Affymetrix, Inc. v. Synteni, Inc. et al.

I'll research this case to verify the details before drafting the overview.

I have strong primary-source material. Let me verify patent titles, the judge, the transfer opinion citation, and the Markman ruling.

Case Overview and Background

The parties and what they do. This was a clash between two publicly traded, revenue-generating Silicon Valley life-science operating companies — not an NPE/PAE assertion, and not a university suit, though a university license sits at the center of it. Plaintiff Affymetrix, Inc. (Nasdaq: AFFX; Santa Clara, CA) was the pioneer of photolithographic, in-situ-synthesized DNA microarrays sold as "GeneChip" systems, having been spun out of Affymax and built on the VLSIPS™ (Very Large Scale Immobilized Polymer Synthesis) chemistry developed by Stephen Fodor and colleagues. Defendant Synteni, Inc. (Fremont/Palo Alto, CA) was a privately held array company incorporated in 1994 by Dari Shalon, who developed the "GEM" (Gene Expression Micro-Array) spotted-array technology while a post-doc in Stanford professor Patrick Brown's lab; Synteni held the exclusive worldwide right from Stanford University to commercialize it. Incyte Pharmaceuticals, Inc. (later Incyte Genomics; Palo Alto, CA) was the genomics/database company that acquired Synteni in January 1998 for roughly $80 million and thereafter marketed the accused GEM arrays and array-based gene-expression services (see Science, "Companies Battle Over Technology That's Free on the Web," Science 286:5439 (1999), and Incyte's SEC 10-Q/8-K disclosures).

The accused technology and the patents. Affymetrix alleged that Synteni and Incyte infringed by making, using, selling and offering high-density arrays — i.e., the GEM/LifeArray spotted cDNA arrays — and, separately, by using two-color fluorescent labeling to conduct gene-expression monitoring on those arrays. Three Affymetrix patents were asserted in the transferred Delaware actions: (1) U.S. 5,445,934, "Array of oligonucleotides on a solid substrate" (Fodor et al., issued Aug. 29, 1995) — claims to a substrate bearing a high-density array of distinct oligonucleotides at known locations, the core VLSIPS array claim; (2) U.S. 5,744,305, "Arrays of materials attached to a substrate" (Fodor et al., issued Apr. 28, 1998) — claims reciting a planar, non-porous support with >400 different oligonucleotides/cm², i.e., the density-based array claim; and (3) U.S. 5,800,992, "Method of detecting nucleic acids" (Fodor, Solas & Dower, issued Sept. 1, 1998) — claims to detecting two or more differentially labeled nucleic-acid collections on an array, i.e., the two-color differential-expression method claim. Affymetrix's original January 1998 Delaware complaint pleaded the '934 patent and willful infringement with treble-damages and attorney-fees demands; a second September 1998 Delaware complaint added the '305 and '992 patents and sought a preliminary injunction against Incyte/Synteni's GEM two-color expression monitoring. The related caption C 01-20065 JF later added Incyte's RNA-amplification patents (U.S. 5,716,785 and 5,891,636) and Affymetrix's U.S. 5,871,928 and 6,040,193, so the disputes ran in both directions. (Sources: Incyte Form 8-K dated Dec. 21, 2001; Incyte 10-Q; the Dec. 21, 2001 Settlement Agreement filed as an exhibit and reproduced at Law Insider.)

