DCT
5:24-cv-04098
Personal Genomics Taiwan Inc v. Pacific Biosciences Of California Inc
I. Executive Summary and Procedural Information
- Parties & Counsel:
- Plaintiff: Personal Genomics Taiwan, Inc. (Taiwan)
- Defendant: Pacific Biosciences of California, Inc. (Delaware)
- Plaintiff’s Counsel: Morris, Nichols, Arsht & Tunnell LLP
- Case Identification: 5:24-cv-04098, D. Del., 09/26/2019
- Venue Allegations: Venue is alleged to be proper in the District of Delaware because the defendant, Pacific Biosciences of California, Inc., is a Delaware corporation and therefore resides in the district.
- Core Dispute: Plaintiff alleges that Defendant’s Sequel and Sequel II single-molecule DNA sequencing systems infringe a patent related to the architecture of bioassay devices.
- Technical Context: The technology pertains to next-generation DNA sequencing, specifically the apparatus for optically detecting single biomolecules in a massively parallel fashion.
- Key Procedural History: The complaint alleges a multi-year history of licensing negotiations between the parties concerning the technology and patent-in-suit, beginning in 2010 and ending in 2015. The complaint also alleges that the defendant cited the patent-in-suit during the prosecution of its own patents. Subsequent to the filing of this complaint, the U.S. Patent and Trademark Office instituted Inter Partes Review (IPR) proceedings (IPR2020-01163, IPR2020-01200) against the patent-in-suit. On May 8, 2024, the USPTO issued an IPR certificate canceling claims 1-6, 9, and 43-58, which includes the representative claim 48 asserted in the complaint.
Case Timeline
| Date | Event |
|---|---|
| 2007-10-25 | ’441 Patent Priority Date |
| 2010-03-03 | PacBio and Plaintiff's predecessor sign NDA |
| 2010-08-03 | ’441 Patent Issue Date |
| 2010-09-XX | Plaintiff PGI founded as a spinoff |
| 2011-07-28 | Parties meet to discuss potential collaboration |
| 2011-12-01 | Defendant suspends collaboration negotiations |
| 2013-09-XX | Licensing discussions resume |
| 2015-06-23 | Final meeting between parties |
| 2015-09-30 | Accused Product "Sequel System" launched |
| 2019-04-24 | Accused Product "Sequel II System" launched |
| 2019-09-26 | Complaint Filing Date |
| 2024-05-08 | USPTO issues IPR Certificate canceling asserted claim 48 |
II. Technology and Patent(s)-in-Suit Analysis
U.S. Patent No. 7,767,441 - “Bioassay system including optical detection apparatuses, and method for detecting biomolecules”
- Patent Identification: U.S. Patent No. 7,767,441, “Bioassay system including optical detection apparatuses, and method for detecting biomolecules,” issued August 3, 2010.
The Invention Explained
- Problem Addressed: The patent’s background section identifies the high cost and complexity of existing high-throughput DNA sequencing technologies. It notes that such systems require "complicated and error-prone image acquisition and analysis steps" and that the molecule being analyzed is often not in "close proximity to a corresponding detecting unit," which limits the strength of the detected signal (’441 Patent, col. 1:48-61).
- The Patented Solution: The invention proposes a bioassay system comprising a massive array of individual optical detection apparatuses. Each apparatus features a light detector with a "linker site" positioned closely above it, where a single biomolecule is affixed. This architecture, illustrated in Figure 2, is designed to maximize the "solid angle of detection" by reducing the distance between the light-emitting molecule and the sensor to 100 micrometers or less, thereby improving signal strength and enabling single-molecule detection without complex scanning optics (’441 Patent, Abstract; col. 2:30-44).
- Technical Importance: This design sought to simplify the hardware and workflow for DNA sequencing, reduce costs, and enable large-scale parallel analysis, addressing the market's push toward the "$1000 genome" paradigm (’441 Patent, col. 1:62-63).
Key Claims at a Glance
- The complaint identifies independent apparatus claim 48 as representative of the infringed claims (Compl. ¶24).
- The essential elements of claim 48 are:
- An apparatus for identifying a single biomolecule, comprising:
- a substrate having a light detector;
- a linker site formed over the light detector, the linker site being treated to affix the biomolecule to the linker site; and
- an excitation light source formed over the substrate;
- wherein the linker site is proximate to the light detector and is spaced apart from the light detector by a distance of less than or equal to 100 micrometers.
- The complaint notes infringement of "one or more claims" and also references method claim 16, reserving the right to assert additional claims (Compl. ¶¶ 23, 54).
III. The Accused Instrumentality
Product Identification
- The accused instrumentalities are the Pacific Biosciences "Sequel" and "Sequel II" DNA sequencing systems, along with their required "SMRT Cell" consumables (Compl. ¶¶ 6, 15-16).
Functionality and Market Context
- The Sequel and Sequel II systems are described as platforms for "single molecule, real-time (SMRT) technology" (Compl. ¶28). The systems require consumable SMRT Cells, which are nanofabricated chips containing millions of "zero-mode waveguides" (ZMWs) (Compl. ¶¶ 30-31, 33).
- The complaint alleges that for the system to function, a single DNA molecule is immobilized within each ZMW, which is positioned over a CMOS optical sensor on a semiconductor substrate (Compl. ¶¶ 33, 38-39, 43). A diagram in the complaint depicts this immobilization process, showing a single DNA molecule anchored within a ZMW (Compl. ¶33, p. 8). The complaint further alleges these systems are marketed for providing "high-quality sequencing" and "highly accurate long reads" (Compl. ¶6).
