US 6607887

I'll search for this specific patent number across the requested sources.

Let me search for litigation and appellate docket information specifically.

Now let me look for appellate docket activity and the full claim set.

Search-scope note

I ran targeted searches for the literal string 6607887 across Google Patents, Espacenet/INPADOC, Justia, PubChem patent records, Plainsite (USPTO application records) and District Court filings. I could not confirm a live USPTO PatentCenter record or any CAFC docket. Two searches returned zero results — including a search expressly for "6607887" CAFC / Federal Circuit 2026 appeal — so I have no evidence of any 2026 (or other) Federal Circuit appeal involving this patent. I found no results for any similar-but-different patent number, and every hit below is for US 6,607,887 or a family member of it.

US 6,607,887 B2 — Bibliographic record

Sources: https://patents.google.com/patent/US6607887/en ; https://pt.espacenet.com/publicationDetails/inpadoc?CC=US&NR=[6607887B2](/patent/6607887B2)&KC=B2

Uncertainty flags. (1) The filing date of 2001-02-27 on application 09/796,071 appears to post-date the title-mate US 6,242,180 B1 (same title, same inventor/assignee, also priority 1994-10-21), so 6,607,887 is almost certainly a continuation in the same family — but I did not retrieve the continuity data field to state the parent chain authoritatively. (2) A USPTO application record on Plainsite for docket AFFYP005C (application shown as "09049805," first inventor Chee, Mark S.) carries a filing date of March 27, 1998; I am not confident this is in the direct line of 09/796,071, and I am flagging the identifier exactly as retrieved rather than interpreting it. (3) The Plainsite record shows examiner Ardin H. Marschel / Art Unit 1631, class 435/6.

Abstract

The abstract wording I could verify comes from the family mate US 6,242,180 B1 (PubChem), which shares this patent's title and priority:

"A computer system (1) for analyzing nucleic acid sequences is provided. The computer system is used to perform multiple methods for determining unknown bases by analyzing the fluorescence intensities of hybridized nucleic acid probes. The results of individual experiments may be improved by processing nucleic acid sequences together. Comparative analysis of multiple experiments is also provided by displaying reference sequences in one area (814) and sample sequences in another area (816) on a display device (3)."

The granted text of 6,607,887 describes the same subject matter: "An improved computer-aided system for visualizing and determining the sequence of nucleic acids is disclosed… improved methods of analyzing fluorescent image files of a chip containing hybridized nucleic acid probes in order to call bases in sample nucleic acid sequences." I could not independently confirm the verbatim abstract paragraph of 6,607,887 itself; treat the quoted text as the family abstract. Source: https://pubchem.ncbi.nlm.nih.gov/patent/US-[6242180](/patent/6242180)-B1

Plain-language overview of the independent claims

The claims I could retrieve verbatim come from the Justia rendering of US 2002/0012925 A1, the pre-grant publication of application 09/796,071. Issued-claim numbering/text may have changed during prosecution, so I flag this as likely but not verified as the exact issued claim set.

Claim 1 — Generic compare-and-call.
In a computer system, a method of identifying an unknown base in a sample nucleic acid: (a) input a plurality of probe intensities, each tied to a nucleic acid probe; (b) the computer compares those intensities, each being substantially proportional to the associated probe hybridizing with at least one nucleic acid sequence, where that at least one sequence includes the sample sequence; and (c) call the unknown base from the comparison. This is the broadest teaching — it does not require a reference sequence or a ratio calculation.

Claim 2 — "Intensity ratio" method (the discriminator).
Same framing, but the plurality of probe intensities are each substantially proportional to the associated probe hybridizing with the sample sequence, and the unknown base is called from the comparison. Plainly: read the four mutation probes at a position and pick the winner.

• Claim 3: the comparison includes calculating a ratio of a higher probe intensity to a lower probe intensity.
• Claim 4: call the base corresponding to the higher-intensity probe if that ratio exceeds a predetermined ratio value.
• Claim 5: that predetermined ratio value is approximately 1.2 — a notable narrowing, matching the specification's worked examples.

Claim 6 — "Reference" method (two-experiment comparison).
A method of identifying an unknown base by (a) inputting a first set of probe intensities, each proportional to a probe hybridizing with a reference nucleic acid sequence; (b) inputting a second set of probe intensities, each proportional to a probe hybridizing with the sample sequence; (c) the computer comparing at least one intensity from the first set against at least one from the second set; and (d) calling the unknown base from that comparison. This is the core of the reference-comparison approach — it detects a mutation as an increase/change against a reference, rather than relying on absolute hybridization discrimination.

• Claim 7: comparing includes calculating first ratios (wild-type reference probe intensity to each reference probe intensity) and second ratios (highest sample probe intensity to each sample probe intensity).
• Claim 8: comparing further includes calculating third ratios of the first ratios to the second ratios ("ratios of ratios").
• Claim 9: call the unknown base according to the probe associated with the highest third ratio.
• Claim 10: another dependent claim on claim 6 defining further comparing-step detail (text truncated in the retrieval).

Additional independent claims I expect but could not verify. The specification separately discloses, and the "Definitions" summary of the granted patent characterizes, several distinct methods — the statistical method (comparing sample probe intensities to means/standard deviations of reference probe intensities across multiple experiments), pooling processing (labeling reference and sample with distinguishable markers and hybridizing them together to cancel experiment-to-experiment variation), the multi-position "bubble"/dark-region method (using hybridization data from more than one base position plus the probe interrogation position to identify single mutations, multiple mutations, and to remove false positives), and the comparative analysis/visualization method (displaying reference sequences in one area and sample sequences in another, with linking and intensity-graph windows). Claims directed to these subject matters very plausibly appear as further independent claims in the issued patent, but I could not retrieve the full numbered claim set or total claim count, so I am not asserting their claim numbers or exact wording.

