US 6242180

I'll search for authoritative information on this patent number.

Let me pull the patent record directly and check for any CAFC/litigation activity.

Let me retrieve the actual claim set for US 6,242,180 specifically.

US 6,242,180 B1 — Identification

Note on the identifier as given: "6242180" is interpreted literally as US Patent No. 6,242,180 B1 (Google Patents renders it "US6242180B1"). All findings below relate to that number only; no similar numbers (e.g., 6,242,185; 6,222,180) were substituted.

Sources: Google Patents (https://patents.google.com/patent/US6242180/en), OSTI/DOE patent record 873772 (https://www.osti.gov/doepatents/biblio/873772), PubChem patent record US-6242180-B1 (https://pubchem.ncbi.nlm.nih.gov/patent/US-6242180-B1), Unified Patents portal (https://portal.unifiedpatents.com/patents/patent/US-6242180-B1).

Abstract (verbatim)

"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)."

USPTO / CAFC 2026 search results

• USPTO records: The authoritative bibliographic data above is consistent across Google Patents, OSTI/DOE, and PubChem. The patent is recorded as expired for failure to pay maintenance fees, with "Anticipated expiration" 2014-10-21 and a subsequent 2015-11-13 reassignment releasing a General Electric Capital Corporation security interest.
• CAFC 2026 dockets: I searched 2026 Federal Circuit material (scheduled-case lists, docketing notices, and Federal Circuit round-up publications) and found no 2026 CAFC appeal, oral argument, or decision captioned to US 6,242,180 or to Affymetrix involving this patent. I cannot rule out a docket entry that is not surfaced by public web search, so treat this as "not found," not as "confirmed none."
• Litigation flag: The Google Patents record carries a generic "Family has litigation / First worldwide family litigation filed" Darts-IP flag for the family. That flag does not identify a specific case, party, or year, and I did not find a named 2026 proceeding behind it. Given the patent expired in 2014, a live 2026 merits appeal on these claims is unlikely.

Plain-language overview of the independent claims — with explicit uncertainty

Important caveat: I was not able to retrieve the verbatim claim text of US 6,242,180 in this search pass. The claim text that surfaced in results belongs to the related but distinct continuation US 6,607,887 (method and computer-program-product claims directed to analyzing a probe intensity from an interrogation position "near the unknown base"), and I am deliberately not presenting that text as the claims of 6,242,180. What follows is a description of the subject matter the specification presents as the invention, which is very likely coextensive with the independent claims given the abstract, but should be verified against the granted claim set (column 1 of the printed patent) before being relied upon.

The specification expressly frames the disclosure as several distinct advances, and the 59-claim set most plausibly includes independent claims in these families:

1. Intensity-ratio base calling. A computer-implemented method/system that takes probe intensities from multiple nucleic acid probes that differ by a single base at an interrogation position, compares the intensities (highest versus next-highest, then successive ratios against a ratio cutoff), and calls the unknown base — assigning an IUPAC ambiguity code when discrimination is insufficient (FIGS. 9).

2. Reference-method base calling. A method/system that calls an unknown base by comparing the probe-intensity pattern of a sample sequence against the corresponding probe intensities of a reference sequence run on the same chip wild-type, flagging significant changes as candidate mutations; a second implementation additionally analyzes neighboring probe positions (ratio-of-ratios and normalized-difference cutoffs) to improve accuracy (FIGS. 10A–11D).

3. Statistical base calling. A method/system that calls an unknown base by comparing sample probe intensities against statistical distributions (means and standard deviations of normalized wild-type and "other" base ratios) computed across multiple reference experiments (FIG. 12).

4. Pooled/multiplexed processing. A method in which a reference nucleic acid and a sample nucleic acid are labeled with distinguishable markers (e.g., fluorescein vs. rhodamine or biotin/phycoerythrin), combined, fragmented, co-hybridized to the same array, and scanned at the two wavelengths, thereby reducing experiment-to-experiment variation (FIG. 13).

5. Dark-region ("bubble") mutation identification. A method of locating mutations and rejecting false positives by using hybridization data from more than one base position: identifying a region where wild-type probe intensity differs between sample and reference, comparing the width of that region to the probe length to classify it as a single mutation (width ≈ probe length), no mutation (width substantially less), or multiple mutations (width greater than probe length), then applying base calling at the positions predicted from the interrogation position within the probe (FIGS. 14A–15).

6. Comparative visualization. A computer-implemented method/system for displaying reference sequences in one display area and sample sequences in another, with linking of sequences, navigation, editing/verification, and per-base intensity graph windows for side-by-side comparison across experiments (FIGS. 16–18).

Whether these map one-to-one onto six independent claims, or are consolidated into fewer independent claims with dependent claims covering the variations (e.g., the "computer program product ... computer readable medium" form, which the specification explicitly contemplates), I cannot confirm without the granted claim text. If you need claim-by-claim fidelity, the authoritative source is the printed patent's claims (column starting at approximately line 1 of the claims section) or the USPTO PatentCenter/Patent Public Search record for application 09/158,765.

I'll research litigation involving US Patent 6242180. Let me run several targeted searches.

Initial searches returned mostly look-alike patents (Kodak's 6,292,218, Masimo's RE47,218). Let me dig deeper with more specific queries.

Let me search litigation-specific databases and the patent's family litigation record.

Summary of Findings — U.S. Patent No. 6,242,180

Caveat up front: I was unable to complete the full set of searches I intended (Unified Patents litigation caselist, PACER, and CAFC dockets) because I hit my tool-use limit mid-research. The results below reflect what I could actually retrieve and verify. I could not identify any specific, named litigation asserting U.S. Patent No. 6,242,180.

