DCT

1:22-cv-00595

10X Genomics Inc v. Vizgen Inc

Log In

I. Executive Summary and Procedural Information

  • Parties & Counsel:
  • Case Identification: 1:22-cv-00595, D. Del., 05/03/2022
  • Venue Allegations: Venue is alleged to be proper as Defendant is a Delaware corporation and thus resides in the district.
  • Core Dispute: Plaintiff alleges that Defendant’s MERSCOPE Platform and associated lab services infringe five patents related to methods for in situ analyte detection and the generation of three-dimensional nucleic acid matrices.
  • Technical Context: The technology relates to spatial genomics, a field focused on analyzing genetic material within its native tissue context, thereby preserving crucial information about the spatial location of molecules.
  • Key Procedural History: The complaint alleges that Plaintiffs provided Defendant with notice of infringement via a letter on or around May 2, 2022, one day prior to filing suit; this allegation forms the basis for the willfulness claims. All asserted patents are owned by Harvard College and are exclusively licensed to 10X Genomics, Inc.

Case Timeline

Date Event
2011-12-22 Earliest Priority Date for ’737, ’051, ’052, and ’054 Patents
2013-03-12 Earliest Priority Date for ’767 Patent
2021-03-XX Defendant announced the launch of MERSCOPE Platform
2021-06-01 U.S. Patent No. 11,021,737 Issues
2021-08-XX Defendant began shipping MERSCOPE Platform
2022-04-05 U.S. Patent Nos. 11,293,051, 11,293,052, and 11,293,054 Issue
2022-04-12 U.S. Patent No. 11,299,767 Issues
2022-05-02 Plaintiff allegedly sent notice letter to Defendant
2022-05-03 Complaint Filed

II. Technology and Patent(s)-in-Suit Analysis

U.S. Patent No. 11,021,737 - "Compositions and Methods for Analyte Detection"

  • Patent Identification: U.S. Patent No. 11,021,737, "Compositions and Methods for Analyte Detection," issued June 1, 2021.

The Invention Explained

  • Problem Addressed: The patent’s background section notes that conventional methods for genetic analysis require extracting nucleic acid molecules from their native environment, which makes it impossible to identify the cellular origin of individual nucleic acids and destroys spatial information critical to understanding their function (U.S. Patent No. 11,021,737, col. 2:50-55).
  • The Patented Solution: The invention provides methods for creating a three-dimensional matrix of nucleic acids in situ, meaning within the cell or tissue sample itself. This process immobilizes, amplifies, and allows for the sequencing of nucleic acids while preserving their original spatial coordinates, creating an information storage medium that can be repeatedly analyzed ('737 Patent, col. 2:5-32, 56-60; Fig. 2).
  • Technical Importance: This approach enables the spatial mapping of gene expression within intact tissues, a key advance for biological research in complex systems ('737 Patent, col. 2:45-49).

Key Claims at a Glance

  • The complaint asserts independent claim 1 (Compl. ¶35).
  • Essential elements of Claim 1 include:
    • Contacting a cell or tissue sample with a detection reagent, where the reagent has a probe that binds to the target analyte and a nucleic acid label with pre-determined subsequences.
    • Detecting a temporal order of signal signatures in the sample associated with those pre-determined subsequences.
    • Using the temporal order of signal signatures to identify the analyte in the sample.
  • The complaint does not explicitly reserve the right to assert dependent claims for the ’737 Patent.

U.S. Patent No. 11,293,051 - "Compositions and Methods for Analyte Detection"

  • Patent Identification: U.S. Patent No. 11,293,051, "Compositions and Methods for Analyte Detection," issued April 5, 2022.

The Invention Explained

  • Problem Addressed: The patent addresses the technical challenge of detecting multiple different analytes within a single sample, particularly where multiplexing is limited by the number of available optical labels (e.g., fluorescent colors) (U.S. Patent No. 11,293,051, col. 20:56-64).
  • The Patented Solution: The invention describes a method of analyzing a sample through sequential readout cycles. In each cycle, a set of "decoding reagents" is associated with a subset of detection reagents bound to analytes, and a signal is detected. By performing multiple distinct readout cycles and removing the signals between them, a temporal order of signal signatures is generated that uniquely identifies each analyte at its specific location within the sample ('051 Patent, col. 4:32-51). Figure 5 illustrates various forms of nucleic acid labels that can be used with probe molecules.
  • Technical Importance: This temporally-sequential detection method allows for a multiplicative increase in the number of analytes that can be distinguished, moving beyond the limitations of spectrally distinct labels ('051 Patent, col. 20:65-col. 21:2).

Key Claims at a Glance

  • The complaint asserts independent claim 1 (Compl. ¶42).
  • Essential elements of Claim 1 include:
    • Performing a first readout cycle by associating a first plurality of decoding reagents with a first subset of detection reagents and detecting a first plurality of signal signatures.
    • Removing the first plurality of signal signatures.
    • Performing a second readout cycle by associating a second plurality of decoding reagents with a second, distinct but overlapping, subset of detection reagents.
    • Using the signal signatures from both cycles to identify a temporal order of signals corresponding to a location and thereby identify an analyte at that location.
  • The complaint does not explicitly reserve the right to assert dependent claims for the ’051 Patent.

