Seer Inc v. Nanomics Biotechnology Co Ltd

I. Executive Summary and Procedural Information

• Parties & Counsel:
  • Plaintiff: Seer, Inc. (Delaware) and The Brigham and Women's Hospital, Inc. (Massachusetts)
  • Defendant: Nanomics Biotechnology Co., Ltd. (China)
  • Plaintiff's Counsel: Wilson Sonsini Goodrich & Rosati PC; Mandell P.C.
• Case Identification: 1:26-cv-05498, N.D. Ill., 05/12/2026
• Venue Allegations: Plaintiffs allege venue is proper in the Northern District of Illinois because Defendant Nanomics maintains its U.S. headquarters in Chicago, has executives and personnel residing and operating in the district, and has committed acts of patent infringement, including offering and using the accused products, within the district.
• Core Dispute: Plaintiffs allege that Defendant's Proteonano Ultraplex Proteomics Platform, which includes automated workstations and nanoparticle-based kits, infringes five U.S. patents related to methods and systems for analyzing proteins in biological samples to identify disease biomarkers.
• Technical Context: The technology at issue is in the field of proteomics, which involves the large-scale study of proteins to gain insights into biological processes and discover biomarkers for diseases, a market of significant interest for diagnostics and personalized medicine.
• Key Procedural History: The complaint notes that in a recent inter partes review proceeding concerning U.S. Patent No. 11,435,360, the Patent Trial and Appeal Board found asserted dependent claim 3 to be not unpatentable, a finding that may be noted by the court in claim construction and validity analyses for that patent.

Case Timeline

Date	Event
2003-05-22	Earliest Priority Date for '948 Patent
2017-12-18	Earliest Priority Date for '360 and '566 Patents
2017-12-XX	BWH grants exclusive license to Seer for '360 and '566 patent families
2019-08-05	Earliest Priority Date for '112 and '222 Patents
2022-09-06	U.S. Patent No. 11,345,360 Issues
2023-04-18	U.S. Patent No. 11,630,112 Issues
2024-06-02	Alleged first use in U.S. commerce of Defendant's "PROTEONANO" mark
2024-07-30	U.S. Patent No. 12,050,222 Issues
2024-11-06	Seer announces Co-Marketing and Sales Agreement with Thermo Fisher Scientific
2025-02-18	U.S. Patent No. 12,228,566 Issues
2025-05-01	Nanomics files for U.S. trademark for "PROTEONANO"
2025-06-01	Seer announces study with Korea University
2025-12-31	Date of Nanomics news article regarding customer locations
2026-02-XX	Nanomics attends conference in St. Louis, Missouri
2026-03-23	PTAB issues Final Written Decision in IPR for '360 Patent
2026-03-31	U.S. Patent No. 12,590,948 Issues
2026-04-09	Seer announces collaboration with Precision Health Research, Singapore
2026-05-12	Complaint Filed

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

U.S. Patent No. 11,435,360 - "System and Sensor Array"

The Invention Explained

• Problem Addressed: The patent addresses the challenge in proteomics of reliably detecting low-abundance proteins in biological samples, which often serve as important disease "biomarkers" Compl. ¶1 These target proteins are typically obscured or "masked" by a small number of high-abundance proteins (e.g., albumin) that dominate the sample (Compl. ¶¶1; Compl. ¶38). Prior approaches to remove high-abundance proteins or enrich for specific low-abundance ones were often ineffective, biased, slow, and expensive Compl. ¶39
• The Patented Solution: The invention proposes a method that contacts a biological sample with a "plurality of particles comprising different particle types" Compl. ¶118 These non-specific particles, each with different physicochemical properties, attract and bind proteins from the sample to form a protein "corona" on their surfaces Compl. ¶40 This counterintuitively expands the dynamic range of analysis, which allows for the detection of low-abundance proteins that might otherwise be missed Compl. ¶40 The proteins in the coronas are then separated from the sample and assayed Compl. ¶118
• Technical Importance: This "unbiased" approach to assaying biological samples represented a new way to gain "deep, rapid, and large-scale access to the body's proteins" without the biases of traditional enrichment or depletion techniques Compl. ¶2