The patent itself (verified, literal)

• Patent number: US 6,242,180 B1 (interpreted literally as written — I did not treat this as 6,292,218 or any other number)
• Title: "Computer-aided visualization and analysis system for sequence evaluation"
• Inventor: Mark S. Chee
• Assignee: Affymetrix, Inc. (original and current)
• Application No.: 09/158,765
• Priority date: 1994-10-21; Filed: 1998-09-23; Granted: 2001-06-05
• Status: Expired – Lifetime (anticipated expiration ~2014-10-21)
• Sources: Google Patents, Unified Patents portal, OSTI

Litigation results

No case specifically naming US 6,242,180 was found in the sources I reached. I want to be explicit rather than fabricate:

One relevant flag — "Family has litigation"

The Google Patents record for US 6,242,180 carries a "Family has litigation" indicator linking to a Darts-IP record (https://patents.darts-ip.com/?family=23276902). This flag relates to the patent family, not necessarily to the '180 patent individually, and the Darts-IP detail page was not retrievable in my searches. Treat this as a lead requiring a direct Darts-IP/Docket Navigator/PACER lookup, not as confirmed litigation against the '180 patent itself.

Context: Affymetrix's litigation campaigns (patents actually named in results)

Affymetrix was an active litigant, but the cases I found named other patents — none confirmed to include 6,242,180:

• Affymetrix v. Synteni/Incyte (D. Del., 1998; later transferred to N.D. Cal.). Asserted U.S. Pat. Nos. 5,445,934; 5,744,305/5,744,308; 5,800,992; 5,871,928; 6,040,193. Settled Dec. 21, 2001 with cross-licenses. (Incyte press release)
• Affymetrix v. Illumina (D. Del., filed July 26, 2004; six patents, five after withdrawal; jury found infringement Mar. 13, 2007; ~$16.7M; multi-phase trial). Patents not enumerated in the sources retrieved. (Illumina 10-K)
• Illumina v. Affymetrix / interference appeal (Agilent) — N.D. Cal. No. C 06-05958 JW, a §146 appeal from Interference No. 105,285 (Schembri patent, 6,513,968). Not the '180 patent. (Justia PDF)
• Affymetrix v. PE Corp. — inequitable conduct/unenforceability dispute; patents not the '180. (Casetext)
• OXG/OGT v. Affymetrix — UK/US patent disputes (2000); not the '180 patent.

Look-alike patents encountered (explicitly NOT 6,242,180)

Per your strict rule, I am flagging these so they are not mistaken for the patent at issue:

• US 6,292,218 (Kodak) — digital camera preview; ITC/Apple/RIM litigation. This is a different patent and appears frequently in searches.
• US RE47,218 (Masimo) — asserted in Masimo v. Sotera Wireless, No. 3:19-cv-01100-BAS-NLS (S.D. Cal.).

Recommended next steps to confirm/deny litigation

1. Search Unified Patents litigation caselist and Docket Navigator directly for "6,242,180."
2. Query PACER for "6:242,180" and CourtListener RECAP.
3. Check the Darts-IP family 23276902 record linked from Google Patents.
4. Cross-check Affymetrix's SEC 10-K litigation disclosures for the relevant years (2004–2008) to see whether the '180 was among the six Illumina patents.

Bottom line: Based on what I could retrieve, I have no confirmed litigation naming U.S. Patent No. 6,242,180. The patent family carries a litigation flag, so litigation involving family members likely exists, but I could not verify any case asserting the '180 patent itself, and I will not speculate beyond the record.

I'll verify the ODP "no proceedings" result against public sources before writing anything up.

Let me probe a few more angles, including the Unified Patents portal entry and any Federal Circuit activity.

PTAB / AIA Trial Landscape — U.S. Patent No. 6,242,180

Patent: U.S. 6,242,180 B1 — "Computer-aided visualization and analysis system for sequence evaluation"
Inventor: Mark S. Chee | Assignee of record: Affymetrix, Inc.
Application: 09/158,765 | Filed: 1998-09-23 | Priority: 1994-10-21 | Granted: 2001-06-05
Status per source: Expired – Lifetime; anticipated expiration 2014-10-21

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Proceedings overview

Total AIA trial proceedings on file: 0. The structured "PTAB proceedings on file" block (USPTO Open Data Portal, most recent ingest) returns no IPR, PGR, or CBM proceeding for U.S. 6,242,180 — zero active, zero with claims invalidated, zero with claims sustained, zero settled, zero institution-denied. I ran eight independent web searches to look for un-indexed or older proceedings (patent number alone; patent number + IPR/PTAB; title + IPR; petitioner-side terms; Federal Circuit; Affymetrix enforcement history; Unified Patents portal; Docket Alarm) and found no evidence of any petition ever being filed against this patent. The defensive bottom line is therefore not "hardened by surviving IPRs" and not "claims canceled by the Board" — it is something stronger and simpler: the patent's term ended on or about 2014-10-21, so there is no live patent to assert. Any demand letter citing US 6,242,180 today is either a mistake or is trading on the fact that the recipient won't check the expiration date. See the caveats in the final section on what I could and could not verify.

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Proceedings

None. There is no proceeding to report, and I will not invent a proceeding number, panel, or FWD to fill this section. Specifically:

• No IPR petition (available for patents filed/issued in relevant part from 2012-09-16 onward) appears in any public source I searched.
• No PGR — this patent's effective filing date (1994-10-21 priority; 1998-09-23 filing) predates the 2013-03-16 PGR cutoff by nearly two decades, so PGR was never available.
• No CBM review — CBM (2012–2020) was limited to patents claiming a financial product/service or a covered business method; a bioinformatics/sequence-analysis patent of this vintage would not have qualified.
• No Federal Circuit appeal of any PTAB decision on this patent, because there was no PTAB decision.

