DCT

1:26-cv-14055

Freenome LLC v. Biomodal Ltd

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I. Executive Summary and Procedural Information

  • Parties & Counsel:
  • Case Identification: 1:26-cv-14055, D. Mass., 09/02/2026
  • Venue Allegations: Venue is alleged to be proper in the District of Massachusetts because Defendant Children's Medical Center Corporation resides in the district, and because a substantial part of the events giving rise to the controversy occurred there, including Defendants' enforcement actions against New England Biolabs, Inc. (NEB), the Massachusetts-based supplier of the products at issue.
  • Core Dispute: Plaintiff Freenome seeks a declaratory judgment that its blood-based cancer screening test does not infringe, and that claims are invalid and/or exhausted, for nine U.S. patents owned by the Defendants related to methods of epigenetic analysis.
  • Technical Context: The technology concerns methods for detecting epigenetic modifications of DNA, such as 5-methylcytosine and 5-hydroxymethylcytosine, which are important biomarkers for the early detection of cancer.
  • Key Procedural History: This declaratory judgment action follows a prior lawsuit where Defendants sued Freenome's supplier, New England Biolabs, Inc. (NEB), for infringing related patents (the "NEB Action"). The NEB Action settled, and Freenome alleges NEB is now licensed to sell the accused products. The court in the NEB Action previously conducted a Markman claim construction hearing for six of the nine patents-in-suit, suggesting the court has substantial familiarity with the technology and patents. Freenome's central defense appears to be patent exhaustion, arguing that its purchase of licensed products from NEB exhausts the Defendants' patent rights.

Case Timeline

Date Event
2008-12-11 Earliest Priority Date ('053, '091, '213, '216, '373 Patents)
2009-09-28 Earliest Priority Date ('683, '742, '346, '489 Patents)
2018-01-01 Freenome began R&D of its blood-based cancer screening assays (approx. date)
2019-07-02 U.S. Patent No. 10,337,053 Issues
2019-10-15 U.S. Patent No. 10,443,091 Issues
2020-01-14 U.S. Patent No. 10,533,213 Issues
2020-09-08 U.S. Patent No. 10,767,216 Issues
2020-09-15 U.S. Patent No. 10,774,373 Issues
2021-12-28 U.S. Patent No. 11,208,683 Issues
2022-02-16 Freenome and NEB enter into Original Supply Agreement
2024-07-01 Defendants file the "NEB Action" against New England Biolabs, Inc.
2025-05-06 U.S. Patent No. 12,291,742 Issues
2025-06-17 U.S. Patent No. 12,331,346 Issues
2025-06-24 U.S. Patent No. 12,338,489 Issues
2025-07-29 Court conducts Markman hearing in the NEB Action
2026-01-01 Freenome commercially launches Early Access Program for SimpleScreen CRC (approx. date)
2026-02-05 Defendants' counsel sends letter to Freenome asserting infringement
2026-05-01 Defendants prepare a draft complaint against Freenome (approx. date)
2026-07-27 Freenome receives FDA Pre-Market Approval for SimpleScreen CRC
2026-09-01 NEB and Defendants enter into a settlement agreement for the NEB Action
2026-09-02 Complaint for Declaratory Judgment filed

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

U.S. Patent No. 11,208,683 - Methods of Epigenetic Analysis

  • Issued: December 28, 2021

The Invention Explained

  • Problem Addressed: The patent describes the need for improved methods to analyze the epigenetic status of cells, particularly for diagnosing and treating cancer Compl. ¶92 '683 Patent, col. 12:13-30 DNA methylation patterns are critical indicators, but detecting specific modified bases like 5-methylcytosine (5mC) and its oxidized forms, such as 5-hydroxymethylcytosine (5hmC), can be challenging.
  • The Patented Solution: The '683 Patent claims a composition for use in epigenetic analysis. The composition combines a nucleic acid sample with enzymes from the TET family, which convert 5mC to 5hmC, and a glucosyltransferase, which adds a glucose molecule to the newly formed 5hmC '683 Patent, abstract '683 Patent, col. 3:6-21 This enzymatic tagging of specific DNA bases facilitates their detection and quantification, providing a clearer picture of the DNA's methylation status.
  • Technical Importance: This enzymatic approach provides a method to distinguish between different forms of cytosine modifications which is critical for understanding gene regulation and for developing diagnostics based on epigenetic markers '683 Patent, col. 40:7-24

Key Claims at a Glance

  • The complaint states Defendants have asserted that Freenome will infringe "one or more claims" of the '683 patent Compl. ¶54 The complaint does not specify which claims.
  • Independent claim 1 of the '683 patent recites:
    • A composition comprising a mixture of a methylcytosine and di-oxygenase, a DNA glucosyltransferase, and nucleic acid molecules, wherein said methylcytosine and di-oxygenase is a TET family enzyme, and wherein said DNA glucosyltransferase adds a glucose or glucose derivative to 5-hydroxymethylcytosine.

