DCT
1:17-cv-12194
Caris MPI Inc v. Foundation Medicine Inc
I. Executive Summary and Procedural Information
- Parties & Counsel:
- Plaintiff: Caris MPI, Inc. (Texas)
- Defendant: Foundation Medicine, Inc. (Delaware)
- Plaintiff’s Counsel: Fish & Richardson P.C.
- Case Identification: 1:17-cv-12194, D. Mass., 11/07/2017
- Venue Allegations: Venue is alleged to be proper in the District of Massachusetts because Defendant has its headquarters and a regular and established place of business in Cambridge, Massachusetts, and has allegedly committed acts of infringement in the district.
- Core Dispute: Plaintiff alleges that Defendant’s genomic profiling products and services for cancer treatment infringe five patents related to systems and methods for determining individualized medical interventions based on molecular profiles.
- Technical Context: The dispute centers on the field of personalized oncology, where molecular information from a patient's tumor is used to guide the selection of targeted cancer therapies.
- Key Procedural History: The complaint asserts that the patented technology was validated in a 2010 clinical study, which found that the molecular profiling approach resulted in longer progression-free survival for a significant percentage of patients compared to conventional therapies. No other procedural history, such as prior litigation or administrative challenges to the patents, is mentioned in the complaint.
Case Timeline
| Date | Event |
|---|---|
| 2006-05-18 | Earliest Priority Date for all Asserted Patents |
| 2010-11-20 | Publication of "2010 Pilot Study" |
| 2012-05-30 | Alleged Commercial Launch of FoundationOne® |
| 2013-12-07 | Alleged Commercial Launch of FoundationOne® Heme |
| 2014-11-04 | Issue Date of U.S. Patent No. 8,880,350 |
| 2015-07-28 | Issue Date of U.S. Patent No. 9,092,392 |
| 2016-03-22 | Issue Date of U.S. Patent No. 9,292,660 |
| 2016-05-03 | Alleged Commercial Launch of FoundationACT® |
| 2016-06-21 | Issue Date of U.S. Patent No. 9,372,193 |
| 2016-07-05 | Issue Date of U.S. Patent No. 9,383,365 |
| 2017-11-07 | Complaint Filing Date |
II. Technology and Patent(s)-in-Suit Analysis
U.S. Patent No. 8,880,350 - "System and Method for Determining Individualized Medical Intervention for a Disease State", issued November 4, 2014
The Invention Explained
- Problem Addressed: The patent addresses the limitations of the "one-size-fits-all" approach to cancer treatment, where therapy is selected based on the cancer's anatomical origin or "lineage" rather than its underlying molecular characteristics. This traditional approach often leads to trial-and-error treatment with poor efficacy because patients with the same cancer type can respond differently to the same therapy (Compl. ¶9; ’350 Patent, col. 1:36-54).
- The Patented Solution: The invention is a system for identifying individualized cancer treatments independent of the cancer's lineage. It involves performing molecular profiling of a patient's tumor to measure a large number of molecular targets (e.g., genes, proteins), comparing these measurements to a reference, and using a database to identify therapeutic agents that can interact with the specific molecular findings in that patient's tumor (’350 Patent, Abstract; col. 2:17-33). This process aims to find effective treatments that would not normally be considered for a particular cancer type (Compl. ¶12).
- Technical Importance: The claimed system represents a shift from organ-based oncology to a molecularly-driven paradigm, providing a systematic way to identify viable therapeutic alternatives for patients with advanced or refractory cancers who have exhausted conventional options (Compl. ¶12).
Key Claims at a Glance
- Independent Claim 1 is asserted (Compl. ¶52).
- Essential elements of Claim 1 include:
- A system for generating a report identifying a therapeutic agent.
- At least one device configured to assay a specific plurality of molecular targets in a biological sample, wherein the targets comprise EGFR, KIT, TOP1, MLH1, PTEN, PDGFRA and ESR1.
- At least one computer database comprising reference values for the molecular targets and a listing of available therapeutic agents for those targets.
- Computer-readable program code with instructions to compare the sample's test values with the reference values.
- Computer-readable program code with instructions to access the database and identify a therapeutic agent where the comparison indicates a likely benefit.