Identifiers/adjacent matters that are NOT proceedings on this patent — flagged because they are easy to conflate and I want to be explicit that I am not counting them:

• US 6,992,180 (Enzo Life Sciences) and US 7,064,197 (Enzo) are different patents from a different family; they appear in the D. Del. litigation and the Enzo/Life Technologies license (e.g., Affymetrix as defendant, D. Del. op. in C.A. 12-104). The "'180 patent" shorthand in those documents refers to 6,992,180, not 6,242,180.
• EPO opposition T 1509/09 (Affymetrix, EP 0 853 679, "Expression monitoring by hybridization to high density oligonucleotide arrays") was a European opposition decided 2012-07-05 involving Agilent, CombiMatrix, Clondiag, and Illumina. European forum, different patent — irrelevant to US PTAB but sometimes cited in blog summaries of "Affymetrix patent challenges."
• The Google Patents family record for US 6,242,180 carries a "Family has litigation" indicator (Darts-IP family 23276902). That is a family-level flag; it is not evidence of any AIA trial on this patent, and Google Patents shows no US litigation or PTAB tab content for the patent itself.

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Strategic summary

Claim status: all claims UNTESTED at the PTAB — but moot. No claim of 6,242,180 has ever been canceled, narrowed, or confirmed by the Board. The patent was never amended in an AIA trial, so the claims stand exactly as granted in 2001: unadjudicated and, from a practical standpoint, unassertable. The controlling fact is the term. Under the Google Patents and Unified Patents records, the patent expired on/around 2014-10-21 (twenty years from the 1994-10-21 priority date; Unified lists 2014-10-20, Google lists 2014-10-21 — the one-day spread is a listing artifact, not a substantive dispute). Google's "Expired – Lifetime" designation (as opposed to "Expired – Fee Related") indicates expiration by operation of term rather than a maintenance-fee lapse. That means there is no ongoing infringement to enjoin and, under 35 U.S.C. § 286, damages are limited to infringement occurring within six years before a complaint is filed. A suit filed now could reach, at most, acts on or before 2014-10-21 — a shrinking and largely time-barred window.

Estoppel landscape: no § 315(e)(2) estoppel exists, because no IPR reached a final written decision. That cuts against a defendant in the narrow sense that the patent owner also bears no adverse Board findings — but it is academic. There is no petitioner whose § 315(e)(2) estoppel could bind anyone, and there is no privity chain to trace. If you needed to invalidate the claims (for example, to defeat a retrospective royalty theory or to clear a cloud on a contract), every prior-art ground remains available: § 102 and § 103 over patents and printed publications, plus § 101 and § 112 challenges that an IPR could never have reached. Note, though, that a district court invalidity defense to an expired patent still requires Article III standing to seek a declaratory judgment of invalidity — a real procedural hurdle if there is no reasonable apprehension of suit.

Pattern signals: none, and structurally there could not be many. There is no repeat petitioner, no Unified Patents-funded challenge campaign, and no patent-owner appellate history on this patent. Affymetrix's actual enforcement era against Illumina (D. Del., filed 2004-07-26; jury verdict of infringement 2007-03-13; ~$16.7M retroactive royalty; later settlement/licensing) predated the IPR regime entirely — IPRs only became available 2012-09-16, and this patent expired roughly two years later. So the absence of IPR activity here is not the weak "well-asserted patents eventually attract IPRs" signal from the standard playbook; it is a function of timing (enforcement predating the AIA) plus an imminent term expiry that removed any petitioner's incentive. Anyone who tells you "no IPRs means the patent is a survivor, so pay" has the inference exactly backwards here.

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Recommended next steps

1. If you have received a demand letter citing US 6,242,180: do not file an IPR — there is nothing to institute against. Instead, verify the expiration and put the sender on notice in writing. Cite the Google Patents legal-status field ("Expired – Lifetime"; anticipated expiration 2014-10-21, https://patents.google.com/patent/US6242180/en) and the Unified Patents record listing Expiration Date 2014-10-20 (https://portal.unifiedpatents.com/patents/patent/US-6242180-B1). Under 35 U.S.C. § 286, pre-suit damages are limited to the six years before filing, and here the entire enforceable period ended in 2014. A letter asserting this patent against post-2014 conduct is a candidate for fee-shifting under § 285 and, depending on the state, a state-law unfair-competition claim.
2. Check the family, not just this patent. Google Patents shows continuations claiming priority to this patent's chain, including US 6,607,887 B2 (from application 09/796,071) and US 2004/0175718 A1 (from 10/616,228), plus the parent US 5,974,164. Any continuation claiming the same 1994-10-21 priority shares the same expiration date, so the whole family's core is expired — but confirm each member's term and any terminal disclaimers independently before you rely on it. I have not verified the claim-by-claim priority chains of those family members.
3. If a live claim is asserted against you from another Affymetrix/Thermo Fisher patent: treat this patent as background art and licensing-context only. Affymetrix was acquired by Thermo Fisher Scientific (2016); the Google Patents "current assignee" field still lists Affymetrix, Inc., and there is a recorded 2015 release of a GE Capital security interest against Affymetrix, Inc. Confirm current ownership of record via the USPTO Assignment database (https://assignment.uspto.gov) rather than relying on patent databases, which lag.
4. Verify the null result yourself before you rely on it in a filing. My search was thorough but bounded. The authoritative negative comes from the ODP block supplied in the prompt; I could not directly render PTAB E2E (https://ptab.uspto.gov) or Docket Alarm result pages inside this task, and my Docket Alarm / targeted PTAB queries returned no results rather than a clean "zero hits" page. A five-minute confirmation on PTAB E2E by patent number, and on CourtListener (https://www.courtlistener.com) by "6242180," will close the residual gap. If either surfaces a proceeding I did not find, the estoppel and claim-status analysis above would need to be rerun — but nothing I found suggests one exists.

Confidence: High that no AIA trial proceeding has ever been filed against US 6,242,180 (consistent ODP data plus eight negative web searches across multiple independent databases). High that the patent's term expired in October 2014 based on two independent listings. Moderate on the exact expiration date (2014-10-20 vs. 2014-10-21 — a one-day discrepancy between sources) and on the current ownership of record, which I did not verify in the assignment database.

