Board upon the same record. …
Any request to reopen prosecution before the examiner under 37 C.F.R.
§ 41.77(b)(1) shall be limited in scope to the "claims so rejected." Accordingly, a
request to reopen prosecution is limited to issues raised by the new ground(s) of
rejection entered by the Board. A request to reopen prosecution that includes
issues other than those raised by the new ground(s) is unlikely to be granted.
Furthermore, should the patent owner seek to substitute claims, there is a
presumption that only one substitute claim would be needed to replace a cancelled
claim.
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A requester may file comments in reply to a patent owner response.
37 C.F.R. § 41.77(c). Requester comments under 37 C.F.R. § 41.77(c) shall be
limited in scope to the issues raised by the Board's opinion reflecting its decision to
reject the claims and the patent owner's response under paragraph 37 C.F.R.
§ 41.77(b)(1). A newly proposed rejection is not permitted as a matter of right. A
newly proposed rejection may be appropriate if it is presented to address an
amendment and/or new evidence properly submitted by the patent owner, and is
presented with a brief explanation as to why the newly proposed rejection is now
necessary and why it could not have been presented earlier.
Compliance with the page limits pursuant to 37 C.F.R. § 1.943(b), for all
patent owner responses and requester comments, is required.
The examiner, after the Board's entry of a patent owner response and
requester comments, will issue a determination under 37 C.F.R. § 41.77(d) as to
whether the Board's rejection is maintained or has been overcome. The proceeding
will then be returned to the Board together with any comments and reply submitted
by the owner and/or requester under 37 C.F.R. § 41.77(e) for reconsideration and
issuance of a new decision by the Board as provided by 37 C.F.R. § 41.77(f).

AFFIRMED; 41.77(b)

GUEST, Administrative Patent Judge, concurring.
I disagree with the majority’s interpretation of the claim language “capture
primer is coupled to the enrichment beads.” I agree with Patent Owner’s argument
that it is error to assign claim 1 a claim interpretation that excludes the
embodiment of Figure 3, particularly because the excluded embodiment is the only
embodiment with written descriptive support in the ’690 patent.
The claims must be read in view of the specification, of which they are a
part. The specification “is always highly relevant to the claim construction
analysis. Usually, it is dispositive; it is the single best guide to the meaning of a
disputed term.” Phillips v. AWH Corp., 415 F.3d 1303, 1315 (Fed. Cir. 2005)
(quoting Vitronics Corp. v. Conceptronic, Inc., 90 F.3d 1576, 1582 (Fed. Cir.
1996)).
We note that the ’690 patent includes descriptive support for a species in
which the capture primer is hybridized to the target nucleic acid prior to being
attached to the enrichment bead. ’690 patent, col. 12, ll. 22-62; col. 20, l. 59 to col.
21, l. 41; Fig. 3; col. 26, l. 30 to col. 28, l. 33. Yet, we have not been directed to
descriptive support in the ’690 patent for the embodiment adopted by the Examiner
and the majority, namely where the capture primer is attached to the enrichment
bead prior to hybridization, and we find no such support.
The “disclosure of a species may be sufficient written descriptive support for
a later claimed genus including that species.” Bilstad v. Wakalopulos, 386 F.3d
1116, 1124 (Fed. Cir. 2004). If the difference between members of the group is
such that the person skilled in the art would readily discern that other members of
the genus would perform similarly to the disclosed members, i.e., if the art is
predictable, then disclosure of more species is not necessary to adequately show
possession of the entire genus. Id., at 1125. Thus, in limited situations, our
reviewing court has found enabling and written descriptive support for a genus
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claim where the description is only to a species. However, it is rarely appropriate
to interpret a claim as narrowly directed to an undisclosed species. The present
case is a situation where the skilled artisan would have readily discerned that the
order of attaching the enrichment bead to the capture primer and attaching
hybridizing the capture primer to the target nucleic acid is not critical and altering
the order of attachment would have been within the skill of an ordinary artisan.
Accordingly, I conclude that the broader interpretation proposed by Patent
Owner, in which the phrase “capture primer is coupled to the enrichment beads” is
generic to the order in which it is coupled, is the broadest reasonable interpretation
that is consistent with the specification of the ’690 patent and as the skilled artisan
would read the claim in light of the specification of the ’690 patent. In re Am.
Acad. of Sci. Tech. Ctr., 367 F.3d 1359, 1364 (Fed. Cir. 2004) (quoting In re Bond,
910 F.2d 831, 833 (Fed. Cir. 1990)) (During reexamination, “claims . . . are to be
given their broadest reasonable interpretation consistent with the specification, and
. . . claim language should be read in light of the specification as it would be
interpreted by one of ordinary skill in the art.”). In this case, not only is the
generic interpretation more consistent with the specification, but it is also broader
than the interpretation proposed by Requester and adopted here by the majority.
I find it relevant that claim 50 was not incorporated exactly as written into
claim 45 during prosecution of the application that became the ’690 patent.
Rather, the words “a capture primer disposed on the enrichment beads” was added
as “wherein the capture primer is coupled to the enrichment beads.” We have no
way of knowing the reason why the language was not adopted verbatim from claim
50. Yet, the original claim language of claim 50 reflects an embodiment not
described in the ’690 patent, while the amended language of claim 45 is subject to
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a reasonably broader interpretation, for which there is written descriptive support,
and which is consistent with the generic scope of original claim 45. Applicant’s
argument with respect to the amendment to claim 45 are directed to the newly
added requirement of hybridization not being taught by the prior art. See
Amendment and Response to Non-Final Office Action 9-12, dated June 19, 2009.
Applicant does not argue the particular order of hybridization and bead attachment
for the capture primer.
13

