Free Letter - District Court of Delaware - Delaware

Case 1 :04-cv-00901-JJF Document 401 Filed O3/O2/2007 Page 1 of 4
l\/Iomus , N 1oHoLs , ARSHT & TUNNELL LLP
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MARYELLEN Noruzrxa
302 351 9278
302 425 3011 Fax
[email protected] M3fQh 2:
BY E-FILING & BY HAND
The Honorable Joseph J. Faman, Jr.
United States District Court
844 King Street
Wilmington, DE 19801
Re: Affmgetrix, Inc. v. lllmnina Inc., C.A. No. 04—CV—901 JJF
Dear Judge Faman:
As directed by the Court at the Pretrial Conference, attached are the Illumina
slides to which Affymetrix objects. While there are a number of slides, Affymetrix’s objections
can be grouped by issue, and some of the issues may be resolved in connection with the Court’s
rulings on the motions in limine currently pending.
1. Demonstratives Improperly Construing Claims Before The Jg
Affymetrix objects to Illumina’s slides nos. 3, 5, 6, 9,17, 18, 21, 22, 23, 24, 25,
28, 29, 33, 40, 41, 42, 43, 47, 72, 73, 74, 75, 81, 82, 84, 85, 88, 89, 92, 102, 104 on the basis that
they put claim construction arguments in front of the jury. For example:
Slide 47 — Illumina purports to construe the Court’s construction of the term
substrate. It highlights the words "a" and "surface" in the Court’s defmition to
argue to the jury that the substrate is limited to a single surface — a position the
Court rejected during claim construction.
Slide 3 — Illumina includes the Court’s construction for one of the terms (in
yellow) and then argues a construction of two other terms (one in pink and one in
green). lllumina’s slide nos. 21, 22, 23, 24, 25, 40, 88 are similar.

Case 1 :04-cv-00901-JJF Document 401 Filed O3/O2/2007 Page 2 of 4
The Honorable Joseph J. Farnan
March 2, 2007
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Slide 6 — Illumina presents snippets from the file wrapper to argue that the patent
does not cover enzyme-based assays or tags, notwithstanding the lack of any such
limiting language in the claims.
Slide 9 — Illumina asserts that the term "biological chip plate" in the preamble is a
limitation and defines it for the jury.
Slide 29 — Illumina purports to present the jury with a slide from Ai`fymetrix’s
Markman presentation entitled "Deposition of Arrays Defined By Affymetrix."
Slide 74 — Illumina compares two claims of the ‘7l6 patent, ptuportedly making a
claim differentiation argument to the jury.
Slide 84 — Illtunina quotes from a declaration by Affymetrix’s validity expert,
Robin Felder" to argue what "attaching" means in the ‘5 31 patent.
Illumina’s attempts to construe the claims in front of the jury and its constructions of the Court’s
. constructions is addressed in Affymetrix’s motion in limine no. 7.
2. Demonstratives Improperly Referring to Prior Art
Affymetrix objects to Illumina’s slide nos. 15, 16, 49, 50, 84, 85, 119, 120 and
165 to the extent they reference prior art. Slides 49, 50, 81 and 82 in Illumina’s "infringement"
slides include figures taken from prior art references. Slides 119 and 120 are time lines that
include references to technology prior to Af`fymetrix’s priority application. This issue is
addressed in Affymetrix’s motion in limine no. 1.
Slide 120 is also objectionable to the extent it suggests that Illumina carmot
infringe because the application that issued as the ‘243 patent was filed after Illumina latmched
its products. Affymetrix is entitled to the priority date of its earlier application and thus, that
whether the application that ultimately issued was filed before or after Illumina began selling its
products is irrelevant.
3. Demonstratives Cutting Off Damages Prior To 2006.
Affymetrix objects to Illumina’s damages demonstrative slides (including nos.
126, 196, 215, 217, 219, 221, 222, 241, 242 and 243), which portray to the jury Illumina’s
damages calculations only through November of 2005 and omit damages for 2006. This issue is
the subject of March 1, 2007 correspondence with the Court.
4. Demonstratives Containing Information
Not Produced In Discovery
Affymetrix objects to Illumina’s demonstrative slides nos. 14, 30, 48 and 63, all
of which appear to portray a bead floating in well. Illumina produced no discovery supporting