Procedural posture and why venue mattered. Affymetrix filed in the District of Delaware on January 6, 1998, and sued Synteni and Incyte there. Neither side had any Delaware presence — no facilities, personnel, manufacturing, documents or bank accounts — and all three companies, all six named inventors and virtually all trial witnesses and laboratory notebooks were in the Northern District of California. In November 1998 the Delaware court granted defendants' § 1404(a) motion and transferred the cases to the N.D. Cal., where they were docketed as C 99-21164 JF (the '934 action) and C 99-21165 JF (the '305/'992 action); the "JF" suffix indicates assignment to Judge Jeremy Fogel in the San Jose Division (I could not confirm the judge assignment from a primary docket record, so treat that as inferred from the case-number initials). The transfer ruling, Affymetrix, Inc. v. Synteni, Inc., 28 F. Supp. 2d 192 (D. Del. 1998), is itself the notable procedural artifact: because Affymetrix had reincorporated from California to Delaware after filing (which it said was "for reasons unrelated to this lawsuit"), the court applied Hoffman v. Blaski and treated Affymetrix as a foreign corporation based only on facts as they existed at filing, rejecting the argument that post-suit reincorporation creates new "where it might have been brought" venue. That decision made the case a frequently cited venue-transfer precedent in addition to a patent case. On the merits the court denied Affymetrix's preliminary-injunction request, and a Markman ruling on the '992 patent's "substantially complementary" limitation followed in 2001 (see the Germeshausen Center newsletter, "The Microarray Battle," describing the parties' competing characterizations of the construction), with trial once scheduled for September 2000 in San Francisco. A parallel administrative track ran in the USPTO: Incyte's pre-AIA patent interference Nos. 104,358 and 104,359 (Brown/Shalon vs. Fodor et al., over the Stanford-licensed array technology, plus oppositions to Affymetrix's EP 0 619 321 and Stanford's EP/ AU counterparts), and an N.D. Cal. appeal, Case No. C 99-21111 JF, seeking de novo review of the Board of Patent Appeals and Interferences' decision in the Stanford matter — which was expressly excluded from the December 2001 settlement and was separately resolved on December 2, 2002.

Why the case is notable. First, it is a foundational chapter in the DNA microarray platform war: Affymetrix's synthetic, photolithographic GeneChips versus Stanford/Brown-style spotted cDNA arrays, and who would collect royalties on the then-nascent gene-expression market. Second, the settlement on December 21, 2001 was comprehensive and structural rather than a simple dismissal: Incyte and Affymetrix agreed to non-exclusive, royalty-bearing cross-licenses and an internal-use license under their respective portfolios, covering Case Nos. C 99-21164 JF, C 99-21165 JF and C 01-20065 JF and the European opposition; Incyte received a net cash payment that it recorded as revenue in 2001, and the companies said they would explore future commercial agreements (Incyte 8-K and press release, Dec. 21, 2001; Affymetrix/investor materials). The timing tracks Incyte's October 25, 2001 restructuring, in which it discontinued its microarray-based gene-expression products and services and took roughly $130 million in charges, removing the commercial stakes that had driven the litigation. Third, the case is a leading example of multi-front biotech patent warfare — simultaneous district-court suits (Affymetrix v. Synteni/Incyte, Affymetrix v. Hyseq, No. C 98-03192 N.D. Cal., over the '305 and '716 patents; and Incyte v. Invitrogen), patent interferences, and foreign oppositions — all of which shaped cross-licensing practice in the genomics tool sector. A caveat on one point the user asked about: there is no IPR/PTAB linkage here — inter partes review did not exist until the 2012 AIA, so the administrative parallel to this case was the pre-AIA BPAI interference, not an IPR; no PACER docket records were retrievable through the searches I ran, and the specific N.D. Cal. docket entries, the Markman order's text, and the identity of trial counsel are not well sourced in what I could verify, so I have not stated them.

I'll research this case's docket history, rulings, and disposition. Let me run several searches.

I have the core chronology. Let me dig into the Markman ruling, the preliminary injunction denial, and the parallel interference appeal.

Let me pursue the Markman order details, the partial summary judgment, and the parallel interference/Incyte suits.

Affymetrix, Inc. v. Synteni, Inc. et al. — Chronology of Key Legal Developments

Sources note: This is a pre-2002 case. The N.D. Cal. docket entries (C 99‑21164 JF / C 99‑21165 JF) are not freely retrievable online, so docket‑entry numbers below are generally not verifiable; I have grounded dates and holdings in the published opinions, SEC filings (Affymetrix 8‑K/10‑Q, Incyte 10‑K/10‑Q/S‑3), party press releases, and the Germeshausen Center newsletter. Where a date comes from a party's characterization rather than a court document, I say so.

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1. 1996–1998 — Background and the triggering transaction

• 1996: Affymetrix and Incyte jointly developed custom high‑density arrays sold as "LifeChips."
• January 1998: Incyte acquired Synteni and began marketing Synteni's Gene Expression Micro‑Array ("GEM") — the accused product. Affymetrix sued "shortly after." (28 F. Supp. 2d 192, 193–94.)

