DCT

1:25-cv-00602

Illumina Inc v. Element Biosciences Inc

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I. Executive Summary and Procedural Information

  • Parties & Counsel:
  • Case Identification: 1:25-cv-00602, D. Del., 09/09/2025
  • Venue Allegations: Venue is based on Defendant's incorporation in the state of Delaware, which deems it a resident of the district.
  • Core Dispute: Plaintiff alleges that Defendant’s AVITI line of genetic sequencing systems and associated consumable kits infringe seven U.S. patents related to the automation of instrument design, sample handling, and fluidics.
  • Technical Context: The technology at issue is next-generation sequencing (NGS), a high-throughput method for determining the sequence of DNA that has significantly reduced the cost and time of genomic analysis, enabling broad applications in research and clinical diagnostics.
  • Key Procedural History: The complaint alleges that Defendant was founded by former Illumina employees familiar with the patented technology, acquired Plaintiff’s commercial MiSeq and MiniSeq instruments (which allegedly practice the patents-in-suit) to aid in developing the accused products, was on notice of the patents via a virtual marking website, and had a request for a broad covenant not to sue declined by Plaintiff prior to litigation.

Case Timeline

Date Event
2007-01-01 Illumina Genome Analyzer launch
2011-01-10 Earliest Priority Date for '241, '781, '130, '116 Patents
2011-01-01 Illumina MiSeq instrument launch
2015-02-10 '781 Patent issued
2016-01-01 Illumina MiniSeq sequencer launch
2017-01-01 Element Biosciences founded
2017-01-03 Earliest Priority Date for '702, '028, '301 Patents
2019-02-01 Element purchases Illumina MiSeq instrument
2021-05-01 Element requests covenant not to sue from Illumina
2021-09-14 '130 Patent issued
2022-01-01 Element launches AVITI sequencer
2023-01-01 Element launches AVITI LT sequencer
2023-07-11 '116 Patent issued
2024-04-01 Element announces AVITI24 sequencer
2024-11-26 '241 Patent issued
2025-03-18 '702 Patent issued
2025-06-10 '028 Patent issued
2025-08-26 '301 Patent issued
2025-09-09 Second Amended Complaint filed

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

U.S. Patent No. 12,151,241

  • Patent Identification: U.S. Patent No. 12,151,241, "Systems, Methods, and Apparatuses To Image a Sample for Biological or Chemical Analysis," issued November 26, 2024.

The Invention Explained

  • Problem Addressed: The complaint alleges that early next-generation sequencing (NGS) systems required significant manual effort from highly trained personnel for tasks such as aligning the sample "flow cell" and connecting fluidic components, introducing possibilities for user error that could lead to wasted samples, costly reagents, and failed sequencing runs (Compl. ¶¶31-32).
  • The Patented Solution: The invention claims an integrated and automated system for genetic sequencing that combines an optical imaging system, a fluid storage system, and a specialized device holder for the flow cell (Compl. ¶¶33-35, 75). As described in a related patent, the system is designed to reduce manual intervention by, for example, automating the delivery of reagents from a tray to the flow cell via movable "sipper tubes" and simplifying the loading and securing of the flow cell for imaging ('130 Patent, Abstract; col. 1:31-40).
  • Technical Importance: This automated "load and go" approach is alleged to have made sequencing faster, more reliable, and more accessible to a wider range of users by minimizing manual preparation and reducing hands-on time from hours to minutes (Compl. ¶¶7, 36, 38).

Key Claims at a Glance

  • The complaint asserts infringement of at least independent Claim 1 (Compl. ¶74).
  • Essential elements of Claim 1 include:
    • An optical system comprising an excitation light source, an imaging detector, and an optical train;
    • A device holder for a fluidic device (flow cell), the holder itself comprising a support structure, a rotatable cover biased toward an open position, and a latch to hold the cover closed;
    • A fluid storage system comprising an enclosure with a door, a transport platform holding an array of sipper tubes, and a drive motor to move the platform; and
    • A casing enclosing the entire system.
  • The complaint reserves the right to assert additional claims, including dependent claims 2-3, 7-12, 14, 15-16, 17, and 18-20 (Compl. ¶74).

U.S. Patent No. 8,951,781

  • Patent Identification: U.S. Patent No. 8,951,781, "Systems, Methods, and Apparatuses To Image a Sample for Biological or Chemical Analysis," issued February 10, 2015.

