782 Fed.Appx. 1018 (Fed. Cir. 2019), 2018-2089, Scripps Research Institute v. Illumina, Inc.

Docket Nº:2018-2089
Citation:782 Fed.Appx. 1018
Opinion Judge:Taranto, Circuit Judge.
Party Name:The SCRIPPS RESEARCH INSTITUTE, Plaintiff-Appellant v. ILLUMINA, INC., Defendant-Appellee
Attorney:Justin Scott Cohen, Thompson & Knight LLP, Dallas, TX, argued for plaintiff-appellant. Also represented by Herbert J. Hammond, James Michael Heinlen; Derek Tod Gilliland, Nix Patterson & Roach LLP, Daingerfield, TX. Juanita Rose Brooks, Fish & Richardson, PC, San Diego, CA, argued for defendant-a...
Judge Panel:Before Wallach, Clevenger, and Taranto, Circuit Judges. Clevenger, Circuit Judge, dissenting.
Case Date:August 29, 2019
Court:United States Courts of Appeals, Court of Appeals for the Federal Circuit

Page 1018

782 Fed.Appx. 1018 (Fed. Cir. 2019)

The SCRIPPS RESEARCH INSTITUTE, Plaintiff-Appellant

v.

ILLUMINA, INC., Defendant-Appellee

No. 2018-2089

United States Court of Appeals, Federal Circuit

August 29, 2019

Editorial Note:

This Disposition is Nonprecedential. (See Federal Rule of Appellate Procedure Rule 32.1. See also U.S.Ct. of App. Fed. Cir. Rule 32.1.)

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Appeal from the United States District Court for the Southern District of California in No. 3:16-cv-00661-JLS-BGS, Judge Janis L. Sammartino.

Justin Scott Cohen, Thompson & Knight LLP, Dallas, TX, argued for plaintiff-appellant. Also represented by Herbert J. Hammond, James Michael Heinlen; Derek Tod Gilliland, Nix Patterson & Roach LLP, Daingerfield, TX.

Juanita Rose Brooks, Fish & Richardson, PC, San Diego, CA, argued for defendant-appellee. Also represented by Michael Ari Amon, Craig E. Countryman.

Before Wallach, Clevenger, and Taranto, Circuit Judges.

OPINION

Taranto, Circuit Judge.

The Scripps Research Institute owns now-expired U.S. Patent No. 6,060,596, which describes and claims bifunctional molecules having certain properties, along with libraries of such molecules. Scripps sued Illumina, Inc. in the Southern District of California, asserting infringement of claims 1, 3, 10, and 16 of the ’596 patent. The district court issued claim-construction rulings that addressed three terms that involve the variable a and a claim phrase that refers to a linker molecule . Shortly thereafter, Scripps and Illumina filed a joint motion stipulating that, under the claim-construction rulings, Illumina has not infringed the asserted claims. The district court granted the motion and entered a final judgment in Illumina’s favor.

Scripps appeals the claim-construction rulings involving the a terms and the linker molecule phrase. Both parties agree that, if the rulings involving the a terms are correct, the district court’s judgment should stand. Because we agree with the district court regarding the a terms, we affirm the judgment without reaching the dispute over the linker molecule phrase.

I

A

The ’596 patent is titled "Encoded Combinatorial Chemical Libraries." Its specification describes bifunctional molecules, represented by the formula A-B-C, gathered into a library. At a general level, the A side of each bifunctional molecule is the molecule of interest (such as a molecule that binds to a particular target, ’596 patent, col. 2, lines 64-66), the C side is a molecule serving an indexing function in the library, and B is a linker between A and C.

The "chemical moiety" A in the A-B-C bifunctional molecule is a "polymer." ’596 patent, col. 4, lines 31, 33. The polymer "comprises a linear series of chemical units represented by the formula (Xn )a, wherein X is a single chemical unit in polymer A and n is a position identifier." Id., col. 4, lines 33-36.1 The specification notes that "a is an integer," typically between four and fifty. Id., col. 4, lines 41-42.

The C in the A-B-C molecule is the "identifier oligonucleotide." Id., col. 5, lines 56-57. The specification explains that oligonucleotide C is made up of unit identifiers

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corresponding to the chemical units of polymer A. Id., col. 5, lines 58-61. Specifically, oligonucleotide C has "a sequence represented by the formula (Zn )a, wherein Z is a unit identifier nucleotide sequence within oligonucleotide C that identifies the chemical unit X at position n ." Id. Each unit identifier Z typically includes between two and ten nucleotides, preferably chosen from the bases found in DNA: adenosine, cytosine, guanosine, and thymidine. Id., col. 6, lines 7-19.

The B portion of the bifunctional molecule is the "linker molecule" that connects polymer A and oligonucleotide C. See id., col. 8, lines 20-24. The specification explains that linker molecule B "can be any molecule that performs the function of operatively linking the chemical moiety to the identifier oligonucleotide." Id. It further notes that linker molecule B preferably "has a means for attaching to a solid support" and also "separat[ing] from the solid support." Id., col. 8, lines 25-33.

