Take2 & CUHK v. PacBio: SMRT Sequencing Patent Dismissed With Prejudice After 581 Days
Take2 Technologies and The Chinese University of Hong Kong brought a patent infringement action against Pacific Biosciences over the Revio and Sequel II sequencing platforms, asserting US11091794B2 covering DNA methylation detection in long-read sequencing. After 581 days of litigation in the Northern District of California, both parties agreed to a joint stipulation of dismissal with prejudice, each side bearing its own costs.
Methylation-Detection Patent Clash Ends in Mutual Dismissal With Prejudice
On 16 August 2023, Take2 Technologies Limited and The Chinese University of Hong Kong (CUHK) filed suit in the Northern District of California against Pacific Biosciences of California, Inc. (PacBio), asserting infringement of US11091794B2. The patent relates to DNA methylation detection methods central to long-read sequencing, and the accused products included PacBio’s flagship Revio systems running SMRT Link software v11.0 and later, the Sequel IIe, and Sequel II platforms — the core of PacBio’s commercial sequencing portfolio.
On 19 March 2025, the parties jointly filed a stipulation of dismissal with prejudice under Federal Rule of Civil Procedure 41, which the court entered as an order. All claims and counterclaims were extinguished, with each side bearing its own attorneys’ fees, costs, and expenses. A dismissal with prejudice operates as a final adjudication on the merits, permanently barring Take2 and CUHK from re-asserting the same patent claims against PacBio on the same grounds.
The 581-day duration and the mutual cost-bearing arrangement are consistent with a negotiated resolution — whether a licensing agreement, cross-licence, or commercial settlement — reached before trial, though the public record does not disclose financial terms or licensing arrangements. The decision to dismiss with prejudice rather than without suggests both parties sought finality, which may reflect either an agreed commercial outcome or PacBio’s successful challenge to the patent’s applicability. The underlying terms, if any, remain confidential.
Filing to Dismissed with Prejudice in 581 days
581 days from filing to closure — roughly typical for N.D. Cal. patent cases that settle pre-trial
Dismissed with prejudice: what the joint stipulation means for both sides
Rule 41 dismissal with prejudice: claims are permanently extinguished
Under Federal Rule of Civil Procedure 41, a voluntary dismissal with prejudice operates as a final adjudication on the merits. Take2 and CUHK cannot re-file these claims against PacBio based on US11091794B2 for the accused products. Unlike a dismissal without prejudice, there is no ability to refile. This finality typically reflects either a negotiated resolution or a strategic decision that further litigation was unlikely to succeed.
Permanent bar on re-filingTake2 and CUHK permanently relinquish claims against PacBio
By agreeing to dismiss with prejudice, Take2 and CUHK have foreclosed any future assertion of US11091794B2 against PacBio’s Revio, Sequel IIe, and Sequel II product lines on the same grounds. The public record does not disclose whether a licensing fee or settlement payment accompanied the dismissal. If no compensation was received, the dismissal represents a full retreat; if a licence was secured, the dismissal is the procedural close of a successful enforcement campaign.
Enforcement concluded — terms undisclosedPacBio secures litigation closure across its core sequencing portfolio
Pacific Biosciences obtains a permanent dismissal covering its most commercially significant platforms — Revio with SMRT Link v11.0+, Sequel IIe, and Sequel II. The with-prejudice designation means PacBio faces no future exposure from Take2 or CUHK under this patent on these products. Each party bearing its own costs is a common indicator of a negotiated exit, and suggests neither party achieved a clear-cut litigation victory in court proceedings.
Portfolio cleared of this claimMethylation-detection IP risk persists for the long-read sequencing sector
US11091794B2 remains granted and was not invalidated in this proceeding. Other sequencing platform developers working in SMRT-based or competing long-read methylation detection technologies should treat this patent as an active enforcement risk — particularly as epigenomic analysis becomes a standard feature of next-generation sequencing workflows. The resolution without public merits ruling provides no precedent on claim scope or validity that competitors can rely upon.