Litigation — what is and is not confirmed

• The Google Patents record for 6,607,887 carries a "Family has litigation" flag (Darts-ip family 23276902) and links to Delaware District Court case 1:04-cv-00901. Source: https://patents.google.com/patent/US6607887/en
• That case is Affymetrix, Inc. v. Illumina, Inc., C.A. No. 04-901-JJF, before Judge Joseph J. Farnan, Jr. Filings I retrieved reference asserted patents such as the '432 patent and the '716 patent, and mention two Affymetrix patents from related priority applications plus parallel Affymetrix v. Incyte and Oxford Gene Technology v. Affymetrix (C.A. 99-348-JJF) litigation. The '432 patent was subject to an Illumina summary-judgment motion of invalidity (Doc. 284, 2006-07-17), and a Phase II trial on validity/willfulness was being scheduled into 2008 (Doc. 450, 2007-10-08).
• I could not confirm that US 6,607,887 itself was an asserted patent in 1:04-cv-00901. The litigation link is recorded at the patent-family level, and the court documents I retrieved name other patents. Treat "6,607,887 was asserted in Affymetrix v. Illumina" as unverified.

Sources: https://portal.unifiedpatents.com/litigation/Delaware%20District%20Court/case/1%3A04-cv-00901 ; https://www.findforms.com/single_form.php/form/63690/... ; https://www.findforms.com/single_form.php/form/63452/...

CAFC / 2026 dockets

No results. My explicit searches for 6607887 in connection with the Federal Circuit and 2026 appellate dockets returned nothing, and the patent's own record shows it lapsed for non-payment of maintenance fees in 2015 and reached its anticipated expiration on 2014-10-21. On that record, a 2026 CAFC appeal involving this patent would be surprising. I state this as an absence of evidence, not as proof of nonexistence — I did not have direct query access to the CAFC docket system.

Explicit uncertainties

1. Verbatim abstract text of 6,607,887 — taken from family mate US 6,242,180.
2. Exact issued claim set and total claim count — the claim text above is from the pre-grant publication US 2002/0012925 A1 and may differ from the granted claims.
3. Whether 6,607,887 was actually asserted in Delaware 1:04-cv-00901.
4. The parent/continuation chain of application 09/796,071 (likely a continuation of the US 6,242,180 line, not verified).
5. No live USPTO PatentCenter or CAFC docket record was retrieved during this search.

I'll research litigation involving US patent 6607887 (Affymetrix / "Computer-aided visualization and analysis system for sequence evaluation"). Let me run several targeted searches.

Let me dig deeper into the Affymetrix v. Illumina case and check for any other cases involving the '887 patent.

Let me check for any other cases involving the '887 patent, including the family litigation and any other defendants.

Litigation involving US Patent 6,607,887

Based on my searches of litigation sources (Unified Patents litigation portal as linked from the patent record, District of Delaware filings mirror, SEC 10-K disclosures, and news/press coverage), I located one case in which US 6,607,887 was asserted. I found no other case naming this patent.

Case 1: Affymetrix, Inc. v. Illumina, Inc.

Details and chronology (re: the '887 patent):

• Affymetrix's July 26, 2004 complaint asserted six Affymetrix patents against Illumina's BeadArray products: U.S. Patent Nos. 5,545,531; 5,795,716; 6,355,432; 6,399,365; 6,607,887; and 6,646,243. The '887 patent was Count 5 of the complaint.
  • Source (Patent/Trademark Report to Commissioner, D. Del., filed 01/16/2008): https://www.findforms.com/single_form.php/form/63424/Patent_Trademark_Report_to_Commissioner_District_Court_of_Delaware_District_Court_of_Delaware_Delaware
• Illumina answered (Sept. 15, 2004) and counterclaimed for declaratory judgment of non-infringement, invalidity, and unenforceability; inequitable-conduct and antitrust allegations were added by first amended answer/counterclaims (allowed Feb. 15, 2006).
• In March 2006 Affymetrix notified Illumina it was dropping one of the six patents; the court dismissed that patent on June 30, 2006. That dropped patent was the '887 patent.
  • Source (Illumina 10-K describing "decision to drop one of the six patents"): https://www.sec.gov/Archives/edgar/data/[1110803](/patent/1110803)/0000936397... (Illumina 10-K) / https://companiesmarketcap.com/illumina/sec-reports-10k/0000936392-07-000158/
• A stipulated proposed order (Doc. 266, filed June 23, 2006) formally dismissed, as to the '887 patent:
  1. Count 5 of Affymetrix's complaint — with prejudice; and
  2. Count V of Illumina's First Amended Answer and Counterclaims (DJ of non-infringement, invalidity, unenforceability) — without prejudice.
  • Source: https://www.findforms.com/single_form.php/form/63711/Proposed_Order_District_Court_of_Delaware_District_Court_of_Delaware_Delaware
• The case continued on the remaining five patents (claim construction ruling Aug. 16, 2006; jury verdict for Affymetrix in March 2007 including ~$16.7 million in damages).
• The entire action was dismissed with prejudice by stipulated order (Docs. 470/471, filed Jan. 14–16, 2008) as part of a global settlement in which Illumina paid Affymetrix $90 million (Jan. 2008) resolving multiple suits brought in the U.S., Germany, and the U.K. between 2004 and 2007.
  • Sources: https://www.findforms.com/single_form.php/form/63423/... and https://www.genomeweb.com/microarrays-multiplexing/cases-closed-wisconsin-court-dismisses-two-illumina-ip-suits-against

Important caveats

• The Delaware case is the only litigation I could confirm naming US 6,607,887. The patent record itself flags that the family has litigation, and the Unified Patents link embedded in the patent page points to the same Delaware case (case 1:04-cv-00901): https://portal.unifiedpatents.com/litigation/Delaware%20District%20Court/case/1%3A04-cv-00901
• Note that the later Illumina v. Affymetrix suits (W.D. Wis., concerning U.S. 7,510,841 and 7,612,020) and the Dr. Anthony Czarnik v. Illumina inventorship suit do not involve US 6,607,887 and are therefore not included above.
• I did not find any litigation outcome in which the '887 patent was adjudicated valid, invalid, infringed, or not infringed — it was withdrawn/dismissed before any merits determination.
• The patent is now expired (anticipated expiration Oct. 21, 2014; legal status "Expired – Fee Related"), so no pending litigation should exist.

Confidence note: The existence, parties, court, case number, and dismissal terms for the '887 patent are well corroborated by primary court documents. The precise date on which Affymetrix formally dropped the patent (reported as June 30, 2006 in Illumina's 10-K) versus the stipulation date (June 23, 2006) differs slightly between sources; both are reported above.

I'll start by verifying the ODP-derived baseline and searching for any AIA trial proceedings on this patent.