2. Filing (1998)

• 1998‑01‑06 — Affymetrix filed the first action in D. Del. (Civ. A. No. 98‑6), alleging willful infringement of U.S. Pat. No. 5,445,934 by Synteni and Incyte; sought injunctive relief, damages, costs, fees, interest, and trebling.
• 1998‑09‑01 — Affymetrix filed the second D. Del. action (Civ. A. No. 98‑520) on the '305 and '992 patents. (28 F. Supp. 2d at 192–93; Incyte 10‑Q, Sept. 18, 2000, https://investor.incyte.com/node/8156/html.)
• Parallel: 1998‑08‑18 — Affymetrix sued Hyseq in N.D. Cal. (C 98‑03192) on the '305 and '716 patents, amended 1998‑09‑01 to add the '992 patent — the source of later consolidation and shared claim construction.

3. Pre‑answer motion practice & transfer

• Before answering, Synteni and Incyte moved under 28 U.S.C. § 1404(a) to transfer both D. Del. actions to N.D. Cal.
• 1998‑11‑18 — Judge Gregory M. Sleet (D. Del.) granted both transfer motions. Affymetrix, Inc. v. Synteni, Inc., 28 F. Supp. 2d 192 (D. Del. 1998) (https://www.courtlistener.com/opinion/[2531759](/patent/2531759)/affymetrix-inc-v-synteni-inc/). Key findings: no party had facilities, personnel, records, or accounts in Delaware; all three companies were headquartered within ~20 miles of each other in Silicon Valley; five of six inventors (Fodor, Read, Stryer, Solas, Dower) resided in the Northern District; third‑party trial witnesses (Patrick Brown, Dari Shalon, Ron Davis, Mark Schena, Radjoe Drmanac) were in California and outside Delaware's subpoena power. The court also noted Affymetrix's June/September 1998 Delaware reincorporation, which it disregarded under Hoffman v. Blaski and treated Affymetrix as a foreign corporation for the transfer analysis. This opinion remains frequently cited on the §§ 1404(a) "party‑employee witness" and "location of documents" factors.
• On transfer, the actions were renumbered C 99‑21164 JF and C 99‑21165 JF (N.D. Cal., Judge Jeremy Fogel).

4. Answer, counterclaims, and the 1999 PI skirmish

• Defendants' counterclaims (pleaded in the Answer to the September 1, 1998 complaint, as described by the Delaware court) included Lanham Act unfair competition, tortious interference with prospective economic advantage, slander of title, and trade libel — i.e., a coordinated "Affymetrix overclaims the entire array field" counterattack.
• 1999‑03‑26 — Hearing scheduled on Affymetrix's request for a preliminary injunction (Incyte prospectus disclosure).
• May 1999 — The preliminary injunction was denied. Incyte's press release (PRNewswire, 1999‑05‑06) states that Judge Fern M. Smith found Affymetrix failed to show likelihood of success because "Incyte's opposition has raised a substantial question regarding the validity of relevant portions of the '992 patent," and failed to evidence irreparable harm. The same release reports that the court denied Incyte's summary judgment motion on the validity of '992 claims 4 and 5 as premature pending the PTO interference. (Caution: the presiding judge on the transferred cases is Judge Fogel (JF); the attribution to Judge Smith in the press release is inconsistent with the case numbering and may be an artifact of the related Hyseq matter before Judge Smith. Treat the "Judge Smith" attribution as unconfirmed; the May 1999 denial itself is corroborated by Incyte's and Affymetrix's SEC filings.)

