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Trial Date in Affy vs. Illumina Pushed Back To January in Wake of Markman Hearing

The final showdown in Affymetrix’s patent infringement suit against genotyping rival Illumina won’t happen next month as previously scheduled. According to court documents filed last week with the US District Court for the District of Delaware, attorneys for the two parties have agreed to push the trial date back to January 2007, giving the legal teams for both firms more time to prepare after receiving the results from a mid-August Markman hearing.
According to the court documents, Affy and Illumina requested and were granted the new scheduling order, which calls for a pretrial conference to be held in Wilmington during the week of December 11. The new trial date has not been set, but the court said it will “commence on a date on or soon after January 29, 2007.”
Affymetrix first sued Illumina in 2004, and Affy and Illumina were originally due in court on October 16. But since the court’s Markman ruling was handed down on Aug. 16, the parties jointly requested more time from the court. According to the recent filing, the extra time was requested “not for purpose of delay, but to allow the parties adequate time to complete expert discovery and prepare for trial in view of the Court’s August 16, 2006, order setting forth terms and phrases of the patents-in-suit.”
Markman Ruling
Affymetrix sued Illumina on July 26, 2004, for allegedly infringing six patents in the DNA microarray field and related technology. Affy dropped one of the patents from the suit in March. The Markman hearing in the case was held in April (see BAN 4/18/2006).
Illumina has said it does not infringe Affymetrix' patents and that these patents are, in any event, invalid and unenforceable. Affymetrix is seeking remedies including lost profits, a royalty, trebled damages for willfulness, and a permanent injunction.
Following the Markman ruling last month, both Illumina and Affymetrix claimed that the district judge's interpretation of key terms in the patent-infringement case favored their respective positions. Judge Joseph Farnan issued the Markman order to interpret 15 disputed claim terms in the five patents in contention (see sidebar).
According to Affymetrix, the judge ruled in its favor for most terms and adopted only two of Illumina's proposed constructions.
In a statement, Affymetrix said the court found that the patents in question are not limited to in situ synthesis; to probes chemically linked to a single surface; or to the placement of probes at predetermined locations, despite Illumina’s claims to the contrary.
Illumina’s motion to dismiss one of the patents in the case — US Patent No. 5,795,716, “Computer-aided visualization and analysis system for sequence evaluation” — was denied by the court.
Illumina had argued that Affymetrix never had legal title to the ‘716 patent and therefore could not sue for infringement of that patent. Illumina argued that the invention covered in the patent was conceived in 1992, before Affymetrix existed, and that the company where the inventors were employed — Wagner and Associates — never officially transferred those rights to Affymax Research Institute, the progenitor of Affymetrix, when Wagner and ARI signed an agreement in 1991.

"We have strongly believed since this suit was filed that Affymetrix's allegations are without merit, and that this suit is a result of Affymetrix' unfortunate decision to compete in the courtroom rather than in the marketplace.”

Affy successfully argued, however, that the 1991 agreement covered future inventions and so the ‘716 patent was transferred to Affy under that agreement.
Despite these apparent setbacks, Illumina said in a statement that the Markman order adopted its position as the "proper interpretation."
"We have strongly believed since this suit was filed that Affymetrix's allegations are without merit, and that this suit is a result of Affymetrix' unfortunate decision to compete in the courtroom rather than in the marketplace,” Illumina CEO Jay Flatley said in a statement.
“We believe this ruling supports our non-infringement and invalidity positions and counterclaims in this case and we look forward to obtaining favorable results to that effect,” he added.
Still, while Affy and Illumina claim victory, the Markman ruling may not shed much light on who will emerge as the real victor next year. Scott Bornstein, an attorney representing Enzo Biochem in its patent infringement suit against Affymetrix and six other defendants, told BioArray News that “nobody wins” a Markman ruling “in and of itself.”
“You cannot win a case or lose a case by a Markman ruling,” Bornstein said. “All it does is position a case to go forward so that you can present your case to a jury one day” (see BAN 8/8/2006).
Representatives from Affymetrix and Illumina declined to discuss the case with BioArray News outside of the information contained in last month’s statements.

Patents in Dispute in Affymetrix vs. Illumina
In its July 26, 2004, lawsuit against Illumina, Affymetrix alleged that Illumina infringed six of its patents. Illumina fired back in September of last year, stating that it is not infringing and that the Affy patents should be invalidated. In March, Affy dropped US Patent No. 6,607,887 from the suit. Illumina tried to have a second patent, US Patent No. 5,795,716, dismissed, but the motion was denied by the court last month. Details on the patents involved in the case follow.
Title: Computer-aided visualization and analysis system for sequence evaluation
Number: 5,795,716
Received: August 18, 1998
Lead Inventor: Mark Chee
Assignee: None
The patent describes a method of identifying an unknown base in a sample nucleic acid sequence comprising measuring probe intensities for a plurality of nucleic acid probes that differ by a base at an interrogation position corresponding to the unknown base, where each probe intensity indicates hybridization affinity between a nucleic acid probe and the sample nucleic acid sequence. The patent also describes a method for analyzing the probe intensities and at least one probe intensity from a nucleic acid probe with an interrogation position corresponding to a position near the unknown base in the sample nucleic acid sequence, and generating a base call identifying the unknown base according to results of the analysis. A computer analysis method is also described.

Title: Methods for making a device for concurrently processing multiple biological chip assays
Number: 5,545,531
Received: August 13, 1996
Lead Inventor: Robert Rava
Assignee: Affymax
The patent describes methods for processing multiple biological chip assays. A biological chip plate comprising a plurality of test wells is described where each test has a molecular probe array. According to the patent, the method involves introducing samples into the test wells; subjecting the biological chip plate to manipulation by a fluid handling device that automatically performs steps to carry out reactions between target molecules in the samples and probes; and subjecting the biological chip plate to a biological chip plate reader that interrogates the probe arrays to detect any reactions between target molecules and probes.

Title: Products for detecting nucleic acids
Number: 6,355,432
Received: March 12, 2002
Lead Inventor: Stephen Fodor
Assignee: Affymetrix
The patent provides methods and apparatus for sequencing, fingerprinting and mapping biological macromolecules, typically biological polymers. The methods make use of a plurality of sequence specific recognition reagents which can also be used for classification of biological samples, and to characterize their sources, the patent states.

Title: Bioarray chip reaction apparatus and its manufacture
Number: 6,399,365
Received: June 4, 2002
Lead Inventor: Donald Besemer
Assignee: Affymetrix
Methods and devices for packaging a substrate having an array of probes fabricated on its surface are described in the patent. According to the patent, a substrate having an array of probes is attached to a cavity inside a body using an adhesive. The body includes inlets that allow fluids into and through the cavity, according to the patent. A seal is provided for each inlet to retain the fluid within the cavity. An opening is formed below the cavity to receive a temperature controller for controlling the temperature in the cavity. By forming a sealed thermostatically controlled chamber in which fluids can easily be introduced, a medium for sequencing by hybridization is provided, the patent states.

Title: Nucleic acid reading and analysis system
Number: 6,646,243
Received: November 11, 2003
Lead Inventor: Michael Pirrung
Assignee: Affymetrix
A method and apparatus for preparation of a substrate containing a plurality of sequences are described. Photoremovable groups are attached to a surface of a substrate and selected regions of the substrate are exposed to light so as to activate the selected areas. A monomer, also containing a photoremovable group, is provided to the substrate to bind at the selected areas, the patent's abstract states. The process is repeated using a variety of monomers such as amino acids until sequences of a desired length are obtained. Detection methods and apparatus are also disclosed in the patent.

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