Free Letter - District Court of Delaware - Delaware

Case 1:04-cv-00901-JJF Document 173 Filed 01/10/2006 Page 1 of 4
MORRIS, JAMES, HITCHENS & WILLIAMS LLP
222 Delaware Avenue, 10th Floor
. Wilmington, Delaware 19801-1621
(302) 888-6800
Facsimile (302) 571-1751
www.morrisjames.com
Richard K. Herrmann Mailing Address
(302) 888-6816 P.o. Box 2306
[email protected] January 10, 2006 Wilmington, DE 19899-2306
VIA ELECTRONIC FILING
The Honorable Joseph J. Farnan, Jr.
United States District Court
District of Delaware
844 King Street
Wilmington, DE 19801
Re: Ajjunetrzhc, Inc. v. Illumina, Inc., D. Del., C.A. N0. 04-901-JJF
Your Honor:
Illumina submits the following summary of the issues it would like to raise to the Court’s
attention at the upcoming hearing on January 12, 2006.
1. Aff@etrix’ Refusal to Produce Key Prior Art Documents
Affymetrix refuses to produce highly relevant prior art-related documents because
Illumina’s specific request for these documents "was served several months after the deadline for
document discovery imposed in the Court’s Rule 16 Scheduling Order." This is false, and in any
event a gross misreading of the Court’s Scheduling Order. Affymetrix cannot be allowed to
unilaterally shut off legitimate document discovery and shield very important evidence from
discovery.
Illumina served its third set of document requests on December 7, 2005, specifically
requesting documents relating to, inter alia, the prior art work of Dr. Andrei Mirzabekov, Dr.
Yuri Lysov, the Engelhardt Institute of Molecular Biology, Dr. Alexendar Chetverin, Dr. Fred
Kramer, the Public Health Research Institute, Dr. Radoje Drmanac, Dr. Radomir Crkvenjakov,
Dr. Robert Foote, Dr. Richard Sachleben, and the University of Tennessee. These persons or
entities represent the key sources of prior art in this case, and Illumina requested documents from
Affymetrix relating to their knowledge of and relationships with them. Illumina sent a cover
letter along with these requests noting that its previous document requests (served 11 months
ago) had generally sought this information -- e.g., Document Request No. 27 sought all
documents and things relating to the invalidity or unenforceability of the Affymetrix Patents --
but that it was serving these narrowly-tailored requests to leave no doubt that Illumina wanted
and requested these documents. Affymetrix has refused to produce any of these documents.
Affymetrix’ attempt to withhold highly relevant discovery, and then declare document
discovery over after Illumina has independently unearthed the relevant information, is without
any basis. As set forth in Illumina’s pending motion for leave to file an amended answer and
Dover (302) 678-8815 Broom Street (302) 655-2599 Newark (302) 368-4200

Case 1:04-cv-00901-JJF Document 173 Filed 01/10/2006 Page 2 of 4
Momus, JAMES, HITCHENS & WILLIAMS LLP
The Hon. Joseph J. Farnan, Jr.
January 10, 2006
Page 2
counterclaims, Illumina believes that Affymetrix possesses documents that show that Affymetrix
knew of highly material prior art without citing it to the Patent Office. All of the requested
documents were responsive to Illumina’s document requests served months ago, but Affymetrix
has not produced them. Simply because Illumina has clarified the exact scope of documents it
now wants from its prior requests should not give Affymetrix a free-pass on this discovery.
In order for Illumina to be able to use these documents in the upcoming depositions of
Affymetrix witnesses, Illumina respectfully requests that Affymetrix be ordered to produce all
documents responsive to these requests by no later than January 16, 2006.
2. Aff@etrix’ Failure To Supplement Its Validity Contentions
Illumina requests an order from the Court immediately requiring Affymetrix to
supplement its response to Illumina’s Interrogatory No. 16, which seeks Affymetrix’ contentions
as to why each of the prior art references cited by Illumina (and discussed in detail in Illumina’s
claim charts provided in response to Affymetrix’ Interrogatory No. 10) do not invalidate the
asserted claims of each patent. Illumina provided Affymetrix a supplemented response with
additional prior art claim charts nearly three months ago. Affymetrix has refused to date to
supplement its response to Interrogatory No. 16 to explain why these prior art references do not
invalidate the claims. Illumina believes that Affymetrix should either be required to supplement
its interrogatory responses immediately or be precluded from offering evidence in response to
Illumina’s invalidity contentions.
3. Illumina’s Motion for Leave To File an Amended Answer and Counterclaims
Last week Illumina filed its Motion for Leave to File an Amended Answer and
Counterclaims, seeking to add allegations for (1) inequitable conduct with respect to all six
asserted patents; (2) a violation of Section 2 of the Sherman Act based on assertion of patents
procured by fraud and other anticompetitive activity; and (3) unclean hands. Illumina has timely
` brought this motion in advance of the Court’s deadline for amending pleadings of January 15,
2006. Moreover, Illumina has pled ample facts to show the merit of these allegations -- which
relate to very serious instances of inequitable conduct and fraud on the patent office, and antitrust
violations for asserting these patents to maintain Affymetrix’ monopoly -- and it is expected that
they will form the centerpiece of Illumina’s defense in this case. Illumina does not request any
extension of discovery or the overall schedule based on this amendment, as the claims overlap in
large part with the unfair competition claims and invalidity defenses already in the case. Thus,
Illumina respectfully requests that the Court grant Illumina’s motion and allow it to file its First
Amended Answer and Counterclaims.
4. Prior Litigation Documents From OGT and Incyge Litigations
At the last status conference, the Court rejected Illumina’s request to have all pleadings
and documents produced from Affymetrix’ prior litigations with OGT and Incyte. Because this

