PTAB

IPR2014-01310

GeneDx Inc v. Myriad Genetics Inc

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Key Events
Petition
petition

1. Case Identification

2. Patent Overview

  • Title: Consensus Sequence of the Human BRCA1 Gene
  • Brief Description: The ’155 patent is directed to methods for genetic testing related to the human BRCA1 gene. The challenged claims cover methods for identifying an individual's susceptibility to breast or ovarian cancer by detecting the presence or absence of seven specific polymorphisms in the BRCA1 coding sequence and comparing them to a reference consensus sequence (SEQ. ID. NO: 1).

3. Grounds for Unpatentability

Ground 1: Claims 2 and 4 are obvious over Friedman in view of Miki.

  • Prior Art Relied Upon: Friedman (a December 1994 journal article, "Confirmation of BRCA1 by analysis of germline mutations...") and Miki (an October 1994 journal article, "A Strong Candidate for the Breast and Ovarian Cancer Susceptibility Gene BRCA1").
  • Core Argument for this Ground:
    • Prior Art Mapping: Petitioner argued that Friedman and Miki collectively disclosed all elements of the claimed methods. Friedman taught methods of identifying both cancer-predisposing mutations and non-disease-causing polymorphisms in the BRCA1 gene by amplifying and sequencing an individual's DNA and comparing it to a reference. Friedman specifically disclosed five of the seven polymorphisms recited in the challenged claims. Miki similarly taught methods of screening for BRCA1 variants and disclosed the remaining two polymorphisms recited in the claims. Claim 2 covers a method for identifying a BRCA1 sequence not associated with cancer based on the presence of the seven polymorphisms, while claim 4 covers detecting increased susceptibility based on the absence of those specific polymorphisms in favor of a mutation. Petitioner asserted that both references teach the fundamental concept of distinguishing benign polymorphisms from harmful mutations.
    • Motivation to Combine: Petitioner contended a person of ordinary skill in the art (POSITA) would combine the teachings of Friedman and Miki to create a more comprehensive basis for genetic testing. A POSITA would have known that creating a consensus sequence—a sequence representing the most common nucleotides at polymorphic locations—was a natural and useful starting point for distinguishing benign variants from disease-causing mutations. Upon reviewing Friedman's disclosure of several polymorphisms, a POSITA would have been motivated to consult other contemporary literature, such as Miki, to identify additional known polymorphisms to develop a more accurate consensus sequence for diagnostic use.
    • Expectation of Success: A POSITA would have had a reasonable expectation of success because Friedman and Miki disclosed all seven required polymorphic sites and described using conventional, well-understood laboratory techniques (e.g., PCR, dideoxy sequencing) to identify them. Combining the known polymorphisms from these two sources into a single consensus sequence was presented as a straightforward design choice, not a complex undertaking.

Ground 2: Claims 2 and 4 are obvious over Friedman in view of Bowcock.

  • Prior Art Relied Upon: Friedman (as in Ground 1) and Bowcock (a 1993 journal article, "Molecular Cloning of BRCA1: a gene for early onset familial breast and ovarian cancer").
  • Core Argument for this Ground:
    • Prior Art Mapping: This ground relied on Friedman for its disclosure of specific polymorphisms and sequencing methods, but used Bowcock to establish a broader motivation and roadmap for characterizing the BRCA1 gene. Bowcock described the importance and general methodology for identifying BRCA1 mutations, including positional cloning, PCR amplification, and DNA sequencing. Crucially, Bowcock taught that once a variant is detected, "one needs to confirm that it is not a polymorphism," establishing the need to distinguish between benign and harmful genetic variations. Friedman’s work was presented as a direct and successful application of the methods and goals outlined in Bowcock.
    • Motivation to Combine: Petitioner argued that Bowcock provided a clear roadmap and compelling rationale for identifying and characterizing the BRCA1 gene for cancer screening. A POSITA, guided by Bowcock's teachings on the importance of filtering out polymorphisms, would have looked to contemporary research that was actively implementing this roadmap. Friedman represented such research, having successfully used the techniques described by Bowcock to identify five specific polymorphisms. The teachings of Bowcock would have urged a POSITA to build upon Friedman's initial findings by seeking to identify additional polymorphisms to achieve a more complete characterization of the gene locus, thereby creating a robust consensus sequence for genetic testing.
    • Expectation of Success: A POSITA would have had a high expectation of success because Bowcock taught conventional and well-understood methods, and Friedman demonstrated the successful application of those very methods to the BRCA1 gene. This demonstrated success would have encouraged a POSITA to follow the same path to identify the remaining common polymorphisms using routine and predictable techniques. Petitioner also argued that any "obvious to try" counterargument would fail because the prior art provided clear direction and involved a finite number of predictable solutions, not a vague exploration.

4. Key Claim Construction Positions

  • "SEQ. ID. NO: 1": Petitioner argued that this term should be construed as "a consensus sequence, the sequence of which is listed in the patent." The patent specification describes this sequence as having been "determined by calculating the percentage of occurrence of each polymorphism and inserting the more frequently occurring polymorphism into the published BRCA1" sequence. This construction was central to Petitioner's obviousness argument, framing the creation of the claimed sequence as the routine and obvious step of compiling known polymorphisms from the prior art into a reference sequence.

5. Relief Requested

  • Petitioner requests institution of an inter partes review and cancellation of claims 2 and 4 of Patent 5,654,155 as unpatentable under 35 U.S.C. §103.