Illumina, Inc. v. Affymetrix, Inc.

I'll research this case thoroughly before drafting the overview.

Let me dig into the specific patents, the earlier related litigation, and the procedural history.

Let me verify the '243 patent's ownership/subject matter and check for IPR activity and the mandamus ruling.

Overview & Background

Parties. Both sides are life-sciences tools operating companies — not NPEs/PAEs. Illumina, Inc. (San Diego) sells sequencing and array-based genomic analysis instruments and consumables, and Affymetrix, Inc. (Santa Clara) was the pioneer of photolithographically synthesized GeneChip® microarrays. The Stanford NPE Litigation Database classifies Illumina as a "practicing entity" and records case 3:09-cv-00665 as a non-declaratory-judgment action (Stanford NPE Database). The two firms were decade-long rivals whose dispute dates to 2004, when Affymetrix sued Illumina in D. Del. (No. 04-901-JJF, Judge Joseph Farnan) on six patents; a March 13, 2007 jury verdict found infringement of five Affymetrix patents and awarded $16.7 million at a 15% royalty, and the parties settled on January 10, 2008, with Illumina paying $90 million and receiving a perpetual covenant not to sue (with a four-year covenant on future technology) (Illumina press release, Jan. 10, 2008; GenomeWeb; Law.com). The 2009 W.D. Wis. suits were a counter-offensive in which Illumina, for the first time, asserted its own array patents.

Accused technology and patents. Illumina filed 3:09-cv-00277-bbc on May 4, 2009, accusing Affymetrix's GeneChip HT Array Plate and HT Array Plate Scanner of infringing U.S. Patent 7,510,841, "Methods of Making and Using Composite Arrays for the Detection of a Plurality of Target Analytes" (issued Mar. 31, 2009), and seeking an injunction plus damages (IBO, May 5, 2009). It filed 3:09-cv-00665-bbc on Nov. 2, 2009, asserting U.S. Patent 7,612,020, "Composite Arrays Utilizing Microspheres with a Hybridization Chamber," against the GeneTitan platform, GeneAtlas, and ArrayStation and associated products; Illumina requested findings of validity/enforceability, willfulness, treble damages, and a permanent injunction (GenomeWeb, Dec. 15, 2010). Both patents are Illumina's bead-based "composite array" family (priority to Dec. 28, 1998; inventors Stuelpnagel, Chee, and Auger), claiming a first substrate with assay locations (e.g., microtiter wells) and a second substrate with discrete bead wells holding encoded microspheres bearing bioactive agents, plus decoding — the core of Illumina's BeadArray technology. Caveat on the metadata: the case metadata lists 6,646,243 as the patent at issue, but the record does not support that. The '243 patent is Affymetrix's "Nucleic Acid Reading and Analysis System" (Pirrung/Read/Fodor/Stryer; a VLSIPS-family divisional descending from U.S. 5,143,854) claiming a capillary polynucleotide analysis apparatus with argon-laser excitation (~488 nm), a CCD detector, and a data system converting fluorescence into sequence information. The '243 was one of the patents Affymetrix asserted against Illumina in the 2004 Delaware case and was reexamined at Illumina's request (reexam 90/008,889, ordered Nov. 27, 2007) (GenomeWeb, Dec. 2007). The patents actually pleaded in the consolidated W.D. Wis. actions were the '841 and the '020; the '243 attribution appears to be a database conflation with the earlier Delaware round, and I flag it rather than treat it as verified.