Let me run more targeted searches to check for any PTAB activity, including older proceedings and related litigation.

Let me check the PTAB portals directly and any reexamination history, plus the Federal Circuit outcome of the Delaware litigation.

PTAB Proceeding Analysis — U.S. Patent No. 6,607,887

Patent: US 6,607,887 B2 — "Computer-aided visualization and analysis system for sequence evaluation"
Patent owner / current assignee: Affymetrix, Inc. (now part of Thermo Fisher Scientific)
Priority date: 1994-10-21 · Application filed: 2001-02-27 (App. No. 09/796,071) · Granted: 2003-08-19
Legal status per structured data: Expired – Fee Related (anticipated expiration 2014-10-21)

Proceedings overview

Total AIA trial proceedings on file: zero. The structured "PTAB proceedings on file" block — the canonical USPTO Open Data Portal list — returns no IPR, no PGR, and no CBM proceeding against US 6,607,887. My independent web checks (RPX PTAB Insight, Unified Patents litigation portal, PTAB decision coverage, general docket searches) surfaced no AIA trial petition naming this patent either, in any filing year from 2012 through today. There is therefore no "claims invalidated / sustained / settled / institution-denied" breakdown to give: the breakdown is 0 active, 0 invalidated, 0 sustained, 0 settled, 0 institution-denied.

The bottom-line defensive posture is unusual and worth stating precisely, because it is not "the patent has been hardened by surviving IPRs." It is closer to the opposite: this patent has never been PTAB-tested at all, and the reason is that the AIA trial regime effectively arrived too late for it. The patent's entire enforcement life — the Affymetrix v. Illumina campaign, D. Del. Case No. 1:04-cv-00901-JJF — predates IPR availability (first IPRs filed 2012). The '887 patent was dropped from that suit in 2006 and its count dismissed, and the patent then expired on 2014-10-21. A defendant today is not facing claims that survived an IPR; it is facing an expired patent that was never tested, in 20 years of enforceability, through a single AIA trial. That cuts both ways: the patent owner cannot point to any PTAB win for leverage, but no § 315(e)(2) estoppel attaches to anyone, so the full prior-art universe remains open on the district-court side.

Below, the one non-AIA proceeding that actually shaped this patent's enforceability is summarized, because it is the only real record of what happened to the '887 claims.

No AIA trial proceeding — and the closest thing to one (D. Del. 1:04-cv-00901-JJF)

• Type: Not an AIA proceeding — 2004–2006 district court infringement action in which the '887 patent was asserted and then voluntarily withdrawn.
• Filed / asserted: Complaint filed 2004-07-26 in the U.S. District Court for the District of Delaware (Judge Joseph J. Farnan, "JJF"). Affymetrix asserted six patents, including the '887 patent. This is the litigation captured in the structured data's Darts-IP family link (family=23276902) and the Unified Patents Delaware case link (case/1:3A04-cv-00901).
• Counterclaim posture: Illumina's First Amended Answer added Count V — declaratory judgment of non-infringement, invalidity, and unenforceability of the '887 patent. Note the unenforceability plea: this action was the vehicle for the inequitable-conduct and ownership/inventorship disputes (the Affymax/Wagner/Lipshutz chain) that shadowed several Affymetrix array patents in this period.
• Termination as to the '887 patent: Affymetrix dropped the '887 patent from suit in March 2006 (reported 2006-03), and the parties stipulated to dismissal. A Proposed Order filed 2006-06-23 (Doc. 266) dismissed Count 5 of Affymetrix's Complaint with prejudice and Count V of Illumina's counterclaims (DJ of non-infringement, invalidity, unenforceability) without prejudice. So the '887 patent ended its only assertion on dismissal-with-prejudice of the infringement count and dismissal-without-prejudice of Illumina's invalidity counterclaim — i.e., no merits ruling on validity or infringement of the '887 patent was ever issued by any tribunal.
• Judge panel: N/A (district court, not PTAB).
• Petition grounds: N/A — no AIA petition was ever filed. Because the 2004 Delaware complaint was served, any Illumina-filed IPR would in any event have been time-barred under § 315(b) (and IPRs did not exist until 2012), which is a clean explanation for the absence of PTAB art on this patent.
• Institution / FWD: N/A.
• Settlement: The broader Affymetrix–Illumina dispute resolved globally years later — Illumina paid Affymetrix a one-time $90 million, Affymetrix dismissed its suits with prejudice, Illumina dismissed its counterclaims, and Affymetrix granted Illumina a perpetual covenant not to sue (extended four years for future-technology products), covering all fields except photolithography. Per press coverage, the covenant expressly excluded the photolithography field "in which Illumina does not operate." (I could not verify the exact settlement execution date from the sources retrieved; the reporting places it after the 2006–2007 Delaware trial phase, and the related Illumina-v.-Affymetrix suits over US 7,510,841 / 7,612,020 were dispatched on summary judgment with CAFC affirmance reported 2011-08-19.) The '887 patent's own count was already out of the case before that settlement.
• Appeal: No Federal Circuit appeal as to the '887 patent — the dismissal was stipulated, and a stipulated dismissal of the infringement count with prejudice removes the jurisdictional predicate for appeal on that patent. The 2011 CAFC affirmance concerns different patents (7,510,841 / 7,612,020) and a different case, and should not be cited as '887 appellate history.
• Defensive value: There is no FWD to link to and no claim-level disposition to quote — the '887 patent was never adjudicated. The practical legacy is (a) an expired patent (anticipated expiration 2014-10-21), so injunctive relief is off the table and any damages case reaches only conduct within the § 286 six-year lookback of the complaint date; and (b) an ample 2004–2006 invalidity record (Illumina's DJ counterclaim pleadings, the Markman briefing in the case, and the inequitable-conduct/ownership record) that a modern defendant can mine. Note that the 2006-08-16 Markman Order covered the remaining patents after '887 was dropped, so there is no '887-specific claim construction on the public record from that case.

Strategic summary

Claim status: everything is UNTESTED. Not canceled, not sustained — simply never reviewed. I was unable to obtain the '887 claim set from the material available to me and will not guess at claim numbers; the authoritative text (26 claims per the printed patent, per the front-page to be verified) should be read directly from the patent. What is certain is that no claim of US 6,607,887 has ever been canceled or confirmed by the PTAB, and no claim has been held invalid or non-infringed by a district court. The patent's entire validity history is a counterclaim that was dismissed without prejudice, which has zero preclusive effect in either direction.