Case 1:04-cv-00901-JJF Document 173 Filed 01/10/2006 Page 3 of 4
Momus, JAMES, HITCHENS & WILLIAMS LLP
The Hon. Joseph J. F aman, Jr.
January 10, 2006
Page 3
ruling would require Illumina to recreate and redo much discovery that has already taken place in
these prior litigations, Illumina respectfully asks that the Court reconsider this issue.
Although not its intent, the Court’s prior ruling has made the discovery process much
more, not less, burdensome on the parties. For at least one deposition -- the deposition of Ann
Pease —- Illumina will agree to drop her deposition if it is permitted discovery of her deposition
transcripts from the OGT and lncyte cases. For several other depositions, their length and
complexity will be greatly reduced if Illumina can obtain the prior deposition transcripts and not
have to re—pl0w ground that has already been covered. Moreover, there are expert reports from
these prior cases that can short circuit a significant amount of the work that will otherwise have
to be undertaken in this case.
Illumina respectfully suggests that it is not fair to allow Affymetrix to withhold very
relevant deposition testimony and documents relating to the same patent disclosures and issues
that are asserted in this case. lf the Court is concerned about the scope of this prior litigation
discovery, Illumina can narrowly tailor its request to cover only a limited number (e. g. 10) of the
prior deposition transcripts and related deposition exhibits, and identify a specific number of
pleadings or expert reports that will be produced. The Court should simply not allow Affymetrix
to completely bury this highly relevant litigation material from discovery in this case.
5. The Date By Which Illumina Must Decide On The Advice—Of-Counsel Defense
Due to Affymetrix’ continuing delays in scheduling inventor depositions, Illumina
reluctantly asks (hopefully for the last time) to move the decision on the advice—of-counsel
defense back by two weeks, to February 15, 2006. Right after the last hearing with the Court, at
which the current date of January 30, 2006 was set, Affymetrix offered Dr. Stephen Fodor for
deposition starting on January 31. Dr. Fodor is @ key witness in the case, being an inventor on
three of the six asserted patents and CEO of Affymetrix. When Illumina asked for the prior
extension of the deadline, it was with the understanding that Dr. Fodor would be deposed in
December (as noticed) or at the latest early January. Now that Affymetrix has strategically
delayed Dr. Fodor’s deposition until January 31, Illumina requests that the deadline for this
decision be moved back to allow consideration of Dr. Fodor’s and other testimony in making the
critical decision of whether to rely on the advice of counsel defense.
Illumina’s request to extend this deadline again is merely an effort to effectuate the
Court’s original reasoning in setting the deadline in the first place. The Court has previously
agreed with Illumina’s position that Illumina should not be required to make a decision about its
advice-of-counsel defense until after significant discovery regarding the patent issues
(infringement and defenses) has been completed. Moreover, the Court has also agreed with
Affymetrix that willfulness—related discovery will be permitted past the fact discovery deadline,
and there is ample time left to take this discovery prior to trial. Thus, Illumina respectfully
requests that the Court reset the deadline by which Illumina must decide on the advice—of-
counsel defense to February 15, 2006.

Case 1:04-cv-00901-JJF Document 173 Filed 01/10/2006 Page 4 of 4
Moruus, ]AMEs, H1TcHENs & WILLIAMS LLP
The Hon. Joseph J. Faman, Jr.
January 10, 2006
Page 4
6. Modest Extension of Fact Discovery Deadline
There are currently about 30 scheduled or outstanding deposition notices, and another l0
or so outstanding third party subpoenas for depositions. More importantly, Affymetrix has
strategically scheduled lllumina’s most important inventor depositions (of Dr. Stephen Fodor and
Dr. Richard Rava) and Illumina’s 30(b)(6) depositions for the final days of discovery, despite the
fact that they were noticed for much earlier in the discovery process. Affymetrix’ strategic
gambit leaves Illumina no time to conduct any follow-up discovery that may flow from these
depositions.
Given the current realities facing the parties and the Court, Illumina believes that a
modest three—week extension of the current fact discovery deadline should be granted, allowing
fact discovery until February 24, 2006. This should have no impact on the trial date of October
16, 2006, nor affect the parties’ or the Court’s preparation for the Markman hearing scheduled
for March 8, 2006. Illumina is prepared to do the hard work of completing the massive amount
of discovery remaining in the next six weeks, but believes this modest extension is appropriate
and warranted given the circumstances.
7. Scheduling an Additional Status Conference with the Court
Much progress has been made in discovery, but there is still much left to do in order for
the parties to complete fact discovery. Affymetrix has unfortunately engaged in a "run out the
clock" strategy of delaying depositions of its most important fact witnesses until the final week
or two of discovery, leaving Illumina little to no time for follow-up discovery after these
depositions. Moreover, as discussed above, Affymetrix still has not produced very material and
important documents relating to the key sources of prior art in this case. To ensure Affymetrix’
compliance with its discovery obligations, Illumina thus believes it appropriate to establish one
more discovery status conference, preferably the week of February 6, to address any issues that
may arise over the next month.
Respectfully,
¤’°¤*gLJtum`?$ °`e. A ‘ ‘°*. ,
. `i
Richard K. Herrmami, I.D. No. 405
[email protected]
cc: Dr. Peter T. Dalleo, Clerk of the Court (via electronic filing)
MaryEllen Noreika, Esq. (via electronic filing)
Michael J. Malecek, Esq. (via facsimile)