Procedural posture and why it matters. Both actions sat before Chief then Senior Judge Barbara B. Crabb in the Madison division of the W.D. Wis. — a famously fast "rocket docket" that Illumina openly chose for speed (Dkt. 44 venue order). Affymetrix moved to transfer to the N.D. Cal.; Judge Crabb denied it on Sept. 18, 2009, weighing the interests of justice and docket speed and finding the witness-convenience factors neutral, and the Federal Circuit denied Affymetrix's mandamus petition on April 13, 2010 (docketed at Dkt. 64 in both cases) (Justia docket). Claim construction followed on July 14, 2010 (Dkt. 80), construing "second substrate," "bioactive agents," and "discrete sites" (Justia docket). The construction of "second substrate" — adopted closer to Affymetrix's proposal, requiring a material modifiable to contain discrete sites for bead attachment — proved dispositive: because Affymetrix's arrays are made by in-situ photolithographic synthesis and do not use beads, the court granted Affymetrix's motion for summary judgment of noninfringement on Dec. 15–16, 2010 (Dkt. 222 in '277; Dkt. 178 in '665), dismissed Affymetrix's invalidity/unenforceability counterclaims without prejudice, and entered amended judgments Mar. 18, 2011 (Dkt. 239 / Dkt. 195) (GenomeWeb; Reuters, Dec. 15, 2010). The Federal Circuit affirmed on Aug. 18, 2011 in a nonprecedential Rule 36 judgment, 427 F. App'x 898 (Newman, Prost, Reyna, JJ.) (Fed. Cir. judgment). The case is notable as a non-NPE, operating-company patent war in a concentrated microarray market; as a demonstration that claim construction alone can end a biotech array case (the bead-vs-photolithography distinction); and as a venue/mandamus data point in the long-running debate over plaintiffs' ability to steer patent suits into swift districts like W.D. Wis. — a controversy later addressed in TC Heartland (2017) and the Judicial Conference's random-assignment practices. It also illustrates the durability of the Illumina–Affymetrix rivalry, which continued until Thermo Fisher acquired Affymetrix in 2016.

Sourcing notes / open items: (1) The '243 patent's connection to these docket numbers is unverified; every primary source I found ties the 2009 W.D. Wis. cases to the '841 and '020 patents only, so the metadata's '6646243' should be treated as unconfirmed pending PACER review of the complaints. (2) I could not verify any IPR or PGR proceedings on the '841 or '020 patents (my searches were truncated); AIA post-grant review postdates most of this litigation, so any IPR activity would have been later and would need separate confirmation on the PTAB docket. (3) The district-court filings are largely under seal; the descriptions of the accused products and claim-construction reasoning above come from the court's public orders and contemporaneous trade press rather than the sealed briefing.

I'll research this case systematically across the docket, opinions, and PTAB records.

Key nuance emerging: the '243 patent may be Affymetrix's patent from the separate Delaware case. Let me verify the Wisconsin docket and case 665.

Now let me pin down the '243 patent's role, the consolidation, and the claim construction/summary judgment opinions.

Threshold note on the patent at issue ('243)

Before the chronology, one record-check worth flagging, because it affects how you brief this case: the metadata lists U.S. 6,646,243 ("Nucleic acid reading and analysis system") as the patent at issue, but the docket record I found ties that patent to a different Illumina–Affymetrix litigation. The '243 patent is Affymetrix's patent, asserted by Affymetrix against Illumina in D. Del. No. 04-901-JJF (filed 2004-07-26), and it was one of four Affymetrix patents put into ex parte reexamination at Illumina's request on 2007-10-19 (Patent Docs, 2008-01-02; GenomeWeb). It was construed by Judge Farnan in Delaware on 2006-08-16 ("substrate" = "a material having a rigid or semi-rigid surface"; "target nucleic acids" = nucleic acids "deliberately exposed to" the attached nucleic acids) (Markman opinion).

The two Western District of Wisconsin cases in the metadata (3:09-cv-277 and 3:09-cv-665) were Illumina's own affirmative infringement suits on U.S. 7,510,841 and U.S. 7,612,020 — not the '243 patent. I could not find any docket entry in 277/665 pleading the '243 patent. I therefore treat the '243/reexam material as context (and as the origin of the parties' prior Delaware dispute) rather than as part of this case's merits, and I say so explicitly rather than silently asserting it was pleaded. Everything below is sourced to the docket/opinions I could retrieve.

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I. Pre-history: the Delaware action and the reexaminations (2004–2008)

This is the strategic backdrop: Illumina responded to an adverse jury verdict not with an appeal alone but with a parallel USPTO validity attack, and then opened a second front in Wisconsin on its own array-processing patents. The Delaware and Wisconsin matters were part of the same commercial war over microarray platforms.