Patent remains enforceableFull party and counsel information
| Role | Name | Type | Detail |
|---|---|---|---|
| Plaintiff | Take2 Technologies Limited | Company | DNA sequencing IP licensing entity and CUHK — joint holders of US11091794B2Search in Eureka ↗ |
| Co-Plaintiff | The Chinese University of Hong Kong | Individual | Search in Eureka ↗ |
| Defendant | Pacific Biosciences of California, Inc. | Company | Pacific Biosciences: long-read SMRT DNA sequencing platform developer and manufacturerSearch in Eureka ↗ |
| Plaintiff counsel | Courtney M. Prochnow | Attorney | Counsel for Take2 Technologies LimitedSearch in Eureka ↗ |
| Plaintiff counsel | Doris Alvarez-Reyes | Attorney | Counsel for Take2 Technologies LimitedSearch in Eureka ↗ |
| Plaintiff counsel | James L. Higgins | Attorney | Counsel for Take2 Technologies LimitedSearch in Eureka ↗ |
| Plaintiff counsel | Joseph Preston Hamilton | Attorney | Counsel for Take2 Technologies LimitedSearch in Eureka ↗ |
| Plaintiff counsel | Kyle R. Canavera | Attorney | Counsel for Take2 Technologies LimitedSearch in Eureka ↗ |
| Plaintiff counsel | Lara J. Dueppen | Attorney | Counsel for Take2 Technologies LimitedSearch in Eureka ↗ |
| Plaintiff counsel | Melanie K. Sharp | Attorney | Counsel for Take2 Technologies LimitedSearch in Eureka ↗ |
| Plaintiff counsel | Michael J. Wise | Attorney | Counsel for Take2 Technologies LimitedSearch in Eureka ↗ |
| Plaintiff counsel | Michael Jonathan Wise | Attorney | Counsel for Take2 Technologies LimitedSearch in Eureka ↗ |
| Plaintiff counsel | Nathan Kelley | Attorney | Counsel for Take2 Technologies LimitedSearch in Eureka ↗ |
| Plaintiff counsel | Taylor E. Hallowell | Attorney | Counsel for Take2 Technologies LimitedSearch in Eureka ↗ |
| Plaintiff counsel | William M. Pierce | Attorney | Counsel for Take2 Technologies LimitedSearch in Eureka ↗ |
| Plaintiff law firm | Perkins Coie LLP | Law Firm | Representing Take2 Technologies LimitedSearch in Eureka ↗ |
| Plaintiff law firm | Young Conaway Stargatt & Taylor, LLP | Law Firm | Representing Take2 Technologies LimitedSearch in Eureka ↗ |
| Defendant counsel | August Melcher | Attorney | Counsel for Pacific Biosciences of California, Inc.Search in Eureka ↗ |
| Defendant counsel | Brian E. Farnan | Attorney | Counsel for Pacific Biosciences of California, Inc.Search in Eureka ↗ |
| Defendant counsel | Derek C. Walter | Attorney | Counsel for Pacific Biosciences of California, Inc.Search in Eureka ↗ |
| Defendant counsel | Edward R. Reines | Attorney | Counsel for Pacific Biosciences of California, Inc.Search in Eureka ↗ |
| Defendant counsel | Edward Robert Reines | Attorney | Counsel for Pacific Biosciences of California, Inc.Search in Eureka ↗ |
| Defendant counsel | Kathryn Leicht | Attorney | Counsel for Pacific Biosciences of California, Inc.Search in Eureka ↗ |
| Defendant law firm | Farnan LLP | Law Firm | Representing Pacific Biosciences of California, Inc.Search in Eureka ↗ |
| Defendant law firm | Jones Day | Law Firm | Representing Pacific Biosciences of California, Inc.Search in Eureka ↗ |
| Defendant law firm | Paul, Weiss, Rifkind, Wharton & Garrison LLP | Law Firm | Representing Pacific Biosciences of California, Inc.Search in Eureka ↗ |
| Defendant law firm | Weil, Gotshal & Manges LLP | Law Firm | Representing Pacific Biosciences of California, Inc.Search in Eureka ↗ |
| Presiding judge | Judge N/A | Judge | California Northern District CourtSearch in Eureka ↗ |
Official order — verbatim text
The joint stipulation language — ‘each and every count, claim, and counterclaim’ dismissed with prejudice — is deliberately comprehensive, ensuring no residual claim survives between these parties. The explicit inclusion of counterclaims suggests PacBio had filed affirmative defences or invalidity counterclaims, all of which are now extinguished. Neither party concedes wrongdoing or validity. The mutual cost-bearing provision, standard in negotiated dismissals, is consistent with a confidential commercial resolution and does not reflect a court determination on the merits of infringement or validity.