Case 1 :04-cv-00901-JJF Document 401 Filed O3/O2/2007 Page 3 of 4
The Honorable Joseph J. Farnan
March 2, 2007
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its current theory that the beads "float" in wells. Instead, its expert Dr. Lusis simply opined at
his deposition that he was told that by an Illumina employee. Affymetrix has had no ability to
take discovery on this issue and would be prejudiced if the slides were to be shown to the jury.
Similarly, Affymetrix objects to Illumina’s demonstratives 11, 12, 13, 129, 130,
150-156 and 200, all of which refer to purported "design alternatives" which were not disclosed
during discovery. This issue is the subject of Affymetrix’s motion in limine no. 6.
5. Arggentative Demonstratives
Affymetrix has objected to Illumina’s slide nos. 1, 2, 4, 5, 6, 7, 10, 14, 15, 16, 17,
18, 19, 20, 28, 31, 32, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 75, 72, 73, 78, 79, 80, 81,
82, 83, 89, 90, 91, 92, 93, 113, 115, 116, 117, 118 and various of IllLunina’s damages slides to
the extent they are argumentative. For example:
Slide 4 — This slide is entitled "Illumina’s Assays and GenCall Are Substantially
Different From ‘71 6 Patent Claims" and goes on to characterize the ‘71 6 patent as
inter alia resulting in "inaccurate base ca1ls.”
Slide 89 — This slide is argues "The Accused Spatial Location "Map" Is Not A
Property Of The Bead." (A position directly contrary to the Court’s
memorandum opinion.)
Slides 90-91 — These slides argue that "Illumina’s Beads Have No ‘Encoding
System’ Separate F rom The Binding Polymer."
Slide 92 — This slide argues that ‘432 Patent Claims 2 and 9 Not Infringed
Because No ‘Encoding System."’
Consistent with the Court’s Trial Management Order, Affymetrix asked Illtunina to agree not to
use argumentative slides in opening. Illumina declined to agree.
6. Other Issues
Affymetrix objects to Illumina’s demonstrative nos. 133, 134, 138, 140, 141, 144,
145 and 146 to the extent they refer to "I1lumina‘s Patents" and its independent development of
its arrays. This issue is addressed in Affymetrix’s motion in limine no. 3.
Affymetrix objects to Illumina’s demonstrative nos. 12 and 46 as unduly
prejudicial. Slide no. 12 purports to show a non-covalent attachment of an oligonucleotide to a
bead in solution. The bead is not on an array and is not the type of beads on products accused of
infringement in this case. Slide no. 46 similarly refers to beads that are not in an array.
Affymetrix objects to Illumina’s demonstrative nos. 182, 183, 231, 232 and 233,
which include hearsay statements from third parties. Three of the slides including statements

Case 1 :04-cv-00901-JJF Document 401 Filed O3/O2/2007 Page 4 of 4
The Honorable Joseph J. Faman
March 2, 2007
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from parties during license negotiations and are the subject of Affymetrix’s motion in limine no.
5(c).
Affymetrix objects to IllLunina’s demonstrative no. 204, which contains one
sentence from a deposition devoid of the question and the remaining part of the answer.
Affymetrix requests that Illtunina include the question and entire answer to put the sentence into
context.
Affymetrix objects to Illumina’s demonstrative nos. 58 through 64 on the grounds
of relevance and prejudice. Slides 58 and 64 address making "in situ” arrays (like some of
Affymetrix’s arrays) and the slides in between appear to be part of a comparison of lllumina’s
arrays with "in situ” arrays. The patents, however, are not limited "in situ” arrays and thus such
a comparison is inappropriate and irrelevant. This issue is addressed to some extent in
Affymetrix’s motion in limine no. 2.
Finally, one additional issue Affymetrix would like to address with the Court is
disclosure of Illumina’s actual witness list. Affymetrix provided its list of witnesses (three fact
witnesses and three experts) last night at 5 p.m. Prior to the Court’s determination that trial
would last five days, the parties had agreed that lllumina would provide its witness list on
Sunday March 4 based on the expectation that Illumina’s witnesses would not testify until the
end of the week or the beginning of the following week. In light of the trial time, Illumina’s
witnesses will testify earlier than that. Affymetrix has asked lllumina to move its disclosure up
one day in order to facilitate our preparation of cross examinations. lllumina has refused.
lllumina has currently listed 17 live witnesses for trial, l0 of whom are potentially relevant to
infringement and damages issues. Affymetrix should not be put to the task of unnecessarily
preparing to cross all of those witnesses when Illtunina knows who it will be calling. Thus,
Affymetrix requests some assistance from the Court.
Respectfully,
f j { x 3
°Maryellé;iNore1ka (#3208)
Enclosures
cc: Dr. Peter T. Dalleo, Clerk O3y electronic filing)
Richard K. Herrmarm, Esquire (By Hand and electronic tiling)
Marcus E. Semel, Esquire (By email)
I Affymetrix received the Court’s trial management Order shortly before sending the email. We are
checking with our client regarding the witness list.