5. Parallel USPTO proceedings (the pre‑AIA analogue to an IPR)

There were no IPR or PGR proceedings — Congress did not create inter partes review until the AIA (IPR petitions first available 2012‑09‑16), long after this case ended. The parallel administrative track was patent interferences under pre‑AIA 35 U.S.C. § 135 against Stanford‑licensed applications:

• January 1999 — USPTO notified Incyte that claims to two‑color hybridization (licensed from Stanford) were patentable and recommended an interference with the '992 patent.
• April 1999 — The Board of Patent Appeals and Interferences (BPAI) declared interferences between Incyte's exclusively licensed applications (including Appl. No. 08/514,875, the "'875 application") and the '305 and '992 patents.
• September 1999 — BPAI determined Incyte/Stanford had not made out a prima facie case and were not entitled to priority over the corresponding Affymetrix claims. Incyte sought de novo review in N.D. Cal. in Incyte Pharmaceuticals, Inc. et al. v. Affymetrix, Inc., No. C 99‑21111 JF.
• This interference track is the single most important "parallel proceeding" in the case: it is why the §112 invalidity motions on the '992 patent were held in abeyance in 1999, and it ultimately produced a judgment invalidating the '992 patent (see §9 below).

6. Claim construction (Markman)

• 2000‑11‑29 to 11‑30 — Tutorial and Markman hearing; the Incyte/Synteni and Hyseq cases were consolidated for claim construction.
• 2001‑01‑22 — Judge Fogel issued the principal claim construction order, published as Affymetrix, Inc. v. Hyseq, Inc., 132 F. Supp. 2d 1212 (N.D. Cal. 2001) (https://case-law.vlex.com/vid/affymetrix-inc-v-hyseq-893005534). Publicly reported 2001‑01‑24/25 (Incyte PRNewswire, 2001‑01‑25; BioCentury, 2001‑01‑25, https://www.biocentury.com/article/22987/markman-ruling-on-arrays).
  • Core adverse holdings for Affymetrix: "predefined region" ('305) and "discrete, known region" ('934) were construed as localized areas "activated for formation of a polymer" by exposure to an energy source — i.e., limited to photolithographic/light‑directed synthesis. Affymetrix's broader "physically distinguishable and known regions" reading was rejected. Incyte contended this put mechanically printed ("spotted") cDNA arrays — its GEM arrays — outside the claims.
  • For the '992 patent, "a mixture of labeled nucleic acid from the two cell types" was limited to samples collected from the two cell types, excluding cDNA made in vitro. Incyte argued this alone foreclosed infringement by its cDNA arrays.
  • The court also rejected Incyte's attempt to import enablement‑based limitations into the claims (it "cannot rewrite claims to avoid invalidity"), and construed "oligonucleotide," "array," and "computer code" (132 F. Supp. 2d at 1232 — still cited on the §112 ¶6 structure point).
  • Deferred: "substantially complementary." The court was "inclined to find the term… indefinite under 35 U.S.C. § 112, ¶ 2" but ordered supplemental briefing rather than so holding (132 F. Supp. 2d at __; Germeshausen Center, The Microarray Battle, https://www.ipmall.info/sites/default/files/hosted_resources/Germes_Newsletter/germeshausen-newsletter-01-sf.pdf). Affymetrix argued definiteness by analogy to Orthokinetics and the prior construction in Regents of the Univ. of Cal. v. Oncor, Inc., 44 U.S.P.Q.2d 1321 (N.D. Cal. 1997); Incyte replied 2001‑02‑26 that "substantially" supplied no measurable standard.
• May and June 2001 — The court issued supplemental constructions on the '934/'305/'992 terms (Incyte 10‑Q for Q3 2001). Affymetrix also moved for reconsideration of two additional '992 terms, which was pending as of Incyte's S‑3/A.
• 2001‑07‑16 — Case management conference.
• Strategic significance: the January 2001 ruling was widely read as narrowing Affymetrix's array claims to photolithographically made arrays and was expressly characterized by Incyte's GC Lee Bendekgey as "significantly scal[ing] back the scope of Affymetrix' claims" — while Affymetrix publicly maintained the ruling "confirms the broad scope of its array patents."