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II. The Wisconsin litigation (2009–2011)

A. Filing and initial pleadings

• 2009-05-04/05 — Case No. 3:09-cv-277-bbc filed. Illumina sues Affymetrix in W.D. Wis. (Madison), asserting U.S. 7,510,841 ("Methods of making and using composite arrays for the detection of a plurality of target analytes," issued 2009-03-31) against the GeneChip HT Array Plate and HT Array Plate Scanner. Illumina seeks an injunction and unspecified damages (docket; IBO, 2009-05-05). Note the timing: the '841 patent issued barely a month before suit.
• 2009-06-09 — Affymetrix files its memorandum in support of a motion to transfer venue to the Northern District of California (D.I. 12). (Affymetrix's answer and counterclaims, and Illumina's rule 12 response, are not individually verified from the docket text I retrieved; by later filings Affymetrix was asserting invalidity and unenforceability counterclaims, which the court ultimately dismissed without prejudice.)
• 2009-11-02 — Case No. 3:09-cv-665-bbc filed. Illumina's second W.D. Wis. suit, asserting U.S. 7,612,020 against Affymetrix's GeneTitan system (FTC filing citing "No. 3:09-cv-00665 (W.D. Wis. filed Nov. 2, 2009)"; Stanford NPE database). The two cases were treated together (the Federal Circuit later described them as "consolidated Case Nos. 09-CV-0277 and 09-CV-0665"); docket entries after 2010 routinely issue in both numbers.
• 2009-12-07 — Joint Preliminary Pretrial Report filed.

B. Pre-trial motions of substance

1. Venue / transfer — denied, then mandamus denied. Judge Barbara B. Crabb denied Affymetrix's transfer motion on 2009-09-18 (docketed 2009-09-21, D.I. 44). The opinion held the convenience factors were largely neutral (employee and even third-party witnesses would appear voluntarily; the GeneTitan could be shipped or shown by video) and that the "interests of justice" — specifically W.D. Wis.'s docket speed — weighed "determinatively" in favor of retaining the case (D.I. 44). Affymetrix petitioned the Federal Circuit for a writ of mandamus; denied 2010-04-13 and docketed in both Wisconsin cases on 2010-04-16 (D.I. 64).
2. Claim construction motions — granted 2010-05-07 (D.I. 73), setting the Markman hearing for 2010-06-04.
3. Leave to amend (inventorship defense). Affymetrix moved for leave to amend on 2010-07-20 to add an inventorship-based attack: Affymetrix contended that a person named Kirk was the true inventor of the '841/'020 subject matter (via a Kirk email), which would undercut Illumina's title/standing. Illumina moved for reconsideration of the leave-to-amend order (2010-08-30); Affymetrix opposed (2010-08-31); the court denied reconsideration on 2010-09-02.
4. Jurisdictional motion to dismiss. Affymetrix moved to dismiss for lack of jurisdiction on 2010-09-17 (standing/inventorship theory). Briefing ran through October; the court ordered supplemental briefing on 2010-10-28/29 (D.I. 192), with responses due 11/8 and 11/10/2010.
5. Cross-motions for summary judgment (both filed 2010-09-17). Affymetrix moved for summary judgment of noninfringement; Illumina moved for partial summary judgment. Affymetrix also moved to strike the expert report of Cameron Weiffenbach (2010-09-14) and to extend the deposition of Dr. Milan Mrksich (2010-09-03). Expert reports (Mrksich on infringement/validity) were served in early September 2010.
6. No stay pending IPR was sought or granted — not surprising, since IPR did not exist until the AIA's 2012-09-16 effective date and the USPTO challenges here were ex parte reexaminations.

C. Claim construction (Markman)

• Hearing: 2010-06-04.
• Order: 2010-07-14 (D.I. 80), construing "second substrate," "bioactive agents," and "discrete sites." Critically, the court construed "substrate" as "a material that can be modified to contain discrete individual sites appropriate for the attachment or association of beads and is amenable to at least one detection method" — language lifted verbatim from the '841 specification (col. 7, ll. 32–36) (SJ opinion, Dkt. 221, at 4-5).
• Strategic effect: the bead-centric construction effectively decided the case. It is undisputed that Affymetrix's accused microarrays are made by photolithographic in situ synthesis on glass wafers and use no beads. Illumina's own contemporaneous/analyst commentary recognized that the court had rejected Illumina's narrower reading of the claims and predicted the noninfringement outcome. See also the Duke/UMKC case studies describing the court as adopting "Affymetrix's relatively narrow construction" and holding the accused technology outside the claims.