U.S. Patent No. 11,293,052 - "Compositions and Methods for Analyte Detection"

  • Patent Identification: U.S. Patent No. 11,293,052, "Compositions and Methods for Analyte Detection," issued April 5, 2022.
  • Technology Synopsis: This patent is directed to methods of analyzing a biological sample by performing multiple, sequential readout cycles. The method involves binding detection reagents to analytes, associating decoding reagents with subsets of the detection reagents in distinct cycles, detecting signal signatures, and using the temporal order of those signals to identify the analytes in situ ('052 Patent, Abstract; col. 1:19-35).
  • Asserted Claims: Independent claim 1 (Compl. ¶49).
  • Accused Features: The complaint alleges that the MERSCOPE Platform and Lab Services program practices the claimed methods (Compl. ¶49).

U.S. Patent No. 11,293,054 - "Compositions and Methods for Analyte Detection"

  • Patent Identification: U.S. Patent No. 11,293,054, "Compositions and Methods for Analyte Detection," issued April 5, 2022.
  • Technology Synopsis: This patent describes a detection reagent comprising a probe (e.g., an antibody or nucleic acid) conjugated to a nucleic acid label. The label contains pre-determined subsequences that can be detected in a temporally-sequential manner to form a unique identifier for the probe, enabling highly multiplexed analyte detection ('054 Patent, Abstract; col. 6:51-col. 7:2).
  • Asserted Claims: Independent claim 1 (Compl. ¶56).
  • Accused Features: The MERSCOPE Platform and its components are alleged to constitute the claimed detection reagents (Compl. ¶56).

U.S. Patent No. 11,299,767 - "Method for Generating a Three-Dimensional Nucleic Acid Containing Matrix"

  • Patent Identification: U.S. Patent No. 11,299,767, "Method for Generating a Three-Dimensional Nucleic Acid Containing Matrix," issued April 12, 2022.
  • Technology Synopsis: This patent focuses on methods for generating a three-dimensional matrix of nucleic acids within a biological sample. The method involves permeabilizing a sample, generating the matrix with attached nucleic acids that preserve their spatial orientation, and then selectively removing non-nucleic acid components to facilitate analysis ('767 Patent, Abstract; col. 1:29-41).
  • Asserted Claims: Independent claim 1 (Compl. ¶63).
  • Accused Features: The MERSCOPE Platform workflow is alleged to perform the steps of the claimed method (Compl. ¶63).

III. The Accused Instrumentality

Product Identification

The "Accused Instrumentalities" are identified as all products and services related to Vizgen's MERSCOPE Platform and Lab Services program (Compl. ¶21). This includes the MERSCOPE Instrument, Analysis Computer, Visualizer Software, and various reagents and consumables (Compl. ¶19).

Functionality and Market Context

  • The MERSCOPE Platform is based on MERFISH (Multiplexed error-robust fluorescence in situ hybridization) technology (Compl. ¶18). It is described as a system for providing multiplexed, single-molecule in situ spatial imaging analysis to customers, either through the sale of the platform or as a service (Compl. ¶18, 20). The complaint alleges that Vizgen launched the MERSCOPE Platform in March 2021 and began shipping products to customers as early as August 2021 (Compl. ¶18).
  • No probative visual evidence provided in complaint.

IV. Analysis of Infringement Allegations

The complaint references exemplary claim charts in Attachments A and B for the ’737 and ’051 patents, respectively, and incorporates them by reference (Compl. ¶35, 42). However, these attachments were not provided with the complaint document. The infringement theory is therefore summarized below in prose based on the narrative allegations in the complaint.

U.S. Patent No. 11,021,737 Infringement Allegations

The complaint alleges that Vizgen directly infringes one or more claims, including at least claim 1, by making, using, selling, or importing the Accused Instrumentalities (Compl. ¶35). The infringement allegations are directed at the use of the MERSCOPE Platform and workflow, either by Vizgen itself in its Lab Services program or by its customers following Vizgen's instructions (Compl. ¶20, 36). The core of the allegation is that the MERSCOPE process for in situ spatial imaging analysis practices the patented method of identifying analytes through temporally-sequential detection of signals from nucleic acid labels.

U.S. Patent No. 11,293,051 Infringement Allegations

Similar to the allegations for the ’737 Patent, the complaint alleges that Vizgen's MERSCOPE Platform and services infringe one or more claims of the ’051 Patent, including claim 1 (Compl. ¶42). The infringement theory centers on the multi-cycle readout process allegedly used by the MERSCOPE Platform. The complaint alleges this process involves performing distinct readout cycles with different sets of decoding reagents to generate a temporal order of signals that identify analytes, thereby practicing the patented method (Compl. ¶42-43).