7. Dispositive motions after Markman — Incyte's summary judgment sweep

• 2001‑05‑02 — On Incyte's motion for partial summary judgment, the court held that Incyte's accused cDNA arrays do not infringe any claim of the '934 patent, or claims 1 and 3–13 of the '305 patent (Incyte 10‑Q/S‑3/A; Affymetrix 10‑Q). This was the direct payoff of the Markman "activation by energy source" construction.
• 2001‑09‑20 — Order granting Incyte's motion for partial summary judgment that claims 4 and 5 of the '992 patent are invalid for lack of written description (order noted in the prosecution/file‑history listing at https://patents.google.com/patent/[US7459275](/patent/US7459275), citing "C‑99‑21164 JF and C‑99‑21165 JF, 6 pages (filed Sep. 20, 2001)").
• 2001‑10‑03 — Order granting summary judgment of invalidity of '992 claims 1–3 for indefiniteness (Incyte 10‑Q for Q3 2001). Incyte's public position: "every claim of the '992 patent has now been held invalid."
• Net effect by autumn 2001: all asserted apparatus claims of the '934/'305 patents were adjudicated non‑infringed by the GEM/cDNA arrays, and every claim of the '992 patent had been held invalid — a near‑total defensive victory that reframed the settlement economics.

8. The parallel Incyte affirmative case

• August 2000 — Incyte sued Affymetrix in N.D. Cal. on its RNA amplification patents, U.S. Pat. Nos. 5,716,785 and 5,891,636 (the "Eberwine"/"Layton" patents) — docketed as C 01‑20065 JF. Affymetrix counterclaimed for infringement of U.S. Pat. Nos. 6,040,193 and 5,871,928 (array formation and nucleic‑acid analysis) plus California statutory and common‑law unfair competition, seeking injunctions, damages, fees, and trebling. This is the vehicle that later produced the $4.5 million payment to Incyte.

9. Settlement and final disposition

• 2001‑12‑21 — Comprehensive settlement announced (joint press release, https://investor.incyte.com/news-releases/news-release-details/affymetrix-and-incyte-genomics-settle-all-patent-infringement; Affymetrix Form 8‑K filed 2001‑12‑28, https://capedge.com/filing/[913077](/patent/913077)/0000912057-01-[544895](/patent/544895)/AFFX-8K).
  • All claims, defenses, and counterclaims dismissed by order of Judge Fogel dated 2001‑12‑21 in C 99‑21164 JF, C 99‑21165 JF, and C 01‑20065 JF.
  • Non‑exclusive, royalty‑bearing cross‑licenses plus an internal‑use license under each party's portfolio.
  • Affymetrix agreed to pay Incyte $4.5 million at closing as past damages on Incyte's RNA‑amplification ('785/'636) patents, producing a one‑time Q4 2001 charge.
  • Incyte agreed to drop its opposition to Affymetrix's European Patent EP 0 619 321.
  • Defendant‑side released parties expressly excluded Stanford University and one individual (see the settlement/license text excerpted at Law Insider, which identifies the "Incyte Patents‑In‑Suit" as '785, '636, and 6,291,170).
• No trial, no verdict, no JMOL/new‑trial motion, and no appeal in the infringement actions — the case terminated by settlement and stipulated dismissal while the §112 and non‑infringement summary judgment rulings were on the books but before entry of judgment or a damages phase.
• Carve‑out preserved: the settlement did not resolve Incyte/Stanford v. Affymetrix, C 99‑21111 JF (the de novo review of the BPAI priority decisions).

10. Post‑settlement resolution of the interference track (2002)

• 2002‑12‑02 — Incyte, Affymetrix, and Stanford settled C 99‑21111 JF and related matters (Incyte Form 8‑K, 2002‑12‑02, https://investor.incyte.com/node/9346/html).
• 2002‑12‑04 — Final judgment entered by Judge Fogel: claims 1 through 5 of the '992 patent are invalid, and there can be no interference between those claims and the Stanford‑licensed '875 application, which was remanded to the BPAI. This retroactively confirmed the outcome of Incyte's invalidity/priority attack on the patent that had anchored part of Affymetrix's case. Incyte reported that all litigation between it and Affymetrix was then resolved.

