DCT

1:25-cv-00602

Illumina Inc v. Element Biosciences Inc

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Amended Complaint
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I. Executive Summary and Procedural Information

  • Parties & Counsel:
  • Case Identification: Illumina, Inc. v. Element Biosciences, Inc., 1:25-cv-00602, D. Del., 07/14/2026
  • Venue Allegations: Venue is alleged to be proper as Defendant Element Biosciences, Inc. is a Delaware corporation and is therefore deemed to reside in the district.
  • Core Dispute: Plaintiff alleges that Defendant's AVITI line of genetic sequencing instruments and associated consumable kits infringe seven U.S. patents related to the automation of genetic sequencing instruments and flow cell cartridges.
  • Technical Context: The technology at issue is Next-Generation Sequencing (NGS), a foundational technology for modern genomics research, diagnostics, and personalized medicine that enables rapid, large-scale DNA sequencing.
  • Key Procedural History: The complaint alleges that Defendant was founded in 2017 by former Illumina employees. Plaintiff alleges Defendant acquired one of Plaintiff's MiSeq sequencing instruments in 2019, which was marked with a reference to Plaintiff's patent portfolio. In May 2021, Defendant allegedly requested a broad covenant not to sue on any patents in Plaintiff's portfolio, which Plaintiff declined. This filing is a Third Amended Complaint.

Case Timeline

Date Event
1998-01-01 Illumina was founded Compl. ¶5
2003-01-01 Human Genome Project completed Compl. ¶27
2007-01-01 Illumina launched Genome Analyzer instrument Compl. ¶6
2011-01-01 Illumina introduced MiSeq instrument Compl. ¶6
2011-01-10 Earliest priority date for '241, '781, '130, '116 Patents Ex. 3, '781 Patent, p. 1 Ex. 4, '130 Patent, p. 1 Ex. 5, '116 Patent, p. 1 Ex. 2, '241 Patent, p. 1
2011-10-14 '781 Patent filed Compl. ¶46
2015-02-10 '781 Patent issued Compl. ¶46
2016-01-01 Illumina released MiniSeq instrument Compl. ¶38
2017-01-01 Element Biosciences was founded Compl. ¶¶8, 52
2017-03-24 Earliest priority date for '702, '028, '301 Patents Ex. 6, '702 Patent, p. 1 Ex. 7, '028 Patent, p. 1 Ex. 8, '301 Patent, p. 1
2019-02-01 Element purchased a MiSeq instrument from Illumina Compl. ¶¶55, 105
2020-05-14 '130 Patent filed Compl. ¶47
2021-05-01 Element requested a covenant not to sue from Illumina Compl. ¶58
2021-09-14 '130 Patent issued Compl. ¶47
2022-01-01 Element launched the AVITI sequencer Compl. ¶60
2022-04-05 '116 Patent filed Compl. ¶48
2023-01-01 Element launched the AVITI LT sequencer Compl. ¶60
2023-07-11 '116 Patent issued Compl. ¶48
2024-02-23 '241 Patent filed Compl. ¶45
2024-04-01 Element announced the AVITI24 sequencer Compl. ¶61
2024-09-06 '702 Patent filed Compl. ¶49
2024-11-26 '241 Patent issued Compl. ¶45
2025-02-11 '028 Patent filed Compl. ¶50
2025-03-18 '702 Patent issued Compl. ¶49
2025-05-05 '301 Patent filed Compl. ¶51
2025-06-10 '028 Patent issued Compl. ¶50
2025-08-26 '301 Patent issued Compl. ¶51
2026-01-01 Element announced the AVITI Dx sequencer Compl. ¶61
2026-07-14 Complaint Filing Date Compl. p. 1