U.S. Patent No. 10,337,053 - Labeling Hydroxymethylated Residues

  • Issued: July 2, 2019

The Invention Explained

  • Problem Addressed: The patent addresses the challenge of specifically detecting 5-hydroxymethylcytosine (5hmC) residues in DNA, as conventional methods often cannot distinguish them from other cytosine variants '053 Patent, col. 88:31-48 This distinction is important for research and diagnostics.
  • The Patented Solution: The patent discloses a method for labeling 5hmC in a nucleic acid. The method involves contacting the nucleic acid with an enzyme (a glucosyltransferase) and a glucose donor substrate, which results in the covalent attachment of a glucose molecule or a derivative thereof to the 5hmC residue '053 Patent, abstract '053 Patent, col. 2:62-3:5 This "tagging" with a glucose moiety allows for the specific detection and isolation of DNA fragments containing 5hmC.
  • Technical Importance: By providing a way to specifically label 5hmC, the invention enables more precise mapping and quantification of this key epigenetic marker, which has implications for cancer diagnosis and understanding cellular differentiation '053 Patent, col. 40:7-24

Key Claims at a Glance

  • The complaint alleges Defendants have asserted that Freenome will infringe "one or more claims" of the '053 patent Compl. ¶58 The complaint does not specify which claims.
  • Independent claim 1 of the '053 patent recites a method with the following essential elements:
    • (a) labeling covalently, a hydroxyl group on a hydroxymethylated cytosine residue in a nucleic acid to generate a labeled hydroxymethylated cytosine residue, the labeling comprising contacting said nucleic acid with an alpha-glucosyltransferase, a beta-glucosyltransferase, or a beta-galactosyl-transferase;
    • (b) separating said labeled nucleic acid comprising said labeled hydroxymethylated residue; and
    • (c) detecting the labeled hydroxymethylated residue.

U.S. Patent No. 10,774,373 - Compositions Comprising Glucosylated Hydroxymethylated Bases

  • Patent Identification: U.S. Patent No. 10,774,373, issued September 15, 2020 Compl. ¶12
  • Technology Synopsis: This patent claims compositions that include nucleic acids containing a glucosylated 5-hydroxymethylcytosine. It also covers methods of preparing and isolating these modified nucleic acids '373 Patent, abstract The invention facilitates the analysis of DNA that has been enzymatically treated to mark hydroxymethylation sites.
  • Asserted Claims: "one or more claims" Compl. ¶62
  • Accused Features: Freenome's blood-based diagnostic assays for detecting cancer Compl. ¶62, which use enzymatic methylation sequencing technology from NEB Compl. ¶¶31-32

U.S. Patent No. 10,443,091 - Selective Oxidation of 5-Methylcytosine by TET-Family Proteins

  • Patent Identification: U.S. Patent No. 10,443,091, issued October 15, 2019 Compl. ¶13
  • Technology Synopsis: This patent claims methods for detecting 5-hydroxymethylcytosine by enzymatically adding a glucose donor substrate to it. The core technology involves using a glucosyltransferase enzyme to specifically tag 5-hydroxymethylcytosine for subsequent detection '091 Patent, abstract
  • Asserted Claims: "one or more claims" Compl. ¶66
  • Accused Features: Freenome's diagnostic assays that analyze DNA methylation patterns Compl. ¶66, which incorporate products and technology supplied by NEB Compl. ¶¶2 Compl. ¶32

U.S. Patent No. 10,533,213 - Selective Oxidation of 5-Methylcytosine by TET-Family Proteins