IV. Analysis of Infringement Allegations
’441 Patent Infringement Allegations
| Claim Element (from Independent Claim 48) | Alleged Infringing Functionality | Complaint Citation | Patent Citation |
|---|---|---|---|
| a substrate having a light detector | The accused Sequel system’s SMRT Cell contains a microchip with a semiconductor substrate and CMOS optical sensors which function as light detectors (Compl. ¶¶ 36-39). | ¶40 | col. 4:57-58 |
| a linker site formed over the light detector, the linker site being treated to affix the biomolecule to the linker site | The bottom of the ZMW in the SMRT Cell is alleged to be the linker site, where a "DNA template-polymerase complex is immobilized" (Compl. ¶43). A video screenshot shows this immobilization, which the complaint alleges constitutes the required treatment to affix the biomolecule (Compl. ¶43, p.10). | ¶44 | col. 4:58-59 |
| an excitation light source formed over the substrate | The accused SMRT technology allegedly uses an excitation light source that illuminates each ZMW "from below" (Compl. ¶48). A visual from a PacBio video is provided to show this illumination method (Compl. ¶48, p. 11). | ¶49 | col. 6:35-37 |
| wherein the linker site is proximate to the light detector and is spaced apart... by a distance of less than or equal to 100 micrometers | The complaint alleges that the linker site in the SMRT Cell microchip is separated from the light detector by a distance of "less than 20 micrometers," satisfying the proximity requirement (Compl. ¶52). | ¶53 | col. 2:38-40 |
- Identified Points of Contention:
- Claim Validity: The primary issue in the case is the validity of the asserted claims. The post-filing IPR certificate, a provided document, indicates that representative claim 48 and all other apparatus claims (49-54, 58) have been canceled by the USPTO. This raises the fundamental question of whether a viable claim for infringement remains.
- Scope Questions: Should a viable claim remain, a key dispute may concern the term "formed over." The complaint alleges the accused system's excitation light source illuminates the reaction site "from below," raising the question of whether this configuration meets the claim limitation of an "excitation light source formed over the substrate," which patent embodiments depict in a stacked arrangement.
- Technical Questions: A factual question concerns whether the accused product's ZMW, in which a polymerase complex is anchored, is structurally and functionally equivalent to the patent's "linker site being treated to affix the biomolecule." The court would need to determine if anchoring a polymerase constitutes "treating" the site itself, as described in the patent.
V. Key Claim Terms for Construction
The Term: "linker site"
Context and Importance: The plaintiff’s infringement theory equates the bottom surface of the defendant's ZMW with the claimed "linker site." The construction of this term is therefore critical to determining whether the accused product's structure falls within the claim's scope.
Intrinsic Evidence for Interpretation:
- Evidence for a Broader Interpretation: The claim language broadly defines the term functionally as a site "formed over the light detector" and "treated to affix the biomolecule" (’441 Patent, col. 28:14-16). This may support an interpretation that covers any treated location above a detector where a molecule is held for analysis.
- Evidence for a Narrower Interpretation: Embodiments in the patent describe the linker site (220) being formed within a "pinhole" (235) in a "blind sheet" (230) (’441 Patent, col. 5:6-10; Fig. 2). A party could argue this disclosure limits the term to a specific physical structure distinct from the integrated well of a ZMW.
The Term: "formed over"
Context and Importance: This term is used to define the spatial relationship of both the "linker site" relative to the "light detector" and the "excitation light source" relative to the "substrate." The defendant's alleged illumination "from below" the ZMW makes the construction of "formed over the substrate" a potential point of non-infringement.
Intrinsic Evidence for Interpretation:
- Evidence for a Broader Interpretation: A party might argue that "over" in the context of semiconductor fabrication refers to a general position in a layered build-up on a substrate, not necessarily a direct vertical stacking order from bottom to top.
- Evidence for a Narrower Interpretation: The patent's Figure 4 depicts the excitation light source (40) as a layer built on top of other layers that are themselves on the substrate (10), suggesting a specific physical hierarchy (’441 Patent, Fig. 4). This could support a narrower definition requiring the light source to be physically above the substrate in the final structure.
VI. Other Allegations
- Indirect Infringement: The complaint alleges induced infringement based on the defendant's alleged pre-suit knowledge of the ’441 patent from years of licensing discussions and its own patent prosecution history. It is alleged that the defendant intended to cause infringement by providing customers with products, instructions, manuals, and software that guide them to perform infringing uses (Compl. ¶¶ 55-56). The complaint also pleads contributory infringement, alleging the accused products are a material part of the invention with no substantial non-infringing use (Compl. ¶57).
- Willful Infringement: The willfulness claim is based on alleged pre-suit knowledge. The complaint cites the history of licensing negotiations from 2010-2015 and the defendant's citation of the ’441 patent as prior art as evidence of long-standing and deliberate disregard for the plaintiff's patent rights (Compl. ¶¶ 55, 59).
VII. Analyst’s Conclusion: Key Questions for the Case
- Case Viability: The central, dispositive question for this litigation is one of claim survival: following the USPTO’s cancellation of representative claim 48 and all other asserted apparatus claims in a post-filing IPR, does the plaintiff retain any valid and enforceable patent claims upon which to base its infringement suit?
- Definitional Scope: If the case proceeds, a core issue will be one of spatial construction: can the claim term "excitation light source formed over the substrate" be construed to read on the accused device's architecture, which allegedly illuminates the reaction site "from below"?
- Structural Equivalence: A key evidentiary question will be one of functional correspondence: does the accused product's zero-mode waveguide (ZMW), where a DNA-polymerase complex is anchored, constitute a "linker site...treated to affix the biomolecule" as that term is defined and described within the context of the ’441 patent's specification and embodiments?