Key Claims at a Glance

• The complaint asserts dependent claim 3 Compl. ¶120, which relies on independent claim 1.
• The essential elements of independent claim 1 are:
  • A method for assaying a biological sample comprising:
  • Contacting the sample with a plurality of particles of different types to form coronas, where the coronas differ by particle type and comprise overlapping and distinct proteins;
  • Separating a subset of the particles with coronas from the sample, producing a subset of proteins; and
  • Assaying that subset of proteins with an instrument to detect proteins across a dynamic range of at least 6 orders of magnitude. Compl. ¶118
• The complaint notes that it is not presently asserting claims 1, 4, 6, 17, 22, and 25 Compl. ¶120, fn. 3

U.S. Patent No. 11,630,112 - "Systems and Methods for Sample Preparation, Data Generation, and Protein Corona Analysis"

The Invention Explained

• Problem Addressed: The patent background identifies a "bottleneck in scientific research" that prevented the early detection of diseases like cancer Compl. ¶81 This was due to the large number of proteins in the proteome and a "lack of convenient molecular tools for proteome analysis," especially for low-abundance proteins Compl. ¶80
• The Patented Solution: The patent describes an automated system designed to implement the protein corona analysis method. The system comprises multiple integrated units, including a multichannel fluid transfer instrument, storage units for samples and reagents, and a "sensing unit" Compl. ¶82 This sensing unit includes a "magnetic sensor array" containing a plurality of magnetic particles with different physicochemical properties, which are used to bind and analyze proteins from the biological sample '112 Patent, col. 29:1-15 A control unit with processors is programmed to automate the steps of contacting the sample with the particles, incubating, washing, and preparing the bound proteins for mass spectrometry Compl. ¶82
• Technical Importance: The invention provides an automated and integrated platform for performing the novel protein corona analysis, enabling "rapid and automated sample preparation, processing of proteomic data, and identifying key biomarkers" Compl. ¶79

Key Claims at a Glance

• The complaint asserts independent claim 1 Compl. ¶82
• The essential elements of independent claim 1 are:
  • An automated system for distinguishing states of a biological sample using a plurality of magnetic particles with different physicochemical properties, comprising:
  • A fluid transfer unit with a multichannel instrument;
  • A sample storage unit;
  • A sensing unit with a magnetic sensor array containing partitions with the plurality of magnetic particles, configured to bind at least 300 different proteins;
  • Storage units for reagents, waste, and consumables;
  • A magnetized support; and
  • A control unit with processors programmed to perform the steps of contacting the sample with the particles, incubating, washing away unbound components, desorbing the bound analytes, and preparing them for mass spectrometry. Compl. ¶82
• The complaint does not explicitly reserve the right to assert dependent claims for the '112 Patent.

U.S. Patent No. 12,050,222 - "Systems and Methods for Sample Preparation, Data Generation, and Protein Corona Analysis"

• Technology Synopsis: Described as a continuation of the '112 patent, this patent relates to automated systems for preparing biological samples for mass spectrometry using a plurality of magnetic particles Compl. ¶¶98, 101 The system is designed to address the bottleneck in detecting low-abundance protein biomarkers for early disease detection Compl. ¶100
• Asserted Claims: Independent claim 16 is asserted Compl. ¶101
• Accused Features: The accused features are the Defendant's Proteonano Enrichment Kits, which allegedly include a plurality of magnetic particles with different physicochemical properties, and the Proteonano Workstations, which allegedly provide the automated, multichannel fluid handling capabilities Compl. ¶¶103-104

U.S. Patent No. 12,228,566 - "System and Method for Protein Corona Sensor Array For Early Detection of Diseases"

