PTAB

IPR2019-00164

Foundation Medicine Inc v. Caris MPI Inc

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Key Events
Petition

1. Case Identification

2. Patent Overview

  • Title: System for Generating a Report Identifying Potential Cancer Therapeutics
  • Brief Description: The ’350 patent is directed to a system for generating a report that identifies potential cancer therapeutics based on an individual's molecular profile. The system analyzes a plurality of molecular targets, compares them to reference values in a database, matches molecular aberrations to known therapies, and generates a report.

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 taught a computerized decision support system for cancer treatment that met most limitations of claim 1. Lu’s system analyzed a patient’s molecular profile (e.g., gene expression), compared it to a database of known mutations and drug outcomes, and generated a report with recommended therapies. However, Lu only expressly disclosed assaying some of the molecular targets required by claim 1 (ESR1 and EGFR). Petitioner asserted that Illumina, a technical bulletin describing a commercially available 502-gene cancer panel, supplied the missing targets. Illumina’s DASL Cancer Panel specifically included all seven targets recited in claim 1: EGFR, KIT, TOP1, MLH1, PTEN, PDGFRA, and ESR1. The combination of Lu’s system with Illumina’s comprehensive gene panel allegedly rendered all limitations of independent claim 1 obvious. Petitioner further argued the combination taught the limitations of dependent claims 2-14, which add conventional features like remote data input, electronic reports, and analysis of post-therapy samples.
    • Motivation to Combine: Petitioner contended a person of ordinary skill in the art (POSA) would combine Lu and Illumina to improve the capabilities of Lu's system. Lu’s system used lower-throughput methods like RT-PCR, while Illumina disclosed a more advanced microarray capable of assaying hundreds of gene targets simultaneously, efficiently, and at a lower cost per target. A POSA seeking to create a comprehensive molecular profiling tool, a recognized goal in personalized medicine, would have been motivated to incorporate Illumina’s well-vetted panel of high-priority cancer genes into Lu's foundational analysis and reporting framework to achieve a more powerful and clinically relevant diagnostic system.
    • Expectation of Success: A POSA would have had a reasonable expectation of success. Both references addressed the same technical field of personalized oncology. The technologies involved—microarrays, gene expression analysis, and computerized databases—were well-known and their integration was routine. Illumina’s DASL Assay was commercially available and explicitly designed for the type of expression profiling described conceptually in Lu.

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 specifically addressed dependent claims 2 and 3, which require that molecular profile test values be input into the system from a remote location (claim 2) and over an internet connection (claim 3). Petitioner argued that while Lu and Illumina taught the core system of claim 1, Muraca explicitly disclosed these networking features. Muraca described a specimen-linked database system that was "accessible remotely by the user" through a network and noted the user device could comprise an "Internet browser, for accessing the network."
    • Motivation to Combine: A POSA would have been motivated to add Muraca's remote access capabilities to the Lu/Illumina system for practical and well-understood reasons. Implementing remote and internet-based data input would maximize the system's utility by allowing clinicians and researchers at different physical locations to access and contribute to the database. This arrangement was a common and logical design choice for health information systems by 2006 to facilitate collaboration and broaden data accessibility.
    • Expectation of Success: Success was predictable, as creating networked database systems with remote and web-based interfaces was a conventional and well-established practice in information technology and bioinformatics at the time.

Ground 3: Claims 7, 11, and 12 are obvious over Lu, Illumina, and McDoniels-Silvers

  • Prior Art Relied Upon: Lu, Illumina, and McDoniels-Silvers (a 2002 peer-reviewed journal article).
  • Core Argument for this Ground:
    • Prior Art Mapping: This ground targeted dependent claims reciting that the molecular profile is determined after an individual has received drug therapy (claim 7) or after the individual has been treated and failed to respond to a cancer therapeutic (claims 11 and 12). Petitioner asserted that McDoniels-Silvers taught these limitations. McDoniels-Silvers described analyzing gene expression profiles from lung cancer patients, including samples from a patient "previously treated with chemotherapy five times" and another "treated with radiation," implicitly teaching analysis of patients who had failed prior therapies.
    • Motivation to Combine: A POSA would have been motivated to apply the Lu/Illumina diagnostic system in the post-treatment context described by McDoniels-Silvers. It was a vital and common practice in oncology to monitor patients during and after treatment to assess therapeutic efficacy, detect resistance, and guide subsequent treatment decisions. Applying a comprehensive molecular profiling tool like the combined Lu/Illumina system to monitor treatment response was a natural and obvious extension of its use, allowing clinicians to make more informed decisions when initial therapies failed.
    • Expectation of Success: There was a high expectation of success, as the underlying assay techniques (microarrays) were equally applicable to pre- and post-treatment patient samples. The practice of monitoring biomarkers after therapy was standard in oncology, ensuring a POSA would know how to implement such a system.

4. Relief Requested

  • Petitioner requested the institution of an inter partes review and cancellation of claims 1-14 of the ’350 patent as unpatentable under 35 U.S.C. §103.