Assignment & Ownership Chain — US 6,242,180 B1

Scope note. Building on the identification section above: this patent is expired (anticipated expiration 2014-10-21), the owner of record never changed away from the Affymetrix entity, and the earlier CAFC/PEDS pass found no 2026 appeal. This section therefore reconstructs the (short) recorded chain and tests it against the NPE rubric. One methodological caveat up front: USPTO Assignment Center is a JavaScript application and returned no crawlable record text to web search, so reel/frame and correspondent data below were verified on sibling Affymetrix patents recorded on the identical event dates and cross-matched to the Google Patents legal-events table for 6,242,180. Where I infer rather than read the record directly, I say so.

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Inventors

Unusual pattern — flagged. The application that issued as 6,242,180 was filed 1998-09-23, and Chee is widely credited with co-founding Illumina, Inc. in 1998 (with David Walt, Larry Bock, John Stuelpnagel and Anthony Czarnik) — i.e., the sole inventor appears to have left the original assignee in the same window as the filing. Two important qualifications:

• This is not evidence of a portfolio fire-sale here. Under the 1994 priority date the invention was already Affymetrix's; the continuation filing was prosecuted and issued to Affymetrix in 2001, and Affymetrix continued to own it through expiration. A departing-inventor pattern is only a fire-sale precursor when the original assignee subsequently dumps the portfolio — which did not happen (see below).
• The co-founding-of-Illumina point comes from general knowledge, not from the assignment record or the patent front page. Treat it as context, not as a citation.

No inventor→company assignment instrument for the 1994 priority application appears in the 6,242,180 record; the applicant of record was Affymetrix itself, consistent with a pre-existing employment/assignment obligation.

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Original assignee

Google Patents still lists the current assignee as "Affymetrix Inc," which is consistent with there being no recorded post-expiration transfer to Thermo Fisher for this number.

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Assignment timeline

Three substantive records exist. All are corporate-housekeeping or securitization events; none is a transfer to a third-party owner.

• 1998-09-28 (executed) / recorded 1999-09-08 — Reel 010215/0164 (reel/frame inferred — verified on sibling Affymetrix patent US 6,491,871, same event date)

  • Conveyance: Merger (with survivorship) — recorded by the assignee itself, "MERGER (SEE DOCUMENT FOR DETAILS)"
  • Assignor: Affymetrix, Inc., a California corporation
  • Assignee: Affymetrix, Inc., a Delaware corporation
  • Correspondent: Not retrieved (Assignment Center correspondent field not crawlable; see signal 3)
  • Context: Internal reorg / corporate re-domestication — the pre-IPO California entity merged into the Delaware parent; no change in beneficial ownership.

• 2012-06-25 (executed) / recorded 2012-06-27 — Reel 028465/0541

  • Conveyance: Security Agreement (collateral assignment of IP to secure a $100,000,000 credit facility)
  • Assignor: Affymetrix, Inc., California/Delaware (record lists owner as Affymetrix, Inc., California)
  • Assignee: General Electric Capital Corporation, as Agent (Bethesda, MD; c/o GE Healthcare Financial Services)
  • Correspondent: Not retrieved
  • Context: Securitization — pledged as collateral under the Affymetrix credit agreement dated 2012-06-25 (filed as an SEC exhibit) and the June 2012 indenture for the 4.00% Convertible Senior Notes due 2019. This is a lien, not a sale; Affymetrix retained title.

• 2015-10-28 (executed) / recorded 2015-11-13 — Reel 037109/0132

  • Conveyance: Release by Secured Party
  • Assignor: General Electric Capital Corporation, as Agent
  • Assignee: Affymetrix, Inc.
  • Correspondent: Not retrieved
  • Context: Discharge of the 2012 lien on satisfaction/payoff — restores clean title to Affymetrix. (The release postdates the patent's 2014-10-21 expiration, so it is a portfolio-wide filing.)

Bottom line of the record: apart from the technical California→Delaware merger and a two-year collateral pledge to GE, US 6,242,180 never left Affymetrix. The chain terminates with title back at the operating company. There is no record of any assignment to an LLC, licensing vehicle, or aggregator.

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Timeline diagram

timeline
    title Ownership of US 6242180
    1994 : Priority application filed
    1998 : Application filed by Affymetrix California
    1999 : Merged into Affymetrix Delaware
    2001 : Patent issued to Affymetrix
    2012 : Security interest pledged to GE Capital
    2014 : Patent expires
    2015 : GE security interest released
    2016 : Affymetrix acquired by Thermo Fisher

(Event text deliberately kept short and punctuation-free per parser constraints; see the table above for exact dates and reel/frame.)

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NPE / troll-pattern signals

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Verdict

Operating-company assertion.

Every recorded instrument on US 6,242,180 is an operating-company event: the 1998-09-28 / recorded 1999-09-08 California→Delaware merger (Reel 010215/0164), the 2012-06-25 / recorded 2012-06-27 collateral pledge to GE Capital as Agent (Reel 028465/0541), and the 2015-10-28 / recorded 2015-11-13 release of that pledge back to Affymetrix (Reel 037109/0132). The patent never left Affymetrix, expired in 2014, and shows zero of the eight NPE signals — so no NPE classification is supportable.

Caveats, stated plainly: (i) the "assertion" prong of this verdict is not established for this specific patent — I found no suit naming it, so read the label as "operating-company ownership, no NPE involvement," not as "this patent was enforced"; (ii) reel/frame numbers are verified on sibling Affymetrix filings on identical dates and inferred to apply here; (iii) the correspondent-of-record field was not retrievable, so signal 3 is an evidence gap rather than a clean negative — if you need it nailed down, pull the three recordings directly at the USPTO Assignment Center (search patent number 6242180): https://assignmentcenter.uspto.gov/ (mirror: https://assignment.uspto.gov/patent/index.html).

I'll search for the USPTO record and citation data for US 6,242,180.

Now let me pull the authoritative "References Cited" list and the granted claims.

Let me obtain the front-page "References Cited" list from an independent full-text source.

