PTAB

IPR2019-00203

Foundation Medicine Inc v. Caris MPI Inc

Log In
Key Events
Petition
petition

1. Case Identification

2. Patent Overview

  • Title: System for Generating a Report Identifying Therapeutic Agents
  • Brief Description: The ’660 patent describes a system for generating a report that identifies potential therapeutic agents for an individual with lung cancer. The system works by analyzing the individual's molecular profile against a specific plurality of molecular targets and matching any identified aberrations with known therapies.

3. Grounds for Unpatentability

Ground 1: Obviousness of Claims 17 and 19 over Von Hoff, Bibikova, Illumina, and Gautam

  • Prior Art Relied Upon: Von Hoff (Application # 2008/0014146), Bibikova (a 2004 journal article), Illumina (a 2005 technical bulletin), and Gautam (a 2003 journal article).
  • Core Argument for this Ground:
    • Prior Art Mapping: Petitioner argued that the combination of Von Hoff, Bibikova, and Illumina taught all limitations of independent claim 1. Von Hoff disclosed a generic system for determining cancer therapies based on molecular profiling. Bibikova taught applying a similar microarray-based profiling method (the DASL Assay described in Illumina) specifically to lung cancer tissue. Illumina disclosed a cancer gene panel that included the specific molecular targets recited in claim 1 (PTEN, CTNNB1, cKIT, BRAF, and PIK3CA). For dependent claim 17, which adds the target RRM1, Petitioner asserted that Gautam taught RRM1 is an important biomarker for lung cancer. For dependent claim 19, which requires determining the RRM1 value via immunohistochemistry (IHC) testing, Petitioner pointed to Von Hoff’s disclosure of using IHC for molecular profiling.
    • Motivation to Combine: A POSITA would combine these references to solve the well-known problem of personalizing cancer treatment. Petitioner argued it would have been obvious to apply Von Hoff's general system to the specific context of lung cancer as taught by Bibikova. To improve the system, a POSITA would incorporate the comprehensive, high-priority gene panel from Illumina. Because Gautam identified RRM1 as a key biomarker in lung cancer suppression, a POSITA would have been motivated to add RRM1 to the panel to increase the system's diagnostic utility.
    • Expectation of Success: The underlying technologies, such as microarrays and IHC, were conventional and commercially available. Combining known biomarkers for a known purpose (lung cancer profiling) using standard, predictable techniques would have presented a POSITA with a reasonable expectation of success.

Ground 2: Obviousness of Claims 20 and 24 over Von Hoff, Bibikova, Illumina, and Gnirke

  • Prior Art Relied Upon: Von Hoff (Application # 2008/0014146), Bibikova (a 2004 journal article), Illumina (a 2005 technical bulletin), and Gnirke (a 2009 journal article).
  • Core Argument for this Ground:
    • Prior Art Mapping: This ground built upon the same combination for claim 1 as Ground 1, but added Gnirke to teach the limitations of claims 20 and 24. Claim 20 requires that the molecular profile test values be determined by sequencing. While Von Hoff and Illumina taught using microarrays for gene expression analysis, Gnirke taught using sequencing to obtain molecular data, including for targets captured using microarray-like techniques. Claim 24 requires the device be configured to identify specific types of nucleic acid variations (e.g., mutation, polymorphism, deletion). Gnirke explicitly taught that its targeted sequencing method could detect these variations.
    • Motivation to Combine: Petitioner argued a POSITA would have been motivated to substitute or supplement the microarray analysis of Von Hoff and Illumina with the sequencing methods of Gnirke to obtain more detailed genetic information. Sequencing can detect specific mutations (e.g., insertions, deletions) that are not discoverable by gene expression profiling alone, thus enriching the molecular profile and improving therapeutic matching. Gnirke itself disclosed adapting microarray hybridization techniques for targeted sequencing, suggesting a natural motivation to combine the technologies.
    • Expectation of Success: By the patent's priority date, sequencing was a mature and widely used technology. Gnirke demonstrated a successful and reliable method of combining hybridization capture with high-throughput sequencing. Therefore, a POSITA would have had a high expectation of success in applying this established technique to the known panel of cancer-related genes disclosed in Illumina.

Ground 3: Obviousness of Claim 21 over Von Hoff, Bibikova, Illumina, Gautam, and Gnirke

  • Prior Art Relied Upon: Von Hoff, Bibikova, Illumina, Gautam, and Gnirke.
  • Core Argument for this Ground:
    • Prior Art Mapping: This ground addressed claim 21, which depends on claim 17 (adding RRM1) and requires a hybrid analysis. Specifically, claim 21 requires (i) sequencing of the core molecular targets (PTEN, CTNNB1, etc.) and (ii) IHC analysis of PTEN and RRM1. Petitioner argued that Gnirke taught the sequencing element (i), as established in Ground 2. The IHC element (ii) was taught by Von Hoff, which disclosed using IHC to analyze protein expression for targets like PTEN. The inclusion of RRM1 in this IHC analysis was rendered obvious by Gautam, which taught a functional relationship between RRM1 and PTEN in lung cancer.
    • Motivation to Combine: A POSITA would combine sequencing and IHC to create a more robust diagnostic system. Petitioner asserted that sequencing provides gene-level information (mutations), while IHC provides protein-level information (expression), and that it was well known that gene expression is an inexact proxy for protein levels. Using both techniques provides complementary and confirmatory data. The known biological link between RRM1 and PTEN (per Gautam) would specifically motivate a POSITA to analyze both targets at both the gene and protein level to fully understand their role and identify therapeutic options.
    • Expectation of Success: All the constituent technologies were conventional. Combining them to generate complementary data sets was a routine and logical approach in biomedical research. A POSITA would have reasonably expected each well-known technology to function predictably within the combined system.

4. Key Technical Contentions (Beyond Claim Construction)

  • Priority Date Challenge: A central argument underpinning all grounds was that the ’660 patent was not entitled to a priority date earlier than February 12, 2010. Petitioner contended that prior applications in the patent's family lacked written description support for the claimed combination of molecular targets, specifically the required inclusion of CTNNB1. This effective priority date rendered Von Hoff (published 2008) and Gnirke (published 2009) available as prior art against the challenged claims.

5. Relief Requested

  • Petitioner requested institution of an inter partes review and cancellation of claims 17, 19-21, and 24 of the ’660 patent as unpatentable under 35 U.S.C. §103.