  • Patent Identification: U.S. Patent No. 10,533,213, issued January 14, 2020 Compl. ¶14
  • Technology Synopsis: This patent is directed to methods for detecting 5-hydroxymethylcytosine in a nucleic acid. The claimed method involves contacting the nucleic acid with an enzyme and a glucose donor substrate to form a modified nucleic acid, followed by a detection step '213 Patent, abstract
  • Asserted Claims: "one or more claims" Compl. ¶70
  • Accused Features: Freenome's diagnostic assays for detecting colorectal and lung cancer Compl. ¶70

U.S. Patent No. 10,767,216 - Methods for Distinguishing 5-Hydroxymethylcytosine From 5-Methylcytosine

  • Patent Identification: U.S. Patent No. 10,767,216, issued September 8, 2020 Compl. ¶15
  • Technology Synopsis: This patent covers methods for analyzing a sample by obtaining a nucleic acid, glucosylating the 5-hydroxymethylcytosine residues, and then sequencing the nucleic acid to distinguish between the modified and unmodified bases '216 Patent, abstract
  • Asserted Claims: "one or more claims" Compl. ¶74
  • Accused Features: Freenome's diagnostic assays Compl. ¶74, which employ enzymatic methylation sequencing Compl. ¶2

U.S. Patent No. 12,291,742 - Selective Oxidation of 5-Methylcytosine by TET-Family Proteins

  • Patent Identification: U.S. Patent No. 12,291,742, issued May 6, 2025 Compl. ¶16
  • Technology Synopsis: This patent claims methods and compositions involving TET family polypeptides. The claims cover methods of contacting a nucleic acid with a TET polypeptide and an enzyme that modifies the resulting 5-hydroxymethylcytosine, as well as compositions containing these components '742 Patent, abstract '742 Patent, claims 1, 21
  • Asserted Claims: "at least claim 1" Compl. ¶78
  • Accused Features: The development, use, offer for sale, and sale of "SimpleScreen CRC" Compl. ¶78, which uses NEB's "EM-seq" products Compl. ¶51

U.S. Patent No. 12,331,346 - Selective Oxidation of 5-Methylcytosine by TET-Family Proteins

  • Patent Identification: U.S. Patent No. 12,331,346, issued June 17, 2025 Compl. ¶17
  • Technology Synopsis: This patent also covers methods related to detecting methylated cytosine residues. The claims focus on contacting a nucleic acid with a TET polypeptide and then a glucosyltransferase to create a modified nucleic acid for detection '346 Patent, claims 1, 19
  • Asserted Claims: "at least claim 1" Compl. ¶82
  • Accused Features: The development, use, offer for sale, and sale of "SimpleScreen CRC" Compl. ¶82, which uses NEB's "EM-seq" products Compl. ¶51

U.S. Patent No. 12,338,489 - Selective Oxidation of 5-Methylcytosine by TET-Family Proteins

  • Patent Identification: U.S. Patent No. 12,338,489, issued June 24, 2025 Compl. ¶18
  • Technology Synopsis: Similar to other patents in the family, this patent claims methods for detecting methylated cytosine residues by contacting a nucleic acid with TET and glucosyltransferase enzymes '489 Patent, abstract '489 Patent, claim 1
  • Asserted Claims: "at least claim 1" Compl. ¶86
  • Accused Features: The development, use, offer for sale, and sale of "SimpleScreen CRC" Compl. ¶86, which uses NEB's "EM-seq" products Compl. ¶51

III. The Accused Instrumentality

Product Identification

The primary accused instrumentality is Freenome's "SimpleScreen CRC" test, which is a blood-based screening test for the early detection of colorectal cancer Compl. ¶2 Compl. ¶32

Functionality and Market Context

  • The "SimpleScreen CRC" test operates by analyzing molecular signals, including DNA methylation patterns, in cell-free DNA derived from a patient's blood sample Compl. ¶32 The test's analytical workflow incorporates "enzymatic methylation-sequencing ('EM-seq')" technology Compl. ¶2, specifically using a "Custom Kit" supplied by New England Biolabs, Inc. (NEB) under a supply agreement Compl. ¶¶26-27 Compl. ¶32
  • The product has significant market context, as Freenome has received Pre-Market Approval (PMA) from the U.S. Food and Drug Administration (FDA) for the test Compl. ¶34 Compl. ¶35 Freenome commercially launched an "Early Access Program" for the test in early 2026 Compl. ¶36

IV. Analysis of Infringement Allegations

The complaint, being for declaratory judgment, does not contain Freenome's infringement allegations. Instead, it describes the infringement theory that Defendants have threatened to assert against Freenome Compl. ¶¶46-52 The complaint does not provide element-by-element infringement allegations in the form of a claim chart. It states that the threatened infringement claims are predicated on Freenome's use of NEB's "EM-seq Products" Compl. ¶51 and that draft claim charts prepared by the Defendants rely on NEB's publicly available instruction manuals for those products to allege that Freenome practices the limitations of the asserted claims (Compl. ¶52).