Prior-Art Analysis for US 6,242,180 B1 — "Computer-aided visualization and analysis system for sequence evaluation"

0. Important corrections to the earlier section

Two things I have now been able to verify, one of which contradicts the previously generated summary:

(a) The granted claim text of US 6,242,180 is now available and it is not the "intensity ratio / reference / statistical" claim set. Two independent full-text mirrors reproduce the same claim 1 (Espacenet claims view for US6242180B1, and EveryPatent's reproduction of the printed patent):

1. A computer implemented method of calling unknown bases in a sample nucleic acid sequence, comprising: inputting a plurality of probe intensities, each probe intensity indicating hybridization affinity between a nucleic acid probe and the sample nucleic acid sequence; calling bases of the sample nucleic acid sequence according to the plurality of probe intensities; identifying a mutant base call that has indicated that a base at a position in the sample nucleic acid sequence is suspected as being a mutation; analyzing probe intensities of at least one position that is near the position of the suspected mutation; and changing the mutant base call to a nonmutant base call if the probe intensities of at least one position that is near the position of the suspected mutation are inconsistent with a mutation.

Claim 8 is the parallel computer-program-product claim; claim 10 is the parallel computer-system claim. This is the dark-region / "bubble" false-positive-removal family (FIGS. 14A–15 of the specification), not the intensity-ratio method (FIG. 9). The earlier section explicitly warned it could not retrieve the claim text and speculated the independent claims would cover the intensity-ratio/reference/statistical methods; that speculation should be treated as superseded. The prior-art relevance ranking below is therefore built on the verified claim 1/8/10 language.

Sources: https://pt.espacenet.com/publicationDetails/claims?CC=US&NR=[6242180B1](/patent/6242180B1)&KC=B1&FT=D&ND=10&date=20010605&DB=EPODOC ; http://www.everypatent.com/comp/pat6242180.html

(b) Claim count. The earlier section noted Espacenet's original-document record showing "59/59 Claims." I could retrieve claims 1–23 verbatim (with snippet truncation of claims 4, 12–15, 18–21). Claims 24–59 are not retrieved in this pass — so I cannot rule out further independent claims (e.g., directed to the visualization/comparative-display subject matter, which would change the prior-art mapping for the later claims).

(c) Small bibliographic discrepancy, unresolved. Unified Patents states application date 1998-09-22 / priority 1994-10-20 / grant 2001-06-04, while Google Patents and Espacenet state 1998-09-23 / 1994-10-21 / 2001-06-05. The 1-day discrepancy is carried forward, unreconciled.

Methodological caveat: I only have web search available, not a direct Patent Public Search / PatentCenter query session. I therefore reconstructed the "References Cited" list from the PubChem patent record for US-6242180-B1 (which mirrors USPTO front-page data), cross-checked against the count independently reported by Unified Patents. I could not open the printed front page itself.

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1. The cited patent documents (52 references)

PubChem's citation record for US-6242180-B1 enumerates 52 patent documents; Unified Patents independently reports "Patent Art (52)." The counts agree, which corroborates the list. The PubChem record also tags each entry — (APP) = cited by applicant, (SEA) = cited in the examiner's search (only US-5,974,164-A carries the SEA tag in the visible excerpt).

Source: https://pubchem.ncbi.nlm.nih.gov/patent/US-6242180-B1 ; https://portal.unifiedpatents.com/patents/patent/US-6242180-B1

1A. Array synthesis / VLSIPS chemistry (the bulk of the "applicant" citations)

1B. Sequencing by hybridization (SHB) — the most materially relevant cluster

These are the references that could arguably be §102 art against the front half of claim 1 (inputting probe intensities; calling bases from those intensities).

1C. Computer-graphics / image-processing / data-handling cluster (the 1980s US patents)

US 4,720,786; US 4,741,043; US 4,777,597; US 4,802,101; US 4,811,218; US 4,837,733; US 4,885,696; US 4,888,695; US 4,894,786; US 4,939,667; US 4,941,092; US 4,958,281; US 4,965,725; US 4,972,325; US 4,980,827; US 4,982,326; US 5,002,867 (17 references).

• Dates: all fall in the 1988–1991 issuance window (inferred from the number series). All are therefore comfortably pre-1994 and are §102(a)-(b) art.
• Descriptions: I could not verify the individual titles in this search pass, and I will not guess at them. The numerical clustering (sequential 4,7xx,xxx–5,00x,xxx issuances, all tagged "(APP)" i.e. applicant-cited) is the signature of a block citation of background art in computer graphics / image display / data-processing for analytical instruments — consistent with the patent's stated purpose of visualising hybridisation data (FIGS. 16–18: reference-sequence area 814, sample-sequence area 816, per-base intensity-graph windows).
• §102 relevance: these are the references that would matter if claims 24–59 (unretrieved) contain the comparative-visualisation claims. Against vacated claims 1/8/10 they are irrelevant — they contain no nucleic-acid hybridisation base-calling. Flagging explicitly: this block is the weakest-verified part of this analysis; obtain the front page ((56) References Cited) or the Office Actions to get exact titles, dates, and the passages the examiner relied on.

1D. Later US patents cited

1E. Foreign patent documents (15)

• WO 89/10977 A1; WO 90/01564 A1; WO 92/10092 A1; WO 92/10588 A1; WO 92/20824 A1; WO 93/11262 A1; WO 93/18186 A1; WO 94/11837 A1; WO 95/11995 A1; WO 95/35505 A1
• EP 0 514 927 A1; EP 0 549 388 A1; EP 0 631 635 A1; EP 0 671 694 A1
• FR 2 684 688 A1

Timing analysis (this matters): WO 92/10092 (published 1992-06-25) is the only one of these the specification itself identifies and incorporates by reference. The publications up to 1993 are potential §102(a) art. WO 95/11995 and WO 95/35505 (1995 publications) cannot be §102(a) art at all — they published after the 1994-10-21 priority date, and pre-AIA §102(e) did not reach PCT publications as such (only pre-2000 US national-stage filings). Their presence in the applicant's citation list is consistent with an IDS filed in the 1998 application disclosing the then-current art, not with reliance as prior art. Titles/dates for the WO and EP items are unverified in this pass.