Estoppel landscape: there is no IPR estoppel, and there is no patent-owner PTAB win to hide behind. Because no IPR was ever instituted, § 315(e)(2) estoppel never attached to any party — not to Illumina, not to anyone. That means a defendant today faces no estoppel-driven gap in the prior-art arsenal (a genuinely favorable fact), but it also means the patent owner cannot claim "the PTAB already blessed these claims." The two constraints that do bind a modern defendant are procedural, not estoppel: (1) § 315(b) — a petition must be filed within one year of service of a complaint, so timing is entirely within the defendant's control but has a hard fuse; and (2) the expired status of the patent, which undercuts the practical value of any IPR (the Board will still institute against expired claims under Phillips-style construction, but there is no injunctive downside to the patent owner and no ongoing royalty to enjoin). Practically, the strongest validity play here is district-court invalidity using the 2004–2006 Illumina art plus intervening § 102(b) references, not an IPR — unless the defendant needs a stay or a clean § 282 invalidity adjudication on a narrow record.

Pattern signals: none of the classic ones are present. There is no serial petitioner (no party has ever filed even one IPR against this patent), no PTAB appeal activity by the patent owner on this patent (nothing to appeal), and no defensive aggregator in the chain — Unified Patents' involvement is limited to hosting the Darts-IP/Unified litigation metadata link for the 2004 Delaware case, not to any funded challenge. Affymetrix as patent owner never had occasion to defend this patent at the PTAB. The absence of any IPR over a 14-year AIA window is best explained by two things: the patent was already expired by 2014-10-21, and its one litigation assertion was abandoned in 2006, meaning no accused infringer ever had both a live § 315(b) window and a commercial reason to pay for an IPR.

Recommended next steps

1. If you are the defendant: do not expect to find an FWD, an institution decision, or a Federal Circuit opinion on US 6,607,887 — none exists. Any demand letter or complaint citing the '887 patent is citing a patent that was asserted once (2004), abandoned by the patent owner in 2006, and expired 2014-10-21. Your first moves: (a) confirm expiry and maintenance-fee status through USPTO Patent Center (the structured data shows "Expired – Fee Related" with anticipated expiration 2014-10-21); (b) compute § 286 damages exposure (no pre-complaint recovery beyond six years, and likely much less given expiry); and (c) pull the full D. Del. 1:04-cv-00901-JJF docket via PACER/CourtListener to harvest Illumina's 2004–2006 invalidity contentions, which are the closest thing to a ready-made invalidity case.
2. If you want a PTAB vehicle anyway: an IPR remains legally available against expired claims, but weigh it against § 315(b) timing and the fact that the Board's discretionary-denial practice (Fintiv resurrected per the 2025-02-28 rescission of the Vidal memo and the 2025-03-26 Acting Director bifurcation memo) makes an IPR against a long-expired, already-litigated, settled patent a poor use of budget. An ex parte reexamination is a cheaper alternative, though note that the CRU has been denying reexam requests under § 325(d) when they substantially overlap a prior IPR petition — not an issue here, since no IPR was ever filed.
3. Do not overstate the "hardened patent" narrative, and do not accept it from opposing counsel either. The correct statement of the record is: no PTAB activity, no validity adjudication, expired since 2014-10-21, and one abandoned 2004 assertion. If the patent owner represents that this patent "survived IPR," that is factually false and should be corrected on the record.
4. Verify before filing. Two items I could not fully confirm from available sources and that you should check directly on USPTO Patent Center / PTAB E2E before relying on them: (i) whether any ex parte reexamination of the '887 patent was ever requested or granted (I found no evidence of one, but I cannot exclude an unindexed reexam certificate), and (ii) the exact claim count and claim numbering of the '887 patent, which must be read off the printed patent rather than inferred from the specification text I was given.

Sources relied on: the structured PTAB/ODP block supplied with this task (no proceedings); Google Patents US6607887B2 litigation metadata (Darts-IP family 23276902; Unified Patents D. Del. 1:04-cv-00901); the 2006-06-23 Proposed Order (Doc. 266) in D. Del. 1:04-cv-00901-JJF dismissing the '887 counts; Illumina's 2006-08-17 Markman press release (identifying the five patents remaining after '887 was dropped); and Affymetrix/Illumina settlement and CAFC-affirmance press coverage. I did not locate any PTAB Final Written Decision, institution decision, or Federal Circuit opinion addressing US 6,607,887, and I have not speculated about what such a document would have said.

I'll research the assignment record for US 6607887 across multiple sources.

Good — I have the two post-issuance reel/frames. Now let me find the original inventor→Affymetrix assignment and any related family assignments.

Inventors

Mark S. Chee — sole named inventor.

Pattern notes:

• This is an all-Affymetrix inventorship story. There is only one inventor, and the specification itself is an Affymetrix internal-system disclosure (it repeatedly incorporates Affymetrix's own US 5,143,854 and PCT WO 90/15070/92/10092 by reference and describes the company's mask-design → synthesis → scan → analyze pipeline end to end).
• No unusual inventor-departure pattern is determinable from the assignment record. I found no assignment running inventor → third party, which is consistent with the standard employee-invention assignment to Affymetrix. I could not retrieve the reel/frame for that original inventor→Affymetrix assignment (see caveat below), so I cannot date it.

Original assignee

Affymetrix, Inc. (a Delaware corporation; original assignee of record, and the assignee returned to on the patent's final recorded assignment).

Assignment timeline

Sourcing caveat, stated plainly: I was able to retrieve the reel/frame identifiers, conveyance types, execution dates and assignor/assignee names for the post-issuance records below (corroborated via the INPADOC legal-status feed for US6607887: https://pt.espacenet.com/publicationDetails/inpadoc?CC=US&NR=[6607887B2](/patent/6607887B2)&KC=B2&FT=D&ND=11&date=20030819&DB=EPODOC). I was not able to retrieve the correspondent of record (attorney/agent who filed the recordings) for either entry from the sources available to me, and I was not able to retrieve a reel/frame for the original inventor→Affymetrix assignment. I am stating those gaps rather than guessing.

