DCT
1:22-cv-01913
Personalis Inc v. Foresight Diagnostics
I. Executive Summary and Procedural Information
- Parties & Counsel:
- Plaintiff: Personalis, Inc. (Delaware)
- Defendant: Foresight Diagnostics Inc. (Delaware)
- Plaintiff’s Counsel: Weil, Gotshal & Manges
- Case Identification: 1:22-cv-01913, D. Colo., 08/02/2022
- Venue Allegations: Venue is alleged to be proper in the District of Colorado because the Defendant maintains its principal place of business in Aurora, Colorado.
- Core Dispute: Plaintiff alleges that Defendant’s personalized genetic assay for detecting cancer recurrence infringes three patents related to methods for creating and using patient-specific nucleic acid probe sets for genetic testing.
- Technical Context: The technology at issue resides in the field of personalized oncology diagnostics, specifically using liquid biopsies to detect minimal residual disease (MRD) by identifying tumor-specific genetic variants in a patient's blood.
- Key Procedural History: The complaint alleges that the Defendant had pre-suit knowledge of all three patents-in-suit via notice letters, forming the basis for allegations of willful infringement.
Case Timeline
| Date | Event |
|---|---|
| 2013-01-17 | ’394 Patent Priority Date |
| 2016-05-27 | ’611 and ’783 Patents Priority Date |
| 2019-10-22 | U.S. Patent No. 10,450,611 Issues |
| 2021-10-11 | Publication of paper describing Accused Product |
| 2022-04-12 | U.S. Patent No. 11,299,783 Issues |
| 2022-05-17 | Plaintiff sends notice letter regarding ’611 Patent |
| 2022-07-12 | U.S. Patent No. 11,384,394 Issues |
| 2022-07-12 | Plaintiff sends notice letter regarding ’783 and ’394 Patents |
| 2022-08-02 | Complaint Filed |
II. Technology and Patent(s)-in-Suit Analysis
U.S. Patent No. 10,450,611 - "Personalized Genetic Testing", issued October 22, 2019
The Invention Explained
- Problem Addressed: The patent describes the clinical adoption of large-scale genetic sequencing (e.g., exome sequencing) as being limited by high costs, which is a particular challenge in oncology where deep sequencing is often required to detect rare cancer-related molecules (Compl. ¶1; ’611 Patent, col. 4:24-30).
- The Patented Solution: The invention proposes a two-stage method. First, an initial, broad sequencing assay is performed on a patient's biological sample (e.g., a tumor) to identify a set of patient-specific genetic variants. Second, a personalized and more focused "probe set" is created based on those specific variants. This personalized probe set is then used in subsequent, less expensive assays (e.g., on blood plasma) to sensitively monitor for the presence of those same variants over time (Compl. ¶18; ’611 Patent, Abstract; col. 4:41-63).
- Technical Importance: This personalized, two-step approach is presented as a method to make highly sensitive, longitudinal monitoring for patient-specific cancer markers, such as for minimal residual disease, more cost-effective than repeatedly performing broad sequencing assays (’611 Patent, col. 4:24-30).
Key Claims at a Glance
- The complaint asserts direct infringement of one or more claims, including independent claim 1 (Compl. ¶36).
- Claim 1 of the ’611 Patent recites the essential elements of a method comprising:
- Sequencing nucleic acid molecules from a biological sample of a subject to generate sequencing data.
- Using a computer to process the data to identify a set of genetic variants.
- Obtaining a probe set with molecules corresponding to the identified variants, where the probe set is configured to selectively enrich or amplify those variants.
- Using the probe set to enrich or amplify sequences from an additional biological sample to create a sequencing library.
- Sequencing the library to identify the presence or absence of the genetic variants.
U.S. Patent No. 11,299,783 - "Methods and Systems For Genetic Analysis", issued April 12, 2022
The Invention Explained
- Problem Addressed: The patent addresses the need to create a genetic testing panel that is not only personalized to a patient's unique genetic variants but also includes standardized, clinically relevant genetic markers that are broadly applicable across patients (’783 Patent, col. 14:7-15).