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2. Non-patent literature cited (Unified Patents reports 8; OSTI enumerates 6)

Sources: https://www.osti.gov/doepatents/biblio/[873772](/patent/873772) ; https://portal.unifiedpatents.com/patents/patent/US-6242180-B1

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3. § 102 anticipation assessment (pre-AIA §102 applies: application filed 1998, priority 1994)

Framework. Because US 6,242,180 issued from and claims priority to a pre-AIA application, §102(a)/(b)/(e) apply in their pre-AIA form. Critically, three of the cited references (US 5,445,934, US 5,384,261) and the 1995–1999 US patents, plus WO 95/11995 and WO 95/35505, published after the 1994-10-21 priority date, so they are disqualifed as §102(a) art outright and can only bite via §102(e) — which turns on their earliest US filing date relative to the applicant's invention date. That chain has not been verified for any of them.

Element-by-element, claim 1 (identical elements recur in claims 8 and 10):

Bottom line on §102:

1. No cited reference anticipates claim 1, claim 8, or claim 10. Every reference in the list is directed either to (i) making/using arrays (Fodor, VLSIPS/WO cluster), (ii) hybridisation-based sequence determination (Drmanac, Strezoska, Southern), or (iii) generic computer graphics/data processing (the 1980s cluster). None teaches the two-step "look at neighbouring interrogation positions → revoke the mutation call" logic that claim 1 recites.
2. The strongest §102 exposure is to the front half of claim 1 only, i.e., Drmanac US 5,202,231 and the 1991–1992 SHB printed publications. If claim 1 were construed narrowly to exclude the re-call step, those references would be the ones to assert — but under the actual claim language they cannot anticipate.
3. For claims 24–59 (unretrieved), the analysis changes materially. If those claims cover the intensity-ratio method, the reference method, or the reference-sequence-vs-sample-sequence display (areas 814/816), then Southern Genomics 1992, Dear & Staden 1991, Fodor Science 1991, US 5,143,854, US 5,202,231, and the 1980s graphics cluster become directly §102-relevant. I cannot complete that mapping without the claim text.
4. Procedural note. Only one cited reference (US 5,974,164) is tagged as an examiner search hit; the other 51 are applicant-cited (IDS). That pattern — a large applicant IDS dominated by array-chemistry art, with a single examiner-cited item — is consistent with allowance turning on the re-call limitation rather than on the array chemistry.

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4. Citations received (forward citations) — not prior art

For completeness, and so this is not confused with the §102 analysis: Espacenet returns 22 documents citing US 6,242,180, and search reports of EP 1 184 467, EP 1 184 468 and EP 1 655 598 list "US 6242180 B1 05-06-2001" in their citation tables (the EP 1 655 598 hit being an Affymetrix application, "System, method, and product for multiple wavelength detection using single source excitation"). Unified Patents reports Referenced By (54). These are descendants/citing documents published 2004–2017 and have no §102 effect on US 6,242,180. Sources: https://pt.espacenet.com/publicationDetails/citingDocuments?CC=US&NR=6242180B1&KC=B1&FT=D&ND=10&date=20010605&DB=EPODOC ; https://patentimages.storage.googleapis.com/9c/29/f1/39865f91edf203/EP1184467A3.pdf ; http://data.epo.org/pise-server/rest/collections/lgpi/EP1655598A2.pdf

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5. What I could not confirm — do not treat as established

1. Titles, exact publication dates, and cited passages for ~30 of the 52 patent references (the whole 1980s graphics cluster, the 1993–94 chemistry cluster, and most of the WO/EP/FR items). I deliberately did not guess.
2. The 8th non-patent literature item (Unified reports 8; I found 7).
3. Claims 24–59 of the printed patent — the single largest gap in the §102 mapping.
4. The US filing chains of US 5,445,934, US 5,384,261, US 5,665,549, US 5,727,098 and US 5,974,164, which determine whether they qualify as §102(e) art at all. I did not verify any of them.
5. Examiner's substantive reasons for allowance. The IDS-vs-SEA pattern is suggestive but is not a substitute for the file wrapper.

Authoritative verification path: the printed patent's (56) References Cited and (57)/claims columns (Patent Public Search: https://ppubs.uspto.gov/pubwebapp/ ; PatentCenter for application 09/158,765: https://patentcenter.uspto.gov/), plus the file-wrapper Office Actions and the Examiner's Statement of Reasons for Allowance. Those will resolve items 1–5 above and confirm or refute the §102 conclusions in Section 3.

I'll first try to retrieve the two things an obviousness analysis actually requires: (a) the granted claim text of US 6,242,180, and (b) the prior-art citations on the patent's face/page — since the "Prior Art section" referenced in the task was not included in the material I was given.

I now have the actual granted claim text, which materially changes the analysis. Let me retrieve the patent's own front-page references (the true "prior art" of record) and the key Affymetrix/Chee family references.

Obviousness Analysis — U.S. Patent No. 6,242,180 B1 (Chee, Affymetrix)

35 U.S.C. § 103 (pre‑AIA), effective filing date 1994‑10‑21 (presumed)

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0. Three threshold flags before the analysis (read these first)

(a) The "Prior Art section" referenced in the task was not supplied to me. The materials I was given contain only the specification/figure text of the '180 patent plus two previously generated sections (Patent summary, Litigation summary). There is no prior-art dataset in the prompt. The following analysis therefore rests on (i) references expressly cited inside the '180 specification itself, (ii) references I could retrieve from public records in this pass, and (iii) generally known art in the field as of October 1994, with explicit confidence labels. I could not retrieve the printed patent's own "(56) References Cited" front page; a search of the Espacenet record returned only a garbled forward-citation ("documents citing") list, which is not prior art. This is a real evidentiary gap and it materially limits confidence.

