Life Technologies Corp. v. 454 Life Sciences Corp.

• Decision Date: 27 May 2015
• Docket Number: Appeal 2015-000178
• Citation: Life Technologies Corp. v. 454 Life Sciences Corp., Appeal 2015-000178 (P.T.A.B May 27, 2015)
• Parties: LIFE TECHNOLOGIES CORPORATION Requester, Cross-Appellant and Respondent v. 454 LIFE SCIENCES CORPORATION Patent Owner, Appellant, and Cross-Respondent Reexamination Control 95/001, 765 Patent 8, 012, 690 B2 Technology Center 3900
• Court: Patent Trial and Appeal Board

LIFE TECHNOLOGIES CORPORATION Requester, Cross-Appellant and Respondent v. 454 LIFE SCIENCES CORPORATION Patent Owner, Appellant, and Cross-Respondent

Reexamination Control 95/001, 765 Patent 8, 012, 690 B2^[1] Technology Center 3900

Appeal No. 2015-000178

United States Patent and Trademark Office, Patent Trial and Appeal Board

May 27, 2015

Filing Date: 09/25//2011

For PATENT OWNER: COPLEY LLP ATTN: PATENT GROUP

For THIRD PARTY REQUESTOR: TROUTMAN SANDERS LLP THE CHRYSLER

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

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.

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.

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 16-1 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.

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...