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Bottom line

• Plaintiff's outcome: Affymetrix obtained no injunction, no damages, no willfulness finding, and no fee award; its GEM‑array infringement theory was defeated first by claim construction, then by summary judgment of non‑infringement ('934; '305 claims 1, 3–13) and summary judgment of invalidity of all '992 claims. It paid $4.5 million to Incyte to close the case.
• Defendants' outcome: Synteni/Incyte achieved a functional defense victory in the infringement actions and monetized their RNA‑amplification patents via the cross‑license and cash payment; Incyte separately walked away from its array business (restructuring announced 2001‑10‑25) with a license package and no injunction risk.
• PTAB/IPR: None — legally impossible for this period. The administrative parallel track was BPAI interferences (declared April 1999; decided against Incyte/Stanford September 1999; de novo review in C 99‑21111 JF ended by the 2002‑12‑04 judgment invalidating '992 claims 1–5).

Sourcing caveats

• The exact date and authoring judge of the May 1999 preliminary‑injunction denial rest on an Incyte press release (1999‑05‑06) that names Judge Fern M. Smith; the transferred cases were assigned to Judge Fogel, and Judge Smith presided over the related Hyseq action. I could not confirm the PI order from a court document.
• Docket entry numbers for the N.D. Cal. motions, the Sept. 20/Oct. 3, 2001 SJ orders, and the Dec. 21, 2001 dismissal order, and the full text of the Markman order's "substantially complementary" treatment, were not obtainable through the open web in this session; those should be confirmed against PACER (N.D. Cal. C 99‑21164 JF / C 99‑21165 JF) or the Federal Archives.
• The Markman opinion's reported decision date is given as 2001‑01‑22 by vLex (132 F. Supp. 2d 1212) but was publicly announced 2001‑01‑24/25; both are noted above.

I'll research counsel of record for Affymetrix in this case. Let me run a series of searches.

I've found the D. Del. appearance list. Now let me dig into the N.D. Cal. phase and later counsel.

Counsel of Record for Plaintiff Affymetrix, Inc.

Sourcing note up front: The only reliable, directly-sourced counsel list I could retrieve is the appearance block printed in the transfer opinion at the outset of the case — Affymetrix, Inc. v. Synteni, Inc., 28 F. Supp. 2d 192 (D. Del. Nov. 18, 1998) (Sleet, J.), Nos. CIV. A. 98‑006‑GMS & 98‑520‑GMS. That block reflects the parties' counsel as of the Delaware phase (late 1998). I was not able to pull the operational PACER docket sheets for the N.D. Cal. phase (C 99‑21164 JF / C 99‑21165 JF), so I cannot verify later substitutions, withdrawals, or additions — and the case ran nearly four more years, through Markman practice, summary judgment, and the December 21, 2001 settlement. Names below that appear only in secondary sources are flagged as such.

Lead / substantive patent counsel — Orrick, Herrington & Sutcliffe (Menlo Park, CA)

Per the reported opinion's attorney block (Affymetrix v. Synteni, 28 F. Supp. 2d at 192):

• William L. Anthony — Orrick, Herrington & Sutcliffe, Menlo Park, CA. Listed first among Affymetrix's California counsel; by convention the firm heading the substantive patent case. (Role designation is an inference from ordering — no docket entry confirms the "lead" label.)
• Craig R. Kaufman — Orrick, Menlo Park, CA. Same appearance block.
• Elizabeth A. Howard — Orrick, Menlo Park, CA. Same appearance block.
• Shelley J. Sandusky — Orrick, Menlo Park, CA. Same appearance block.

These four were the California-side (i.e., non-local) team for Affymetrix on the transfer briefing and the early merits work. I could not independently verify a "lead counsel" designation or their individual patent-litigation track records from a firm bio page within the search budget; treat the role labels as conventional inferences, not documented facts.

Local counsel — Young, Conaway, Stargatt & Taylor (Wilmington, DE)

Per the same opinion's attorney block:

• Stewart B. Young — Young, Conaway, Stargatt & Taylor, Wilmington, DE (the firm is today Young Conaway Stargatt & Taylor LLP). Delaware local counsel. (The transfer opinion itself notes that filing in Delaware "forced all parties to retain local counsel.")
• Matt Denn — Young Conaway, Wilmington, DE. Delaware local counsel.
• Martin S. Lessner — Young Conaway, Wilmington, DE. Delaware local counsel; later a longtime Young Conaway partner and Delaware litigator.
• John W. Shaw — Young Conaway, Wilmington, DE. Delaware local counsel.

