DCT

1:25-cv-03646

Biomodal Ltd v. Watchmaker Genomics Inc

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Key Events
Complaint

I. Executive Summary and Procedural Information

  • Parties & Counsel:
  • Case Identification: 1:25-cv-03646, D. Colo., 11/13/2025
  • Venue Allegations: Plaintiffs allege venue is proper in the District of Colorado because Defendant resides in the district, is subject to personal jurisdiction, and has committed alleged acts of infringement there.
  • Core Dispute: Plaintiffs allege that Defendant’s DNA library preparation kits infringe two patents related to methods for detecting epigenetic modifications of DNA using TET-family enzymes.
  • Technical Context: The technology relates to the field of epigenetics, specifically the enzymatic detection of DNA methylation (5-methylcytosine) and hydroxymethylation (5-hydroxymethylcytosine), which are crucial markers for gene expression studies in fields such as oncology and developmental biology.
  • Key Procedural History: Plaintiff biomodal is the exclusive licensee of the Asserted Patents since November 28, 2016. The patents claim priority to provisional applications filed in 2008.

Case Timeline

Date Event
2008-09-26 Earliest Priority Date for ’320 and ’742 Patents
2016-11-28 Plaintiff biomodal obtains exclusive license to Asserted Patents
2024-06-25 U.S. Patent No. 12,018,320 Issues
2025-05-06 U.S. Patent No. 12,291,742 Issues
2025-11-05 Alleged Launch of Accused Product
2025-11-13 Complaint Filed

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

U.S. Patent No. 12,018,320 - Selective Oxidation of 5-Methylcytosine by TET-family Proteins (Issued 06/25/2024)

The Invention Explained

  • Problem Addressed: The patent’s background section describes that while DNA methylation is a vital process in mammalian development and disease, the molecular mechanisms of active DNA demethylation were not well understood at the time of the invention (Compl. ¶19; ’320 Patent, col. 3:28-44). Identifying the enzymes and pathways involved was a key challenge in the field of epigenetics.
  • The Patented Solution: The invention is based on the discovery of a "novel and surprising catalytic activity for the family of TET proteins," which are enzymes capable of converting the methylated DNA base 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) through oxidation (’320 Patent, Abstract; col. 3:65-4:5). This enzymatic conversion provides a new method for detecting and analyzing the methylation status of DNA, as illustrated by the chemical reaction shown in Figure 2 of the patent (’320 Patent, Fig. 2).
  • Technical Importance: This discovery provided a molecular basis for a potential active DNA demethylation pathway, offering new tools to regulate and detect epigenetic modifications that are central to gene regulation, cancer, and developmental biology (Compl. ¶¶ 18-19).

Key Claims at a Glance

  • The complaint asserts independent claim 1 and dependent claims 2-4, 6, and 11 (Compl. ¶34).
  • Claim 1 is a method claim with the following essential elements:
    • Providing a polynucleotide with an epigenetic modification and an enzyme from the ten-eleven translocation (TET) family.
    • Oxidizing the epigenetic modification with the enzyme to generate an oxidized epigenetic modification.
    • Using the oxidized epigenetic modification or a derivative to identify the original epigenetic modification.
  • The complaint reserves the right to assert additional claims.

U.S. Patent No. 12,291,742 - Selective Oxidation of 5-Methylcytosine by TET-family Proteins (Issued 05/06/2025)

The Invention Explained

  • Problem Addressed: As with its family member, the ’742 Patent addresses the technical challenge of accurately mapping DNA methylation, a process known to be highly aberrant in diseases like cancer, for which the underlying enzymatic pathways were not fully characterized (’742 Patent, col. 1:64-2:9).
  • The Patented Solution: The patent discloses methods that leverage the catalytic activity of TET-family enzymes to convert 5-methylcytosine to 5-hydroxymethylcytosine (’742 Patent, Abstract). The claims combine this enzymatic step with subsequent chemical conversion and sequencing steps to provide a comprehensive method for analyzing DNA methylation status at base-level resolution. The process is depicted chemically in Figure 2 of the patent (’742 Patent, Fig. 2).
  • Technical Importance: The claimed methods provide a specific workflow for epigenetic analysis, potentially enabling more accurate sequencing-based detection of 5mC by differentiating it from unmodified cytosine (Compl. ¶¶ 18-19).

Key Claims at a Glance

  • The complaint asserts independent claim 21 and dependent claim 30 (Compl. ¶43).
  • Claim 21 is a method claim with the following essential elements:
    • Contacting a nucleic acid molecule containing cytosine and 5-methylcytosine with an isolated TET polypeptide enzyme in an amount effective to convert all of the 5-methylcytosine to an oxidized derivative.
    • Converting the cytosine in the nucleic acid molecule to uracil.
    • Conducting a sequencing reaction to obtain the sequence of the nucleic acid molecule.
  • The complaint reserves the right to assert additional claims.

III. The Accused Instrumentality

Product Identification

The accused instrumentality is the "Watchmaker DNA Library Prep Kits with TAPS+" (the "Accused Product") (Compl. ¶27).

Functionality and Market Context

The complaint alleges that the Accused Product is a kit used for preparing DNA libraries for scientific analysis, particularly for studying epigenetics, including 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) (Compl. ¶28). The infringement allegations are based on the use of the Accused Product "in accordance with Defendant Watchmaker's explicit instructions" by Defendant's personnel, customers, or other users (Compl. ¶31). Defendant allegedly began selling the Accused Product on or about November 5, 2025 (Compl. ¶29).