The Invention Explained

  • Problem Addressed: As with the '241 Patent, this invention addresses the problems of early NGS systems that relied on a user's ability to precisely and manually place samples into the instrument, a process prone to misalignment, leaks, and other errors (Compl. ¶¶31-33).
  • The Patented Solution: The invention claimed is a "fluidic device holder" designed to automate the precise positioning of a fluidic device (e.g., a flow cell) for analysis (Compl. ¶107). The holder uses a combination of fixed "reference surfaces" (such as pins) and a "movable locator arm" driven by an "actuator." When engaged, the locator arm presses the fluidic device against the reference surfaces, securing it in a fixed, correct position for imaging relative to the X, Y, and Z axes ('130 Patent, Abstract; col. 3:1-10).
  • Technical Importance: This mechanism automates the critical step of flow cell alignment, removing a key source of user error and improving the reliability and repeatability of the sequencing process (Compl. ¶¶33-34).

Key Claims at a Glance

  • The complaint asserts infringement of at least independent Claim 30 (Compl. ¶106).
  • Essential elements of Claim 30 include:
    • A support structure with a base surface and a plurality of reference surfaces in an XY-plane;
    • An alignment assembly with an actuator and a movable locator arm having an engagement end;
    • The actuator moves the locator arm between retracted and biased positions, where in the biased position, the engagement end presses the fluidic device against the reference surfaces to hold it in a fixed position; and
    • The locator arm includes a finger which includes the engagement end.
  • The complaint reserves the right to assert additional claims, including dependent claims 31, 38-39, and 42-43 (Compl. ¶106).

Multi-Patent Capsules

  • Patent Identification: U.S. Patent No. 11,117,130, "Systems, Methods, and Apparatuses To Image a Sample for Biological or Chemical Analysis," issued September 14, 2021.

  • Technology Synopsis: The patent claims a system that integrates an optical deck, a slidable sample deck that supports a fluidic device and includes a thermal module to control its temperature, and a separate fluid storage system with a fluid removal assembly using an elevator mechanism to move an array of sipper tubes bidirectionally along a Z-axis (Compl. ¶130).

  • Asserted Claims: Independent Claim 1 (Compl. ¶129).

  • Accused Features: The complaint alleges the overall architecture of the AVITI Systems infringes, mapping the claimed optical deck, slidable and thermally-controlled sample deck, and fluid storage system to corresponding components in the accused instruments (Compl. ¶¶132-161).

  • Patent Identification: U.S. Patent No. 11,697,116, "A DNA sequencing instrument comprising," issued July 11, 2023.

  • Technology Synopsis: The patent claims a DNA sequencing instrument with a detailed fluid removal assembly. This assembly includes an elevator mechanism with a drive motor and lead screw, a transport platform for sipper tubes that carries a "flag," a guide plate for the tubes, and a location sensor configured to detect the flag to determine the position of the sipper tubes (Compl. ¶172).

  • Asserted Claims: Independent Claim 1 (Compl. ¶171).

  • Accused Features: The allegations target the specific mechanics of the AVITI Systems' fluid aspiration technology, including the elevator mechanism that moves the sipper tubes, the guide plate that aligns them with reagent wells, and the use of a flag and sensor to determine their vertical position (Compl. ¶¶186-214).

  • Patent Identification: U.S. Patent No. 12,251,702, "Flowcell Cartridge with Floating Seal Bracket," issued March 18, 2025.

  • Technology Synopsis: The patent claims a microfluidic cartridge containing a frame, a microfluidic plate (e.g., glass slide) that "floats" relative to the frame, and a support bracket that also "floats" relative to the plate and frame. The bracket has seals and alignment holes that engage with indexing features on an analysis device to align the fluidic ports (Compl. ¶223).

  • Asserted Claims: Independent Claim 1 (Compl. ¶222).

  • Accused Features: The allegations focus on the design of the Element Sequencing Kits, particularly the assertion that the glass substrate (plate) and the seal bracket can move relative to the plastic cartridge (frame) to allow for precise alignment when installed in the AVITI instrument (Compl. ¶¶226-227, 231-233).

  • Patent Identification: U.S. Patent No. 12,325,028, "Flowcell Cartridge with Floating Bracket," issued June 10, 2025.

