Illumina Inc. v. Complete Genomics, Inc.
| Decision Date | 26 March 2013 |
| Docket Number | No. C -10-05542(EDL),C -10-05542(EDL) |
| Parties | ILLUMINA INC. and SOLEXA, INC., Plaintiff, v. COMPLETE GENOMICS INC., Defendant. |
| Court | U.S. District Court — Northern District of California |
This patent infringement case involves DNA sequencing technology. Plaintiffs Illumina, Inc. and Solexa, Inc., (collectively, "Illumina") accuse Defendant Complete Genomics, Inc. ("CGI") of infringing U.S. Patent No 6,306,597 ("the '597 patent"). On May 31, 2012, CGI moved for summary judgment, arguing that several claims of the '597 patent are invalid as anticipated and obvious. The Court held a hearing on this motion on September 4, 2012. For the reasons stated at the hearing and in this Order, Defendant's motion for partial summary judgment of invalidity is granted. The Court heard Illumina's reconsideration motion on January 29, 2013. The Court has issued a separate order denying that motion, but sta ted at the hearing that it would amend this summary judgment order to correct two minor errors that do not affect the merits.
Illumina filed this patent infringement action against CGI in the District Court for the District of Delaware on August 3, 2010. The parties are competitors in the field of DNAsequencing. Illumina designs, manufactures, and sells several platforms for high-throughput DNA sequencing, including its Genome Analyzer and HiSeq sequencing instruments. CGI offers DNA sequencing services to its customers through its Complete Genomics Analysis Service ("CGA™ Service"). In performing its CGA™ Service, CGI employs its Complete Genomics Analysis Platform ("CGA™ Platform"), which includes its Combinatorial Probe-Anchor Ligation ("cPAL™") read technology, among other technologies.
Illumina alleges that through CGI's use of its CGA™ Platform to perform DNA sequencing services, CGI infringes three Illumina patents, specifically U.S. Patent No. 6,306,597 ("the '597 patent"), U.S. Patent No. 7,232,656 ("the '656 patent"), and U.S. Patent No. 7,598,035 ("the '035 patent") (collectively "the Illumina Patents").
CGI denies that it infringes any of the Illumina Patents. CGI further alleges that all of the Illumina Patents are invalid; this motion is specific to the '597 patent.
By order dated November 9, 2010, the court granted CGI's motion to transfer venue to the Northern District of California. Judge Alsup denied CGI's motion to consider whether this action is related to an earlier filed action, Applera Corp. - Applied Biosystems Group v. Illumina, et al., No. C 07-02845 WHA ("Applera"). Docket No. 42. Upon consent of the parties, this action was reassigned to this Court by Judge Breyer. The parties stipulated to dismissal without prejudice of all claims and counterclaims related to the '656 and '035 patents. Docket No. 75.
In Applera, Applied Biosystems ("AB") filed suit against Illumina for ownership of the '597 patent and 2 related patents (U.S. Patent Nos. 5,750,341 and 5,969,119). AB alleged that the inventor, Dr. Stephen Macevicz, invented the subject matter of the patents while he was in-house patent counsel for AB and breached the terms of an Invention Agreement by, among other things, failing to disclose inventions to AB, applying for patents on the inventions in his own name, and purporting to assign the inventions and patents to Lynx, a spinoff corporation of AB, which subsequently merged with Solexa. AB alleged that Macevicz's conduct, as well as Illumina andSolexa's conduct, gave rise to claims for interference with contract, breach of fiduciary duty, constructive fraud, conversion, imposition of constructive trust, and unfair competition. Illumina countersued AB for infringement.
Judge Alsup issued a claim construction order on February 21, 2008, which construed terms from one of the '597 patent's sibling patents, some of which also appear in the '597 patent. See Applera, Case No. 07-2845 WHA, Docket No. 133. Judge Alsup issued a supplemental claim construction on terms from Claim 1 of the '597 patent and the parties stipulated that AB infringed Claim 1 and that the Southern prior art reference rendered Claim 1 invalid. Applera, Docket Nos. 383-1, 384-1, 402 (). The parties agreed before the claim construction hearing that Judge Alsup's construction of the terms applied to the '597 patent.
Following a jury trial, on February 3, 2008, Judge Alsup entered judgment for Illumina on AB's claim of ownership of the Macevicz patents and entered judgment for AB on Illumina's claim that AB infringed the '119 patent.