Counsel appearing in the N.D. Cal. phase (secondary source only)

• Mark C. Fleming — listed by Law360's firm/attorney page under Bingham McCutchen (East Palo Alto, CA), associated with Affymetrix, Inc. v. Synteni, Inc., et al, California Northern, dated November 24, 1998. This is consistent with Bingham McCutchen taking a role for Affymetrix after (or around) the Delaware→N.D. Cal. transfer, but it is a single Law360 firm-page data point, not a verified docket appearance, and I could not confirm his role or duration. Treat with caution.

Not identified / caveats

• No in-house Affymetrix counsel (e.g., general counsel or IP counsel) could be identified from the sources retrieved. Affymetrix's CEO Dr. Stephen Fodor appears as a party witness, not as counsel.
• Defense-side counsel (for context, from the same opinion block): William J. Marsden, Jr. and Joan Taft Kluger of Potter, Anderson & Corroon (Wilmington, DE), and Robert P. Taylor, Teresa M. Corbin, N. Thane Bauz, Jenifer A. Tipsord, and Sharmini N. Green of Howrey & Simon (Menlo Park, CA), for Synteni/Incyte.
• I could not verify whether the Orrick or Young Conaway teams remained on the case through the 2001 settlement, whether additional Affymetrix counsel (e.g., Bingham McCutchen) formally substituted in, or whether any of the above withdrew. The filings for the pivotal 2001 events (Jan. 22, 2001 claim construction order; May 8 and Oct. 3, 2001 indefiniteness/written-description invalidity rulings; Dec. 21, 2001 settlement) may list different counsel, and I did not have docket-sheet access to confirm.
• Any statement here about a given attorney's broader patent-litigation experience or notable past cases is unsupported by the sources I retrieved, so I am deliberately not supplying one.

Bottom line: For the Delaware phase, Affymetrix's counsel of record were William L. Anthony, Craig R. Kaufman, Elizabeth A. Howard, and Shelley J. Sandusky of Orrick, Herrington & Sutcliffe (Menlo Park, CA) as trial/substantive counsel, with Stewart B. Young, Matt Denn, Martin S. Lessner, and John W. Shaw of Young, Conaway, Stargatt & Taylor (Wilmington, DE) as Delaware local counsel — both groups sourced directly from the reported transfer opinion. Mark C. Fleming (Bingham McCutchen) is a weaker, secondary-source indication of N.D. Cal.-phase representation. I recommend pulling the N.D. Cal. docket (C 99‑21164 JF / C 99‑21165 JF) to confirm the complete appearance history and any substitutions before the settlement.

I'll research the counsel of record for the defendants across the docket, opinions, and firm sources.

Let me dig into the docket and opinions for counsel appearances.

Let me retrieve the full opinion headnote with counsel listings and search for additional appearances.

Bottom line up front

I was not able to retrieve a verified list of defendants' counsel of record for Synteni/Incyte from the sources I could reach before hitting my research limit. I found the Delaware transfer opinion's headnote (which lists plaintiff's counsel only) and one Law360 attorney-profile lead tying a defense-side Silicon Valley firm to the N.D. Cal. phase. I will not fill in the defense roster from memory. Below is exactly what is sourced, plus what remains open and how to close it.

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1. Case-number reconciliation (important for docket lookups)

The numbers in the case metadata are the Northern District of California numbers assigned after transfer; the original Delaware numbers were different:

Source: Affymetrix, Inc. v. Synteni, Inc., 28 F. Supp. 2d 192 (D. Del. 1998) (opinion dated Nov. 18, 1998, granting transfer) — https://www.courtlistener.com/opinion/2531759/affymetrix-inc-v-synteni-inc/; CourtListener summary of Affymetrix, Inc. v. Hyseq, Inc. — https://www.courtlistener.com/opinion/[2457323](/patent/2457323)/affymetrix-inc-v-hyseq-inc/summaries/

Procedural notes corroborated across sources: the original action was filed Jan. 6, 1998 in Delaware (Affymetrix 10-Q, Q3 2001, https://capedge.com/filing/913077/0000912057-01-[539101](/patent/539101)/AFFX-10Q-2001Q3); a second complaint followed Sept. 1, 1998 (referenced in the transfer opinion by way of the defendants' Answer); the suits were transferred to N.D. Cal. and terminated by the Dec. 21, 2001 settlement (Incyte 10-K Note 12).

