DECISION ON APPEAL AND CROSS-APPEAL
LEBOVITZ, Administrative Patent Judge.
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.
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 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;
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.
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.
6. Claims 20-28, 39-47, and 57-65 under 35 U.S.C.
§314(a) as enlarging the scope of the patent.
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 16-1 9 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.
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.
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...