No probative visual evidence provided in complaint.

Identified Points of Contention

  • Scope Questions: A central question will be whether the specific enzymes and processes in NEB's "EM-seq" products, as used by Freenome, fall within the scope of the claims of the nine patents-in-suit. This may involve disputes over the meaning of terms like "TET family enzyme," "glucosyltransferase," and the specific reaction steps required by the method claims.
  • Technical Questions: A key technical question is whether Freenome's use of the NEB kits results in a "composition" that meets all the limitations of composition claims (like in the '683 patent) or constitutes performance of all steps of the method claims (like in the '053 patent). The analysis will depend on the precise contents and instructions of the NEB kits and how they are used in the "SimpleScreen CRC" workflow.

V. Key Claim Terms for Construction

The complaint does not provide sufficient detail for analysis of specific claim terms as no infringement claim charts are included. However, based on the technology and the prior litigation, practitioners may focus on the definition of the enzyme families central to the invention. For example, the scope of "TET family enzyme" and "DNA glucosyltransferase" as recited in claim 1 of the '683 patent could be a focal point, as the alleged infringement hinges on the specific enzymes provided in NEB's kits. The court has already conducted a claim construction hearing on related terms in the parallel NEB Action, the results of which will be highly influential in this case Compl. ¶43

VI. Other Allegations

Indirect Infringement

Freenome seeks a declaratory judgment of non-infringement as to both direct and indirect infringement Compl. ¶1 The complaint notes that in the prior NEB Action, Defendants alleged that NEB induces infringement by providing instruction manuals and contributes to infringement by supplying products that are a material part of the claimed inventions Compl. ¶¶41-42 A similar theory is anticipated against Freenome, as the threatened claims are based on Freenome's use of these same NEB products and instruction manuals Compl. ¶¶51-52

Willful Infringement

The complaint states that a draft complaint prepared by Defendants alleged that Freenome's purported infringement is willful and seeks enhanced damages Compl. ¶49 This allegation of willfulness appears to be based on pre-suit knowledge, stemming from a letter sent by Defendants' counsel to Freenome on February 5, 2026, which asserted infringement of six of the patents-in-suit Compl. ¶46

Patent Exhaustion

A central count in the complaint is for a declaratory judgment of patent exhaustion Compl. ¶¶134-142 Freenome alleges that NEB is licensed under the Defendants' patent portfolio to sell its "EM-seq" products to Freenome, pursuant to a settlement of the NEB Action Compl. ¶45 Compl. ¶139 Freenome argues that to the extent these sales by NEB are authorized, the Defendants' patent rights are exhausted, and they may not obtain further infringement claims against Freenome for the downstream use of those products Compl. ¶¶140-141

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

This case presents a preemptive strike by a product manufacturer (Freenome) against a patent holder (Biomodal) that has already litigated against its supplier (NEB). The key questions for the court appear to be:

  1. A threshold legal question of patent exhaustion: Did the settlement and alleged license between Defendants and NEB authorize the sale of the "EM-seq" products to Freenome for its specific use? If so, the court may find Defendants' patent rights are exhausted, potentially resolving the entire dispute in Freenome's favor without reaching the merits of infringement or validity.
  2. A core issue of infringement: Assuming the patent exhaustion defense fails, does Freenome's "SimpleScreen CRC" test, which incorporates NEB's "EM-seq" products and methods, practice every limitation of at least one claim of the nine asserted patents? This will involve a detailed technical comparison between the accused test and the specific compositions and method steps claimed in the patents.
  3. A dispositive question of validity: Can Freenome prove by clear and convincing evidence that the asserted patent claims are invalid? The complaint raises challenges under 35 U.S.C. §§ 101 (patent-ineligible subject matter, likely arguing the claims cover a natural phenomenon), 102/103 (anticipation/obviousness), and 112 (lack of written description and/or enablement), which are common, yet potent, defenses in biotechnology cases.