  • Technology Synopsis: The patent claims a complete analysis system comprising both a microfluidic cartridge (with a floating plate and a floating bracket/gasket) and a sequencer configured to receive it. The sequencer's receiver includes a chuck and multiple sets of "indexing features" (e.g., pins) that correspond to alignment holes and apertures on the cartridge to align the components (Compl. ¶260).

  • Asserted Claims: Independent Claim 1 (Compl. ¶259).

  • Accused Features: The allegations target the interaction between the Element Sequencing Kits (the cartridge) and the AVITI instruments (the sequencer). Specifically, the complaint points to the pins and protrusions within the AVITI's "nest" as the claimed indexing features that engage with holes on the accused cartridges to achieve alignment of the fluidic ports (Compl. ¶¶270-282).

  • Patent Identification: U.S. Patent No. 12,397,301, "Flowcell Cartridge with Floating Bracket," issued August 26, 2025.

  • Technology Synopsis: The patent claims an analysis system similar to the '028 Patent, further specifying that each seal on the floating support has a "through-hole" that fluidically connects the microfluidic plate's ports to the analysis device's ports once alignment is achieved via engagement of pins (Compl. ¶290).

  • Asserted Claims: Independent Claim 1 (Compl. ¶289).

  • Accused Features: The allegations again focus on the interaction between the AVITI instruments and Element Sequencing Kits, emphasizing how the system's pins align the cartridge's floating bracket such that the through-holes in its seals create a fluidic path from the flow cell to the instrument's ports (Compl. ¶¶296-311).

III. The Accused Instrumentality

Product Identification

The accused instrumentalities are Defendant’s AVITI, AVITI LT, and AVITI24 genetic sequencing instruments (collectively, "AVITI Systems") and their associated consumable "Element Sequencing Kits," which include the Cloudbreak, Trinity, and Teton product lines (Compl. ¶¶60-61, 71).

Functionality and Market Context

The AVITI Systems are identified as next-generation sequencing (NGS) instruments that utilize a dual-flow cell design (Compl. ¶¶62, 77). The complaint describes their functionality as including an optical system with lasers and cameras for imaging, a "nest bay" that holds two flow cell cartridges via a hinged lid, and an automated fluid storage and delivery system that uses "sippers" to aspirate reagents from a refrigerated bay (Compl. ¶¶80, 82, 85, 89, 146). The complaint alleges the AVITI LT is a software-limited version of the AVITI, and the AVITI24 is a related benchtop model (Compl. ¶¶63-64). The "Element Sequencing Kits" are described as consumables containing a flow cell, comprising a glass substrate encased in a plastic cartridge, for use with the AVITI systems (Compl. ¶¶71, 114).

The complaint alleges these products compete directly with Plaintiff’s products and that by 2023, Defendant had exceeded 160 orders and generated over $25 million in revenue from the accused products (Compl. ¶¶8, 60).