During reexamination, original claims are not subject to reexamination
under 35 U.S.C. § 112. See 35 U.S.C. §§ 301(a) and 311(a) (reexamination must
be based on “prior art consisting of patents or printed publications...or statements
of the patent owner . . . in which the patent owner took a position on the scope of
any claim of a particular patent.”); see also In re NTP, Inc., 654 F.3d 1268, 1276
(Fed. Cir. 2011) (“other challenges to the patentability of original claims—such as
qualification as patentable subject matter under § 101 or satisfaction of the written
description and enablement requirements of § 112—may not be raised in
reexamination proceedings.”).
In NTP, the Federal Circuit concluded that the Board’s claim interpretation
was consistent with the specification and was reasonable in view of the
specification as viewed by a person of ordinary skill in the art. See NTP, 654 F.3d
at 1274. Thus, the further discussion in NTP related to 35 U.S.C. § 112 support is
only with respect to whether prior applications were awarded priority under 35
U.S.C. § 120. See id. at 1278. NTP states:

13
Even if the intent of the amendment during initial prosecution was to narrow the
scope of claim 45 to an embodiment in which the capture primer is attached prior
to hybridization, the claim is not entitled to such a narrow interpretation. Thus, the
broader interpretation is appropriate.
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Whether the examiner actually considered [written descriptive
support in the parent application under 35 U.S.C. § 120] can only be
determined by reviewing the prosecution history. The history here
fails to support NTP’s contention that the examiner made such a
considered judgment. Deciding whether a patent application satisfies
§ 112 requires a distinct and separate analysis from deciding whether
that application satisfies § 120. When an examiner decides whether
an application satisfies § 112, the examiner reviews only the
application. Deciding whether that same application is entitled to an
earlier priority date requires the examiner to determine whether
pending claims are supported by the written description of the parent
application. 35 U.S.C. § 120.
Id. (emphasis added).
The Federal Circuit may be recognizing a presumption that the Examiner
reviews each application for 35 U.S.C. § 112 support of the claims, but that there is
no further presumption that the Examiner has reviewed the claims for 35 U.S.C. §
112 support in any documents for which priority is claimed. Cf. In re Etter, 756
F.2d 852, 858 (Fed. Cir. 1985) (en banc) (holding that there was no presumption of
validity in reexamination cases, but only applying that lack of presumption to prior
art rejections based on patents or printed publications, which are the only
appropriate rejections in a reexamination). Further, in the present case, there is
evidence that Examiner reviewed claims 45-69 for 35 U.S.C. § 112 issues, during
the initial examination of the application that became the ’690 patent, because
claim 45 was rejected under 35 U.S.C. § 112, second paragraph, during the initial
examination. See Non-final Office Action 2, dated March 20, 2009.
A substantial new question of patentability (SNQ) cannot be based on
unpatentability under 35 U.S.C. § 112. Accordingly, during reexamination, while
a patent owner has the opportunity to correct patented claims for which 35 U.S.C.
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§ 112 problems exist, such issues cannot be raised by a third party requester, by an
Examiner, or by the Board on appeal. Thus, the limited situation where an issued
claim in not supported by the specification, the only appropriate approach would
be to interpret original patent claims, if possible, such that a substantial new
question of patentability under 35 U.S.C. § 112 is not raised, namely under the
broadest reasonable interpretation consistent with the specification such that the
original patented claims would be valid under 35 U.S.C. § 112.
14
At the very least,
it would be improper to interpret the claims as only directed to an embodiment
which is not described in the patent.
Accordingly, I further disagree with the majority that there is not support for
original claim 1 in the ’540 provisional application and in the ’899 Application for
the claims as interpreted by the Patent Owner. It is notable that the disclosure of
the ’540 provisional application and the ’899 Application are consistent with the
disclosure of the ’690 patent, to the extent that only the embodiment of Fig. 3 is
described.
In light of my belief that the claims are entitled to a different claim
interpretation, I would have reversed the Examiner’s rejections based on 35 U.S.C.
§314(a). I would have also have reversed the Examiner’s rejections based on
Dressman, as Dressman would not have been prior art at the time of the invention.
However, the alternative claim interpretation proposed by Patent Owner
does not affect the majority’s analysis reversing the Examiner’s determination not
to adopt the rejections based on Holliger and Drmanac. The new grounds of

14
As the Federal Circuit in NTP recognized, claims added during reexamination
and claim amendments are properly available for rejection under 35 U.S.C. § 112.
See NTP, 654 F.3d at 1276, n. 6.
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rejection are appropriate even under the broader interpretation proposed by Patent
Owner, as the rejection encompasses the interpretation adopted by the majority.
Thus, I concur in the majority’s determination to enter new grounds of rejection.

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ack

for PATENT OWNER:

COOLEY LLP
ATTN: PATENT GROUP
1299 PENNSYLVANIA AVENUE, NW
SUITE 700
WASHINGTON, DC 2004

for THIRD PARTY REQUESTOR:

TROUTMAN SANDERS LLP
THE CHRYSLER BUILDING
405 LEXINGTON AVENUE
NEW YORK, NY 10174