DCT

1:22-cv-01913

Personalis Inc v. Foresight Diagnostics

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I. Executive Summary and Procedural Information

  • Parties & Counsel:
  • Case Identification: 1:22-cv-01913, D. Colo., 08/17/2022
  • Venue Allegations: Venue is alleged to be proper in the District of Colorado because the Defendant maintains its principal place of business in the state.
  • Core Dispute: Plaintiff alleges that Defendant’s personalized genetic testing service, the Solid Tumor Recurrence Test, infringes four patents related to methods for creating and using patient-specific nucleic acid probes for detecting and monitoring cancer.
  • Technical Context: The technology at issue involves tumor-informed liquid biopsies, a method for non-invasively detecting and quantifying minimal residual disease (MRD) in cancer patients by analyzing trace amounts of tumor DNA in the bloodstream.
  • Key Procedural History: The complaint alleges that Plaintiff provided Defendant with pre-suit notice of each of the four asserted patents, which may form the basis for its claim of willful infringement.

Case Timeline

Date Event
2013-01-17 Priority Date for ’394 and ’033 Patents
2016-05-27 Priority Date for ’611 and ’783 Patents
2019-10-22 ’611 Patent Issued
2022-04-12 ’783 Patent Issued
2022-05-17 Alleged notice of ’611 Patent provided to Defendant
2022-07-12 ’394 Patent Issued
2022-07-12 Alleged notice of ’783 and ’394 Patents, and pending ’033 application, provided to Defendant
2022-08-09 ’033 Patent Issued
2022-08-17 First Amended Complaint Filed

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

No probative visual evidence provided in complaint.

U.S. Patent No. 10,450,611 - Personalized Genetic Testing

  • Patent Identification: U.S. Patent No. 10,450,611, entitled “Personalized Genetic Testing,” issued on October 22, 2019 (’611 Patent).

The Invention Explained

  • Problem Addressed: The patent’s background section notes that the clinical adoption of large-scale genetic sequencing, such as exome sequencing, has been limited by its high cost, a problem that is particularly acute in cancer diagnostics where very deep sequencing (e.g., >500x coverage) is often required (’611 Patent, col. 4:24-31).
  • The Patented Solution: The invention proposes a two-stage method to create a cost-effective, personalized assay for longitudinal patient monitoring. First, an initial, broad sequencing assay is performed on a biological sample to identify a patient-specific set of genetic variants. Second, a customized, smaller set of nucleic acid probes is created to specifically target only those identified variants. This personalized probe set is then used in subsequent, less expensive assays on later samples from the patient to monitor for the presence of those specific variants over time (’611 Patent, Abstract; col. 4:41-63). The general information flow is depicted in the patent’s Figure 1 (’611 Patent, FIG. 1).
  • Technical Importance: This approach enables the creation of a patient-specific "liquid biopsy" panel that can be used for highly sensitive, targeted, and repeated monitoring of minimal residual disease at a potentially lower cost than repeatedly performing broad, exome-scale sequencing (Compl. ¶17-18).

Key Claims at a Glance

  • The complaint asserts infringement of at least independent claim 1 (Compl. ¶42).
  • Claim 1 of the ’611 Patent includes the following essential elements:
    • Sequencing nucleic acid molecules from a subject's biological sample to generate sequencing data.
    • Processing the sequencing data with a computer to identify a set of genetic variants.
    • Obtaining a probe set with nucleic acid molecules configured to selectively enrich or amplify sequences containing that set of genetic variants.
    • Using the probe set to enrich or amplify sequences in an additional biological sample to create a sequencing library.
    • Sequencing the resulting library to identify the presence or absence of at least a subset of the original genetic variants.
  • The complaint does not explicitly reserve the right to assert dependent claims.

U.S. Patent No. 11,299,783 - Methods and Systems For Genetic Analysis

  • Patent Identification: U.S. Patent No. 11,299,783, entitled “Methods and Systems For Genetic Analysis,” issued on April 12, 2022 (’783 Patent).