D. Discovery milestones with strategic significance

• 2009-07-02 — Illumina's first interrogatories (Nos. 1–8) and first RFPs (Nos. 1–53) served on Affymetrix; 2009-07-13 — first set of RFAs (Nos. 1–196); 2009-07-14 — second set of RFAs (Nos. 197–228). The volume of admission requests signals an early push for element-by-element infringement admissions.
• 2009-07-22 — Affymetrix motion for protective order (early discovery-scope fight).
• 2009-07-31/2009-08-03 — Initial disclosures and Affymetrix's responses to interrogatories and RFPs.
• 2010-02-10 — Illumina's first RFPs (Nos. 1–47) in the '665 case (GeneTitan discovery, a separate products/systems inquiry).
• 2010-04-30 — Illumina's responses to Affymetrix's second interrogatory set (Nos. 9–16).
• 2010-06/07/08 — Repeated supplemental interrogatory responses by Affymetrix, and 2010-09-15 supplemental responses by Illumina — consistent with claim construction and infringement-contentions shifting mid-discovery.
• 2010-09-03/09-14/09-16 — Expert discovery battles: motion to extend the Mrksich deposition (with a declaration of Affymetrix's Roger J. Chin on expenses incurred), and Affymetrix's motion to strike the Weiffenbach report.
• Inventorship discovery (the Kirk/Augur conception dispute) was the central factual battleground: Illumina argued Augur conceived the '841/'020 inventions before Kirk's email, defeating a decision on inventorship as a matter of law (Dkt. 221).

E. Dispositive ruling; no trial

• 2010-12-14 — Opinion, D.I. 221 (Judge Crabb). Summary judgment of noninfringement for Affymetrix. Key holdings:
  • Standing: Illumina's standing "remains intact until the patent has been corrected," so there was no jurisdictional bar to reaching the merits — the court rejected Affymetrix's Rule 12(b)(1) theory.
  • Inventorship/§ 256: the court declined to decide inventorship, noting Affymetrix "did not raise a separate counterclaim under § 256 for correction of the patents," and observed Affymetrix and Kirk could bring a standalone § 256 case.
  • Infringement: with "substrate" construed to require bead-compatible discrete sites, and it being "undisputed that the accused products … do not use beads," no reasonable jury could find literal or equivalent infringement.
  • The court expressly declined to reach the "thorny questions about inventorship or the other invalidity defenses."
  • Claims asserted: '841 — claim 1 and claims 2-3, 8, 10, 13-21, 24-26; '020 — claims 1, 20, 36, 51, 64 and numerous dependents.
  • No justiciable controversy in validity remained once all claims were dismissed for noninfringement.
• 2010-12-16 — Judgment entered, D.I. 222, in favor of Affymetrix; counterclaims for invalidity dismissed without prejudice (judgment PDF). Reuters reported the ruling on 2010-12-15 (Reuters).
• 2011-03-18 — Amended Judgment, D.I. 239, granting Affymetrix's summary judgment motion on noninfringement and dismissing "its claims for invalidity and unenforceability without prejudice." The amendment broadened the dismissed counterclaims to include unenforceability. No JMOL, new-trial, or fee motion is reflected in the docket as the operative disposition.
• No trial and no verdict. Both asserted patents were resolved on paper — an unusual outcome for a patent case litigated this hard (RFA sets of 200+, expert strikes, five motions filed on a single day, 2010-09-17).

F. Appeal and final disposition

• 2011-08-18 — Federal Circuit Nos. 2011-1145, -1146: AFFIRMED under Fed. Cir. R. 36 (unpublished; reported at 427 F. App'x 898). Per curiam (Newman, Prost, Reyna) (opinion text). Judgment issued 2011-08-22.
• Counsel of record on appeal (verified): for Illumina — Gregory A. Castanias, Jones Day (argued); Jeffrey N. Costakos and Kimberly K. Dodd, Foley & Lardner (Milwaukee); George E. Quillin. For Affymetrix — Richard P. Bress, Latham & Watkins (argued); Roger J. Chin (Latham), Ron E. Shulman; of counsel Thomas T. Carmack, Wilson Sonsini.
• 2011-08-19 — Affymetrix announces the affirmance, quoting GC Rick Runkel (Benzinga; News-Medical). Affymetrix characterized the result as affirmance of "dismissal of the patent infringement lawsuits … regarding U.S. Patent Nos. 7,510,841 and 7,612,020."
• Posture: Case 3:09-cv-00665 is recorded as closed 2011-05-11 in one aggregator database (AI Lab case page); the practical final disposition is judgment for Affymetrix on noninfringement, affirmed, with Affymetrix's invalidity and unenforceability counterclaims dismissed without prejudice (i.e., unadjudicated). To the extent the case summary describes this as "settled/dismissed," the record I found shows a merits judgment plus Rule 36 affirmance, not a settlement. The dismissal component is limited to the without-prejudice dismissal of Affymetrix's counterclaims.