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

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 describes early next-generation sequencing (NGS) systems as requiring highly trained personnel for time-consuming and error-prone processes, such as manually aligning a flow cell, applying immersion oil, and clamping fluidic manifolds Compl. ¶31 These manual steps created risks of reagent leakage, imaging obstruction, and wasted samples, which increased costs and reduced reliability Compl. ¶¶31-32
  • The Patented Solution: The patent describes an automated system designed to reduce manual user interaction Compl. ¶33 The invention combines a device holder that automatically aligns and secures a flow cell for imaging with a fluid storage system that automatically handles reagents Compl. ¶¶34-35 Key components include a device holder with a rotatable cover biased toward an open position and a latch, and a fluid storage system with "sipper tubes" on a transport platform that descend into a reagent tray to extract and deliver fluids '241 Patent, abstract '241 Patent, col. 53:36-54:4
  • Technical Importance: This automation transformed a specialized, error-prone process into a reliable, "load and go" endeavor performable by users with limited training, which dramatically increased the accessibility and efficiency of genetic sequencing Compl. ¶7

Key Claims at a Glance

  • The complaint asserts independent claim 1 Compl. ¶76
  • The essential elements of independent claim 1 include:
    • An optical system (excitation light source, imaging detector, optical train).
    • A device holder for a fluidic device, which itself comprises: a support structure with a base surface and loading region; a rotatable cover biased toward an open position; and a latch to hold the cover closed.
    • A fluid storage system, which itself comprises: an enclosure with a cavity and a door; a transport platform holding an array of sipper tubes; and a drive motor to move the transport platform.
    • A casing enclosing the optical system, device holder, and fluid storage system.
  • The complaint also asserts dependent claims 2-3, 7-12, 14, 15-16, 17 and 18-20 Compl. ¶75

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: The patent's background describes the need for improved systems for performing assay protocols, highlighting that prior systems could have limited capabilities and not be cost-effective '781 Patent, col. 2:1-6 The complaint elaborates that precise manual placement of samples and reagents was a key source of error, time, and cost in early NGS systems (Compl. ¶31; Compl. ¶32; Compl. ¶33).
  • The Patented Solution: The patent discloses a fluidic device holder that automates the precise alignment of a fluidic device (e.g., a flow cell) for imaging. The solution uses a support structure with reference surfaces and an "alignment assembly" containing a movable "locator arm." The locator arm is moved by an actuator to press the fluidic device against the reference surfaces, holding it in a fixed, correct position for analysis '781 Patent, abstract '781 Patent, col. 3:1-11
  • Technical Importance: This automated alignment mechanism improved the reliability and efficiency of sequencing by removing the need for a user to precisely place samples into the instrument, a key step in making the technology more accessible Compl. ¶33

Key Claims at a Glance

  • The complaint asserts independent claim 30 Compl. ¶109
  • The essential elements of independent claim 30 include:
    • A fluidic device holder configured to orient a fluidic device.
    • A support structure with a base surface and a plurality of reference surfaces.
    • An alignment assembly comprising an actuator and a movable locator arm with an engagement end.
    • The locator arm presses the fluidic device against the reference surfaces in a biased position.
    • The locator arm includes a finger, which includes the engagement end.
  • The complaint also asserts dependent claims 31, 38-39 and 42-43 Compl. ¶108

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 describes an integrated system for biological analysis that includes an optical deck, a sample deck with a slidable platform and thermal module, and a fluid storage system '130 Patent, abstract The fluid storage system has a fluid removal assembly with an elevator mechanism and a stage assembly holding an array of sipper tubes that move bidirectionally along a Z-axis to deliver fluids '130 Patent, col. 53:38-67

  • Asserted Claims: Independent claim 1 and dependent claims 2-7, 10-19, and 21-23 are asserted Compl. ¶132

  • Accused Features: The complaint alleges that the overall architecture of the AVITI Systems, including their optical deck, slidable sample deck with nests, and fluid storage and removal systems, infringes the '130 Patent Compl. ¶¶134-167

  • Patent Identification: U.S. Patent No. 11,697,116, "Systems, Methods, and Apparatuses To Image a Sample for Biological or Chemical Analysis," issued July 11, 2023.

