DCT

2:14-cv-00150

Counsyl Inc v. Myriad Genetics Inc

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I. Executive Summary and Procedural Information

  • Parties & Counsel:
  • Case Identification: 2:14-cv-00150, N.D. Cal., 09/20/2013
  • Venue Allegations: Plaintiff Counsyl alleges venue is proper in the Northern District of California because Defendant Myriad conducts substantial business in the district, employs a sales and marketing force, generates significant revenue, and has made substantial investments there.
  • Core Dispute: Plaintiff seeks a declaratory judgment that its genetic testing services for BRCA1 and BRCA2 genes do not infringe, and/or that the asserted claims are invalid, for eight of Defendant's patents related to genetic cancer susceptibility testing.
  • Technical Context: The technology involves methods and materials for detecting mutations in the human BRCA1 and BRCA2 genes, which are linked to a significantly increased hereditary risk for breast and ovarian cancer.
  • Key Procedural History: This declaratory judgment action was filed in the wake of the U.S. Supreme Court's decision in Association for Molecular Pathology v. Myriad Genetics, Inc., which invalidated claims directed to isolated human genomic DNA. The complaint alleges that Defendant has continued to aggressively enforce its remaining patent claims against other genetic testing companies, creating a controversy that necessitates this preemptive suit by Plaintiff.

Case Timeline

Date Event
1994-08-12 Earliest Priority Date for ’999, ’282, ’441, and ’497 Patents
1995-12-18 Earliest Priority Date for ’492, ’857, and ’379 Patents
1998-01-20 U.S. Patent No. 5,709,999 Issued
1998-04-02 Earliest Priority Date for ’721 Patent
1998-05-05 U.S. Patent No. 5,747,282 Issued
1998-05-19 U.S. Patent No. 5,753,441 Issued
1998-11-17 U.S. Patent No. 5,837,492 Issued
2000-03-07 U.S. Patent No. 6,033,857 Issued
2000-04-18 U.S. Patent No. 6,051,379 Issued
2005-10-04 U.S. Patent No. 6,951,721 Issued
2007-07-31 U.S. Patent No. 7,250,497 Issued
2013-06-13 U.S. Supreme Court decision in Association for Molecular Pathology v. Myriad Genetics, Inc.
2013-07-09 Myriad sues Ambry Genetics Corp. for patent infringement
2013-07-10 Myriad sues Gene by Gene, Ltd. for patent infringement
2013-09-20 Complaint for Declaratory Judgment Filed

II. Technology and Patent(s)-in-Suit Analysis

U.S. Patent No. 5,709,999 - "LINKED BREAST AND OVARIAN CANCER SUSCEPTIBILITY GENE"

The Invention Explained

  • Problem Addressed: The patent describes the challenge of identifying individuals with a genetic predisposition to breast and ovarian cancer, noting that a significant fraction of cases are attributable to inherited, dominant susceptibility genes (’999 Patent, col. 2:45-51). The background highlights the difficulty in localizing and isolating the specific gene, BRCA1, responsible for this susceptibility (’999 Patent, col. 4:10-21).
  • The Patented Solution: The invention claims to provide methods and materials for isolating and detecting the human BRCA1 gene and its mutations (’999 Patent, Abstract). The patent describes methods for analyzing a patient's BRCA1 gene sequence and comparing it to a wild-type sequence to identify alterations, which can be used to diagnose a predisposition to cancer (’999 Patent, col. 4:32-52).
  • Technical Importance: The identification of the BRCA1 gene and methods for detecting its mutations enabled the development of predictive genetic tests for one of the most significant forms of hereditary cancer risk (’999 Patent, col. 4:26-31).