- Computer-readable program code with instructions to generate a report listing the beneficial molecular targets and the identified therapeutic agent.
- The complaint also asserts infringement of claim 5 and reserves the right to assert additional claims (Compl. ¶53).
U.S. Patent No. 9,372,193 - "System and Method for Determining Individualized Medical Intervention for a Disease State", issued June 21, 2016
The Invention Explained
- Problem Addressed: The patent addresses the same problem as the ’350 Patent: the need for a systematic method to determine individualized medical interventions based on molecular profiling, independent of the cancer's diagnosed lineage (Compl. ¶12; ’193 Patent, col. 2:28-35).
- The Patented Solution: The ’193 Patent claims a system nearly identical in structure and function to that of the ’350 Patent. It provides for assaying molecular targets, comparing results to a reference value in a database, and generating a report that identifies a therapeutic agent predicted to be beneficial. The primary distinction is the specific combination of molecular targets recited in the claims (’193 Patent, Abstract; col. 1:40-50).
- Technical Importance: This patent extends the core inventive concept to a different combination of molecular targets, suggesting a platform approach to identifying non-conventional treatment options across a range of molecular profiles (Compl. ¶15).
Key Claims at a Glance
- Independent Claim 1 is asserted (Compl. ¶60).
- Essential elements of Claim 1 are structurally identical to Claim 1 of the ’350 Patent, but recite a different combination of molecular targets:
- The plurality of molecular targets comprises AR, EGFR, HER2, KIT, MLH1, PTEN, and PDGFRA.
- The complaint also asserts infringement of claim 5 and reserves the right to assert additional claims (Compl. ¶61).
Multi-Patent Capsules for Additional Patents-in-Suit
U.S. Patent No. 9,383,365: Titled "System and Method for Determining Individualized Medical Intervention for a Disease State", issued July 5, 2016.
- Technology Synopsis: This patent claims a system structurally similar to the ’350 and ’193 patents. It is directed to identifying non-conventional treatment options by assaying a specific panel of molecular targets in a patient’s tumor, comparing the results to a database, and generating a report of potentially beneficial therapies (Compl. ¶15, ¶68).
- Asserted Claims: Claim 1 (independent) and Claim 5 are asserted (Compl. ¶69).
- Accused Features: The accused FoundationOne® and FoundationOne® Heme products are alleged to infringe by assaying a panel of targets that includes those recited in the claims and generating reports that identify therapeutic agents (Compl. ¶69).
U.S. Patent No. 9,092,392: Titled "Molecular Profiling of Tumors", issued July 28, 2015.
- Technology Synopsis: This patent claims a system for generating a therapeutic report specifically for an individual with colorectal cancer. It recites using a nucleic acid sequencing device to assay a specific panel of molecular targets (BRAF, PIK3CA, EGFR, and PTEN) and using a database to identify therapies based on the results (Compl. ¶16, ¶76).
- Asserted Claims: Claim 1 (independent) and Claim 5 are asserted (Compl. ¶77).
- Accused Features: The accused FoundationOne® and FoundationACT® products are alleged to infringe by performing molecular profiling for colorectal cancer patients that includes the claimed targets and generating reports with treatment options (Compl. ¶77).
U.S. Patent No. 9,292,660: Titled "Molecular Profiling of Tumors", issued March 22, 2016.
- Technology Synopsis: This patent is analogous to the ’392 Patent but is directed specifically to lung cancer. It claims a system for generating a therapeutic report by assaying a specified plurality of molecular targets (PTEN, CTNNB1, cKIT, BRAF and PIK3CA) and using a database to identify likely beneficial agents (Compl. ¶16, ¶84).
- Asserted Claims: Claim 1 (independent) and Claim 5 are asserted (Compl. ¶85).
- Accused Features: The accused FoundationOne® and FoundationACT® products are alleged to infringe by performing molecular profiling for lung cancer patients that includes the claimed targets and generating reports with treatment options (Compl. ¶85).
III. The Accused Instrumentality
Product Identification
- The accused instrumentalities are Defendant’s molecular profiling products, including FoundationOne®, FoundationOne® Heme, and FoundationACT® (Compl. ¶39).