The Invention Explained

  • Problem Addressed: The patent addresses the same general problem of creating cost-effective and clinically useful personalized genetic tests (’783 Patent, col. 4:26-32).
  • The Patented Solution: The invention is a method using a "personalized probe set" that comprises two distinct components: a "variable portion" containing probes designed based on a patient’s unique sequencing results, and a "fixed portion" containing probes that are independent of that specific patient's results. This fixed portion can target content such as known cancer driver genes, pharmacogenomic markers, or variants for sample identification. The combined probe set is then used on subsequent samples to generate a report informing therapeutic choices (’783 Patent, Abstract; col. 8:6-15).
  • Technical Importance: This hybrid approach combines patient-specific variant tracking with simultaneous monitoring of a standard panel of clinically actionable genetic markers, offering a more comprehensive tool for monitoring disease progression and informing treatment decisions (Compl. ¶24).

Key Claims at a Glance

  • The complaint asserts infringement of at least independent claim 1 (Compl. ¶48).
  • Claim 1 of the ’783 Patent includes the following essential elements:
    • Obtaining a personalized probe set comprising: (i) at least one variable portion derived from a sequencing assay result and (ii) at least one fixed portion independent of that result.
    • Using the personalized probe set on an additional biological sample to identify the presence or absence of genetic variants.
    • Generating a report that identifies the presence or absence of a disease and/or genetic variants that inform a therapy choice.
  • The complaint does not explicitly reserve the right to assert dependent claims.

U.S. Patent No. 11,384,394 - Methods and Systems for Genetic Analysis

  • Patent Identification: U.S. Patent No. 11,384,394, entitled “Methods and Systems for Genetic Analysis,” issued on July 12, 2022 (’394 Patent) (Compl. ¶25).

Technology Synopsis

The ’394 Patent claims a method for longitudinal genetic analysis. The method involves performing whole genome sequencing on a first biological sample, creating a set of capture probes based on identified polymorphisms, using those probes to sequence a second sample from a later time point, and generating a biomedical report on the findings (Compl. ¶29-30).

Asserted Claims

Independent claim 1 (Compl. ¶54).

Accused Features

The complaint alleges that Defendant’s Accused Product infringes by performing a method of analyzing nucleic acid samples over time using capture probes based on an initial sample analysis (Compl. ¶53-55).

U.S. Patent No. 11,408,033 - Methods and Systems For Genetic Analysis

  • Patent Identification: U.S. Patent No. 11,408,033, entitled “Methods and Systems For Genetic Analysis,” issued on August 9, 2022 (’033 Patent) (Compl. ¶31).

Technology Synopsis

The ’033 Patent claims a method for analyzing nucleic acid samples over time. The method includes producing a set of capture probes that hybridize to polymorphisms located in sequences encoding genes with known "biomedically interpretable variants," contacting a sample with the probes, sequencing the captured molecules, and repeating the process on a subsequent sample (Compl. ¶35-36).

Asserted Claims

Independent claim 1 (Compl. ¶60).

Accused Features

The complaint alleges that Defendant’s Accused Product infringes by employing a method of analyzing samples over time using capture probes that target known variants (Compl. ¶59-61).

III. The Accused Instrumentality

Product Identification

The accused instrumentality is Defendant’s “Solid Tumor Recurrence Test,” identified in the complaint as “the Accused Product” (Compl. ¶37, ¶41).

Functionality and Market Context

The Accused Product is described as a service offering a personalized assay for the detection of minimal residual disease (MRD) for solid tumors (Compl. ¶37). The complaint alleges the method involves a multi-step process: (a) performing whole genome sequencing of a patient’s tumor sample, (b) identifying genetic variants from that sequencing, (c) creating probes designed to selectively enrich for those specific genetic variants, (d) using the custom probes to enrich for the variants in a subsequent blood or plasma sample, and (e) sequencing the enriched sample to determine the presence or absence of the variants (Compl. ¶39).

IV. Analysis of Infringement Allegations

The complaint references, but does not include, claim chart exhibits detailing its infringement allegations (Compl. ¶43, ¶49, ¶55, ¶61). The narrative infringement theory is summarized below.