Key Claims at a Glance

  • The complaint seeks a declaratory judgment of non-infringement and invalidity of independent claim 6 (Compl. ¶¶ 23, 27). Claim 6 depends on independent claim 1.
  • The essential elements of independent claim 1 are:
    • A method for detecting a germline alteration in a BRCA1 gene in a human subject which comprises
    • analyzing a sequence of a BRCA1 gene from a human sample or analyzing a sequence of BRCA1 RNA from the subject or a sequence of BRCA1 cDNA made from mRNA from said subject
    • and comparing the sequence with the wild-type BRCA1 gene or wild-type BRCA1 cDNA,
    • wherein a difference in the sequence of the BRCA1 gene, BRCA1 RNA or BRCA1 cDNA of the subject from wild-type indicates a germline alteration in said BRCA1 gene.
  • Claim 6 further specifies that the detection of a germline alteration is performed by "hybridizing a BRCA1 gene probe which specifically hybridizes to an allele of said BRCA1 gene isolated from said sample and detecting the presence of a hybridization product."

U.S. Patent No. 5,747,282 - "17Q-LINKED BREAST AND OVARIAN CANCER SUSCEPTIBILITY GENE"

The Invention Explained

  • Problem Addressed: As with the related ’999 Patent, this patent addresses the need for tools to diagnose susceptibility to breast and ovarian cancer linked to the BRCA1 gene (’282 Patent, col. 1:17-26).
  • The Patented Solution: The invention claims the purified, isolated DNA molecules that code for the BRCA1 protein (’282 Patent, Abstract). Specifically, it claims the isolated DNA having the nucleotide sequence of the BRCA1 gene (SEQ ID NO:1) and the DNA that codes for the corresponding amino acid sequence (SEQ ID NO:2) (’282 Patent, col. 154:62-65, col. 155:1-3).
  • Technical Importance: The isolation and claiming of the DNA sequence itself was a foundational step for creating diagnostic tools like probes and primers, as well as for research into the gene's function and potential therapeutic applications (’282 Patent, col. 4:27-31).

Key Claims at a Glance

  • The complaint seeks a declaratory judgment of non-infringement and invalidity of claims 5 and 6 (Compl. ¶¶ 31, 35). These claims depend on independent claims 1 and 2.
  • The essential elements of the base independent claims are:
    • Claim 1: An isolated DNA coding for a BRCA1 polypeptide, said polypeptide having the amino acid sequence set forth in SEQ ID NO:2.
    • Claim 2: The isolated DNA of claim 1, wherein said DNA has the nucleotide sequence set forth in SEQ ID NO:1.
  • Claims 5 and 6 respectively claim "An isolated DNA having at least 15 nucleotides of the DNA of claim 1" and "An isolated DNA having at least 15 nucleotides of the DNA of claim 2."

U.S. Patent No. 5,753,441 - "17Q-LINKED BREAST AND OVARIAN CANCER SUSCEPTIBILITY GENE"

  • Technology Synopsis: Belonging to the same family as the ’999 and ’282 patents, this patent also relates to methods and materials for detecting the BRCA1 gene and its mutations to diagnose predisposition to breast and ovarian cancer. The claims cover various methods for screening and detecting alterations (’441 Patent, col. 155:15-158:48).
  • Asserted Claims: Claims 8, 23, and 33 (Compl. ¶¶ 39, 43).
  • Accused Features: Plaintiff's "genetic sequencing and analysis of the BRCA1 gene" (Compl. ¶ 41).

U.S. Patent No. 6,951,721 - "METHOD FOR DETERMINING THE HAPLOTYPE OF A HUMAN BRCA1 GENE"

  • Technology Synopsis: This patent describes methods for determining the haplotype of a human BRCA1 gene by analyzing multiple polymorphic sites. This information is presented as useful for distinguishing between different "normal" alleles and identifying those associated with cancer risk.
  • Asserted Claims: Claim 5 (Compl. ¶¶ 47, 51).
  • Accused Features: Plaintiff's "genetic sequencing and analysis of the BRCA1 gene" (Compl. ¶ 49).