Not an assignment (listed for completeness, so it is not mistaken for one): Google Patents records a "2003-07-08 Priority to US10/616,228" event. That is a continuation/family-branching event (the child published as US 2004/0175718 A1), not a transfer of ownership.

1. Original inventor → Affymetrix (reel/frame not retrievable)

• Date not retrieved (pre-issuance; expected 1994–2001 window) / recorded not retrieved — Reel not retrieved
  • Conveyance: Assignment (employment/obligation assignment, inferred from the record's designation of Affymetrix as original assignee)
  • Assignor: Mark S. Chee
  • Assignee: Affymetrix, Inc.
  • Correspondent: not retrieved
  • Context: internal/inbound employee-invention assignment — the ordinary route by which Affymetrix became original assignee.

2. Affymetrix → GE Capital (IP collateral pledge)

• 2012-06-25 (executed) / recorded 2012-06-27 — Reel 028465/0541
  • Conveyance: Security Agreement (recorded in the assignment database under event code "AS / ASSIGNMENT", with the record text reading SECURITY AGREEMENT;ASSIGNOR:AFFYMETRIX, INC.;REEL/FRAME:028465/0541)
  • Assignor: Affymetrix, Inc.
  • Assignee: General Electric Capital Corporation, as Agent (address of record given as Maryland / MA in INPADOC)
  • Correspondent: not retrieved
  • Context: securitization — this is not a sale. It is the perfecting record for a lien on Affymetrix's patent estate granted under the $100,000,000 Credit Agreement dated as of June 25, 2012, by and among Affymetrix, Inc. (Borrower), General Electric Capital Corporation (as Agent), Silicon Valley Bank (as Syndication Agent), and the lender parties. Note the execution date (2012-06-25) is the same day as the credit agreement, and the "effective date" recorded is 2012-06-25 — a strong corroboration that this is the credit facility's collateral filing and nothing more. (Credit agreement: https://contracts.justia.com/companies/affymetrix-inc-22525/contract/[628359](/patent/628359)/). The same reel/frame 028465/0541 was recorded against other Affymetrix patents in the same portfolio (e.g., US 6,630,308), confirming a blanket portfolio pledge rather than a patent-specific deal.

3. GE Capital → Affymetrix (lien release)

• 2015-10-28 (executed) / recorded 2015-11-13 — Reel 037109/0132
  • Conveyance: Release By Secured Party (record text: RELEASE BY SECURED PARTY;ASSIGNOR:GENERAL ELECTRIC CAPITAL CORPORATION, AS AGENT;REEL/FRAME:037109/0132)
  • Assignor: General Electric Capital Corporation, as Agent
  • Assignee: Affymetrix, Inc. (address of record given as California in INPADOC)
  • Correspondent: not retrieved
  • Context: release of collateral / internal reorg of the security chain, not a sale. The lien was discharged, returning the record to Affymetrix as sole owner. This is the terminal recorded event for the '887 patent.

4. No assignment to Thermo Fisher is on this record

Despite Affymetrix's 2016 acquisition by Thermo Fisher Scientific, no recorded assignment of US 6,607,887 to Thermo Fisher (or a Thermo Fisher subsidiary) appears in the patent's legal-event record. The plausible explanations are (a) the patent had already expired (2015) and was not carried into the acquisition schedule, or (b) the acquisition was effected at the corporate/entity level rather than by per-patent recordals. I am flagging this as an open item rather than asserting a transfer that I did not find recorded.

Maintenance-fee / lapse events that bracket entries 2–3 (not assignments, but they explain the odd ordering — the release was recorded after the patent lapsed):

• 2015-03-27 — maintenance fee reminder mailed
• 2015-08-19 — lapse for failure to pay maintenance fees
• 2015-10-06 — lapsed due to failure to pay maintenance fee
• 2015-09-14 — patent discontinued / expired under 37 CFR 1.362

Timeline diagram

timeline
    title Ownership of US 6607887
    1994 : Priority date 21 October
    2001 : Application 09 796 071 filed
    2003 : Patent issued to Affymetrix
    2004 : Affymetrix sues Illumina on this patent
    2012 : IP lien recorded to GE Capital
    2014 : Anticipated expiration
    2015 : Lien released back to Affymetrix
         : Patent lapses for unpaid maintenance fees
    2016 : Affymetrix acquired by Thermo Fisher

NPE / troll-pattern signals

Preface: this chain contains exactly two post-issuance recordings, both of which are the two halves of a single secured-lending transaction (pledge + release). There is no third-party acquirer anywhere in the chain.

Verdict

Operating-company assertion

Justification: The only recorded post-issuance entries are Reel 028465/0541 (security agreement executed 2012-06-25, recorded 2012-06-27, Affymetrix → General Electric Capital Corp. as Agent — collateral for the $100M credit facility of even date) and Reel 037109/0132 (release by secured party executed 2015-10-28, recorded 2015-11-13, back to Affymetrix). Neither is a transfer of ownership to an asserter; the second merely discharges the first. Throughout the patent's enforceable life the owner of record was Affymetrix, Inc., a company that shipped the GeneChip probe-array products and analysis software embodying the claims, and that asserted the '887 patent itself against a direct competitor, Illumina, Inc. (D. Del. No. 1:04-cv-00901-JJF, Count 5, later dismissed with prejudice in 2006). There is no shell LLC, no known NPE, no cascading transfer, no fire-sale, and no defense-aggregator endpoint anywhere in the record — the sole genuine signal is securitization, which is a financing event, not an NPE pattern.

Verification link (USPTO Assignment Center, search by patent number): https://assignmentcenter.uspto.gov/ ; legacy front end: https://assignment.uspto.gov/patent/index.html . Search the patent number 6607887; reels to inspect are 028465/0541 and 037109/0132.

Open items / low-confidence points I want on the record rather than smoothed over:

1. The original inventor→Affymetrix assignment reel/frame and its correspondent were not retrieved; only Affymetrix's status as original assignee is established.
2. Correspondents of record for reels 028465/0541 and 037109/0132 were not retrieved, so signal #3 is honestly reported as "unclear" rather than scored.
3. No Thermo Fisher assignment was found on this patent's record — I have not asserted one.

I'll research the prior art citations for US 6,607,887, starting with the patent's own reference lists (both US patent citations and non-patent literature).

I found the Justia reference list. Let me pull the complete "Referenced Cited" list and the non-patent references.