IV. Analysis of Infringement Allegations

'241 Patent Infringement Allegations

Claim Element (from Independent Claim 1) Alleged Infringing Functionality Complaint Citation Patent Citation
an optical system comprising an excitation light source, an imaging detector, and an optical train The AVITI Systems' four-color optical system, which includes excitation lasers ("excitation lines"), "multiple cameras for simultaneous imaging" (imaging detectors), and objective and tube lenses (optical train) to guide light. ¶80 '130 Patent, col. 4:32-47
a device holder to orient a fluidic device for imaging by the optical system, the fluidic device comprising a flow cell The "nest" within the AVITI Systems' nest bay, which holds the flow cell cartridge (the fluidic device) for imaging. An annotated product photo shows the nest bay holding two loaded flow cells. (Compl. ¶36). ¶82 '130 Patent, col. 3:11-20
a support structure including a loading region to receive the fluidic device, the loading region including a base surface to have the fluidic device positioned thereon The nest itself is the support structure, containing a loading area with three silver registration pins that fit into holes on the flow cell cartridge to ensure proper alignment and seating on a base surface. ¶¶83-84 '130 Patent, col. 3:14-17
a rotatable cover that is coupled to the support structure and moveable about an axis between an open position and a closed position...to secure the fluidic device The hinged "flow cell lid" on each nest, which moves about an axis, opens to a 40° angle to permit insertion of the flow cell, and closes to secure it in place for imaging. A video screenshot shows the cover's axis of rotation. (Compl. ¶40). ¶¶85-86 '130 Patent, col. 40:48-55
wherein the cover is biased toward the open position The nest lid automatically opens to the 40° angle when unlatched, indicating it is biased open. The complaint provides a photo allegedly showing a spring that provides this bias. (Compl. ¶41). ¶87 '130 Patent, col. 41:25-28
a latch to releasably hold the cover in the closed position A tab on the lid that "snaps into place" to secure the flow cell and a button that "unlatches" the lid. A photo shows the cover latched in the closed position. (Compl. ¶42). ¶88 '130 Patent, col. 41:35-39
a fluid storage system comprising: an enclosure having a cavity, a door openable to provide access to the cavity The AVITI Systems' pump and reagent bays, which are enclosed with bay doors. The complaint provides an unboxing video screenshot showing the enclosure and cavity opening. (Compl. ¶45). ¶¶89-90, 93 '130 Patent, col. 20:30-38
a transport platform holding an array of sipper tubes...a drive motor operatively coupled to the transport platform...to position the array of sipper tubes The sipper tubes used to aspirate reagents are attached to a transport platform that is moved up and down by a drive motor, allowing the sippers to descend into and ascend from the reagent wells. ¶¶94-96 '130 Patent, col. 36:57-64
a casing enclosing the optical system, the device holder, and the fluid storage system therein The "Exterior shells" of the AVITI instrument, which enclose the internal components, including the optical system, nest bay (device holder), and reagent/pump bays (fluid storage system). ¶97 '130 Patent, col. 18:6-10
  • Identified Points of Contention:
    • Scope Questions: The complaint presents a comprehensive mapping of a multi-part system claim onto the accused device. A central question may be whether every recited element exists in the AVITI systems and is arranged as claimed. For instance, the functionality of the "transport platform holding an array of sipper tubes" as described in the patent will need to be compared to the specific mechanism in the accused device.
    • Technical Questions: A potential point of dispute is the "biased toward the open position" limitation. The complaint alleges a spring provides this function (Compl. ¶87), but the specific force, reliability, and manner of operation of this biasing mechanism may be scrutinized to determine if it meets the claim requirement as understood in the context of the patent.

'781 Patent Infringement Allegations

Claim Element (from Independent Claim 30) Alleged Infringing Functionality Complaint Citation Patent Citation
A fluidic device holder configured to orient a fluidic device with respect to mutually perpendicular X, Y, and Z-axes The nest and nest lid within the AVITI system, which together hold and orient the flow cell cartridge (the fluidic device) for imaging along the X, Y, and Z axes. ¶¶108, 111 '130 Patent, Abstract
a support structure configured to receive a fluidic device, the support structure including a base surface that faces in a direction along the Z-axis... The nest, which includes a loading area with a base surface. The fluidic device is positioned on this base surface. ¶¶112-113 '130 Patent, col. 3:14-17
a plurality of reference surfaces facing in respective directions along an XY-plane The surfaces of the three silver pins in the nest's loading area. These pins fit into holes on the cartridge, limiting its movement in the XY-plane. ¶¶114-116 '130 Patent, col. 3:18-19
an alignment assembly comprising an actuator and a movable locator arm... the actuator moving the locator arm between retracted and biased positions to move the engagement end away from and toward the reference surfaces The mechanism coupled to the nest lid. The complaint alleges that closing the lid acts as the "actuator," which in turn moves an internal component ("locator arm") that pushes the fluidic device along the X-axis. This moves the device from a retracted (un-pressed) state to a biased (pressed) state. A video screenshot comparison shows the fluidic device shifting upon lid closure. (Compl. ¶63). ¶¶117-118 '130 Patent, col. 3:20-27
wherein the engagement end presses... the fluidic device against the reference surfaces when the locator arm is in the biased position such that the fluidic device is held...in a fixed position When the lid is closed, the engagement end of the locator arm allegedly presses the fluidic device in the X-direction against the silver pins (reference surfaces), securing it in a fixed position relative to the nest. ¶¶119-120 '130 Patent, col. 3:27-31
wherein the locator arm includes a finger, the finger including the engagement end The internal component that acts as the "locator arm" is alleged to be a projecting machine part, which fits the definition of a "finger," and the part of it that contacts the fluidic device is the "engagement end." ¶121 '130 Patent, col. 54:38-40
  • Identified Points of Contention:
    • Scope Questions: The primary dispute will likely center on the claim term "alignment assembly comprising an actuator and a movable locator arm." The complaint's theory equates the manual action of closing the lid with the function of an "actuator" that drives a "locator arm." It raises the question of whether a manually operated lid mechanism can be considered an "actuator" as the term is used in the patent, or if the patent requires a separate, automated component.
    • Technical Questions: Evidence will be required to demonstrate that the internal part alleged to be the "locator arm" actually functions as claimed, moving between distinct "retracted and biased positions" and pressing the fluidic device against the "reference surfaces" to achieve a "fixed position."