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III. Parallel USPTO proceedings

• No PTAB IPR/PGR proceedings on the asserted '841/'020 patents appear in the record; the IPR regime postdates the relevant events (available only for petitions filed on/after 2012-09-16), and I found no later IPR/PGR filings on either patent.
• Ex parte reexaminations (pre-AIA) were the operative USPTO track, and they attached to the Delaware patents, not the Wisconsin patents:
  • 90/008,889 — U.S. 6,646,243 (the patent identified in the metadata), requested 2007-10-19 by Illumina, ordered 2007-12-21.
  • 90/008,885 ('432), 90/008,888 ('531), 90/008,886 ('716), with a fifth request on '365 awaiting decision as of late 2007.
  • Effect on the litigation: the reexaminations were Illumina's principal counterweight to the 2007 Delaware verdict and, together with the second Wisconsin suit over GeneTitan, converted a single infringement case into a multi-front war. The Wisconsin cases did not turn on these reexams, because the asserted Wisconsin patents were different and were resolved on noninfringement rather than validity.
• Foreign parallel: the record references a Technical Board of Appeal 3.3.04 decision of 2009-06-26 (T 0384/08-3304) and an Opposition Brief filed 2010-03-31 against European Patent No. 1 593 967, both cited in the '841/'020 litigation papers — i.e., the parties were simultaneously fighting European oppositions over counterpart subject matter, and the European outcome was fed into the U.S. record.

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IV. One-page chronology

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V. Gaps and things I could not verify

1. The '243 patent's presence in the Wisconsin cases — I found no docket entry pleading it. If your engagement requires that linkage, it should be confirmed against the actual 277/665 dockets in PACER, because the metadata's patent list appears to conflate this case with the Delaware 04-901-JJF action.
2. Exact dates/extent of Affymetrix's original answer and counterclaims in 277, and the precise consolidation order date (the Federal Circuit treats the cases as consolidated; the district docket entries caption both).
3. Docket items I only saw indirectly (e.g., the 2010-11-10 and 2011-03-08 documents referenced in patent specifications/press materials) — file dates are stated in secondary sources, not confirmed docket text.
4. Whether the broader Illumina–Affymetrix dispute was later resolved globally (e.g., a cross-license) — I found no sourced confirmation, so I make no assertion.
5. Fee motions / bill of costs — none appeared in the docket excerpts retrieved; absent confirmation, treat the amended judgment as the terminal district-court event.

I'll research the counsel of record for Illumina in this case.

Good start — I have the Federal Circuit panel. Now let me find the district court docket and counsel of record.

Let me pull the actual docket sheets and attorney appearance lists.

Counsel of Record for the Plaintiff — Illumina, Inc.

Note on scope/verification: I was able to verify Illumina's appellate and trial-team counsel from the Federal Circuit opinion, the Federal Circuit docket, and W.D. Wis. filings referenced in the record. I could not fully retrieve the PACER attorney-appearance list (the "ATTY TO BE NOTICED / LEAD ATTORNEY" entries) for either docket before hitting my research limit, so the list below may not be exhaustive of every pro hac vice entrant. Everything below is sourced; where I can't source it, I say so.

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Verified counsel for Illumina, Inc.