U.S. Patent No. 7,250,497 - "LARGE DELETIONS IN HUMAN BRCA1 GENE AND USE THEREOF"

  • Technology Synopsis: This patent discloses the discovery of large deletions in the BRCA1 gene and provides methods for detecting these specific genetic variants. The presence of these large deletions is alleged to indicate a predisposition to breast and ovarian cancer.
  • Asserted Claims: Claims 1-20 (Compl. ¶¶ 55, 59).
  • Accused Features: Plaintiff's "genetic sequencing and analysis of the BRCA1 gene" (Compl. ¶ 57).

U.S. Patent No. 5,837,492 - "CHROMOSOME 13-LINKED BREAST CANCER SUSCEPTIBILITY GENE"

  • Technology Synopsis: This patent relates to the BRCA2 gene, a second major gene associated with hereditary breast cancer. The invention covers isolated DNA molecules for the BRCA2 gene, as well as methods for their use in diagnosing predisposition to cancer.
  • Asserted Claims: Claims 5, 9, 29, and 30 (Compl. ¶¶ 21, 63, 67).
  • Accused Features: Plaintiff's "genetic sequencing and analysis of the BRCA2 gene" (Compl. ¶ 65).

U.S. Patent No. 6,033,857 - "CHROMOSOME 13-LINKED BREAST CANCER SUSCEPTIBILITY GENE"

  • Technology Synopsis: This patent, also related to the BRCA2 gene, claims methods for screening for alterations in the BRCA2 gene by comparing a sample sequence to the wild-type sequence. It also claims specific primers for use in analyzing the gene.
  • Asserted Claims: Claim 4 (Compl. ¶¶ 21, 71, 75).
  • Accused Features: Plaintiff's "genetic sequencing and analysis of the BRCA2 gene" (Compl. ¶ 73).

U.S. Patent No. 6,051,379 - "CANCER SUSCEPTIBILITY MUTATIONS OF BRCA2"

  • Technology Synopsis: This patent claims isolated nucleic acids that contain specific, enumerated mutations of the BRCA2 gene. It also covers methods of detecting these specific mutations.
  • Asserted Claims: Claims 1-25, 40-42 (Compl. ¶¶ 22, 79, 83).
  • Accused Features: Plaintiff's "genetic sequencing and analysis of the BRCA2 gene" (Compl. p.12, ¶1).

III. The Accused Instrumentality

Product Identification

  • The accused instrumentalities are Plaintiff Counsyl's "genetic tests and related services related to sequencing and analysis of BRCA1 and BRCA2 genes" (Compl. ¶ 5).

Functionality and Market Context

  • The complaint describes Counsyl as a "technology company in the United States focusing on the development of genetic testing and services for various hereditary diseases and traits" (Compl. ¶ 2). It alleges that Counsyl has made a "substantial research and development investment in improving genetic tests and providing more access at lower cost" (Compl. ¶ 16). The complaint does not provide sufficient detail for analysis of the specific technical steps or processes used in its genetic testing services. No probative visual evidence provided in complaint.

IV. Analysis of Infringement Allegations

The complaint is for a declaratory judgment of non-infringement and does not contain affirmative infringement allegations or a claim chart. Instead, it makes blanket denials of infringement for the asserted claims. For example, regarding the ’999 Patent, the complaint states that Counsyl "has not directly or indirectly infringed and is not directly or indirectly infringing claim 6 of the ’999 patent" (Compl. ¶ 24). Similar denials are made for all other patents-in-suit. The complaint does not specify which elements of the claims are not met by its services.

  • Identified Points of Contention:
    • Scope Questions: A primary question for the method claims (e.g., ’999 Patent, claim 6) will be whether the terms "analyzing" and "comparing" can be construed to read on modern, automated DNA sequencing and bioinformatics pipelines, or if they imply a more limited set of laboratory techniques contemplated at the time of invention. For the composition claims (e.g., ’282 Patent, claims 5 and 6), a central question is whether the term "isolated DNA" can be validly construed to cover synthetic DNA primers used in a diagnostic process, an issue at the heart of the Supreme Court's Myriad decision.
    • Technical Questions: What evidence does the complaint provide that its "sequencing and analysis" methods avoid the specific steps claimed in Myriad's patents? For instance, with respect to claim 6 of the ’999 Patent, a key technical question is whether Counsyl's process utilizes a "BRCA1 gene probe" for hybridization to detect an alteration, as opposed to other methods like direct sequencing. The complaint does not offer this level of technical detail.