  • Identified Points of Contention:
    • Scope Questions: A central question may be whether the term "detection reagent" as used in the patents, which comprises a probe and a nucleic acid label, reads on the probes and labeling system used in the accused MERFISH technology. Does the MERFISH process of sequential hybridization of imaging probes meet the claim limitation of "detecting a temporal order of signal signatures"?
    • Technical Questions: The complaint does not provide specific details on how the MERSCOPE Platform technically performs its analysis. A key question for the court will be what evidence demonstrates that the accused process performs each step of the asserted multi-step method claims, such as associating distinct pluralities of "decoding reagents" with "detection reagents" in sequential, overlapping cycles as required by claim 1 of the ’051 Patent.

V. Key Claim Terms for Construction

  • The Term: "detecting in a temporally-sequential manner" ('737 Patent, Claim 1)

  • Context and Importance: This phrase is at the core of the claimed invention, distinguishing it from prior art methods that rely on simultaneous detection of multiple distinct colors. The definition of this term will be critical for determining whether the accused MERFISH process, which involves multiple rounds of hybridization and imaging, constitutes infringement. Practitioners may focus on whether this term requires active signal removal between steps or simply sequential data acquisition.

  • Intrinsic Evidence for Interpretation:

    • Evidence for a Broader Interpretation: The specification states that a temporal order of signal signatures "can be unique for each subpopulation of the detection reagents" ('737 Patent, col. 22:42-46), which may suggest that any method of generating a unique time-based code meets the limitation.
    • Evidence for a Narrower Interpretation: The specification describes embodiments where "unbound detection reagents" are removed before detection, and signals from a prior step can be removed by methods like "washing, heating, photo-bleaching, displacement... [or] enzymatic digestion" ('737 Patent, col. 23:32-41). This could support a narrower construction requiring an active signal removal step between detection events, not just sequential imaging.

  • The Term: "detection reagent" ('051 Patent, Claim 1)

  • Context and Importance: Claim 1 of the ’051 Patent recites distinct pluralities of "decoding reagents" being associated with subsets of "detection reagents." The relationship and definition of these two types of reagents will be central to the infringement analysis. The dispute may turn on whether the probes used in the accused MERFISH technology can be bifurcated into these two claimed categories.

  • Intrinsic Evidence for Interpretation:

    • Evidence for a Broader Interpretation: The patent defines a "detection reagent" broadly as comprising "at least one probe reagent and at least one nucleic acid label" ('051 Patent, col. 23:51-53). A "decoder probe" is defined as an oligonucleotide complementary to a sequence on the nucleic acid label ('051 Patent, col. 24:53-56). This could support an interpretation where the main MERFISH probes are "detection reagents" and the fluorescently labeled oligos that sequentially bind to them are "decoder probes."
    • Evidence for a Narrower Interpretation: The detailed description and figures illustrate specific configurations, such as a probe reagent conjugated to a particle that acts as a hub for multiple nucleic acid labels ('051 Patent, Fig. 6A, 6B). A defendant may argue that the term should be limited to these more complex disclosed structures, potentially distinguishing them from the accused product's architecture.

VI. Other Allegations

  • Indirect Infringement: For all five patents, the complaint alleges induced infringement based on Defendant's instructional materials, such as user guides and product bulletins, which allegedly instruct customers on how to use the MERSCOPE Platform in an infringing manner (e.g., Compl. ¶36, 43, 50, 57, 64). It also alleges contributory infringement, asserting that the MERSCOPE Platform components are a material part of the patented inventions, are specifically designed for infringing use, and have no substantial non-infringing uses (e.g., Compl. ¶37, 44, 51, 58, 65).
  • Willful Infringement: Willfulness is alleged for all five patents based on Defendant’s alleged knowledge of the patents as of "on or around May 2, 2022," the date Plaintiffs allegedly sent a notice letter with infringement claim charts to Defendant (e.g., Compl. ¶35, 42, 49, 56, 63). The complaint alleges infringement has been willful since at least that date.

VII. Analyst’s Conclusion: Key Questions for the Case

  • A core issue will be one of claim construction and technical comparison: How does the accused MERFISH technology, which relies on sequential hybridization of fluorescent probes to target RNA, map onto the patent claims' requirements for "detection reagents," "decoding reagents," and the generation of a "temporal order of signal signatures"? The resolution will depend on whether the court construes these terms broadly enough to cover the specific components and processes of the accused platform.
  • A second central question will be evidentiary: Given the absence of the complaint's claim chart exhibits, what technical evidence will Plaintiffs present to demonstrate that the accused MERSCOPE Platform and its workflow actually perform each and every step recited in the asserted multi-step method claims, particularly the complex, multi-cycle process of claim 1 of the ’051 patent?
  • A third question relates to damages and willfulness: Can Plaintiffs establish that Defendant had the requisite knowledge and intent for induced infringement, and does the alleged May 2, 2022 notice letter provide a sufficient factual basis to support a finding of willful infringement for conduct occurring after that date?