US11091794B2 — DNA Methylation Detection in Long-Read SMRT Sequencing
US11091794B2, filed under application number US16/995607, protects methods and systems for detecting DNA methylation in the context of single-molecule real-time (SMRT) sequencing. Methylation detection is a critical component of epigenomic analysis, enabling researchers to identify gene expression regulation patterns without separate bisulfite conversion assays. The patent’s co-ownership by CUHK — a leading genomics research institution — and commercialisation by Take2 Technologies suggests the invention originated from academic research and was subsequently positioned for commercial enforcement.
The commercial significance of this patent is substantial. PacBio’s Revio system represents the current flagship of its long-read sequencing portfolio, with SMRT Link software enabling methylation calling as a standard analytical feature. The breadth of accused products — spanning three distinct system generations — suggests the asserted claims are not narrowly drawn to a single hardware implementation but may cover software-enabled methylation detection workflows more broadly. For any company developing platforms, analysis pipelines, or consumables in the SMRT or competing long-read sequencing space, this patent warrants careful FTO evaluation.
Should your team run an FTO analysis against US11091794B2?
Any organisation developing, manufacturing, or commercialising long-read DNA sequencing platforms with methylation detection capability — including SMRT-based systems, Oxford Nanopore-adjacent workflows, or software-enabled epigenomic analysis pipelines — should assess freedom-to-operate against US11091794B2. The patent was actively enforced against PacBio’s full commercial portfolio, and the case resolved without any public finding of invalidity. Product and R&D teams launching sequencing platforms with integrated methylation calling functionality are particularly exposed.
PatSnap Eureka’s FTO Search Agent can map the claim landscape of US11091794B2 against your product’s technical specification, identify prior art that may narrow or challenge claim scope, and flag related pending applications from the same family or inventors. Given CUHK’s institutional IP portfolio and Take2’s enforcement posture, monitoring continuation applications and related filings in this family is strongly recommended for any player in the long-read sequencing market.
Run a freedom-to-operate analysis on US11091794B2 to assess your product’s exposure
Run FTO in Eureka →Similar Patent Cases in DNA Sequencing & Genomics Technology
Explore patent infringement actions involving DNA sequencing, methylation detection, and SMRT technology in the Northern District of California and related venues.
What this case signals for the long-read sequencing IP landscape
A with-prejudice dismissal with no public merits ruling leaves the patent’s enforceability intact and its claim scope untested — a live risk for the sector.
US11091794B2 was never invalidated — enforcement risk persists for sequencing rivals
No court ruled on validity or claim scope. Any competitor deploying SMRT-based or methylation-detection sequencing workflows should assess exposure to US11091794B2 independently. The absence of a merits ruling means there is no public record weakening the patent’s enforceability against third parties.
Mutual cost-bearing is a hallmark of a negotiated exit, not a plaintiff capitulation
When both parties bear their own costs and dismiss with prejudice, it typically suggests a commercial resolution was reached — possibly including a licence, royalty arrangement, or cross-licensing deal. R&D and IP teams at genomics companies should monitor whether CUHK and Take2 pursue similar actions against other platform providers.
Take2 v Pacific — key questions answered
The case was dismissed with prejudice on 19 March 2025 by joint stipulation under Rule 41 of the Federal Rules of Civil Procedure. All claims and counterclaims were extinguished, with each party bearing its own costs. The dismissal is permanent — Take2 and CUHK cannot re-assert the same patent claims against PacBio on the same grounds.
The plaintiffs asserted US11091794B2, filed under application number US16/995607. The patent covers DNA methylation detection methods in the context of single-molecule real-time (SMRT) sequencing — a core capability of PacBio’s Revio and Sequel product lines.
The accused products included PacBio’s Revio systems equipped with or used with SMRT Link software v11.0, v11.1, or later, Sequel IIe Systems, and Sequel II systems — effectively PacBio’s primary commercial long-read sequencing portfolio at the time of filing.
No. A dismissal with prejudice by joint stipulation carries no finding on the merits of infringement or validity. The patent remains granted and enforceable. The dismissal simply bars Take2 and CUHK from re-suing PacBio on these specific claims. Third parties cannot rely on this outcome as a validity determination.
The public record does not disclose the reason. The mutual cost-bearing arrangement and with-prejudice designation are consistent with a negotiated commercial resolution — possibly a licence or settlement agreement — though this is not confirmed. Both parties may also have concluded that continued litigation was not commercially justified. The underlying terms, if any, remain confidential.
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