DCT
1:19-cv-01810
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; Irell & Manella LLP
- Case Identification: 1:19-cv-01810, D. Del., 09/26/2019
- Venue Allegations: Venue is asserted as proper in the District of Delaware because Defendant 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 using semiconductor-based optical detectors.
- Technical Context: The technology concerns next-generation DNA sequencing, specifically methods for immobilizing and detecting single biomolecules on a semiconductor chip to enable high-throughput, parallel analysis.
- Key Procedural History: The complaint alleges a long history of pre-suit interactions, including multiple rounds of licensing and collaboration discussions between the parties (and their predecessors) from 2010 to 2015. The complaint also notes that the asserted patent was cited by the Defendant during the prosecution of its own patent applications. Subsequent to the filing of this complaint, the asserted representative claim (Claim 48) was cancelled in inter partes review proceedings (IPR2020-01163, IPR2020-01200), a development that would be dispositive for any infringement theory relying on that claim.
Case Timeline
| Date | Event |
|---|---|
| 2007-10-25 | ’441 Patent Priority Date |
| 2010-03-03 | Defendant first contacts Plaintiff's predecessor (ITRI) about licensing |
| 2010-08-03 | U.S. Patent No. 7,767,441 Issues |
| 2010-09 | Plaintiff (as Crackerbio Taiwan, Inc.) is founded |
| 2010-11-18 | Plaintiff's predecessor receives exclusive license from ITRI |
| 2011-12-01 | Defendant suspends licensing negotiations |
| 2013-09 | Defendant re-initiates contact with Plaintiff regarding a license |
| 2015-06-23 | Final alleged meeting between the parties |
| 2015-09-30 | Defendant launches the accused Sequel System |
| 2019-04-24 | Defendant launches the accused Sequel II System |
| 2019-06-10 | Plaintiff becomes the assignee of the ’441 Patent |
| 2019-09-26 | Complaint Filed |
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
The Invention Explained
- Problem Addressed: The patent describes the high cost and complexity of conventional, high-throughput DNA sequencing technologies. It identifies specific problems including error-prone image acquisition and analysis steps, and the physical distance between the molecule being analyzed and the light detector, which limits the strength of the detected signal (’441 Patent, col. 1:45-62).
- The Patented Solution: The invention proposes a bioassay system comprising a large array of independent optical detection apparatuses. Each apparatus features a light detector on a substrate with a "linker site" positioned directly over and in close proximity to the detector (’441 Patent, col. 2:21-28; Fig. 2). This close arrangement is designed to maximize the light collected from a single biomolecule (manifested as a "large solid angle of detection"), thereby improving signal strength and simplifying the system by avoiding the need for complex scanning optics (’441 Patent, col. 2:26-31, 11:24-29).
- Technical Importance: This approach aims to create a more efficient, less error-prone, and lower-cost platform for single-molecule analysis, a key goal in making personalized genomics more accessible (’441 Patent, col. 1:41-44).
Key Claims at a Glance
- The complaint asserts apparatus claim 48 as representative and also references method claim 16 (Compl. ¶¶24, 54).
- Independent Claim 48 recites the following essential elements:
- A substrate having a light detector
- A linker site formed over the light detector, treated to affix a biomolecule
- An excitation light source formed over the substrate
- A proximity requirement, where the linker site is spaced from the light detector by a distance of 100 micrometers or less
- The complaint reserves the right to assert other claims (Compl. ¶23).
III. The Accused Instrumentality
Product Identification
- The accused instrumentalities are Defendant's "Sequel" and "Sequel II" DNA sequencing systems, which utilize consumable "SMRT Cells" (Single Molecule, Real-Time) (Compl. ¶¶6, 30).
Functionality and Market Context
- The complaint describes the accused systems as platforms for "single molecule, real-time (SMRT) technology" (Compl. ¶28). The SMRT Cells are described as nanofabricated consumables containing millions of "zero-mode waveguides" (ZMWs) (Compl. ¶¶31, 33). In operation, a single DNA molecule is immobilized at the bottom of each ZMW, where its sequencing is observed in real-time (Compl. ¶33). The complaint presents a diagram from Defendant's materials illustrating how light is emitted as labeled bases are incorporated by a polymerase anchored in the ZMW. This diagram shows how light signals correspond to the sequence of a DNA strand (Compl. ¶33, p. 8).