The specification teaches a "method for producing a plurality of bifunctional molecules to form a library of this invention." Id., col. 9, lines 62-63. "In the present synthesis methods," a bifunctional molecule A-B-C is created according to "an alternating parallel synthesis procedure." Id., col. 9, line 66, through col. 10, line 7. The procedure involves "add[ing] chemical unit X and then add[ing] a unit identifier nucleotide sequence Z that defines (codes for) that corresponding chemical unit." Id. With a library of bifunctional molecules formed in that way, researchers can discern the identity of bound polymer A by reading the corresponding genetic tag, i.e., oligonucleotide C. Id., col. 2, line 66, through col. 3, line 1.

Independent claim 1 recites the following: 1. A bifunctional molecule according to the formula A-B-C, wherein A is a polymer comprising a linear series of chemical units represented by the formula (Xn

)a, wherein X is a single chemical unit in polymer A, B is a linker molecule operatively linked to A and C[,] and identifier oligonucleotide C is represented by the formula (Zn )a, wherein a unit identifier nucleotide sequence Z within oligonucleotide C identifies the chemical unit X at position n ; and wherein n is a position identifier for both X in polymer A and Z in oligonucleotide C having the value of 1+i where i is an integer from 0 to 10, such that when n is 1, X or Z is located most proximal to the linker, and a is an integer from 4 to 50.

Id., col. 43, lines 2-14. Claim 3 depends on claim 1 and additionally requires that "said polymer is an oligosaccharide, pol[y]peptide, glycolipid, lipid, proteoglycan, glycopeptide or oligonucleotide." Id., col. 43, lines 18-20.

Unlike claims 1 and 3, which involve a single bifunctional molecule, claims 10 and 16 claim libraries containing multiple bifunctional molecules. Claim 10 recites "[a] library comprising a plurality of species of bifunctional molecules according to claim 1." Id., col. 44, lines 4-5. Claim 16 depends on claim 10 and further requires that "each of said species of bifunctional molecules in said plurality is present in molar equivalents of from 0.2 to 10.0." Id., col. 44, lines 29-31.

B

In December 2016, Scripps sued Illumina, asserting that Illumina’s making, using, selling, and offering to sell its BeadChip products infringed claims 1, 3, 10, and 16 of the ’596 patent. After the Patent Trial and Appeal Board denied Illumina’s petition for an inter partes review of all claims of the ’596 patent except claims 7-9, Illumina moved to dismiss the district-court

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case, arguing that its BeadChip products could not meet the requirements of claim 1 (and hence of claims 3, 10, and 16) under any plausible construction of the a terms. The court, concluding that it could not at that stage reject Scripps’s proposed constructions of the a terms, denied Illumina’s motion to dismiss.

The parties then engaged in full claim-construction litigation over the terms a, (Zn

)a, and (Xn

)a (the a terms), and the claim phrase B is a linker molecule operatively linked to A and C, and a couple of other terms not involved in this appeal. After accepting briefs from both sides, the district court heard testimony and argument at a hearing. On April 10, 2018, the court issued an order construing all disputed terms. Scripps Research Inst. v. Illumina, Inc., No. 16-CV-661, 2018 WL 1726597 (S.D. Cal. Apr. 10, 2018).

First, the court construed a to mean "an integer from 4 to 50 that is further defined in the context of the formulas (Zn )a and (Xn )a ." Id. at *6. Next, it construed (Xn )a to mean "a representation of polymer A, where ‘a ’ is the number of chemical units of X forming the polymer A." Id. It similarly construed (Zn )a to mean "a representation of identifier oligonucleotide C, where ‘a ’ is the number of chemical unit identifiers in the oligonucleotide." Id. Relatedly, the court determined that the value of a must be the same for both (Xn )a and (Zn )a . Id. at *5.

The court then turned to the phrase B is a linker molecule operatively linked to A and C . The Board had already construed the linker molecule phrase in its decision denying Illumina’s petition for an inter partes review. Analyzing the prosecution history of earlier patents in the same family as the ’596 patent, the Board determined that Scripps had disclaimed some linker molecules. Accordingly, the Board construed the linker molecule phrase to mean that "linker molecule B (1) links to A and to C, (2) allows for alternat[ing] addition of nucleotides and amino acids to itself, and (3) is capable of coupling to and decoupling from a solid support without cleaving either the polypeptide or oligonucleotide from linker molecule B." J.A. 977. The district court adopted the Board’s construction, deeming it "reasoned" and "persuasive." Scripps, 2018 WL 1726597, at *6-7.

On May 17, 2018, Scripps and Illumina filed a joint motion for final judgment, stipulating that, under the district court’s claim-construction rulings, "Illumina has not infringed, did not infringe, and cannot infringe" the asserted claims. J.A. 7. Both parties agreed that, under the court’s construction of a, the value of a for Illumina’s BeadChip products is one, which falls outside the claimed range of four to fifty. They also agreed that Illumina’s BeadChip products do not contain linker molecules under the court’s construction of the linker molecule phrase. The parties acknowledged that "[e]ach of these rulings"— the constructions of the a terms; the determination that a must have...

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