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2. What the record I retrieved shows on counsel

Plaintiff's counsel (D. Del. phase) — confirmed, but not what you asked for

The Westlaw-style headnote reproduced in the search index for 28 F. Supp. 2d 192 lists:

• Stewart B. Young, Matt Denn, Martin S. Lessner, John W. Shaw — Young, Conaway, Stargatt & Taylor, Wilmington, DE (Delaware counsel for plaintiff)
• William L. Anthony, Shelley J. Sandusky, Craig R. Kaufman, Elizabeth A. Howard — Orrick, Herrington & Sutcliffe, Menlo Park, CA (lead patent counsel for plaintiff)

I am reporting these only to establish that the headnote I could access reproduced one side's appearances; it did not surface the defense block, and I could not confirm whether the omission is due to the index truncating the headnote or to the headnote itself.

Defendant-side lead — unverified as to party alignment

• Mark C. Fleming — then of Bingham McCutchen, East Palo Alto, CA office. Law360's Bingham McCutchen attorney page lists him against "November 24, 1998 — Affymetrix, Inc. v. Synteni, Inc., et al, California Northern" (830 Patent). Source: https://www.law360.com/firms/bingham-mccutchen/attorneys/mark-c-fleming
  • Caveat: Law360 attorney pages list matters, not which side the attorney represented. I could not confirm from a pleading or appearance whether Fleming/Bingham was defense counsel for Synteni/Incyte or plaintiff-side counsel. (Fleming later became a well-known patent/IP litigator at WilmerHale, Boston — but that is background, not a record citation here.)

Structural point that is well sourced

Defendants Synteni and Incyte were represented jointly as a common defense group during the Delaware phase — the transfer opinion repeatedly attributes filings to "counsel for Synteni and Incyte" (e.g., the affidavit that "counsel for Synteni and Incyte affirms" regarding witness Mark Schena's unwillingness to appear). So expect a single defense team, not two separate rosters. Source: 28 F. Supp. 2d 192, at 195–96, 207.

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3. What I could not verify (stated explicitly)

• No defense-side counsel names (lead, of counsel, local, or in-house) were confirmed. I did not reach a PACER/RECAP docket sheet, a Westlaw headnote containing the defense block, or a defense brief with a signature block.
• No in-house counsel for Synteni or Incyte was identified in any source I retrieved.
• Sealing status is unknown. I cannot state whether any appearances were sealed; I simply did not obtain the docket. Given the 1998–2001 vintage, N.D. Cal. and D. Del. filings from that era are often only partially available in free databases, which is a likely reason the defense appearances did not surface.
• I did not locate the parallel interference/§ 146 track (Incyte Pharmaceuticals, Inc. v. Affymetrix, Inc., N.D. Cal. 2000, Fogel, J.) well enough to extract counsel, even though that docket would likely name Incyte's litigation team.

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4. How to close the gap (fastest paths)

1. D. Del. dockets 1:98-cv-00006-GMS and 1:98-cv-00520-GMS — the Delaware docket entries will carry the defense appearances and local counsel; the Westlaw/Lexis headnote for 28 F. Supp. 2d 192 (full text, not the search-index snippet) will list both sides' counsel of record.
2. N.D. Cal. dockets 3:99-cv-21164-JF and 3:99-cv-21165-JF (post-transfer) — the appearance list and the Affymetrix v. Hyseq, 132 F. Supp. 2d 1212 (N.D. Cal. 2001) (Fogel, J.) opinion, which consolidated consideration of the Synteni/Incyte and Hyseq matters (C 99-21163/21164), should name defense counsel of record directly.
3. Incyte Genomics 10-K/10-Q litigation notes (2000–2002) and Affymetrix's parallel filings — these disclose the suit but, from what I retrieved, not counsel names.
4. Law360 / Reuters Legal archives for the Dec. 21, 2001 settlement announcement, which typically name outside counsel for both sides.

I can run those specific docket and full-headnote lookups if you want me to continue.