Let me fetch the full reference lists directly.

Prior Art Analysis — US 6,607,887

1. Threshold identification (per the authoritative patent text)

Critical framing for §102. Because the effective priority date is 1994-10-21, only references that (a) published more than one year before that date (§102(b)), (b) published/filed before it (§102(a)/(e)), or (c) fall within the statutory exceptions, can anticipate. References with later dates are §103 art at best, or are the applicant's own family. Note also that '887 is a continuation in the Chee "computer-aided visualization" family — US 5,795,716 (same title) is the earlier member and is asserted in the Delaware litigation you summarized; it is a family member, not prior art.

2. IMPORTANT LIMITATION ON THIS REPORT

My tool budget was exhausted before I could retrieve the complete front-page "References Cited" list, the Non-Patent Citations (NPL) list, or the examiner's actual §102/§103 rejections from the file history. What I did retrieve is the opening portion of Justia's "Referenced Cited → U.S. Patent Documents" table for US 6,607,887 (the list was truncated after U.S. 5,727,098). The list below reproduces exactly what was retrieved, and I flag where I am inferring subject matter rather than confirming it. I have not fabricated any reference number, date, or inventor.

3. References Cited (US patent documents) — as retrieved

Source: Justia "Referenced Cited" table for US 6,607,887 — https://patents.justia.com/patent/[6607887](/patent/6607887)

⚠️ What is missing: I could not retrieve (a) the remainder of the US-patent list beyond item 36, (b) the foreign patent documents cited, (c) the Non-Patent Citations (NPL) — which in this family likely include key base-calling/sequencing-by-hybridization papers and the Affymetrix sister applications — or (d) the examiner's actual rejections, which would identify which reference was applied against which claim. Any of these could contain the true §102 anticipant.

4. References named inside the '887 specification (background / incorporated by reference)

These are affirmatively identified in the patent text itself and are therefore the references most loaded against the disclosure:

These establish the array/hybridization infrastructure as known art well before 1994. None of them, on their face, discloses the '887's distinguishing subject matter — the intensity-based base-calling algorithms (intensity-ratio, reference, statistical methods) and the graphical comparative-visualization interface.

5. Which claim(s) each class of reference could potentially anticipate

Because the visible claims of '887 (from the FPO text) are directed to (i) mutation identification by comparing reference vs. sample probe-intensity sets and analyzing "selected region" characteristics (claim 20 and dependents 21–23) and (ii) graphical display/comparison of multiple sequences (claim 24 and dependents 25–35), the mapping is:

• Claim 20–23 (intensity-comparison mutation calling / "bubble" region analysis): the only listed references with any anticipatory potential are the sequencing-by-hybridization patents — Macevicz 5,002,867, Drmanac 5,202,231 (and, more weakly for lack of pre-1994 date, Drmanac 5,492,806 / 5,525,464). These teach deriving sequence from hybridization (probe) intensities, but I have no evidence they disclose the specific comparison of a reference-intensity set to a sample-intensity set with interrogation-position region analysis. On the record retrieved, none is a clean §102 anticipant.
• Claims 24–35 (display reference sequence in a first area, sample sequence in a second area; linking; indicating differing bases): the image-analysis/cytometry patents (Hara, Shiraishi, Bacus, Rutenberg, Stockham, Hemminger) disclose computer-displayed, annotated biomedical data but not nucleic-acid sequence comparison. They are §102(b) art as to generic "display/compare on a computer" features only — insufficient to anticipate any full '887 claim.
• Pirrung 5,143,854, Fodor 5,445,934, Winkler 5,384,261, Ellman 5,288,514: disclose array synthesis/combinatorial chemistry. They support the "chip" context but do not disclose the claimed base-calling or visualization steps.
• Hunkapiller 4,811,218, Prober 5,306,618 / 5,332,666: disclose sequencing detection hardware; relevant only to any "probe intensity" measurement limitations.

Bottom line on §102: On the references actually retrieved, no single reference appears to disclose every element of any '887 claim, and the front-page list is dominated by (a) pre-1994 image-analysis background and (b) the applicant's own incorporated-by-reference array-synthesis patents. The genuine anticipation risk for this patent would most likely lie in the Non-Patent Citations / foreign documents (e.g., sequencing-by-hybridization base-calling literature and the sibling Affymetrix applications) that I was unable to retrieve — not in the US patent-document list shown above. That is a firm limitation of this report, not a conclusion that no anticipation exists.

6. Explicit confidence statements

• High confidence / confirmed: the bibliographic data in §1; the identity of references #1–36 as listed; that these are the "References Cited" (not "Cited By") of '887; the incorporation-by-reference passages in §4.
• Moderate confidence / inferred: subject-matter descriptions for Macevicz, Pirrung, Drmanac, Winkler, Fodor, Ellman, Pinkel.
• Low confidence / not confirmed: titles and content of the Hara/Shiraishi/Bacus/Rutenberg/Stockham/Hemminger/Weiss/Holmes/Mitsuhashi/Hunkapiller references; the inventor of item 36; and the complete reference and NPL lists (truncated).
• Not performed: review of the '887 file history rejections, which would be required to state definitively which reference was applied under §102 against which claim. If you want, I can target the USPTO PatentCenter/Public-PAIR file wrapper and the Google Patents "Similar Documents"/"Cited By" views (note: "Cited By" = later, forward citations and are not prior art) in a follow-up pass.

One cross-reference flag (no contradiction): your litigation section correctly notes US 5,795,716 (same title) was asserted in Affymetrix v. Illumina, 1:04-cv-00901-JJF. That patent is a family member of '887, not prior art — I mention it only so it is not mistakenly counted as a §102 reference.

I'll first pull the actual prior-art references cited on the face of US 6,607,887 (the fetched page text cut off before the reference list), then analyze the § 103 combinations.

I have the front-page reference list now. Let me verify dates/families of the most on-point references and check the '887's own prosecution/priority chain.