1. Gregory A. Castanias — Jones Day (Washington, D.C.) — Lead appellate counsel; argued the appeal

• Per the Federal Circuit's opinion: "Gregory A. Castanias, Jones Day, of Washington, DC, argued for plaintiff-appellant." Illumina, Inc. v. Affymetrix, Inc., 427 F. App'x 898 (Fed. Cir. 2011) (Nos. 2011-1145, -1146).
• Source: https://cafc.uscourts.gov/opinions-orders/11-1145-1146.pdf
• Experience note: A career patent appellate specialist (Jones Day IP Appellate & Supreme Court practice, D.C.); he was the Jones Day partner who argued Illumina's appeal, which the Federal Circuit affirmed in a nonprecedential per curiam decision on claim construction/noninfringement.
• Caveat: His appearance is documented at the Federal Circuit; I did not verify a district-court pro hac vice appearance for him in W.D. Wis.

2. Jeffrey N. Costakos — Foley & Lardner LLP (Milwaukee, WI) — Trial/lead counsel; of counsel on the appeal brief

• Listed as "of counsel on the brief" for plaintiff-appellant, Foley & Lardner LLP, Milwaukee, WI (427 F. App'x 898; CourtListener attorney listing: https://www.courtlistener.com/opinion/[8465976](/patent/8465976)/illumina-inc-v-affymetrix-inc/).
• Experience note: Foley IP litigation partner in the firm's Milwaukee office; the Milwaukee team (Foley) was Illumina's principal trial-side patent litigation group in this consolidated W.D. Wis. matter.

3. Kimberly K. Dodd — Foley & Lardner LLP (Milwaukee, WI) — District court counsel of record; of counsel on the appeal brief

• Two independent confirmations:
  1. Federal Circuit: "Of counsel on the brief were Jeffrey N. Costakos and Kimberly K. Dodd, Foley & Lardner LLP, of Milwaukee, Wisconsin."
  2. District court filing: the record lists a "Declaration of Kimberly K. Dodd in opposition to Affymetrix's Motion to Dismiss for Lack of Jurisdiction" in Illumina, Inc. v. Affymetrix, Inc., No. 09-cv-277-bbc (W.D. Wis. 2010). See patent-reference listing, e.g., https://patentimages.storage.googleapis.com/68/7f/ac/98db057e3b2863/[US7901897](/patent/US7901897).pdf
• The Justia docket page for the consolidated 3:09-cv-00665 case also shows "Represented By: Kimberly Kristin Dodd" (https://dockets.justia.com/docket/wisconsin/wiwdc/3:2009cv00665/26590).
• Firm profile (https://www.foley.com/people/dodd-kimberly-k/): partner, IP Litigation and Trademark/Copyright & Advertising practices, Milwaukee office; admitted in Wisconsin, California, and before the USPTO; J.D., Univ. of Wisconsin (2003); B.S. in bacteriology/genetics — relevant to the microarray/genomics subject matter. Has tried cases in the W.D. Wis., N.D. Cal., E.D. Cal., E.D. Tex., D. Del., N.D. Ill., S.D. Fla., the ITC, and Wisconsin state courts; first- and second-chair experience.

4. George E. Quillin — Foley & Lardner LLP (Washington, D.C. office) — Of counsel on the appeal brief

• Federal Circuit: "George E. Quillin, of Washington, DC" listed as of counsel for plaintiff-appellant; CourtListener's attorney block attributes him to Foley & Lardner LLP.
• Experience note: Foley's Washington, D.C. IP litigation group; supported the appellate briefing.

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Party / case posture (for context and correction)

• The consolidated cases were Illumina's infringement suits, not a declaratory-judgment action. Docket: 3:09-cv-00277-bbc, filed May 4, 2009 (asserting U.S. Pat. No. 7,510,841), and 3:09-cv-00665-bbc, filed Nov. 2, 2009 (asserting U.S. Pat. No. 7,612,020). They were consolidated before Judge Barbara B. Crabb. (https://dockets.justia.com/docket/wisconsin/wiwdc/3:2009cv00277/22297 ; https://dockets.justia.com/docket/wisconsin/wiwdc/3:2009cv00665/26590)
• Rulings: the court denied Affymetrix's motion to transfer to N.D. Cal. (Dkt. 44, Sept. 18/21, 2009); claim construction order July 14, 2010 (Dkt. 80); summary judgment of noninfringement for Affymetrix, judgment entered Dec. 16, 2010 (Dkt. 222), amended judgment Mar. 18, 2011 (Dkt. 239); Federal Circuit affirmed Aug. 18, 2011; case closed May 11, 2011.
• U.S. Pat. No. 6,646,243: I could not verify that the '243 patent was pleaded in either W.D. Wis. complaint. Every record source I found for these two dockets identifies only the '841 and '020 patents. I flag this because your case metadata already notes it is unverified — the public record I retrieved does not support the '243 being at issue here.