’611 Patent Infringement Allegations

The complaint alleges that the Accused Product directly infringes at least claim 1 of the ’611 Patent (Compl. ¶42). The infringement theory is based on the description of the Accused Product’s methodology, which allegedly maps directly onto the steps of claim 1. Specifically, the complaint alleges the Accused Product performs an initial sequencing of a tumor sample to identify variants (meeting the first two claim elements), creates a set of custom probes for those variants (meeting the "obtaining a probe set" element), and then uses that probe set to test a subsequent blood or plasma sample (meeting the final two claim elements) (Compl. ¶39).

’783 Patent Infringement Allegations

The complaint alleges that the Accused Product directly infringes at least claim 1 of the ’783 Patent (Compl. ¶48). However, the complaint’s description of the Accused Product’s functionality only details steps corresponding to the "variable portion" of the claimed probe set—that is, a set of probes personalized to a specific patient's tumor variants (Compl. ¶39). The complaint does not allege any specific facts suggesting that the Accused Product’s probe set also includes a "fixed portion that is independent of the sequencing assay," which is a required element of claim 1 of the ’783 Patent.

Identified Points of Contention

  • Evidentiary Questions: For all asserted patents, the infringement analysis will depend on evidence detailing the precise technical steps of the Accused Product. The high-level description in the complaint may not capture nuances that could differentiate the accused method from the claimed steps.
  • Scope Questions: A central dispute for the ’783 Patent will be whether the Accused Product meets the "fixed portion" limitation of claim 1. The complaint’s factual allegations appear to describe a purely personalized probe set, which may raise the question of whether there is a fundamental mismatch between the accused method and the claim's requirements.

V. Key Claim Terms for Construction

  • The Term: "fixed portion that is independent of the... sequencing assay" (’783 Patent, claim 1)
  • Context and Importance: The construction of this term appears central to the infringement analysis for the ’783 Patent. Practitioners may focus on this term because the complaint’s allegations describe a personalized ("variable") probe set but do not provide facts supporting the presence of a "fixed" component. The viability of the infringement claim may depend on whether the Accused Product's probes can be shown to contain any element that meets the definition of a "fixed portion."
  • Intrinsic Evidence for Interpretation:
    • Evidence for a Broader Interpretation: A party might argue that the specification supports a broad reading where the "fixed portion" could include a minimal set of probes, such as those used for "genetic sample ID by a fixed panel of genetic variants" (’783 Patent, col. 8:11-13). This could potentially read on control probes or standard markers included in an assay.
    • Evidence for a Narrower Interpretation: A party might argue that the specification consistently contrasts the "variable portion" (e.g., corresponding to a patient's specific Mendelian phenotype) with a "fixed portion" comprising "additional genetic content not related to" that patient-specific condition, such as "cancer driver genes" or "pharmacogenomics" (’783 Patent, col. 8:6-11, 63-65). This could support a narrower construction requiring a substantive, clinically relevant panel of standard probes, not merely administrative or control markers.

VI. Other Allegations

  • Willful Infringement: The complaint alleges willful infringement for all four patents-in-suit. The allegations are based on a series of written notice letters sent to the Defendant. Knowledge of the ’611 Patent is alleged as of May 17, 2022 (Compl. ¶45). Knowledge of the ’783 and ’394 Patents is alleged as of July 12, 2022 (Compl. ¶51, ¶57). Knowledge of the ’033 Patent is alleged as of its issue date, August 9, 2022, based on the prior notice letter that identified the pending application (Compl. ¶63).

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

  • A central evidentiary question will be one of technical implementation: what is the precise composition of the probe set used in Foresight's "Solid Tumor Recurrence Test"? The complaint describes a personalized methodology, but the viability of the infringement claim for the ’783 Patent will depend on evidence demonstrating that the accused probe set also contains a "fixed portion" of patient-independent probes.
  • The case will likely involve a key question of claim scope: can the term "fixed portion" in the ’783 Patent be construed to cover standard control or quality-assurance probes that may be included in an assay, or does the patent require a substantive panel of clinically-relevant, non-personalized probes? The answer to this question may be dispositive for a significant part of the dispute.
  • A third area of focus will be on willfulness: given the plaintiff's allegations of providing pre-suit notice for all asserted patents, the court will likely examine the defendant's conduct after receiving these notices to determine whether any continuing infringement was objectively reckless, which could expose the defendant to enhanced damages.