Functionality and Market Context
- The complaint alleges these products constitute a comprehensive genetic profiling (CGP) service for tumors (Compl. ¶41). The service involves receiving a biological sample (e.g., solid tumor tissue, blood for ctDNA), performing next-generation sequencing (NGS) to identify genomic alterations in hundreds of cancer-related genes, and generating a detailed report (Compl. ¶41-42, ¶48). The resulting report provides physicians with "clinically actionable information," which includes a list of detected alterations, potential targeted therapies associated with benefit, therapies associated with lack of response, and relevant clinical trials (Compl. ¶41, ¶43-44). The sample report for lung adenocarcinoma included in the complaint shows the identification of specific "Genomic Alterations" and lists corresponding "Potential Treatment Strategies" and "Clinical Trials to Consider" (Compl. p. 11-14).
IV. Analysis of Infringement Allegations
'350 Patent Infringement Allegations
| Claim Element (from Independent Claim 1) | Alleged Infringing Functionality | Complaint Citation | Patent Citation |
|---|---|---|---|
| A system for generating a report identifying at least one therapeutic agent for an individual with a cancer comprising: | Defendant provides the FoundationOne® and FoundationOne® Heme products, which are systems that generate reports identifying therapeutic agents for cancer patients. | ¶53 | col. 1:38-44 |
| a. at least one device configured to assay a plurality of molecular targets...wherein the molecular targets comprise EGFR, KIT, TOP1, MLH1, PTEN, PDGFRA and ESR1; | Defendant's system uses NGS-based assays to identify genomic alterations in hundreds of cancer-related genes, which allegedly include the specific targets listed in the claim. | ¶41, ¶53 | col. 2:55-65 |
| b. at least one computer database comprising: i. a reference value for the plurality of molecular targets; and ii. a listing of available therapeutic agents... | Defendant's system allegedly includes a database containing reference information and known associations between molecular targets and therapeutic agents to generate its reports. | ¶41-43 | col. 12:5-10 |
| c. a computer-readable program code comprising instructions to...compare said test values with a corresponding reference value... | Defendant's software compares a patient's genomic alteration data against its internal database of reference values and clinical information to determine significance and potential treatments. | ¶41 | col. 14:41-55 |
| d. a computer-readable program code comprising instructions to...identify at least one therapeutic agent...wherein said comparison...indicates a likely benefit... | Based on the comparison, Defendant's system identifies and lists potential targeted therapies and relevant clinical trials in its reports, such as the link between ERBB2 amplification and HER2-targeted therapies shown in the sample report. | ¶43; Compl. p. 12 | col. 14:56-62 |
| e. a computer-readable program code comprising instructions to generate a report that comprises a listing of the molecular targets wherein said comparison...indicated a likely benefit...along with the...therapeutic agent... | The FoundationOne® report presents a list of molecular targets with detected alterations and corresponding therapies with potential benefit, therapies associated with lack of response, and clinical trials. | ¶41, ¶43-44; Compl. p. 11 | col. 14:63-67 |
'193 Patent Infringement Allegations
| Claim Element (from Independent Claim 1) | Alleged Infringing Functionality | Complaint Citation | Patent Citation |
|---|---|---|---|
| a. at least one device configured to assay a plurality of molecular targets...wherein the plurality of molecular targets comprises AR, EGFR, HER2, KIT, MLH1, PTEN, and PDGFRA; | Defendant's system uses NGS-based assays to identify genomic alterations in hundreds of cancer-related genes, which allegedly include the specific targets listed in the claim. | ¶41, ¶61 | col. 3:1-17 |
| [Remaining elements b, c, d, and e are structurally identical to those in the '350 Patent chart above] | [The alleged infringing functionality for these elements is the same as described for the '350 Patent, involving the use of a database to compare results and a report generator to present findings] | ¶41-44, ¶61 | col. 12:5-10; col. 14:41-67 |
- Identified Points of Contention:
- Scope Questions: A central question may be whether the accused products, which perform comprehensive genomic profiling on hundreds of genes, meet the claim limitation of a "device configured to assay a plurality of molecular targets, wherein the molecular targets comprise [a specific, enumerated list of 7-8 genes]." The defense may argue that its system is not configured for these specific, small panels, but rather for broad, untargeted genomic analysis, and that the claimed combination of genes has no particular technical significance in its system.