• Technology Synopsis: Described as being in the same family as the '360 patent, this patent relates to a method for identifying a pattern of protein biomarkers by incubating a biological fluid from a subject in a disease state with magnetic particles that have different physicochemical properties Compl. ¶¶137-138 The resulting biomolecule coronas are then isolated and analyzed by mass spectrometry to identify a relationship between a biomarker pattern and the disease state Compl. ¶138
• Asserted Claims: Independent claim 1 is asserted Compl. ¶138
• Accused Features: The complaint alleges that the use of the Accused Products infringes, pointing to the Proteonano Enrichment Kits' inclusion of multiple magnetic particle types (PP1, PP2, and PP3) and their use on plasma from subjects in a disease state, as described in a Nanomics publication Compl. ¶¶140-141

U.S. Patent No. 12,590,948 - "Systems and Methods for Discovery and Analysis of Markers"

• Technology Synopsis: The patent relates to a system for analyzing biological samples that includes a sample preparation device configured to "deplete a sample of highly abundant proteins" present at a concentration of at least 10 µg/mL Compl. ¶¶64-65 The system couples this preparation device to a mass spectrometer Compl. ¶65
• Asserted Claims: Independent claim 1 is asserted Compl. ¶65
• Accused Features: The complaint alleges the Proteonano Workstations constitute the "sample preparation device" and that the overall PUP Platform depletes highly abundant proteins like albumin Compl. ¶¶67-68

III. The Accused Instrumentality

Product Identification

• The accused products are collectively identified as the Proteonano Ultraplex Proteomics Platform ("PUP Platform"), which consists of the Proteonano Kit, Nanomics G1 Workstation, and AI-powered proteomics analysis software (collectively, "Accused Products" or "Accused Technology") Compl. ¶51 Specific kits mentioned include the Proteonano Plasma Proteome Enrichment Kit Compl. ¶52

Functionality and Market Context

• The PUP Platform is alleged to enable "protein enrichment by nano-bio interaction" using "superparamagnetic" nanoparticles to "selectively capture low abundant proteins in biological samples" Compl. ¶53 The platform is described as including kits with multiple nanoparticle types functionalized with peptides Compl. ¶54 Compl. Ex. 14 at 2 The Nanomics G1 workstation allegedly provides automated sample processing, including a "heater-shaker module for nanoparticle-plasma incubation" and a "magnetic module for protein corona separation" Compl. ¶55 Compl. Ex. 15 at 7 A visual provided in the complaint shows Nanomics' marketing diagram of its workflow, which Plaintiffs present in direct comparison to Seer's own workflow diagram to illustrate alleged copying Compl. p. 22 After processing, data is allegedly transferred to an "Ai-powered proteomics analysis software" for analysis Compl. ¶57
• The complaint positions the PUP Platform as a "knock-off product" trading on Seer's success and designed to address the same bottlenecks in detecting low-abundance proteins Compl. ¶5 Compl. ¶51 Defendant's website is quoted as stating the platform has been adopted by over 100 institutions and exported overseas, including to the Pacific Northwest National Laboratory in the United States Compl. ¶22

IV. Analysis of Infringement Allegations

U.S. Patent No. 11,435,360 Infringement Allegations

Claim Element (from Independent Claim 1)	Alleged Infringing Functionality	Complaint Citation	Patent Citation
(a) contacting the biological sample with a plurality of particles comprising different particle types to permit biomolecules...to bind...and form coronas...	The Nanomics process allegedly uses a 96 well-plate to incubate biological samples with nanoparticles of different types to form coronas. The G1 workstation includes a "heater-shaker module" for this incubation step.	¶121	col. 7:1-5
wherein the coronas corresponding to the different particle types (i) differ based on particle type, and (ii) comprise overlapping and distinct proteins;	Nanomics publications allegedly describe the Proteonano Kit as being composed of AI-designed polypeptides to bind proteins and as combining multiple nanoparticles into a single reagent.	¶122	col. 9:1-10
(b) separating at least a subset of the plurality of particles comprising the coronas from the biological sample by removing the subset of the plurality of particles...	The Nanomics G1 workstation is alleged to include "a magnetic module for protein corona separation" to separate the particles after corona formation.	¶123	col. 7:6-10
(c) assaying the subset of proteins of (b) with an instrument to detect, in the subset, proteins...at concentrations across a dynamic range comprising at least 6 orders of magnitude...	A Nanomics publication allegedly reported that its workflow detected biomarkers "spanning eight orders of magnitude from a single pooled plasma sample." A graphic from this publication is included in the complaint to support this allegation.	¶124	col. 8:55-60
[from dependent claim 3] wherein the plurality of particles comprise iron oxide.	A Nanomics publication allegedly states that the core layer of its nanoparticles "consists of superparamagnetic Fe3O4 nanoparticles."	¶126	col. 12:45-50

