Foundation Medicine Inc v. Caris MPI Inc

1. Case Identification

• Case #: IPR2019-00171
• Patent #: 9,383,365
• Petitioner(s): Foundation Medicine, Inc.
• Patent Owner(s): Caris MPI, Inc.
• Challenged Claims: 1-14

2. Patent Overview

• Title: System for Generating a Report Identifying Potential Cancer Therapeutics
• Brief Description: The ’365 patent discloses a system for personalized cancer treatment. The system analyzes a patient's molecular profile for a plurality of molecular targets, compares the profile to reference values in a database, and generates a report identifying potential cancer therapies based on detected molecular aberrations.

3. Grounds for Unpatentability

Ground 1: Claims 1-14 are obvious over Lu in view of Illumina.

• Prior Art Relied Upon: Lu (International Publication No. WO 03/017038) and Illumina (a 2005 commercial technical bulletin).
• Core Argument for this Ground:
  • Prior Art Mapping: Petitioner argued that Lu teaches the core system of independent claim 1, including a device to assay molecular targets, a database with reference values and therapeutic information, and software to compare data and generate a report recommending treatment. However, Lu only explicitly mentions assaying a subset of the claimed molecular targets (e.g., EGFR and ERBB2). Illumina, which describes a commercial 502-gene cancer panel, discloses a device configured to assay a plurality of molecular targets that expressly includes all seven targets recited in claim 1 (EGFR, KIT, TOP1, MLH1, PTEN, PDGFRA, and ERBB2). Petitioner contended that the combination of Lu's system with Illumina's comprehensive gene panel teaches every limitation of claim 1. The limitations of dependent claims 2-14 were argued to be disclosed or rendered obvious by Lu and Illumina as well, covering aspects like remote data input, report formatting, and specific assay types (e.g., microarrays).
  • Motivation to Combine: A Person of Ordinary Skill in the Art (POSA) would combine Lu and Illumina to improve the diagnostic and therapeutic utility of Lu’s system. The goal of personalized medicine was to obtain comprehensive molecular profiles. A POSA would have been motivated to replace Lu’s lower-throughput RT-PCR method with Illumina's more efficient and comprehensive microarray assay, which could test for hundreds of well-established cancer biomarkers simultaneously. Incorporating Illumina's widely recognized cancer gene panel would make Lu's system more powerful and clinically relevant.
  • Expectation of Success: A POSA would have had a reasonable expectation of success. Both Lu's system and Illumina's microarray technology were well-established methods for molecular profiling. Combining a known panel of cancer gene targets (Illumina) with a known computerized decision support system (Lu) involved the application of routine and predictable technologies.

Ground 2: Claims 2 and 3 are obvious over Lu, Illumina, and Muraca.

• Prior Art Relied Upon: Lu, Illumina, and Muraca (Application # 2002/0150966).
• Core Argument for this Ground:
  • Prior Art Mapping: This ground builds on Ground 1 to specifically address the limitations of claims 2 and 3, which require that molecular profile test values be input into the system from a remote location, potentially over an internet connection. Petitioner asserted that Muraca explicitly discloses a specimen-linked database system where users can remotely access and add information through a network using an internet browser.
  • Motivation to Combine: If the Lu and Illumina combination was found not to teach remote data input, a POSA would have been motivated to incorporate Muraca's teachings. The ability to input and access data remotely was a well-known and highly desirable feature for bioinformatics systems, as it maximized access to widespread databases and facilitated collaboration. Combining the Lu/Illumina profiling system with Muraca's conventional remote access functionality would have been a logical and predictable improvement.
  • Expectation of Success: Given that web-accessible databases were conventional technology by 2006, integrating remote input capabilities into the Lu/Illumina system would have been a routine task with a high expectation of success.

Ground 3: Claims 7 and 11 are obvious over Lu, Illumina, and McDoniels-Silvers.

• Prior Art Relied Upon: Lu, Illumina, and McDoniels-Silvers (a 2002 scientific paper).
• Core Argument for this Ground:
  • Prior Art Mapping: This ground addresses the limitations of claims 7 and 11, which specify that the molecular profile is determined after an individual has received drug therapy (claim 7) and potentially failed to respond to that therapy (claim 11). Petitioner argued that McDoniels-Silvers discloses obtaining molecular profiles via microarray from lung cancer patients who had been previously treated with radiation and chemotherapy.
  • Motivation to Combine: A POSA would have been motivated to apply the Lu/Illumina system in the manner taught by McDoniels-Silvers to monitor a patient's response to treatment. This was a common and vital practice in oncology to assess whether a therapy was effective and to guide subsequent treatment decisions. Using a comprehensive molecular profiling tool for this purpose was a logical extension of existing clinical practice.
  • Expectation of Success: Monitoring cancer biomarkers during and after treatment was a well-established practice. Applying the combined Lu/Illumina profiling system to this known clinical need would have been a straightforward application of existing technologies with a predictable outcome.

4. Key Claim Construction Positions

• "likely benefit of the at least one therapeutic agent": Petitioner argued that based on the specification and the prosecution history of a related patent, this term should be interpreted broadly to mean any therapeutic agent with "potential efficacy." The ’365 patent itself provides no specific definition or working examples, referring only to agents "capable of interacting" with gene targets. This broad interpretation allows prior art systems that link molecular profiles to drugs with known potential efficacy, like Lu, to meet the claim limitation.

5. Relief Requested

• Petitioner requested the institution of an inter partes review and the cancellation of claims 1-14 of the ’365 patent as unpatentable under 35 U.S.C. §103.