- Technical Questions: The complaint alleges the use of NGS technology, while the patent specifications heavily describe technologies like immunohistochemistry (IHC) and microarrays (’350 Patent, col. 2:55-65). A dispute may arise over whether Defendant's NGS-based platform is the same as or equivalent to the "device configured to assay" contemplated and enabled by the patents. Further, the basis for determining a "likely benefit" will be a key factual question, specifically how Defendant's proprietary algorithms for associating alterations with therapies compare to the methods described in the patents.
V. Key Claim Terms for Construction
The Term: "plurality of molecular targets comprises [list of specific genes]"
- Context and Importance: This term appears in the independent claim of each asserted patent and defines the specific molecular panel that the claimed system is configured to assay. The construction of "comprises" and the significance of the recited list will be dispositive for infringement. Practitioners may focus on this term because the accused products test for hundreds of genes, not just the specific small panels recited. The question will be whether testing a superset that includes the claimed genes is sufficient to meet this limitation.
- Intrinsic Evidence for Interpretation:
- Evidence for a Broader Interpretation: The term "comprises" is typically interpreted in patent law to be inclusive, meaning "including but not limited to." Plaintiff may argue that as long as the accused system is configured to test for the recited genes, it infringes, regardless of how many other genes it also tests for.
- Evidence for a Narrower Interpretation: The patents describe the invention as moving beyond limited, lineage-specific tests to find new options by measuring a "larger number of targets" (’350 Patent, col. 2:17-20). However, the claims themselves recite very specific, relatively small lists. Defendant may argue that the claims are properly limited to systems specifically configured around these enumerated panels, and that a system designed for broad, comprehensive profiling of an entirely different and much larger set of genes does not infringe.
The Term: "device configured to assay"
- Context and Importance: This term defines the hardware component of the claimed system. Its construction is critical to determining whether Defendant’s NGS-based testing platform falls within the scope of the claims.
- Intrinsic Evidence for Interpretation:
- Evidence for a Broader Interpretation: The claim language is broad. The specification mentions that the system may use "various testing techniques to gather molecular information" (’350 Patent, col. 2:34-35). Plaintiff may argue this language supports a broad construction that covers any molecular assay technology, including NGS.
- Evidence for a Narrower Interpretation: The detailed description of the embodiments focuses heavily on IHC and microarray analyses as the methods for performing the test (’350 Patent, col. 2:55-65). Defendant may argue that the scope of "device" should be interpreted in light of these specific disclosures and may not extend to fundamentally different technologies like NGS that were not described in the patent.
VI. Other Allegations
Willful Infringement
- The complaint alleges willful infringement for all asserted patents. The basis for willfulness is Defendant's alleged knowledge of the patents since their respective issue dates. This knowledge is predicated on the allegation that Defendant identifies Plaintiff as a competitor in its public statements and monitors the patent portfolios of its competitors (Compl. ¶56, ¶64). The complaint further cites Defendant's 2016 10-K filing, which acknowledges the risk of patent infringement litigation from competitors, as evidence of awareness of its potential infringement (Compl. ¶56).
VII. Analyst’s Conclusion: Key Questions for the Case
The resolution of this dispute may turn on the following central questions:
- A core issue will be one of definitional scope: does a system that performs comprehensive genomic sequencing of hundreds of genes meet the claim limitation of being "configured to assay" a specific, enumerated panel of seven or eight molecular targets? The case may depend on whether testing a superset of genes infringes a claim directed to a subset.
- A key evidentiary question will be one of technological correspondence: does Defendant’s next-generation sequencing (NGS) platform function in the same or an equivalent way as the "device configured to assay" described in the patents, which are primarily exemplified by microarray and IHC technologies?
- A threshold legal question may concern patent eligibility: whether the asserted system claims—which recite steps of assaying molecular data, accessing a database for comparison, and generating a report with therapeutic suggestions—are directed to patent-eligible subject matter under 35 U.S.C. § 101 or to an abstract idea.