  • Technology Synopsis: The patent claims a DNA sequencing instrument with an optical deck, a sample deck, and a fluid storage system '116 Patent, col. 53:28-54:26 It adds specific details to the fluid removal assembly, including a lead screw coupled to the drive motor, a transport platform carrying a "flag," a guide plate for the sipper tubes, and a location sensor to determine the level of the sipper tube array by detecting the flag '116 Patent, col. 53:50-54:9

  • Asserted Claims: At least Claim 1 is asserted Compl. ¶175

  • Accused Features: The complaint alleges that the AVITI Systems' fluid removal assembly, which uses a motor, lead screw, transport platform, and sensor system to control sipper tube movement, infringes the '116 Patent Compl. ¶¶190-218

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

  • Technology Synopsis: The patent describes a microfluidic cartridge consumable, not the instrument itself. The invention is a cartridge with a frame containing a microfluidic plate and a support bracket that both "float" relative to the frame and to each other '702 Patent, col. 14:7-14 The support bracket has seals and alignment holes that are configured to align with indexing features on an analysis device, ensuring a proper fluidic connection '702 Patent, col. 14:15-34

  • Asserted Claims: Independent claim 1 and dependent claims 2-11 are asserted Compl. ¶227

  • Accused Features: The complaint alleges that the design of Element's Sequencing Kits, including the Cloudbreak, Trinity, and Teton kits, infringes the '702 Patent by incorporating a frame with a floating glass substrate (microfluidic plate) and a floating support bracket Compl. ¶¶229-258

  • 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 bracket) and a sequencer '028 Patent, col. 14:6-19 The sequencer's receiver includes a chuck, analysis ports, and two sets of indexing features that engage with the cartridge's alignment holes and frame apertures to align the fluidic ports and gasket '028 Patent, col. 14:20-34

  • Asserted Claims: Independent claim 1 and dependent claims 2-8 are asserted Compl. ¶265

  • Accused Features: The complaint alleges that the combination of the Element Sequencing Kits (as the cartridge) and the AVITI instruments (as the sequencer) infringes the '028 Patent Compl. ¶¶267-289

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

  • Technology Synopsis: The patent claims a system similar to the '028 Patent, but specifically claims the indexing features as "pins" '301 Patent, col. 14:20-29 It also adds the limitation that each seal on the support bracket has a "through-hole" to fluidically connect the cartridge's fluidic ports to the sequencer's analysis device ports '301 Patent, col. 14:30-34

  • Asserted Claims: At least Claim 1 is asserted Compl. ¶296

  • Accused Features: The complaint alleges that the combination of the AVITI system's receiver pins and the Element Sequencing Kits, which include a support with seals containing through-holes, infringes the '301 Patent Compl. ¶¶298-319