(b) Contradiction with the previously generated "Patent summary" — flagged as required. That section stated (i) the verbatim claim text of US 6,242,180 was not retrieved, and (ii) the "interrogation position 'near the unknown base'" language belonged to the related continuation US 6,607,887, not the '180. Both of those statements are now superseded. I retrieved the granted claims from Espacenet and EveryPatent. US 6,242,180 claim 1 itself recites analyzing probe intensities at a position "near the position of the suspected mutation" and "changing the mutant base call to a nonmutant base call." So the '180's independent claims are not primarily the intensity-ratio / reference / statistical / pooling / visualization claims listed in the earlier summary; they are directed to the nearby-position consistency check (false-positive rejection). The earlier summary's six "subject-matter families" remain a fair description of the disclosure, but the claims as granted are materially narrower. This changes the obviousness analysis substantially.

(c) Priority-date discrepancy partially resolved, and it matters. The earlier summary noted Google Patents (1994‑10‑21) vs Unified Patents (1994‑10‑20). Espacenet's bibliographic record lists priority numbers US19940327525 19941021 and US19950531137 19951016, corroborating 1994‑10‑21 as the earliest date, with the '180 itself filed 1998‑09‑23 (Espacenet: US19980158765 19980923; Unified shows 1998‑09‑22 — unresolved minor discrepancy). Because the claims at issue are directed to a computational post-processing step, whether they are supported under § 112 by the 1994 application (as opposed to only by the 1998 continuation) controls which art is available. This is the single most important open question in the analysis (see § 7).

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1. The claims actually to be analyzed

Retrieved verbatim (Espacenet claims view; EveryPatent). The record shows 59 claims total (the earlier summary's Espacenet count), but the retrieved text exposes claims 1–11 and 16–17, 22–23; claims 4, 12–15, 18–21 were truncated. Analysis below is keyed to claim 1 and its product/system counterparts 8 and 10.

Claim 1 (method): inputting a plurality of probe intensities, each indicating hybridization affinity between a nucleic acid probe and the sample; calling bases of the sample according to those intensities; identifying a mutant base call (a position suspected as a mutation); analyzing probe intensities of at least one position near the suspected mutation; and changing the mutant base call to a nonmutant base call if those nearby intensities are inconsistent with a mutation.

Dependents: cl. 2 ("inconsistent … if the probe intensities do not indicate lower hybridization affinity than is expected"); cl. 3 (near = adjacent); cl. 5 (a plurality of nearby positions); cl. 6 (the plurality surrounds the suspected mutation equal to the length of the probes); cl. 7 (cl. 2 applied to cl. 6).

Claim 8 (computer program product) and claim 10 (computer system) mirror claim 1 element-for-element, with cl. 9 / cl. 11 reciting the medium (memory, hard drive, floppy disk, CD‑ROM, flash memory, tape). Claims 16–17 and 22–23 are the cl. 6/7 analogs for the product/system claims.

Claim 6 is the tell: "plurality … surround the suspected mutation equal to the length of the nucleic acid probes" is the claim's encoding of the "dark region / bubble width ≈ probe length" test described in FIGS. 14A–15 of the specification.

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2. Framework (Graham v. John Deere, 383 U.S. 1 (1966); KSR v. Teleflex, 550 U.S. 398 (2007))

Pre‑AIA § 103 applies (priority 1994; filed 1998). The analysis proceeds: (1) scope and content of the prior art; (2) differences between the prior art and the claims; (3) level of ordinary skill; (4) secondary considerations, with nexus. Critically, the relevant art is that before 1994‑10‑21 — which excludes most of the literature I would normally cite for this patent family.

Level of ordinary skill (proposed): a Ph.D. or M.S. in molecular biology/biochemistry/CS with 2–3 years' experience in nucleic acid hybridization assays and array data analysis, or equivalent; capable of routine programming of intensity-data processing.

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3. The prior-art landscape actually available on a 1994‑10‑21 date

Key observation: the obviousness case therefore has to be built from array-platform art + mismatch-discrimination art + generic data-processing/error-rejection art, not from the (later) Affymetrix array-resequencing papers. And the strongest single piece of evidence — the "footprint of probes flanking the point of variation" concept — sits five days outside the critical date on its face. That is an uncomfortably thin margin, and it is why § 7 matters.

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4. The combinations

Combination A — Fodor '854 + WO 90/15070/92/10092 (+ 08/249,188) + SBH/mismatch-discrimination literature

Mapping to claim 1:

• inputting a plurality of probe intensities, each indicating hybridization affinity between a probe and the sample → Fodor '854/08/249,188: scanner output of fluorescence intensities at known probe locations (the '180 spec itself concedes this is the prior "cell file" workflow).
• calling bases according to the plurality of probe intensities → SBH and Southern 1992: the identity of the base at an interrogation position is read from which of the related probes hybridizes most strongly (perfect match > mismatch).
• identifying a mutant base call → routine consequence of the above: comparing the called base to the expected/wild‑type base yields "a position in the sample suspected as being a mutation."
• analyzing probe intensities near the suspected mutation and changing the call if those are inconsistent with a mutation → this is the only genuinely claim‑specific step, and it is supplied by Combination B.

Motivation to combine: all references are in the same field of endeavor (hybridization-based nucleic acid sequence analysis) and address the same problem — accurately determining a target sequence from array hybridization data. Southern 1992 and Fodor '854 were the recognized foundational platform references; a POSITA building a base-calling pipeline on the Fodor/08/249,188 platform would necessarily read base identity out of the four related probe intensities, because that is what the array is for.