• Identified Points of Contention:
  • Technical Question: A primary factual dispute may concern the "at least 6 orders of magnitude" limitation. The analysis will depend on evidence of the Nanomics PUP Platform's actual performance. While Plaintiffs cite a publication by Nanomics' CEO (Compl. ¶124), Defendant may challenge the testing methodology, the specific products used, or the applicability of those results to the accused process as a whole.
  • Scope Question: The construction of "coronas ... compris[ing] overlapping and distinct proteins" may be a point of contention. The parties may dispute the evidentiary standard required to prove that the coronas formed by the accused process meet both the "overlapping" and "distinct" characteristics as required by the claim.

U.S. Patent No. 11,630,112 Infringement Allegations

Claim Element (from Independent Claim 1)	Alleged Infringing Functionality	Complaint Citation	Patent Citation
(a) a fluid transfer unit comprising a multichannel fluid transfer instrument for transferring fluids between units within the system;	The Proteonano Workstations allegedly include an "8-Channel Pipette" described as providing "High-throughput liquid handling optimized for 96-well Proteonano workflows."	¶85	col. 28:50-55
(c) a sensing unit comprising a support and a magnetic sensor array, wherein the magnetic sensor array...comprises partitions that comprise the plurality of magnetic particles having surfaces with different physicochemical properties...	The Proteonano Enrichment Kits allegedly include a plurality of magnetic particles (PP1, PP2, PP3) with different physicochemical properties. These are allegedly used in a 96 well-plate, which functions as the claimed support with partitions. A diagram from a Nanomics publication depicts this 96-well plate configuration (Compl. p. 25).	¶84	col. 29:1-10
wherein the plurality of magnetic particles are configured to bind to at least 300 different proteins;	A Nanomics publication allegedly describes that mass spectrometers identified "2,987 ± 12 protein groups" from a sample of pooled plasma using the accused technology.	¶87	col. 29:11-15
(g) a magnetized support, wherein the one or more processors are further programmed to transfer the magnetic sensor array to the magnetized support;	Nanomics' G1 workstation allegedly includes a "magnetic module," and videos on its website allegedly show the automated system transferring the 96-well plate (the alleged "magnetic sensor array") to this magnetic module.	¶¶85-86	col. 30:20-25
(h) a control unit comprising one or more processors programmed to perform steps comprising: i. contacting... ii. incubating... iii. removing... iv. adding a solution... v. preparing...for mass spectrometry.	The Accused Products allegedly constitute an "automated system" where processors in the control unit are programmed to perform the claimed steps. Allegations point to the workstation's heater-shaker for incubation, magnetic module for separation, and liquid handler for fluid transfers, all as part of an automated workflow.	¶¶84-87	col. 31:1-20

• Identified Points of Contention:
  • Scope Question: A central issue may be whether Defendant's combination of separate products-kits, a workstation, and software-constitutes a single "automated system" as claimed. Defendant may argue it does not sell the claimed system, but rather components that customers assemble, potentially shifting the focus to indirect infringement.
  • Technical Question: The claim requires the particles be "configured to bind to at least 300 different proteins." This raises a factual question about the inherent capability of the accused nanoparticles. Plaintiffs cite performance data from a Nanomics publication (Compl. ¶87), but the analysis may turn on whether this reflects an inherent "configuration" of the particles themselves or is merely the result of a specific experiment.

V. Key Claim Terms for Construction

• The Term: "automated system" (from '112 Patent, Claim 1)

• Context and Importance: This term appears in the preamble of the asserted independent claim of the '112 patent. The infringement case against the accused PUP Platform-which comprises a kit, a workstation, and software-may depend on whether this collection of components, sold and marketed together, meets the definition of a single "automated system." Practitioners may focus on this term because a narrow construction could suggest that no single entity makes or sells the entire claimed invention.