Obviousness Analysis — US 6,607,887 B2 (Chee, Affymetrix), 35 U.S.C. § 103

Analyst note on sources. The Google Patents page for US 6,607,887 (https://patents.google.com/patent/US6607887/en) supplies only the "Prior art keywords" (base; intensity; sequence; nucleic acid; probe) and classification/CIT tables in the text I was able to retrieve — the fetched document is truncated mid-sentence at FIG. 21 and the "References Cited" tables that normally follow are not present in it. I therefore reconstructed the prior-art section from the Justia front-page mirror of the same patent (https://patents.justia.com/patent/6607887, "Referenced Cited"), cross-checked against the PubChem citation list for the sibling patent US 6,242,180 (https://pubchem.ncbi.nlm.nih.gov/patent/US-6242180-B1). All references discussed below are from that face-of-patent list unless I say otherwise, and I flag every inference about a reference's content that I could not verify from the reference itself.

1. The claims that must be analyzed

Claims 1–13 as granted (per Justia) are narrower than the specification's disclosure. The specification teaches three base-calling methods (intensity-ratio, reference, statistical) plus pooling, "bubble"/dark-region analysis, and a comparative visualization GUI, but the granted claims are limited to:

• Claim 1 — a method of identifying an unknown base in a sample nucleic acid sequence comprising (a) inputting probe intensities for probes "that differ by a base at an interrogation position corresponding to the unknown base"; (b) "analyzing the probe intensities and at least one probe intensity from a nucleic acid probe with an interrogation position corresponding to a position near the unknown base"; and (c) generating a base call.
• Claims 2–6 — the "expected-for-a-mutation" predicates (2–4), the near = adjacent limitation (5), and interrogation position internal to the probe (6).
• Claims 7–13 — the same subject matter as a computer program product, with claim 8 naming the carrier (memory, hard drive, floppy disk, CD-ROM, flash memory, tape).

The point of novelty is element (b): use of intensity data from the neighboring interrogation position, not just the four probes at the position being called. This corresponds to the second implementation of the reference method (the neighboring-ratio computation of FIGS. 11A–11D) and the "dark region"/bubble method of FIGS. 14–15. Everything else in claim 1 is the admitted, well-documented state of the art as of 1994.

2. Threshold issue that controls the entire § 103 analysis: the effective filing date

US 6,607,887 was filed 2001‑02‑27 as a later continuation in the 1994 family (5,795,716 → 5,974,164 → 6,242,180 → 6,600,996 → 6,607,887 → 6,733,964; see the family table at https://patents.google.com/patent/US5525464#21). Google lists the priority date as 1994‑10‑21. Pre‑AIA §§ 102/103 govern (effective filing date well before 2013‑03‑16).

This matters because the two most on-point references in the field were filed within five days of, and published after, 1994‑10‑21:

Two consequences:

1. If claims 1–13 are entitled to 1994‑10‑21, then WO 95/11995 is not prior art at all, and the § 102(e) reach of US 5,837,832 / WO 95/11995 is additionally defeated for § 103 purposes by pre‑AIA § 103(c): both are Affymetrix/Affymax subject matter, and § 103(c) disqualifies art that "qualifies as prior art only under … subsection (e)" when it was commonly owned with the claimed invention. A rejection built on WO 95/11995/US 5,837,832 alone would fail under this scenario.
2. If claims 1–13 are not entitled to 1994‑10‑21 — e.g., because the neighbor-interrogation-position analysis of FIGS. 11 and 14–15 was added by a later continuation and lacks § 112 support in the 1994 parent — then the effective date is 2001‑02‑27, and WO 95/11995 becomes unambiguous § 102(b) art (published 1995, more than one year before 2001‑02‑27). Critically, § 103(c) does not apply to § 102(b) art, so common ownership ceases to be a shield. In that scenario the whole family (US 5,795,716 (1998), US 5,974,164 (1999)) also becomes § 102(b) art against these claims.

I cannot resolve which scenario is correct from the materials available, and I flag it explicitly: I have not verified whether the 1994 parent application contained the "neighboring interrogation position" disclosure. The entire strength of any § 103 ground rises or falls on that question, so it is the first thing to confirm from the file wrapper/priority documents.

3. Person of ordinary skill

A POSITA here is a bioinformatics/software engineer or molecular biologist (B.S./M.S. plus 2–3 years, or Ph.D.) with working knowledge of (i) light-directed oligonucleotide array fabrication and scanning (Fodor 1991; US 5,143,854; US 5,445,934), (ii) sequencing-by-hybridization decoding (Drmanac; Southern), and (iii) routine data-processing/pattern-recognition programming (Dear & Staden; Hunkapiller; Stockham).

4. Claim-element mapping

5. The § 103 grounds

Ground 1 — Fodor/Pirrung + Drmanac + Southern (works under either effective-date scenario)

US 5,143,854 + US 5,445,934 (Fodor/Pirrung) + US 5,202,231/5,525,464 (Drmanac) + Southern 1992 + Strezoska 1991.

Fodor/Pirrung render the array and its readout obvious (the '887 concedes this in its own Background, referring to WO 92/10588 and 95/11995 and to the VLSIPS patents). Drmanac and Southern render the analytical step obvious: both teach that a perfectly matched probe gives the strongest signal, that a single internal mismatch measurably destabilizes duplex formation, and that the base at a position is inferred by comparing the relative intensities across the probe set. Drmanac's decoding algorithms are the strongest bridge to element (b): reconstructing a sequence from the k-tuple "word contents" of a tiled probe set necessarily means the call at position i is made jointly with the signals at positions i±1…i±k. A POSITA reading Drmanac with Fodor would have had every reason to use neighboring-position intensities rather than throwing that data away.

Motivation: same field, same problem (call bases accurately from array intensities), and the neighboring data is not merely available — it is in the same data file, from the same scan, indexed by known probe position. KSR makes the combination of a known method with a known technique for improving it (here: adding the immediately adjacent data points to a comparison already being performed) a paradigm case of obviousness, particularly where the results are as predictable as an intensity ratio moving from 0.9 to 1.48 across a mutation boundary (the '887's own FIG. 11D).

Ground 2 — WO 95/11995 / US 5,837,832 + Fodor/Pirrung + Drmanac + Dear & Staden (conditional on the effective date; the decisive ground)

WO 95/11995 is the single most devastating reference if it is available as art. It expressly discloses (a) the WT + four-substitution-probe set for every base of a reference sequence, (b) the layout in which probes for adjacent reference positions are physically adjacent on the chip, and (c) "comparative hybridization" — hybridizing a reference and a target to the same array and comparing relative specific binding to determine whether they differ, including claims reciting dual labels (WO 95/11995 claims 63–64, text at https://patentimages.storage.googleapis.com/de/f1/4e/ad721eb53b37f1/WO1995011995A1.pdf). Element (b) of claim 1 — reading a neighboring interrogation position — is then a trivial and expressly-incentivized use of the reference's own arrangement. Adding a general-purpose computer to perform it is taught by Hunkapiller (US 4,811,218) and Dear & Staden.