III. The Accused Instrumentality

  • Product Identification: The accused instrumentalities are Defendant's "AVITI Systems" and "Element Sequencing Kits" Compl. ¶73 The AVITI Systems include the AVITI, AVITI LT, AVITI24, and AVITI Dx sequencers Compl. ¶¶60-61, 63, 65 The Element Sequencing Kits include the Cloudbreak, Trinity, and Teton product lines, which contain consumables like flow cells and reagent cartridges for use with the AVITI Systems Compl. ¶¶66-67, 72
  • Functionality and Market Context:
    • The AVITI System is described as a "next-generation sequencing (NGS) system" that uses a dual-flow cell design Compl. ¶¶62, 78 The complaint alleges the system includes nests to hold flow cells, a hinged lid to secure them, reagent and pump bays to store and deliver fluids, and an optical system to perform imaging Compl. ¶¶78, 83, 90 The complaint includes a diagram from an AVITI specification sheet showing the system's major components, including the touchscreen, flow cell nests, and reagent/waste bottles Compl. ¶78 The AVITI LT is alleged to be the same physical machine as the AVITI but with software limitations for lower throughput Compl. ¶63
    • The Element Sequencing Kits provide the consumables, such as flow cells in plastic cartridges, that are loaded into the AVITI Systems to perform sequencing runs Compl. ¶67 The complaint includes an image of a "Cloudbreak" flow cell and plastic cartridge Compl. ¶67
    • The complaint alleges that Defendant has marketed these products as a "disruptive" alternative to Plaintiff's systems and has generated more than $25 million in revenue from over 160 orders Compl. ¶¶55, 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 include an optical system with excitation light sources (lasers), imaging detectors (cameras), and an optical train (lenses and mirrors). ¶81 col. 53:38-40
a device holder to orient a fluidic device for imaging by the optical system, the fluidic device comprising a flow cell... The AVITI Systems contain two "nests" within a nest bay, where each nest and its lid function as a device holder for a flow cell. ¶83 col. 53:41-44
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 serves as the support structure, containing a "loading area" with three silver registration pins and a base surface where the flow cell cartridge is placed. An annotated image from an instrument demonstration video shows the loading area and silver pins. ¶84 col. 53:45-48
a rotatable cover that is coupled to the support structure and moveable about an axis between an open position and a closed position... The nest lid is a rotatable cover, described as a "hinged flow cell lid" that opens to a 40° angle to permit insertion/removal of the flow cell and closes to secure it. ¶86 col. 53:49-56
wherein the cover is biased toward the open position The nest lid automatically opens when unlatched, which the complaint alleges is due to a spring mechanism that biases the cover toward the open position. ¶88 col. 53:57-58
a latch to releasably hold the cover in the closed position A tab on the lid secures the flow cell, and a button unlatches the lid; this mechanism is alleged to be the claimed latch. An annotated image from a video shows the latched cover. ¶89 col. 53:59
a fluid storage system comprising: an enclosure having a cavity, a door openable to provide access... The AVITI Systems have dedicated pump and reagent bays on each side, enclosed with bay doors. The complaint alleges these constitute the claimed enclosure, cavity, and door. ¶¶90-91; ¶94 col. 53:60-63
a transport platform holding an array of sipper tubes...a drive motor operatively coupled to the transport platform... The system uses an array of sipper tubes attached to a transport platform that moves up and down via a drive motor to descend into reagent cartridge wells and aspirate fluids. ¶¶95-97 col. 53:64-54:1
a casing enclosing the optical system, the device holder, and the fluid storage system therein. The "Exterior shells" of the AVITI instrument are alleged to be the casing that encloses the internal components, including the optical system, device holder (nests), and fluid storage system (reagent bays). ¶98 col. 54:2-4

'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 AVITI nest and lid serve as the fluidic device holder and are alleged to orient the flow cell along X, Y, and Z axes. ¶113 col. 55:19-21
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 is the support structure, and it includes a base surface that orients the device in the Z-direction. ¶¶114-115 col. 55:22-26
a plurality of reference surfaces facing in respective directions along an XY-plane The three silver pins in the loading area are alleged to be the reference surfaces, as they limit the movement of the fluidic device along the XY-plane. ¶¶116-118 col. 55:27-29
an alignment assembly comprising an actuator and a movable locator arm... the actuator moving the locator arm between retracted and biased positions... The complaint alleges that the mechanism coupled to the nest lid acts as the alignment assembly. Closing the lid (the actuator) moves a component (the locator arm) that shifts the fluidic device along the X-axis into a biased position. ¶¶119-120 col. 55:30-35
wherein the engagement end presses...the fluidic device against the reference surfaces when the locator arm is in the biased position... A video demonstration allegedly shows that when the lid is closed, the fluidic device shifts and is pressed against the silver pins (reference surfaces), holding it in a fixed position. ¶121 col. 55:35-40
wherein the locator arm includes a finger, the finger including the engagement end. The complaint alleges the part of the locator arm that pushes the fluidic device is a "finger," described as a projecting machine part. ¶123 col. 55:38-40
  • Identified Points of Contention:
    • '241 Patent: A potential point of contention may be whether the accused sipper tube mechanism meets the specific structural definitions of a "transport platform" and "drive motor" as contemplated by the patent. The interpretation of "biased toward the open position" may also be disputed, focusing on whether the 40-degree opening of the accused lid is functionally equivalent to the bias described in the patent's specification.
    • '781 Patent: The central dispute will likely be one of claim construction regarding the term "movable locator arm". The complaint's theory relies on equating the mechanism actuated by the closing lid with the claimed "locator arm." The defense may argue that the accused product achieves alignment through a different mechanism that does not contain a distinct, movable "arm" or "finger" as claimed, raising the question of whether there is a structural and functional mismatch.