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 SMRT Cell 1M contains a microchip with a semiconductor substrate that includes one or more CMOS optical sensors which function as light detectors. | ¶¶38-40 | col. 10:57-66 |
| a linker site formed over the light detector, the linker site being treated to affix the biomolecule to the linker site | The SMRT Cell includes an area within each ZMW for affixing a single DNA molecule over the light detector. The complaint alleges this area, the bottom of the ZMW, is treated to immobilize the biomolecule via an "anchored" polymerase. | ¶¶41-43 | col. 11:50-54 |
| an excitation light source formed over the substrate | The SMRT Cell microchip allegedly has a light-emitting waveguide formed over the semiconductor substrate that illuminates the linker site. The complaint includes a screenshot from Defendant's video showing illumination of the ZMW from below. | ¶¶46-48 | col. 11:33-44 |
| 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 linker site and light detector in the accused SMRT Cell are allegedly separated by a distance of less than 20 micrometers, which is within the claimed range. | ¶52 | col. 11:25-28 |
- Identified Points of Contention:
- Scope Questions: A central question concerns the structural correspondence between the patent's claims and the accused product. The court may need to determine if the "bottom of the ZMW" in the accused SMRT Cell, illuminated from below, constitutes a "linker site formed over the light detector" with an "excitation light source formed over the substrate" as those phrases are used in the patent.
- Technical Questions: The complaint alleges the accused device uses a light-emitting waveguide that illuminates the ZMW from below (Compl. ¶48, p. 11). This raises the question of whether this configuration meets the "formed over the substrate" limitation for the excitation light source, which the patent figures depict as an integrated layer on top of the device structure (’441 Patent, Fig. 4).
V. Key Claim Terms for Construction
The Term: "linker site"
Context and Importance: The definition of "linker site" is critical, as it is the structure where the single biomolecule is physically located for analysis. The infringement theory depends on mapping this term to the bottom of the accused product's ZMW, where a DNA-polymerase complex is immobilized (Compl. ¶¶43-44). Practitioners may focus on this term to dispute whether a nanoscale well (ZMW) is equivalent to the claimed "site."
Intrinsic Evidence for Interpretation:
- Evidence for a Broader Interpretation: The claims define the term functionally as a site "being treated to affix the biomolecule" (’441 Patent, col. 27:19-20). This functional language may support an argument that any location specifically prepared for immobilization, such as the bottom of a ZMW, qualifies.
- Evidence for a Narrower Interpretation: The patent specification and figures depict the "linker site 220" as a defined area on a surface, potentially with a supporting material filled into a pinhole, rather than the bottom of a waveguide structure (’441 Patent, col. 11:22-25; Fig. 2). This could suggest a more limited, surface-based definition.
The Term: "formed over"
Context and Importance: The spatial relationship "formed over" appears in two key limitations: the linker site is "formed over the light detector," and the excitation light source is "formed over the substrate." The accused products allegedly illuminate the analysis site from below the substrate containing the detector. The viability of the infringement case may turn on whether "formed over" requires a specific vertical stacking order or can encompass a broader set of physical arrangements.
Intrinsic Evidence for Interpretation:
- Evidence for a Broader Interpretation: The term "over" is not explicitly defined with a strict directional or stacking requirement. An argument could be made that as long as the components are part of the same integrated apparatus on the substrate, the limitation is met.
- Evidence for a Narrower Interpretation: The patent figures consistently show a stacked arrangement where the linker site 220 is physically on top of the detector 210, and the excitation source 40 is a layer built on top of other structures which are themselves on the substrate (’441 Patent, Figs. 2, 4). This consistent depiction may support a narrower construction requiring a specific vertical assembly.
VI. Other Allegations
- Indirect Infringement: The complaint alleges induced infringement, stating that Defendant had knowledge of the patent from extensive licensing discussions and that its publicly available documentation, user guides, and software "instruct[] customers on uses of PacBio's products that infringe" (Compl. ¶¶55-56). It also alleges contributory infringement, arguing that the SMRT Cells and other system components are material parts of the invention that are not staple articles of commerce and have no substantial non-infringing use (Compl. ¶57).
- Willful Infringement: Willfulness is alleged based on Defendant's purported pre-suit knowledge of the ’441 Patent, stemming from licensing negotiations that began as early as 2010 and continued intermittently until 2015, years before the accused products were launched (Compl. ¶¶12-14, 59).
VII. Analyst’s Conclusion: Key Questions for the Case
- A threshold issue, arising after the complaint was filed, is one of case viability: given that the asserted representative claim (Claim 48) and all other independent claims have been cancelled in inter partes review, can the Plaintiff proceed by asserting any of the surviving dependent claims, and if so, do the infringement allegations in the original complaint provide sufficient notice for such a theory?
- A core technical issue will be one of structural and definitional scope: can the architecture of the accused ZMW-based system, which immobilizes a polymerase at the bottom of a well and provides illumination from below, be construed to meet the claim limitations of a "linker site formed over the light detector" and an "excitation light source formed over the substrate" as described in the patent?
- Finally, should the case proceed on a surviving claim, a key question for damages will be one of intent: does the documented history of extensive, failed licensing negotiations between the parties prior to the launch of the accused products provide a sufficient basis to establish willful infringement?