• Intrinsic Evidence for Interpretation:

  • Evidence for a Broader Interpretation: The patent describes the invention as comprising various "units" (e.g., fluid transfer unit, sample storage unit, sensing unit) that work together '112 Patent, col. 28:50-67 Plaintiffs may argue that as long as the accused products provide all the necessary, interoperable "units" to perform the automated process, they constitute the claimed "system," regardless of being sold in separate boxes.
  • Evidence for a Narrower Interpretation: The specification describes a "loading unit that is movable at least across the substrate" '112 Patent, Abstract This language, along with figures depicting an integrated instrument (e.g.,'112 Patent, Fig. 3), may support an interpretation that the "automated system" must be a single, physically integrated apparatus, not a collection of discrete products that a user assembles.

• The Term: "...assaying the subset of proteins... across a dynamic range comprising at least 6 orders of magnitude" (from '360 Patent, Claim 1)

• Context and Importance: This limitation defines a minimum performance threshold for the claimed method. The infringement analysis will likely require quantitative evidence showing that the accused process meets this specific functional requirement.

• Intrinsic Evidence for Interpretation:

  • Evidence for a Broader Interpretation: Plaintiffs may point to the background section of related patents, which describes the natural proteome as spanning "over 10 orders of magnitude" '112 Patent, col. 18:25-26, to argue the inventors intended "dynamic range" to be understood broadly in the context of large-scale proteomics analysis. The claim language itself does not tie the measurement to a specific instrument or methodology.
  • Evidence for a Narrower Interpretation: Defendant may argue that the meaning of "assaying... across a dynamic range" should be limited to the specific embodiments and examples disclosed in the patent's specification. If the patent's examples demonstrate a particular method for calculating this range, a court could be persuaded to adopt that more limited definition.

VI. Other Allegations

• Indirect Infringement: The complaint alleges inducement to infringe across all asserted patents, stating that Nanomics provides instructions, advertising, marketing materials, and operational manuals that encourage and facilitate direct infringement by customers and end users (Compl. ¶¶70; Compl. ¶89; Compl. ¶108; Compl. ¶128; Compl. ¶143). Contributory infringement is also alleged, based on the assertion that the Accused Products are especially made for infringing use and are not staple articles of commerce suitable for substantial non-infringing use (Compl. ¶¶71; Compl. ¶90; Compl. ¶109; Compl. ¶129; Compl. ¶144).
• Willful Infringement: Plaintiffs allege that Nanomics had actual or constructive pre-suit knowledge of the Asserted Patents. The basis for this allegation includes the claim that the proteomics research field is "close-knit and small," that Nanomics' CEO has mentioned Seer in public online posts, that Nanomics' publications cite articles authored by Seer and inventors of the patents-in-suit, and that Nanomics attended conferences where Seer's technology was presented Compl. ¶¶58-60 The complaint also pleads willfulness based on knowledge acquired no later than the date of service of the complaint (Compl. ¶¶73; Compl. ¶92; Compl. ¶111; Compl. ¶131; Compl. ¶146).

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

• A central evidentiary question will be one of quantitative performance: Can Plaintiffs produce sufficient evidence to demonstrate that the accused Nanomics PUP Platform, as it operates in practice, meets the numerical and functional thresholds required by the claims, such as binding to "at least 300 different proteins" ('112 patent) and assaying proteins across a "dynamic range comprising at least 6 orders of magnitude" ('360 patent)?
• A core issue will be one of system scope: Does the sale of a kit, an automated workstation, and separate analysis software constitute the sale of a single "automated system" as recited in the asserted system claims, or does this sales model insulate the Defendant from direct infringement, shifting the focus to the higher evidentiary burden of indirect infringement?
• A significant question for damages will be one of intent: Do the allegations of Defendant's awareness of Seer, its citation to Seer-affiliated publications, and the visual similarity of its marketing materials, as presented in the complaint, provide a sufficient factual basis to support a finding of willful infringement, which could expose the Defendant to enhanced damages?