V. Key Claim Terms for Construction

  • The Term: "isolated DNA" (’282 Patent, claim 1)

  • Context and Importance: The patentability of claims to "isolated DNA" was the central issue in Association for Molecular Pathology v. Myriad Genetics, Inc. The Supreme Court held that isolated genomic DNA is not patent-eligible subject matter, but that complementary DNA (cDNA) may be. The construction of this term is therefore critical to the validity of the ’282 Patent's asserted claims, which cover DNA fragments of at least 15 nucleotides and could be interpreted to read on primers or probes used in diagnostic testing.

  • Intrinsic Evidence for Interpretation:

    • Evidence for a Broader Interpretation: The specification defines "isolated" or "substantially pure" DNA as being "substantially separated from other cellular components which naturally accompany a native human sequence" (’282 Patent, col. 19:8-12). This language could be argued to encompass any DNA molecule, including a synthetic primer, that is not in its natural cellular environment.
    • Evidence for a Narrower Interpretation: Practitioners may argue that in light of the Supreme Court's ruling, the term cannot be construed to cover any DNA sequence, however purified, whose nucleotide sequence is identical to one found in nature. The abstract distinguishes between the BRCA1 gene and its "mutant alleles," suggesting the claims are directed to naturally occurring sequences (’282 Patent, Abstract).

  • The Term: "analyzing a sequence" (’999 Patent, claim 1)

  • Context and Importance: This term defines a core step of the asserted method claim. Its interpretation will determine whether modern high-throughput sequencing methods, which may not have existed at the time of the invention, fall within the claim's scope. Furthermore, if "analyzing" is construed to include a mental step of diagnosis, the claim's validity could be challenged under the prohibition against patenting abstract ideas.

  • Intrinsic Evidence for Interpretation:

    • Evidence for a Broader Interpretation: The detailed description lists numerous methods for detecting mutations, including "direct DNA sequencing," suggesting "analyzing" should be read broadly to cover various techniques for determining the order of nucleotides in a sample (’999 Patent, col. 13:5-15).
    • Evidence for a Narrower Interpretation: The patent's summary states the invention relates to the "diagnosis of predisposition to breast and ovarian cancer" (’999 Patent, col. 4:38-39). This may support a narrower construction requiring that "analyzing" be part of a diagnostic, rather than merely informational, process.

VI. Other Allegations

  • Indirect Infringement: Counsyl seeks a declaration that it has not "induced infringement of, or contributed to the infringement of" the asserted claims (Compl., p. 12, Prayer for Relief, ¶A). The complaint does not provide specific facts to support its assertion of non-infringement by inducement or contributory infringement beyond a general denial.

VII. Analyst’s Conclusion: Key Questions for the Case

  • A central issue will be one of patentable subject matter: can the asserted composition claims directed to "isolated DNA" fragments (’282 Patent, claims 5 and 6) be validly enforced against the synthetic primers likely used in modern genetic testing, or are such claims invalid under the precedent of Association for Molecular Pathology v. Myriad Genetics, Inc.?
  • A key question of claim scope will be whether the method of "analyzing a sequence ... and comparing" (’999 Patent, claim 1) can be construed to cover modern, automated sequencing and bioinformatic analysis, or whether there is a fundamental mismatch in technical operation and legal scope that places Plaintiff's services outside the claims.
  • A threshold jurisdictional question will be whether Plaintiff can demonstrate a "definite and concrete" controversy sufficient for declaratory judgment, given that the complaint bases its apprehension of suit on Defendant's litigation against third parties rather than on any direct threats against Plaintiff itself (Compl. ¶¶ 14, 17).