Motivation / KSR factors: (i) the reference itself supplies the design incentive (its stated object is detecting single- and multiple-base substitutions relative to a reference sequence); (ii) the neighboring positions are, by the reference's own chip layout, the nearest data to the call being made; (iii) the art recognized a known problem (cross-hybridization causing miscalls in the "dark regions" around a mutation) and the claimed solution is a finite, predictable use of already-collected points; (iv) nothing in the claims reflects an unexpected result — the '887 reports only a 0.28 vs. 0.15 normalized difference (FIG. 11D), squarely within routine signal-to-noise engineering.

But this ground is barred by § 103(c) common ownership if the claims keep the 1994‑10‑21 date, or by the five-day date gap if the reference is relied on under § 102(e).

Ground 3 — Computer-program-product claims (7–13)

Hunkapiller US 4,811,218 + Dear & Staden 1991 + Stockham US 5,273,632 + Hemminger US 5,297,288 + Bacus US 4,741,043.

Claims 7–13 add nothing to claim 1 but a computer readable medium recitation. Hunkapiller discloses automated, computer-implemented calling of bases from intensity data for sequencing; Dear & Staden discloses a general-purpose sequence assembly/editing program that compares neighboring sequence regions; Bacus/Stockham/Hemminger disclose reading, storing and displaying arrayed biological image data. Where the underlying analytical method is known, implementing it in software and storing it on a conventional medium is obvious as a matter of routine engineering. Claim 8's media list (memory, hard drive, floppy, CD-ROM, flash, tape) is a catalogue of conventional 1990s carriers, each of which the '887's own background/FIG. 1–2 discussion acknowledges.

Ground 4 — Dependent limitations

• Claim 5 ("near" = adjacent): directly met by WO 95/11995's adjacent-position chip layout, and inherent in any per-base tiling scheme (Fodor/Pirrung).
• Claim 6 (interrogation position internal): taught by Southern 1992 and WO 95/11995 (11-mers/20-mers with the variable position internal, as the '887 itself describes at FIG. 7 and FIG. 14A's "interrogation position of each probe being at the 12th base position").
• Claims 2–4 and 9–11 ("lower as expected for a mutation" / mutant identified by highest intensity): the mismatch-destabilization knowledge of Southern 1992 and Drmanac 1993 supplies the predicate; the "call the highest intensity probe" rule is the acknowledged baseline ("the intensity should be highest for the probe that binds most strongly to the sample sequence").
• Claims 12–13: same as 5–6 in product form.

Ground 5 — Applicant's own specification as an admission

The '887's specification states, in describing FIG. 8, that "the fluorescent intensities of cells near an interrogation position having a mutation are relatively dark … [because] the cells at interrogation positions near a mutation do not contain probes that are perfectly complementary to the sample sequence." That is an admission that the neighboring-position signal depression was known and observable. Once the phenomenon is known, using the neighboring intensity in the call is the very definition of an obvious improvement, and no secondary consideration (unexpected results, long-felt need, commercial success) appears to attach to the narrow "near-probe" limitation as claimed.

6. Likely rejection structure (assumes the effective date is not 1994‑10‑21)

7. Honest assessment of the strength of these grounds

Where the grounds are strong: if the claims are held not entitled to the 1994‑10‑21 date, they are very likely invalid. WO 95/11995 supplies both the probe-set structure and the adjacent-probe layout, the '887 itself incorporates WO 95/11995 by reference, and implementing the analysis on a computer is documented by the cited Hunkapiller/Dear/Stockham references. The improvement over the disclosed reference method is one additional data input, with no showing of unexpected results.

Where the grounds are weak or unresolved (flags, not conclusions):

1. The date gap. WO 95/11995 was filed 1994‑10‑26 and published 1995‑05‑04; the '887 priority is 1994‑10‑21. If the claims keep that date, the most on-point reference is unavailable.
2. § 103(c). US 5,837,832, WO 95/11995 and US 6,242,180 are all Affymetrix/Affymax and (except 6,242,180, which shares the same priority and would be an obviousness-type double-patenting rather than § 103 issue) qualify as art only under § 102(e)/(g). Common ownership defeats their use in a § 103 ground under pre-AIA § 103(c). Note the '887's face list actually cites US 6,242,180 (Chee) — a same-priority family member — which is indicative of a double-patenting rather than a § 103 posture.
3. Unverified reference content. I confirmed the content statements attributed above to WO 95/11995/US 5,837,832 (adjacent-position layout; WT + four substitution probes; comparative-hybridization claims), Southern 1992 (title/venue) and Fodor 1991 (title/venue) from retrieved text. Statements about US 5,202,231 / 5,492,806 / 5,525,464, US 4,811,218, US 5,273,632, US 5,297,288 and the Hara/Shiraishi family are based on their titles, assignees and examiner citations in the '887's face list — I did not retrieve their specifications, and each should be verified column-by-column before any ground is relied upon.
4. What I could not verify at all: whether the 1994 parent application supported claims 1–13, and whether the WO 95/11995 / US 5,837,832 subject matter relied upon was carried in Ser. No. 08/143,312 (filed 1993‑10‑26) for § 102(e) purposes. Both should be checked against the file wrappers before this analysis is used.

Net opinion: Claims 1–13 of US 6,607,887 would be prima facie obvious under § 103 over WO 95/11995 (or US 5,837,832) in view of Fodor/Pirrung and Drmanac, with Hunkapiller/Dear & Staden for claims 7–13 — if the claims are not entitled to the 1994‑10‑21 priority date. If they are so entitled, the strongest art is date-barred or removed by § 103(c), and the remaining pre-October-1994 art (Fodor, Pirrung, Drmanac, Southern, Strezoska, Macevicz, WO 92/10588) is a genuine but less certain ground, because none of those references, on the face of the citations available to me, expressly teaches the neighboring interrogation position limitation that constitutes the point of novelty of claim 1.