Defendant's counsel (for contrast / completeness)

From the same Federal Circuit opinion: Richard P. Bress, Latham & Watkins LLP (Washington, D.C.) argued for Affymetrix; on the brief were Roger J. Chin, Latham & Watkins (San Francisco) and Ron E. Shulman (Menlo Park, CA); of counsel Thomas T. Carmack, Wilson Sonsini Goodrich & Rosati (Palo Alto, CA). Roger J. Chin also filed declarations in the district court (Dkt. entry, Sept. 16, 2010).

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Gaps and things I could NOT verify (stated explicitly, per instruction not to invent)

1. Full W.D. Wis. appearance list. I did not retrieve the complete PACER attorney list; additional local/pro hac vice counsel may have appeared without surfacing in my sources.
2. Justin Edwin Gray. The Justia docket page for 3:09-cv-00277 shows a "Represented By: Justin Edwin Gray" entry, but I could not confirm which party he represented or his firm. Treat as unverified.
3. Local counsel. W.D. Wis. practice often involves a local-counsel firm; I found no confirmation of an additional local firm beyond Foley & Lardner's Milwaukee team.
4. In-house counsel. No Illumina in-house attorney is named in the public filings I retrieved. Statements about Illumina legal-department personnel (e.g., a chief legal officer) are from unrelated, later matters and should not be attributed to this case.
5. Sealed material. Several Illumina filings in this case were filed under seal (e.g., "Illumina's Motion to File Under Seal," Sept. 10, 2010; redacted briefs), so appearance/role information could be partially obscured.

I'll research the counsel of record for Affymetrix in this consolidated case. Let me search multiple sources.

The Federal Circuit opinion gives me a strong lead. Let me dig into the docket and local counsel.

Excellent leads. Now let me pin down the Wisconsin local counsel and confirm the district-court team via the docket.

I hit the research step limit, so here is my analysis based on what I was able to verify. I'll flag clearly where a fact is confirmed versus inferred.

Counsel of Record — Defendant Affymetrix, Inc.

Illumina, Inc. v. Affymetrix, Inc., Nos. 3:09-cv-00277-bbc & 3:09-cv-00665-bbc (W.D. Wis.) (consolidated)

Important caveat up front

The consolidated W.D. Wis. docket is not fully available through free sources, and there is no complete PACER docket sheet transcription I could retrieve for the district-court appearances. The most authoritative counsel-of-record listing I located is the Federal Circuit opinion on appeal, which lists appellate counsel, plus firm-move press coverage that confirms who ran the district-court defense. I could not independently verify the name of Affymetrix's Wisconsin local counsel on the 2009–2010 district docket (see below). I have not invented any names to fill that gap.

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A. Lead defense / appellate counsel (verified)

Ron E. Shulman — Lead counsel (district court defense team); named on Federal Circuit brief

• Firm: Wilson Sonsini Goodrich & Rosati, Palo Alto / Menlo Park, CA (at the time of this litigation). Shulman later moved to Latham & Watkins (Menlo Park).
• Note: Tried the defense that produced summary judgment of non-infringement for Affymetrix; a Wilson Sonsini IP group that included Shulman was recruited by Latham & Watkins, and press coverage credited that team with "secur[ing] summary judgment for Affymetrix Inc. in a patent infringement case brought by Illumina Inc. over DNA microarrays in the U.S. District Court for the Western District of Wisconsin." Source: Latham & Watkins media coverage, "Latham Nets Wilson Sonsini IP Group," lw.com.
• Citation: Illumina, Inc. v. Affymetrix, Inc., 427 F. App'x 898 (Fed. Cir. 2011) (Nos. 2011-1145, 2011-1146) — brief listed "Ron E. Shulman, of Menlo Park, California."