Combination B — Combination A + mismatch-destabilization / "footprint" knowledge

This is the combination that reaches the heart of claim 1, and the motivation is unusually strong because the underlying phenomenon is not an invention — it is a physical consequence the art already knew:

1. It was known (Southern 1992; Guo 1994; SBH literature) that a single internal base mismatch destabilizes a short duplex and lowers hybridization signal. It follows as a matter of physics, with no inventive step, that a probe overlapping (rather than centered on) a mutation will also show reduced signal — i.e., a mutation necessarily perturbs a neighborhood of probe intensities, not a single cell.
2. It was equally known that isolated low signals arise from artifacts (dust, background, incomplete hybridization, cross-hybridization) and do not produce a coordinated neighborhood pattern.
3. Therefore a POSITA, seeking to suppress false-positive mutation calls, would look at neighboring probe intensities to check whether the low-intensity "mutation" signal is consistent with a real mutation. That is precisely claim 1's step (d)–(e).

KSR rationales available:

• Combination of known elements with predictable results — array readout + base calling + a consistency/outlier filter.
• Known technique, known function ("the improvement is no more than the predictable use of prior art elements according to their established functions"). Looking at neighbors to validate an outlier is a textbook data-processing step.
• Automation of a manual step. The '180's own figures are visualization figures: FIGS. 14A–14C are graphs of wild‑type probe intensity vs. cell position in which a human visually identifies "bubbles." The specification's own words concede that "the characteristics of these 'dark regions' may be utilized to identify mutations and false positives." Once the human visual test is described, implementing it in software is an obvious automation of a known mental/visual procedure (cf. In re Venner; and the general resistance-to-automation rationale).
• Design incentive: driving down false positives in diagnostic base calling.

Reasonable expectation of success: high. Every step operates on already-collected intensity data; no unpredictable biology is required; a POSITA could implement the neighborhood comparison with routine programming.

Combination C — Automated sequencer base-calling art (e.g., Prober '796 / ABI software) + array-platform art

Mapping: Prober/ABI-type software supplies inputting intensity data, calling bases, and suspecting/correcting a call — i.e., elements (a)–(c) and the concept of programmatically revising a base call. Array art supplies the probe-array context. Motivation: common problem (automated, high-accuracy base calling from fluorescence data) and common field (computerized analysis of fluorescence-intensity data for nucleic acid sequencing). The gap the combination must bridge is that sequencer trace data is positional/electrophoretic rather than addressable-array, so the "neighboring probe" step is not directly present — this combination is weaker than A+B.

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5. Dependent claims

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6. Presumed rebuttals, and how they fare

• § 103(c) (pre-AIA) common ownership. Several plausible references (the 08/249,188 application; WO 90/15070, WO 92/10092; US 5,143,854's assignee lineage; later Affymetrix cases) are commonly owned by Affymetrix at the time the invention was made. Under pre‑AIA § 103(c)(1), commonly owned § 102(e)/(f)/(g) art cannot be used in an obviousness combination. This knocks out much of the § 102(e)-only art (e.g., the 08/249,188 application), though not the § 102(a)/(b) printed publications (Fodor '854 is a patent, so § 102(b) applies to it once it granted — but its grant date is 1992, so it is § 102(b) art and immune to § 103(c)). This is a strong defense and should be tested against the file history.
• Secondary considerations. I found no verified evidence of unexpected results, long-felt need, licensing-nexus, or commercial-success-nexus attributable to claim 1. The patent's own expiry in 2014 for failure to pay maintenance fees (Google Patents: anticipated expiration 2014‑10‑21; GE Capital security interest released 2015‑11‑13) is, at most, a weak inference and is not a proper Graham factor. The earlier Litigation summary found no confirmed litigation naming the '180, so there is no adjudicated validity record to rely on either way.
• Teaching away. I found none. The art affirmatively recognized that mismatches reduce signal — that supports the combination.
• Priority/§ 112. See § 7.

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7. The decisive issue: is claim 1 entitled to 1994‑10‑21?

The '180 issued from an application filed 1998‑09‑23, a continuation of a chain rooted in 1994‑10‑21 / 1995‑10‑16 filings. Claim 1's "changing the mutant base call" step reads like a post-hoc algorithmic refinement of the earlier visualization disclosure. If that subject matter is not supported (written description/enablement, § 112 ¶ 1) by the 1994 and 1995 applications, then for § 102/§ 103 purposes the effective date is 1998‑09‑23, and the following become prior art:

• EP 717,113 / WO 95/11995 (Chee et al., Affymetrix) — the "footprint of probes flanking the point of variation between target and reference sequence." This is, on its face, the nearest thing to claim 1 in the record, and it is Affymetrix's own earlier work (raising § 103(c) issues in return).
• Chee et al., Science 274:610–614 (1996) — retrieved and quoted in the record ("Accessing genetic information with high-density DNA arrays"; the reviewer-style summary in EP 1009857 B1 confirms its disclosure of genomic polymorphism analysis with arrays).
• Lockhart et al., Nat. Biotechnol. 14:1675–1680 (1996); Hacia et al. (1996) two-colour analysis; WO 97/29212 (clustering of hybridization intensities).
• The HIV/p53 array resequencing work of 1995–1997.

If the 1998 date applies, claim 1 is very likely obvious (and arguably anticipated by the footprint disclosure combined with routine base calling), and claim 6 in particular collapses.

I cannot resolve this without the file history and the parent applications. I am flagging it rather than asserting an outcome.

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8. Bottom line

What would change this analysis, and what I could not obtain:

1. The printed patent's own (56) References Cited list (not supplied; only a forward-citation list was retrievable).
2. The prosecution file history of 09/158,765 — including any § 103(c) common-ownership statements, terminal disclaimers, and the examiner's own art rejections.
3. The parent applications (US 08/327,525, US 08/531,137) to test § 112 support for claim 1's "changing the mutant base call" step.
4. The full 59-claim set (claims 4, 12–15, 18–21 were truncated in every source I reached), which may contain further independent claims requiring separate analysis.

I have deliberately labeled every reference above by retrieval status and confidence rather than asserting dates or mappings I could not verify.