V. Key Claim Terms for Construction

  • Term: "alignment assembly comprising an actuator and a movable locator arm" ('781 Patent, Claim 30)

  • Context and Importance: This term is central to the infringement theory for the '781 Patent. The Plaintiff's case appears to depend on a broad construction where the user's manual action of closing the nest lid satisfies the "actuator" element, which in turn moves an internal part defined as the "locator arm." Practitioners may focus on this term because if it is construed to require a separate, automated mechanism distinct from the main cover, the infringement allegation could be challenged.

  • Intrinsic Evidence for Interpretation:

    • Evidence for a Broader Interpretation: The body of the '130 Patent (from the same family) may use broad, functional language to describe the alignment assembly that does not explicitly require a motor or independent power source, potentially allowing a mechanical linkage driven by the cover to fall within its scope (e.g., '130 Patent, col. 3:20-27).
    • Evidence for a Narrower Interpretation: The specification may depict embodiments where the "actuator" is an electromechanical component, such as a motor or solenoid, separate from the cover mechanism. The abstract's language of an "actuator moving the locator arm" could suggest a powered component rather than a manually operated one ('130 Patent, Abstract).

  • Term: "biased toward the open position" ('241 Patent, Claim 1)

  • Context and Importance: This term requires the rotatable cover to have a default tendency to open. The complaint alleges a spring performs this function (Compl. ¶87). This is a specific mechanical feature that must be present in the accused device. The dispute may turn on the degree and nature of the "bias" required by the claims versus what is present in the AVITI system's lid.

  • Intrinsic Evidence for Interpretation:

    • Evidence for a Broader Interpretation: The '130 Patent specification may describe the purpose of the bias functionally, such as to "facilitate removal" of the device, which could be satisfied by any mechanism, including a simple spring, that assists in opening the cover ('130 Patent, col. 41:25-28).
    • Evidence for a Narrower Interpretation: The patent's figures or detailed description might illustrate a more complex or specific biasing mechanism, potentially allowing an argument that a simple spring-loaded hinge does not meet the technical requirements envisioned by the inventors.

VI. Other Allegations

  • Indirect Infringement: The complaint alleges inducement of infringement, stating that Defendant’s user manuals, workflow guides, and other product documentation instruct customers on how to use the AVITI Systems in a manner that directly infringes the asserted claims, such as by loading the flow cell cartridges and reagents (Compl. ¶¶101, 124, 166, 217, 255, 285, 314).
  • Willful Infringement: Willfulness is alleged based on pre-suit knowledge of the patents. The complaint asserts that Defendant was aware of the patents through multiple avenues: its founders and key employees are former Illumina employees who worked on the patented technology; it purchased Illumina's MiSeq instrument, which was covered by a virtual patent marking notice that identified the '781 Patent; and it requested a covenant not to sue from Illumina in May 2021, which was declined (Compl. ¶¶52-58, 102-103, 125-126).

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

  • A core issue will be one of definitional scope: can the term "actuator", as part of the claimed "alignment assembly," be construed to cover the manual action of a user closing an instrument lid, or does the patent's context require a distinct, powered component? The resolution of this claim construction dispute may be pivotal for the infringement analysis of the '781 patent family.
  • A second central issue will be one of component-level equivalence: does the design of the "Element Sequencing Kits"—specifically the interaction between the glass substrate, plastic frame, and seal bracket—meet the claim limitations requiring a "floating" microfluidic plate and a "floating" support bracket that engage with the sequencer's indexing features for alignment, as claimed in the '702, '028, and '301 patents?
  • A key evidentiary question will be one of knowledge and intent: what evidence demonstrates that Defendant, allegedly founded by former employees and having acquired Plaintiff's commercial instruments for development, had pre-suit knowledge of the asserted patents and their relevance to the accused AVITI system, which will be central to the claim for willful infringement?