Geneoscopy Inc v. Exact Sciences Corp

1. Case Identification

• Case #: IPR2024-01330
• Patent #: 11,970,746
• Filed: August 20, 2024
• Petitioner(s): Geneoscopy, Inc.
• Patent Owner(s): Exact Sciences Corporation
• Challenged Claims: 1-4, 12-19

2. Patent Overview

• Title: Methods of Preparing Fecal Samples for Analysis
• Brief Description: The ’746 patent discloses methods for processing a fecal sample for colorectal cancer screening. The core method involves separating a freshly collected sample into two portions without freezing, where one portion is combined with a DNA-stabilizing buffer and the other is combined with a blood protein-stabilizing buffer, allowing for separate nucleic acid and blood protein diagnostic tests.

3. Grounds for Unpatentability

Ground I: Claims 1-4 and 14-19 are obvious over Lenhard in view of Itzkowitz and Vilkin.

• Prior Art Relied Upon: Lenhard (a 2005 journal article), Itzkowitz (a 2007 journal article), and Vilkin (a 2005 journal article).
• Core Argument for this Ground:
  • Prior Art Mapping: Petitioner argued that Lenhard taught the foundational method of detecting colorectal cancer (CRC) by separating a stool sample into two aliquots and performing a DNA methylation test on one and a fecal occult blood test (FOBT) on the other. However, Lenhard used an older guaiac-based FOBT (gFOBT) and did not detail at-home collection with stabilizing buffers. Petitioner asserted that a Person of Ordinary Skill in the Art (POSA) would have modified Lenhard’s method by incorporating the superior technologies of Vilkin and Itzkowitz. Vilkin taught replacing the gFOBT with a more sensitive and quantitative immunochemical FOBT (iFOBT) that uses a hemoglobin-stabilizing buffer for sample transport. Itzkowitz taught an at-home fecal collection method using a sealable container and a DNA-stabilizing buffer to prevent degradation during shipment without freezing. The combination of these three references allegedly taught every element of the challenged claims.
  • Motivation to Combine: A POSA would combine these references to improve the known assay of Lenhard. Vilkin’s iFOBT offered clear advantages over Lenhard’s gFOBT, including higher sensitivity and no need for patient dietary restrictions. Itzkowitz’s method for at-home collection with a DNA stabilizer offered improved patient convenience and sample integrity, increasing the sensitivity of the DNA test. Combining these known elements was presented as a predictable solution to improve a known diagnostic method.
  • Expectation of Success: A POSA would have had a reasonable expectation of success because the combination involved substituting improved, well-established components (iFOBT, stabilizing buffers) into an existing, proven framework for dual-marker fecal analysis.

Ground II: Claims 1-4 and 14-19 are obvious over Shuber and Vilkin.

• Prior Art Relied Upon: Shuber (International Application # WO 2005/113769) and Vilkin (a 2005 journal article).
• Core Argument for this Ground:
  • Prior Art Mapping: Petitioner contended that Shuber taught a method for preparing a fecal sample for DNA analysis by depositing it into a sealable container with a DNA stabilizing solution, which could then be shipped to a lab without freezing. Vilkin taught a method for iFOBT analysis where a portion of a fecal sample is collected in a separate sealable container with a hemoglobin-stabilizing buffer. Petitioner argued that combining these two established at-home collection and testing methods would result in the claimed method: collecting a stool sample, separating it into a first portion for DNA analysis (per Shuber) and a second for blood protein analysis (per Vilkin), each in its own stabilized and sealed container.
  • Motivation to Combine: A POSA would have been motivated to combine a DNA-based test like Shuber's with a blood-based test like Vilkin's to create a CRC diagnostic test with improved sensitivity. The petition cited multiple sources showing it was well understood in the art by the priority date that combining DNA and blood protein assays improved overall detection rates for CRC.
  • Expectation of Success: The expectation of success was argued to be high, as it required only the concurrent use of two known, commercially practiced assays on separate portions of a single fecal sample, a routine and predictable practice in the field of diagnostics.

Ground III: Claims 1 and 2 are anticipated by Inbar.

• Prior Art Relied Upon: Inbar (International Application # WO 97/25925).

• Core Argument for this Ground:

  • Prior Art Mapping: Petitioner asserted that Inbar, a 1997 patent application, disclosed every element of claims 1 and 2. Inbar described a system for collecting a stool sample at home and using a sampling device to transfer multiple specimens into separate, sealable containers. Each container held a different "preservation medium" suitable for the specific assay to be performed, such as detecting "cryptic blood" or microorganisms. Inbar explicitly taught that the preservation medium should prevent the deterioration of the substance being tested. This system of collecting, separating, and separately preserving two portions of a single stool sample in different stabilizing buffers was argued to be an express disclosure of the method of claim 1. As Inbar also taught shipping the sealed containers to a laboratory for testing, it was argued to anticipate claim 2 as well.

• Additional Grounds: Petitioner asserted additional obviousness challenges, including combining the references of Ground I with Kanaoka (Application # US 2006/0216714) to teach RNA analysis (claims 12-13) and combining the references of Ground II with Kanaoka for the same purpose. Further grounds alleged obviousness by combining Inbar with Shuber and Vilkin, with and without Kanaoka, arguing it would have been obvious to use Inbar's collection system to perform the specific assays taught by the other references.

4. Key Claim Construction Positions

• Petitioner argued that the claim term "determining expression from a human gene" (recited in claim 4) should be construed to include testing for indirect indicators of gene expression. Specifically, because dependent claims 5 and 6 recite epigenetically-modified and methylated DNA, the broader term in claim 4 must encompass these DNA-based tests, which measure markers that result in diminished gene expression.

5. Arguments Regarding Discretionary Denial

• Petitioner argued that the Board should not exercise its discretion to deny institution under §325(d). Although the asserted prior art was listed in an Information Disclosure Statement (IDS) during prosecution, it was never substantively evaluated or used in a rejection by the Examiner. Petitioner contended this constituted a material error by the USPTO, evidenced by the fact that the Board recently instituted IPR (IPR2024-00459) on the parent ’781 patent based on the same prior art and arguments presented in Grounds I-IV of this petition. Petitioner argued that because the challenged claims of the ’746 patent are broader than those of the parent, the Board's prior institution decision confirms the Examiner's error in allowing the claims.

6. Relief Requested

• Petitioner requested institution of an inter partes review and cancellation of claims 1-4 and 12-19 of the ’746 patent as unpatentable.