DCT

1:22-cv-00595

10X Genomics Inc v. Vizgen Inc

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I. Executive Summary and Procedural Information

  • Parties & Counsel:
  • Case Identification: 1:22-cv-00595, D. Del., 08/01/2022
  • Venue Allegations: Venue is alleged to be proper in the District of Delaware because Defendant Vizgen, Inc. is a Delaware corporation and therefore resides in the district.
  • Core Dispute: Plaintiffs allege that Defendant’s MERSCOPE Platform and associated lab services infringe five patents related to methods for detecting biological analytes in situ and generating three-dimensional nucleic acid matrices.
  • Technical Context: The lawsuit concerns the field of spatial genomics, a technology that allows researchers to map the location of genetic material directly within tissue samples, preserving spatial context crucial for understanding biological systems.
  • Key Procedural History: The patents-in-suit are owned by Harvard and exclusively licensed to 10x Genomics, which has the right to sue for infringement. The complaint alleges that on May 2, 2022, approximately three months prior to filing, 10x provided Vizgen with a notice letter detailing the alleged infringement, forming the basis for the willfulness allegations.

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 Accused MERSCOPE Platform launch announced
2021-06-01 U.S. Patent No. 11,021,737 issues
2021-08-XX Accused MERSCOPE Platform begins shipping
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 sends notice letter alleging infringement to Defendant
2022-08-01 First Amended Complaint filed

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

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

  • Issued: June 1, 2021.

The Invention Explained

  • Problem Addressed: Traditional methods of molecular analysis require extracting nucleic acids like DNA and RNA from their native environment (e.g., a cell or tissue), which makes it impossible to identify the original spatial location or cellular origin of individual molecules (’737 Patent, col. 1:50-57). This loss of positional information hinders the understanding of how gene products function within complex biological systems (Compl. ¶15).
  • The Patented Solution: The invention describes methods for immobilizing nucleic acids within their native environment by creating a three-dimensional matrix. This matrix, which can be formed from materials like polyacrylamide, preserves the spatial orientation of the nucleic acids (’737 Patent, col. 3:35-39; ’737 Patent, Fig. 2). Once fixed in place within this matrix, the nucleic acids can be amplified and sequenced in situ, allowing their identity and original three-dimensional coordinates to be determined (’737 Patent, col. 2:20-32).
  • Technical Importance: This approach enables in situ analysis, which aims to measure and analyze a large number of molecules directly in tissue samples, capturing their precise location at sub-cellular resolutions (Compl. ¶15).

Key Claims at a Glance

  • The complaint asserts independent claim 1 and reserves the right to assert additional claims (’737 Patent, Compl. ¶36).
  • The complaint refers to an exemplary claim chart in "Attachment A," which was not filed with the complaint. The full text of the asserted claims is not provided in the complaint.

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

  • Issued: April 5, 2022.

The Invention Explained

  • Problem Addressed: As with the related ’737 Patent, this invention addresses the loss of spatial information that occurs when biological analytes are removed from their native cellular or tissue environment for analysis (Compl. ¶14-15).
  • The Patented Solution: The technology involves methods of in situ analyte detection that preserve the spatial context of biological molecules. The complaint alleges this family of patents covers foundational methods for creating spatial maps of gene expression within original tissue at cellular resolutions (Compl. ¶17).

Key Claims at a Glance

  • The complaint asserts independent claim 1 and reserves the right to assert additional claims (’051 Patent, Compl. ¶44).
  • The complaint refers to an exemplary claim chart in "Attachment B," which was not filed with the complaint. The full text of the asserted claims is not provided in the complaint.

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

  • Issued: April 5, 2022.
  • Technology Synopsis: This patent, part of the same family as the ’737 and ’051 Patents, is directed at methods for detecting analytes within a sample while preserving their spatial information. The technology enables in situ analysis by creating spatial maps of gene expression directly within tissue at high resolution (Compl. ¶17).
  • Asserted Claims: The complaint asserts independent claim 1 (Compl. ¶52).
  • Accused Features: The accused features are Defendant’s MERSCOPE Platform, its components, and related lab services, which allegedly provide multiplexed, single-molecule in situ spatial imaging analysis (Compl. ¶18, 52).

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

  • Issued: April 5, 2022.
  • Technology Synopsis: Belonging to the same family as the lead patents, this patent describes methods for analyte detection that maintain the native spatial context of the molecules. This allows researchers to generate comprehensive maps tying molecular function to physical location within a biological sample (Compl. ¶14-15).
  • Asserted Claims: The complaint asserts independent claim 1 (Compl. ¶60).
  • Accused Features: The complaint alleges that the MERSCOPE Platform and workflow, which perform in situ spatial imaging, infringe the ’054 Patent (Compl. ¶18, 60).

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 the method of generating a three-dimensional matrix that contains nucleic acids. This matrix immobilizes the nucleic acids within their native environment, such as a cell, preserving their spatial orientation for subsequent in situ amplification, detection, and sequencing.
  • Asserted Claims: The complaint asserts independent claim 1 (Compl. ¶68).
  • Accused Features: The complaint accuses the MERSCOPE Platform and its associated workflows of infringing the ’767 Patent by making and using the claimed methods for generating a three-dimensional nucleic acid matrix (Compl. ¶18-21, 68).

III. The Accused Instrumentality

Product Identification

  • The accused instrumentalities are Defendant Vizgen’s MERSCOPE Platform and its associated Lab Services program (Compl. ¶18). This includes the MERSCOPE Instrument, Analysis Computer, Visualizer Software, and various reagents and consumables such as slides and gene panels (Compl. ¶19).