On March 25, 2010, the Federal Circuit affirmed Judge Alsup's claim construction of the terms that were appealed and stated: "Because the district court properly construed the terms of claim 1 of the '597 patent, we affirm the court's judgment of noninfringement with respect to Applera's accused products, and the court's order, entered pursuant to stipulation, concerning invalidity." Mot. Ex. 13, at 8.
On June 30, 2008, AB filed a request for reexamination of the '597 patent. Three months after the jury trial before Judge Alsup, on May 28, 2009, the PTO issued a non-final Office Action rejecting claim 1 of the '597 patent as being anticipated by several prior art references, including Martinelli (U.S. Patent No. 5,800,994) and either Landegren (U.S. Patent No. 4,988,617) or Whiteley (U.S. Patent No. 4,883,750) taken in view of Martinelli. Mot. Ex. 14.
On June 22, 2009, Illumina filed an information disclosure statement ("IDS") with the PTO regarding the ongoing litigation. Mot. Ex. 15. Illumina attached many litigation-related documentsto the IDS, including the stipulation. In the text of the IDS, Illumina noted that a jury had returned a verdict finding that claim 1 of the '119 patent (the '597 patent's sibling patent) was not invalid for obviousness, but the only mention of the stipulation was that "As a result of the district court's claim construction ruling, the parties entered into a stipulation regarding infringement and invalidity of claim 1 of the '597 patent." Mot. Ex. 15 at 2, 3.
Illumina held an interview with the examiner on July 13, 2009, and filed a response to the office action on August 6, 2009, which included amendments to the claims. Declaration of John Labbe in Support of Illumina's Claim Construction Brief ("Labbe Claim Const. Decl.") Exs. 9, 10. The examiner's interview summary indicates that he and Illumina discussed whether the "Martinelli patent is 'repeating' steps a and b within the meaning of claim 1." Labbe Decl., Ex. 10. In its response to the PTO's Office Action, Illumina summarized the interview as follows:
It was discussed that Martinelli did not disclose repeating steps (a) and (b) on the same polynucleotide that was operated on in the first cycle of the claimed method. It was discussed that claim 1 recites a method that is limited to repeating steps (a) and (b) on the same polynucleotide that was operated on in the first cycle of the method. It was agreed that an unequivocal statement by the Applicant that step (c) of claim 1 of the '597 patent requires repeating steps (a) and (b) on the same polynucleotide acted upon in the first cycle of the recited method would overcome the rejections based on Martinelli.
Labbe Claim Const. Decl., Ex. 9 at 11 . According to Illumina, "Martinelli described its version of [oligonucleotide ligation assay] as a 'hybridization-ligation methodology (HLM),'" which involves binding two probes to a DNA sample to detect whether a mutation is present. Id. at 15; Opening Claim Constr. Br. at 8. Under the Martinelli patent, according to Illumina, "[i]f the two probes can be ligated, the identity of the nucleotide at the site in the sample where the two probes attach to each other can be determined, because ligation could only occur if the mutation is present." Opening Claim Constr. Br. at 8.
In response to the rejection of claim 1 as anticipated by Martinelli and obvious over Landegren and Whiteley in view of Martinelli, Illumina distinguished Martinelli on the ground that Martinelli "did not disclose repeating the steps of its 'HLM' method . . . [and] expressly taught that the HLM reaction was intended to be performed for only one cycle." Labbe Claim Const. Decl., Ex. 9 at 15. In its amendment to Claim 1, Illumina made the following narrowing statement:
As discussed at the interview, the "repeating" step in the claimed method, step (c), requires the repetition of steps (a) and (b) on the same polynucleotide sequence that was acted upon in the first cycle of the recited method. Step (a) of claim 1 recites "extending an initializing oligonucleotide along the polynucleotide." When step (a) is repeated as required by step (c), a (new) initializing oligonucleotide is extended along the same polynucleotide as was acted upon in the first cycle of the recited method ("the polynucleotide").
Labbe Claim Const. Decl., Ex. 9 at 15.
As part of the reexamination, Illumina also submitted an ex parte declaration of Dr. Stephen Macevicz pursuant to 37 C.F.R. § 1.131. Mot. Ex. 16. The declaration said that "[f]rom at least just before February 9, 1995, until April 17, 1995, I spent a number of evenings and weekend days working on the preparation and filing of the '663 application." Id. at 4. This declaration seems to be the first attempt by Illumina to antedate the Southern reference; during the course of the Applera litigation, there had been no attempt to show that Macevicz's earlier conception date (memorialized in his lab notebook) combined with an actual reduction to practice or due diligence, as is required to antedate or swear behind a reference. Mot. Ex. 9, at 2. The Examiner found that Macevicz had exercised...
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