PTAB

IPR2023-00317

Foresight Diagnostics Inc v. Personalis Inc

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Petition
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1. Case Identification

2. Patent Overview

  • Title: Methods and Systems for Genetic Analysis
  • Brief Description: The ’033 patent describes methods for analyzing nucleic acid samples to aid in disease diagnosis, monitoring, and treatment. The claimed method involves producing capture probes for known genetic polymorphisms using a database, contacting a biological sample with the probes, sequencing the captured nucleic acids, and repeating the process on subsequent samples from the same individual.

3. Grounds for Unpatentability

Ground 1: Anticipation by Forshew - Claims 1-7 and 10-23 are anticipated by Forshew.

  • Prior Art Relied Upon: Forshew (a May 2012 article in Science Translational Medicine).
  • Core Argument for this Ground:
    • Prior Art Mapping: Petitioner argued that Forshew disclosed every limitation of the challenged claims. Forshew described a tagged-amplicon deep sequencing (TAm-Seq) method for identifying and monitoring cancer mutations by analyzing plasma DNA from cancer patients. This method involved designing PCR primers (“capture probes”) using a computer program (Primer3) and information from a public mutation database (COSMIC) to target genes with known biomedically interpretable variants. Forshew then contacted patient plasma samples with these primers, conducted sequencing on the resulting amplified DNA, and repeated the workflow on samples taken over time from patients to monitor tumor dynamics. Petitioner asserted this process directly maps to the steps recited in the independent and dependent claims.

Ground 2: Obviousness over Forshew in view of Wagle - Claims 1-23 are obvious over Forshew in view of Wagle.

  • Prior Art Relied Upon: Forshew (a 2012 article) and Wagle (a 2012 article in Cancer Discovery).
  • Core Argument for this Ground:
    • Prior Art Mapping: Petitioner asserted that Forshew taught the core method of longitudinal cancer mutation monitoring using a PCR-based capture system. Wagle taught a similar targeted sequencing approach for detecting genomic alterations but used an alternative, well-known technique of solution-based hybridization with "RNA baits" for target enrichment ("exon capture"). To the extent Forshew’s PCR primers were not considered "capture probes," Wagle disclosed this element. Wagle also disclosed using capture probes in a hybridization array and on solid surfaces like beads, mapping to limitations in claims 8 and 9.
    • Motivation to Combine: A POSITA would combine these references because Forshew cited Wagle, indicating their direct relevance. Wagle presented its hybridization capture method as a known alternative to PCR-based techniques like Forshew's, and a POSITA would have found it obvious to substitute Wagle's well-known hybridization probes for Forshew's PCR primers. The techniques were known to have overlapping applicability and were often used interchangeably for target enrichment.
    • Expectation of Success: A POSITA would have a reasonable expectation of success, as both PCR-based capture and hybridization-based capture were well-established and widely used techniques for enriching target DNA sequences prior to sequencing, with numerous publications demonstrating their effectiveness.

Ground 3: Obviousness over Wagle in view of Chan - Claims 1-9 and 11-23 are obvious over Wagle in view of Chan.

  • Prior Art Relied Upon: Wagle (a 2012 article) and Chan (a 2013 article in Clinical Chemistry).
  • Core Argument for this Ground:
    • Prior Art Mapping: Petitioner argued Wagle taught the foundational method of using hybridization-based capture probes (RNA baits) designed with computer aid to target a panel of "druggable" or "actionable" cancer-related genes from static tumor tissue samples. Chan supplied the missing element of longitudinal monitoring, expressly teaching the use of solution-phase hybridization to serially track tumor-associated polymorphisms in patient plasma over time, including taking samples before and after surgery to monitor cancer non-invasively.
    • Motivation to Combine: A POSITA would be motivated to apply Chan's teaching of longitudinal plasma monitoring to Wagle's robust hybridization capture method. Chan explicitly suggested that a targeted approach, like Wagle's, could be used for serial monitoring of specific mutations to achieve better cancer management. This combination would create a powerful system for non-invasively tracking actionable mutations in patient plasma over time, an explicit goal in the art.
    • Expectation of Success: Success would be expected because the combination merely involved applying a known monitoring protocol (from Chan) to a proven capture and sequencing technology (from Wagle). Chan itself noted that solution-phase hybridization-based capture approaches had already been successfully used for other diagnostic purposes.

4. Key Claim Construction Positions

  • Petitioner argued for constructions of key terms to support its invalidity grounds and asserted that no other terms required express construction.
  • "capture probe": Petitioner asserted this term should be construed broadly to encompass both PCR primer capture probes (as disclosed in Forshew) and solution-based hybridization capture probes or "baits" (as disclosed in Wagle), reflecting the common understanding of a POSA at the time.
  • "biomedical report": Petitioner contended that the claim 2 limitation of "generating a biomedical report" should be given no patentable weight under the printed matter doctrine. The argument was that this step merely recites the content of information and is not functionally related to the underlying physical steps of the method.

5. Relief Requested

  • Petitioner requested the institution of an inter partes review and the cancellation of all challenged claims 1-23 of Patent 11,408,033 as unpatentable.