Functionality and Market Context

  • The complaint alleges that the MERSCOPE Platform is based on MERFISH (Multiplexed error-robust fluorescence in situ hybridization) technology and is used to provide customers with "multiplexed, single-molecule in situ spatial imaging analysis" (Compl. ¶18). Vizgen is alleged to use the platform to provide in-house sample processing and data analysis for customers via its Lab Services program, and also to sell the platform to end-user customers (Compl. ¶19-20). The complaint notes that Vizgen announced the launch of MERSCOPE in March 2021, nearly six months after Plaintiff 10x Genomics acquired ReadCoor, a company founded on related work at Harvard (Compl. ¶16, 18).

IV. Analysis of Infringement Allegations

The complaint references exemplary claim charts for each asserted patent as Attachments A through E but does not include these attachments in the filing. The complaint also does not quote the language of any asserted claim. The infringement theory must therefore be summarized from the narrative allegations.

For each of the five asserted patents, the complaint alleges that Vizgen’s MERSCOPE Platform and Lab Services program directly infringes, induces infringement, and contributes to the infringement of at least claim 1 (Compl. ¶36, 44, 52, 60, 68). The core of the infringement allegation is that the MERSCOPE workflow, in performing multiplexed in situ spatial imaging analysis, practices the patented methods for detecting analytes and generating three-dimensional nucleic acid matrices. The complaint cites Vizgen’s user guides, product bulletins, and other public-facing materials as evidence that Vizgen instructs its customers on how to use the accused products in an infringing manner (Compl. ¶37, 45, 53, 61, 69).

No probative visual evidence provided in complaint.

  • Identified Points of Contention:
    • Scope Questions: A central issue may be whether the term "three-dimensional matrix," as used and defined in the patents, can be construed to cover the technical process employed by Vizgen's MERFISH-based technology. The patent specification describes creating a physical matrix through co-polymerization (’737 Patent, col. 2:50-54); the court will have to determine whether the accused process meets this claim limitation, either literally or under the doctrine of equivalents.
    • Technical Questions: A key evidentiary question will be whether the operational steps of the MERSCOPE Platform perform the specific functions required by the asserted claims. The complaint relies on high-level product descriptions, raising the question of what specific technical evidence Plaintiffs will present to demonstrate that the accused MERFISH process meets each element of the asserted method claims.

V. Key Claim Terms for Construction

The complaint does not provide the language of the asserted claims. However, based on the patent specifications and the nature of the dispute, the construction of the following terms may be central to the case.

  • The Term: "three dimensional matrix"

    • Context and Importance: This term appears to be at the heart of the invention, describing the structure that preserves the spatial information of nucleic acids. Its definition will be critical for determining whether Vizgen’s technology, which may achieve a similar outcome through different technical means, falls within the scope of the claims.
    • Intrinsic Evidence for Interpretation:
      • Evidence for a Broader Interpretation: The specification states that the terms "copolymer, matrix and matrix material may be used interchangeably" (’737 Patent, col. 2:14-16), which may support a broader definition not limited to a specific physical substance.
      • Evidence for a Narrower Interpretation: The detailed description provides specific examples of materials for forming the matrix, such as "polyacrylamide, cellulose, alginate, polyamide, cross-linked agarose," which could be used to argue that the term is limited to such physical gel-like structures (’737 Patent, col. 3:35-39).

  • The Term: "in situ"

    • Context and Importance: The patent's stated goal is to analyze nucleic acids "within their native environment" to preserve spatial data (’737 Patent, col. 2:18-20). The definition of "in situ" will be important, as it may determine whether the claims cover processes performed on fixed and permeabilized cells versus living cells, or other sample preparations.
    • Intrinsic Evidence for Interpretation:
      • Evidence for a Broader Interpretation: The specification broadly refers to generating the matrix "in a cell or tissue sample to preserve the naturally occurring nucleic acid sequence diversity" (’737 Patent, col. 2:20-23), which might support a construction covering a wide range of sample states.
      • Evidence for a Narrower Interpretation: Specific embodiments or examples detailed in the patent may describe the process in the limited context of fixed and sectioned tissues on a slide, which a defendant could argue limits the scope of the term to those specific applications.

VI. Other Allegations

  • Indirect Infringement: The complaint alleges both induced and contributory infringement for all five patents-in-suit. Inducement is alleged based on Vizgen’s user manuals, product bulletins, and other instructional materials, which allegedly instruct and encourage customers to use the MERSCOPE Platform in an infringing manner (Compl. ¶37, 45, 53, 61, 69). Contributory infringement is alleged on the basis that Vizgen provides instruments and reagents that are a material part of the claimed inventions, have no substantial non-infringing use, and are especially made for an infringing use (Compl. ¶38, 46, 54, 62, 70).
  • Willful Infringement: Willfulness is alleged for all five patents based on knowledge stemming from a notice letter sent by 10x to Vizgen on or around May 2, 2022 (Compl. ¶33, 40). The complaint alleges that Vizgen continued to "use, market, sell, ship, and encourage and instruct others to use the infringing MERSCOPE platform" after receiving this notice (Compl. ¶39).

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

  • A core issue will be one of technical scope: does Vizgen's MERFISH technology, which relies on sequential fluorescence in situ hybridization, practice the specific patented method of creating and amplifying analytes within a "three-dimensional matrix" as that term is construed from the patent specification? The case may turn on whether the claims are interpreted to cover only the creation of a physical gel-like matrix or can be read more broadly on other methods of in situ spatial analysis.
  • A second key question will be one of infringement proof: can Plaintiffs demonstrate that the accused MERSCOPE Platform and its workflows perform every step of the asserted method claims? The initial complaint's reliance on high-level marketing materials raises the question of what direct technical evidence will be required to prove that the accused product's actual operation maps onto each limitation of the asserted claims.