IV. Analysis of Infringement Allegations

The complaint references but does not attach claim chart exhibits that detail its infringement theories (Compl. ¶¶ 35, 44). The following summarizes the narrative allegations. No probative visual evidence provided in complaint.

’320 Patent Infringement Allegations

The complaint alleges that the use of the Accused Product as instructed by Defendant directly infringes at least claim 1 of the ’320 Patent (Compl. ¶¶ 31, 35). The narrative theory suggests that the process of using the kit to study 5mC and 5hmC inherently practices the claimed method of providing a polynucleotide, oxidizing an epigenetic modification using a TET-family enzyme, and then using that oxidized modification to identify the original modification (Compl. ¶¶ 2, 28, 31).

’742 Patent Infringement Allegations

The complaint asserts that using the Accused Product as instructed directly infringes at least claim 21 of the ’742 Patent (Compl. ¶¶ 31, 44). The infringement theory appears to be that the "TAPS+" technology in the kit performs a sequence of steps that maps onto the elements of claim 21: first, using a TET enzyme to convert 5mC to an oxidized derivative; second, chemically converting unmodified cytosine to uracil; and third, preparing the DNA for a sequencing reaction (Compl. ¶¶ 2, 28, 31).

Identified Points of Contention

  • Scope Questions: For the ’320 Patent, a central question may be what constitutes "identify[ing] said epigenetic modification" under claim 1. The court may need to determine if the data output from a sequencing run performed after using the kit fulfills this claim element. For the ’742 Patent, a key issue may be the claim requirement to "convert all of said 5-methylcytosine." This raises the question of whether "all" requires 100% conversion efficiency or if it can be construed to mean "substantially all" in the context of the invention.
  • Technical Questions: A primary evidentiary question will be whether the Accused Product's workflow, when used as instructed, actually performs the claimed steps. This will involve establishing that the "TAPS+" technology utilizes a TET-family enzyme for oxidation as required by both patents and, for the ’742 Patent, subsequently converts cytosine to uracil before sequencing. The complaint's own assertion that natural TET enzymes do not convert "all, or more than 98%" of 5mC may be relevant to the factual analysis of what the accused process achieves (Compl. ¶14).

V. Key Claim Terms for Construction

"identify the epigenetic modification" (’320 Patent, Claim 1)

  • Context and Importance: This term defines the purpose and final step of the claimed method. Its construction will determine the scope of activities that constitute infringement, particularly what form of data analysis or detection is required to complete the claimed method.
  • Intrinsic Evidence for a Broader Interpretation: The specification discusses various "downstream applications" and detection methods, including immunochemistry, chromatin immunoprecipitation, and sequencing, which could support a broad interpretation that "identify" covers any method of determining the location of the original modification (’320 Patent, col. 6:45-54).
  • Intrinsic Evidence for a Narrower Interpretation: The patent’s specific examples demonstrate identification using thin-layer chromatography (TLC) and mass spectrometry (’320 Patent, Figs. 7A-E, 9). A party may argue that "identify" should be limited to the specific analytical techniques disclosed in the embodiments.

"an amount effective to convert all of said 5-methylcytosine" (’742 Patent, Claim 21)

  • Context and Importance: The word "all" appears to set an absolute, 100% standard for conversion efficiency. Practitioners may focus on this term because demonstrating perfect conversion is technically challenging, and its construction could be dispositive for the infringement analysis.
  • Intrinsic Evidence for a Broader Interpretation: The patent discusses improving the "efficiency or rate" of various processes, which may suggest that "all" should be understood in the context of achieving a functionally complete conversion for the purpose of accurate sequencing, rather than a literal 100% conversion of every molecule (’742 Patent, col. 4:60-65).
  • Intrinsic Evidence for a Narrower Interpretation: The plain meaning of "all" is unequivocal. A defendant could argue that the patentee chose this absolute term to distinguish the invention from prior art and must be held to it. The complaint's statement that natural TET enzymes do not convert "all, or more than 98%" could be used to argue that the patentees were aware of and intended a distinction between near-complete and fully complete conversion (Compl. ¶14).

VI. Other Allegations

Indirect Infringement

The complaint alleges both induced and contributory infringement for both patents. It asserts that Defendant's "protocols and manuals provide explicit instructions resulting in infringement" (inducement) and that the Accused Product is a material component of the invention, especially adapted for infringement, and not a staple article of commerce (contributory) (Compl. ¶¶ 37-38, 46-47).

Willful Infringement

Willfulness is alleged based on Defendant’s purported actual knowledge or willful blindness to the infringement, with knowledge established "no later than the filing date of this Complaint" (Compl. ¶¶ 36, 45). Plaintiffs seek enhanced damages based on these allegations (Compl. Prayer for Relief ¶(D)).

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

  • A core issue will be one of definitional scope: can the term "all" in Claim 21 of the ’742 Patent be construed to mean "substantially all," or does it impose a strict 100% conversion requirement that may be difficult for the Plaintiff to prove the accused product meets?
  • A key evidentiary question will be one of technical operation: what chemical and enzymatic processes does the "TAPS+" technology in the Accused Product actually perform? Discovery will focus on whether the kit utilizes a TET-family enzyme and, for the ’742 Patent, whether it performs a subsequent cytosine-to-uracil conversion, as required to map onto the asserted claims.
  • A final central question will be one of infringement mapping: for the broad method of the ’320 Patent, does the act of preparing a DNA library with the accused kit and using it for sequencing constitute "using" the oxidized modification to "identify" the original modification, or is an additional, distinct step of analysis required to satisfy the claim?