V. Key Claim Terms for Construction

From the '241 Patent:

  • The Term: "rotatable cover"
  • Context and Importance: This term is central to the device holder element. The accused product uses a "hinged flow cell lid" (Compl. ¶86). The dispute may turn on whether this "hinged lid" falls within the scope of a "rotatable cover," a term that may have a specific meaning defined by the patent's description and figures.
  • Intrinsic Evidence for Interpretation:
    • Evidence for a Broader Interpretation: The patent specification may use "cover," "lid," and "cover assembly" interchangeably, suggesting a broad meaning not limited to a specific geometry beyond being capable of rotation ('241 Patent, col. 3:11-16). The general description of the cover moving about an axis could support reading on a hinge.
    • Evidence for a Narrower Interpretation: The patent figures, particularly in the '130 patent which is part of the same family, depict a specific geometry for the cover assembly (see '130 Patent, FIG. 43-44). The patent's description of how the cover housing, legs, and bridge portion interact may provide a basis for arguing that a simple hinge is structurally different from the claimed invention.

From the '781 Patent:

  • The Term: "movable locator arm"
  • Context and Importance: This term is the core of the asserted infringement theory for the '781 patent. The complaint alleges that a mechanism linked to the closing lid of the AVITI nest functions as the claimed "locator arm" by shifting the flow cell into position (Compl. ¶119). Practitioners may focus on this term because its construction will determine if there is a literal infringement or if the doctrine of equivalents is necessary.
  • Intrinsic Evidence for Interpretation:
    • Evidence for a Broader Interpretation: The patent's abstract describes the arm's function as holding the device against reference surfaces in a biased position '781 Patent, abstract This functional description could support a broader interpretation that covers any mechanical member performing this specific alignment function.
    • Evidence for a Narrower Interpretation: The patent's detailed description and figures (e.g., FIG. 19 of the '781 patent shows locator arm 472) illustrate a distinct, pivoting lever structure designated as the "locator arm." The inclusion of a "finger" on the arm further specifies a particular structure, which could be used to argue that the accused mechanism, which may lack these specific features, falls outside the claim's scope.

VI. Other Allegations

  • Indirect Infringement: The complaint alleges both induced and contributory infringement. Inducement is based on allegations that Element provides product guides, user manuals, and technical support that instruct and encourage customers to use the AVITI Systems and Sequencing Kits in an infringing manner (Compl. ¶¶102, 126, 169). Contributory infringement is based on allegations that the AVITI Systems and Element Sequencing Kits are designed to be used together, are a material part of the claimed inventions, and are not staple articles of commerce suitable for substantial non-infringing use (Compl. ¶¶103, 127, 170).
  • Willful Infringement: The complaint alleges willful infringement based on both pre- and post-suit knowledge. Pre-suit knowledge is alleged based on Element's founding by former Illumina employees, its 2019 purchase of an Illumina MiSeq instrument with a virtual patent marking label pointing to the '781 patent family, and a May 2021 request for a covenant not to sue (Compl. ¶52, Compl. ¶57, Compl. ¶58, Compl. ¶104, Compl. ¶128). Post-suit knowledge is based on prior versions of the complaint in the same action.

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

This litigation presents several critical questions for the court, revolving around claim construction and the technical operation of complex, multi-component systems.

  • A core issue will be one of definitional scope: can the term "movable locator arm" from the '781 patent, which is described in the specification as a distinct pivoting lever, be construed to read on the accused alignment mechanism that is actuated by the closing of the sequencer's lid? This determination will be central to the infringement analysis for a key group of patents.
  • A second central question will be one of structural and functional correspondence for the systems patents ('241, '130, '116). Does the accused AVITI system's method of aspirating reagents using a vertically-moving array of sipper tubes meet the detailed, multi-part limitations of a "fluid removal assembly" that includes an "elevator mechanism" and "stage assembly" as claimed, or is there a fundamental mismatch in the claimed versus accused architecture?
  • A third key battleground will be the mechanics of the consumable interface. For the "floating bracket" patents ('702, '028, '301), the analysis will depend on whether the alleged "floating" of the microfluidic plate and support bracket within Element's cartridges functions in the same way as the claimed invention to achieve alignment with the sequencer's indexing features and fluidic ports.
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