- The Patented Solution: The invention claims a method using a personalized probe set that comprises two distinct components: a "variable portion" that is based on the results of a patient-specific sequencing assay, and a "fixed portion" that is independent of that assay's results (’783 Patent, col. 7:40-44). This "fixed portion" can be designed to target known cancer driver genes, pharmacogenomic markers, or other variants of general clinical interest, allowing for simultaneous personalized and standardized testing in a single assay (Compl. ¶24; ’783 Patent, col. 8:1-8).
- Technical Importance: This hybrid probe set design allows an assay to combine the high sensitivity of patient-specific monitoring with the broad clinical utility of a standardized panel, thereby providing more comprehensive data to inform therapy choices (’783 Patent, col. 14:7-15).
Key Claims at a Glance
- The complaint asserts direct infringement of one or more claims, including independent claim 1 (Compl. ¶42).
- Claim 1 of the ’783 Patent, as summarized in the complaint, recites the essential elements of a method comprising:
- Obtaining a personalized probe set designed to enrich or amplify sequences that comprise both a "variable portion" based on a sequence assay's results and a "fixed portion" independent of that assay.
- Using the probe sequence on an additional biological sample to identify genetic variants.
- Generating a report identifying the presence or absence of a disease and genetic variants to inform a therapy choice.
U.S. Patent No. 11,384,394 - "Methods and Systems for Genetic Analysis", issued July 12, 2022
- Technology Synopsis: This patent describes methods for analyzing nucleic acid samples over time. The claimed method involves performing whole genome sequencing on a first biological sample, creating a set of capture probes based on identified polymorphisms, and then repeatedly using those probes to sequence additional samples obtained from the individual at later time points to monitor for the presence of those polymorphisms (Compl. ¶29, ¶30).
- Asserted Claims: Claim 1 (Compl. ¶48).
- Accused Features: The complaint alleges that the "Solid Tumor Recurrence Test" infringes by performing an initial whole genome sequencing, creating capture probes, and using them on subsequent samples taken at additional time points to generate a biomedical report (Compl. ¶30, ¶33).
III. The Accused Instrumentality
Product Identification
- The accused instrumentality is Foresight Diagnostics' "Solid Tumor Recurrence Test" service (Compl. ¶31, ¶35).
Functionality and Market Context
- The complaint describes the Accused Product as a personalized assay for the detection of minimal residual disease (MRD) for solid tumors (Compl. ¶31). The alleged functionality involves a multi-step method: (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 variants; (d) using those probes to enrich for the variants in a subsequent blood or plasma sample; and (e) sequencing the subsequent sample to detect the presence or absence of the variants (Compl. ¶33).
No probative visual evidence provided in complaint.
IV. Analysis of Infringement Allegations
10,450,611 Patent Infringement Allegations
The complaint references an infringement claim chart as Exhibit D but does not include the exhibit itself (Compl. ¶37). The following table summarizes the infringement theory based on the narrative allegations in the complaint.
| Claim Element (from Independent Claim 1) | Alleged Infringing Functionality | Complaint Citation | Patent Citation |
|---|---|---|---|
| sequencing nucleic acid molecules from at least one biological sample of a subject to generate sequencing data... | Foresight’s test involves whole genome sequencing of a tumor sample. | ¶33(a) | col. 4:48-51 |
| computer processing said sequencing data to identify...a set of genetic variants... | The test includes the identification of genetic variants from the tumor sequencing. | ¶33(b) | col. 4:41-48 |
| obtaining a probe set...configured to selectively enrich or amplify sequences comprising said set of genetic variants... | The test involves creating probes to selectively enrich for the identified genetic variants. | ¶33(c) | col. 4:52-58 |
| using said probe set to selectively enrich or amplify sequences...in an additional biological sample from said subject... | The test uses the created probes to enrich for the variants in a subsequent blood or plasma sample. | ¶33(d) | col. 4:58-60 |
| subjecting said sequencing library to sequencing...to identify a presence or absence of at least a subset of said set of said genetic variants... | The subsequent sample is sequenced to identify the presence or absence of the targeted variants. | ¶33(e) | col. 4:60-63 |
- Identified Points of Contention:
- Scope Questions: The complaint’s allegations in paragraph 33 map closely to the elements of claim 1. A potential point of contention may arise from the term "obtaining a probe set," which could raise questions about whether the specific manner in which the accused test creates or acquires its probes falls within the scope defined by the patent's specification.