Roger J. Chin — Core defense team member; named on Federal Circuit brief

• Firm: Wilson Sonsini Goodrich & Rosati, San Francisco, CA (during the district-court case); later Latham & Watkins, San Francisco.
• Note: Filed at least one substantive declaration in the district case — "Declaration of Roger J. Chin Setting Forth Affymetrix's Expenses" (Sept. 16, 2010), 09-cv-277-bbc — confirming his hands-on role in the W.D. Wis. proceeding. Longtime Illumina-adjacent patent litigator (later involved in Cornell v. Illumina).
• Citation: 427 F. App'x 898; Latham media coverage (lw.com).

Richard P. Bress — Appellate lead counsel (argued the Federal Circuit appeal)

• Firm: Latham & Watkins LLP, Washington, D.C.
• Note: Presented oral argument for Affymetrix on appeal; prominent appellate/patent advocate. He appears on the appeal, not (per available records) on the 2009 trial-court pleadings.
• Citation: Illumina, Inc. v. Affymetrix, Inc., 427 F. App'x 898 (Fed. Cir. 2011) ("Richard P. Bress, Latham & Watkins, LLP, of Washington, DC, argued for defendant-appellee"). URL: cafc.uscourts.gov/opinions-orders/11-1145-1146.pdf.

Thomas T. Carmack — Of counsel (appellate brief)

• Firm: Wilson Sonsini Goodrich & Rosati, Palo Alto, CA.
• Note: Listed as "Of counsel" on the Federal Circuit brief; Wilson Sonsini is the same firm that ran Affymetrix's district-court defense.
• Citation: 427 F. App'x 898.

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B. Wisconsin local counsel (probable, NOT fully verified for this docket)

James R. Troupis — Likely local counsel (role confirmed in the related follow-on action, not confirmed on this docket)

• Firm: Troupis Law Office LLC, Middleton, Wisconsin.
• Note: Signed as Wisconsin counsel for Affymetrix, Inc. (and Gregory L. Kirk) alongside Shulman and Chin in the closely related follow-on action Affymetrix, Inc. v. Illumina, Inc. (W.D. Wis., filed 2011). Because the same Wilson Sonsini defense team appears in both matters, Troupis is the most likely Wisconsin counsel for the 2009–2010 consolidated case as well — but I could not confirm his appearance on the 09-cv-277/665 docket specifically. Treat this as probable, not established.
• Source: Affymetrix, Inc. v. Illumina, Inc. filing (Mar. 14, 2011), patentdocs.typepad.com/files/affymetrix-v-illumina.pdf ("/s/ James R. Troupis, Troupis Law Office LLC … Ron E. Shulman … Roger J. Chin, Wilson Sonsini Goodrich & Rosati … Attorneys for Plaintiffs Affymetrix, Inc. and Gregory L. Kirk").

Open item: I was not able to verify whether a different Wisconsin firm (e.g., a Madison-based firm) served as Affymetrix's local counsel during 2009–2010. This should be confirmed against the actual PACER docket sheet / the ECF "attorney to be noticed" entries for 3:09-cv-00277-bbc.

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C. In-house counsel (verified via public reporting)

Richard "Rick" Runkel — In-house (client-side)

• Role: Executive Vice President, General Counsel & Secretary, Affymetrix, Inc.
• Note: Publicly quoted as the company's GC on the outcome of this litigation ("confirms our position that Illumina's lawsuits were without merit"). In-house attorneys typically do not enter an appearance of record, so he would not appear on the docket.
• Source: GenomeWeb / Genome Technology, "Cases Closed: Wisconsin Court Dismisses Two Illumina IP Suits Against Affymetrix" (Dec. 15, 2010), genomeweb.com.

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D. Explicitly excluded — not defense counsel

Christian G. Cabou — A "Declaration of Christian G. Cabou" appears in the 09-cv-277 record (cited in the court's Sept. 18, 2009 venue opinion at dkt. #19). Cabou was Illumina's Senior Vice President, General Counsel & Secretary from 2006–2013 — i.e., plaintiff-side in-house counsel, not Affymetrix's. Do not attribute him to the defendant. (Sources: MarketScreener/Zonebourse executive profiles for Illumina; Illumina SEC filings signed by Cabou as GC.)

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Summary table

If you need the definitive district-court "attorney to be noticed" list, the next step is to pull the PACER docket for 3:09-cv-00277-bbc (Dkt. #1 appearances and the Answer/Counterclaim signature blocks) — that is the one source I could not fully retrieve within the research window.