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Hearing This Week Could Define Course of Affy vs. Illumina; Documents Shed Light on Evolving Case

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Though Affymetrix and Illumina aren't slated to face each other in court for another six months, a special hearing scheduled to take place this week may ultimately determine who wins the companies' patent-infringement suit (see BAN 8/24/2005).

Attorneys for the two array companies are expected to meet on Thursday in the US District Court in Wilmington, Del., for a Markman hearing, a key event in patent-infringement cases in which the presiding judge gets the final say in defining the scope of the claims involved in the lawsuit.

The Markman hearing is the next step on the road to the companies' Oct. 16 trial date, and documents associated with the hearing offer glimpses of Affymetrix's case and Illumina's defense and counterclaims.

For example, when Affymetrix originally sued Illumina in July 2004, the company claimed its rival was infringing on six of its patents (see Sidebar). But when lawyers for the array firms meet in Wilmington this week, they'll actually be sparring over only five Affy patents, according to legal documents obtained by BioArray News.

In a March 16 letter, Affy counsel Daniel Reed told Illumina's lawyers that information obtained in the case discovery process covering the sixth patent -- US Patent No. 6,607,887, "Computer-aided visualization and analysis system for sequence evaluation" -- has caused Affy to drop that patent from its suit.


Shedding more light on Affy's case and Illumina's counterclaims have been the individuals and companies that have received requests or subpoenas to give depositions in the case.

"Based on the discovery, Affymetrix has ... decided to dismiss the '887 patent from the lawsuit. Therefore, no claims from this patent need be construed," Reed wrote in the letter to Chicago-based Kirkland & Ellis.

The decision to drop that IP represents a minor victory for Illumina. In a March 29 letter to presiding Judge Joseph Farnan, the company's counsel called Affy's claims related to the patent "frivolous."

The five remaining patents under dispute cover a method for analyzing probe intensities, methods for processing multiple biological chip assays, products for detecting nucleic acids, methods and devices for packaging a substrate, and a nucleic acid reading and analysis system.

In a scenario that could benefit Affymetrix, Farnan could decide at the Markman hearing to allow all or most of its claims into the final trial. Yet if the judge decides to dismiss some of Affy's claims -- perhaps even tossing claims of infringement related to specific patents -- Affy's case against Illumina could weaken.

Affy wasn't the only principal in the suit to amend its case over the past few months. In January, Illumina filed an amended list of counterclaims in the case, accusing Affy of fraud and claiming it has violated federal antitrust legislation, according to court documents filed at the time (see BAN 1/10/2006).

Depositions and Subpoenas

Shedding more light on Affy's case and Illumina's counterclaims have been the individuals and companies that have received requests or subpoenas to give depositions in the case.

During the discovery period, Illumina and Affymetrix subpoenad numerous individuals and companies, including Radomir Crkvenjakov, Radoje Drmanac, and Richard Sachleben. Crkvenjakov received his subpoena from Affy, while Drmanac and Sachleben received their subpoenas from Illumina.

Crkvenjakov and Drmanac are former Argonne National Laboratory researchers who founded a company called Hyseq in 1993 with the aim of selling a technology called sequencing by hybridization.

In its subpoena to Drmanac, Illumina requested all documents related to his work on "technology referred to as 'Sequencing by Hybridization' and the miniaturization of SBH by forming arrays of oligonucleotides attached to microbeads," as well as all records of Drmanac's communication with several individuals including Affymetrix head Stephen Fodor.

According to Illumina, Sachleben worked at Oak Ridge National Laboratory in the late 1980s and early 1990s "with technology that may be relevant prior art to the patents-in-suit."

In addition, Sachleben "attended a conference in Moscow in November 1991, and prepared a detailed trip report relating to that conference which is important to certain of Illumina's invalidity and inequitable conduct defenses in this case," Illumina stated in the subpoena. Illumina alleged in its amended answer in January that representatives of what was to become Affymetrix were present in Moscow at that time, and did not disclose knowledge gained from the conference as prior art when applying for the patents in question.

In its January statement, Illumina argued that Fodor "learned of the concept of a 'sequencing chip'... from conference presentations by Radoje Drmanac and Radomir Crkvenjakov that he and others associated with Affymetrix attended in 1989 and 1990."

"Fodor did not disclose these presentations or knowledge of them to the US Patent and Trademark Organization," Illumina stated.

While the subpoenas served to Crkvenjakov, Drmanac, and Sachleben represent an intriguing angle in the case, the other individuals and companies asked to answer questions in Affymetrix vs. Illumina have been nothing short of an array industry Who's who.

Over the past few months, Affymetrix has conducted depositions with Illumina's upper management, including CEO Jay Flatley, chief operating officer and co-founder John Stuelpnagel, co-founder and scientist Mark Chee, vice president of engineering Robert Kain, chief financial officer Christian Henry, chief scientific officer David Barker, and vice president of worldwide sales Tristan Orpin.

Chee in particular has figured prominently in Affy's case. A former Affy scientist, he co-founded Illumina in 1998, and he was a lead inventor on two of the original six Affy patents named in the suit.

Illumina investor CW Group also received a subpoena from Affymetrix in September to answer questions related to the case (see BAN 9/14/2005).

For its part of the discovery process, Illumina has over the past few months taken depositions from Fodor; Affymetrix President Sue Siegel; Greg Yap, vice president of DNA Products; Carl Raimond, market development manager; Richard Rava, senior VP of research at Affymetrix Labs; and Leighton Read, Donald Besemer, and Michael Pirrung, scientists that are or have been affiliated with the company.

Illumina also subpoenaed Gene Logic in January to provide its counsel with "all documents and things referring or relating to correspondence, communications and/or meetings with Affymetrix regarding Illumina and/or its products/services."

All Quiet on the West Coast

Though the Affymetrix vs. Illumina case appears to be heating up, both companies have made few, if any public statements about the case.

A lawyer representing Illumina in the case declined to comment on the upcoming Markman hearing, while Affy's attorneys did not return phone calls seeking comment.

Illumina did reference the litigation in its annual filing with the Securities and Exchange Commission in March. According to the filing, Illumina believes that it has "meritorious defenses against each of the infringement claims alleged by Affymetrix and intends to vigorously defend against this suit."

Affymetrix did not discuss its litigation with Illumina in its annual report, also filed in March.

— Justin Petrone ([email protected])

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