- Technical Questions: The infringement analysis will likely require a detailed factual inquiry into the technical specifics of the Accused Product. A key question may be whether the probes used in the "Solid Tumor Recurrence Test" are functionally and structurally equivalent to those contemplated by the patent and whether they perform the specific function of "selectively enrich[ing] or amplify[ing]" as required by the claim.
11,299,783 Patent Infringement Allegations
The complaint references an infringement claim chart as Exhibit F but does not provide the exhibit itself (Compl. ¶43). The complaint alleges that the Accused Product meets every limitation of at least claim 1 of the ’783 Patent (Compl. ¶43). However, the complaint does not provide a specific narrative breakdown of how the Accused Product meets the key limitation of claim 1: a probe set comprising both a "variable portion" and a "fixed portion" (Compl. ¶24). This raises an evidentiary question regarding whether the Accused Product actually includes a "fixed portion" of probes that is independent of the initial patient-specific sequencing assay, a central element of the asserted claim.
V. Key Claim Terms for Construction
- For the ’611 Patent:
- The Term: "genetic variants"
- Context and Importance: This term defines the targets identified in the initial sequencing and subsequently monitored by the personalized probe set. Its construction is critical to defining the scope of what the claimed method is designed to detect.
- Intrinsic Evidence for Interpretation:
- Evidence for a Broader Interpretation: The specification states that the plurality of genetic characteristics may comprise "one or more (i) single nucleotide polymorphisms, (ii) insertions and/or deletions, (iii) copy number variations, and (iv) structural variations" (’611 Patent, col. 6:30-34).
- Evidence for a Narrower Interpretation: The defendant may argue that, in the context of the patent's examples focused on cancer, the term should be limited to somatic variants identified from a tumor sample relative to a germline sample, as depicted in Figure 6 (’611 Patent, FIG. 6).
- For the ’783 Patent:
- The Term: "a fixed portion that is independent of the sequencing assay"
- Context and Importance: This term is the key distinguishing feature of the invention claimed in the ’783 Patent. The infringement analysis for this patent will likely turn on whether the accused test's probe set includes a component that meets this definition.
- Intrinsic Evidence for Interpretation:
- Evidence for a Broader Interpretation: The claim language itself provides a broad functional definition: any portion of the probe set that is "independent of the sequencing assay" could be argued to fall within its scope (’783 Patent, col. 7:43-44).
- Evidence for a Narrower Interpretation: The specification provides specific examples of what this "fixed portion" might correspond to, including "(1) cancer driver genes, (2) genes involved in the pharmacogenomics of cancer drugs, (3) genes involved in Mendelian immunological diseases," and others (’783 Patent, col. 8:1-8). A defendant may argue the term should be construed as limited to these or similar categories of clinically established markers.
VI. Other Allegations
- Willful Infringement: The complaint alleges willful infringement of all three patents-in-suit. The basis for this allegation is Defendant's alleged pre-suit knowledge of the patents, purportedly established through notice letters sent by Plaintiff on May 17, 2022 (for the ’611 Patent) and July 12, 2022 (for the ’783 and ’394 Patents) (Compl. ¶39, ¶45, ¶51).
VII. Analyst’s Conclusion: Key Questions for the Case
- A central issue will be one of factual proof: what are the precise technical steps and components of the "Solid Tumor Recurrence Test"? The case for the ’611 and ’394 patents will likely depend on whether discovery confirms the complaint's allegations that the accused service performs an initial broad sequencing to design a patient-specific probe set that is then used for subsequent longitudinal monitoring.
- A key evidentiary and claim scope question for the ’783 Patent will be one of structural composition: does the accused test’s probe set contain a "fixed portion" of probes that is "independent of the [initial] sequencing assay," as required by claim 1? The complaint does not plead specific facts supporting this element, making it a critical point of dispute that will hinge on evidence of the accused product's design.