DCT

1:09-cv-04515

Association for Molecular Pathology v. United States Patent Trademark Office

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I. Executive Summary and Procedural Information

  • Parties & Counsel:
  • Case Identification: 1:09-cv-04515, S.D.N.Y., 05/12/2009
  • Venue Allegations: Plaintiffs allege venue is proper in the Southern District of New York as a substantial part of the events giving rise to the claim occurred in the district, and several plaintiffs and one defendant (USPTO, by virtue of its nationwide business) reside or are found there.
  • Core Dispute: Plaintiffs, a coalition of researchers, medical organizations, and patients, seek a declaratory judgment that numerous claims in patents related to the BRCA1 and BRCA2 genes are invalid and unconstitutional, arguing they improperly claim products of nature, laws of nature, and abstract ideas.
  • Technical Context: The technology involves isolating human genes associated with hereditary breast and ovarian cancer (BRCA1 and BRCA2) and analyzing their DNA sequences to identify mutations that correlate with an increased risk of developing these cancers.
  • Key Procedural History: The complaint alleges that Defendant Myriad Genetics, as the exclusive licensee of the patents-in-suit, has enforced its patent rights on at least nine occasions, including sending cease-and-desist letters to researchers at Yale University and the University of Pennsylvania. These enforcement actions are alleged to have chilled research and prevented clinicians and patients from accessing alternative or confirmatory genetic testing.

Case Timeline

Date Event
1990-01-01 Researchers determine a gene correlated with breast/ovarian cancer is located on chromosome 17 (BRCA1)
1994-08-12 Earliest Priority Date for ’473, ’999, ’001, '441 Patents
1996-01-05 Earliest Priority Date for ’282 Patent
1996-04-29 Earliest Priority Date for ’492, ’857 Patents
1997-12-02 U.S. Patent No. 5,693,473 Issues
1998-01-20 U.S. Patent No. 5,709,999 Issues
1998-01-20 U.S. Patent No. 5,710,001 Issues
1998-05-05 U.S. Patent No. 5,747,282 Issues
1998-05-19 U.S. Patent No. 5,753,441 Issues
1998-11-17 U.S. Patent No. 5,837,492 Issues
2000-03-07 U.S. Patent No. 6,033,857 Issues
2005-01-01 Plaintiff Limary diagnosed with breast cancer and seeks BRCA testing
2009-05-12 Complaint Filed

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

U.S. Patent No. 5,747,282 - "17Q-Linked Breast and Ovarian Cancer Susceptibility Gene"

The Invention Explained

  • Problem Addressed: The patent describes a significant unmet need in medical genetics: identifying the specific gene responsible for a hereditary predisposition to breast and ovarian cancer, which was known to be linked to a region on chromosome 17q but had not yet been precisely located and sequenced (U.S. Patent No. 5,747,282, col. 3:25-52). This lack of identification prevented reliable diagnostic testing for at-risk individuals.
  • The Patented Solution: The invention provides the isolated nucleic acid sequence of the human BRCA1 gene, which codes for a specific protein (SEQ ID NO:2) ('282 Patent, Abstract). By isolating and sequencing this gene, the inventors enabled the creation of diagnostic tools, such as probes and primers, to detect mutations that correlate with a predisposition to cancer, and provided materials for developing potential therapeutics ('282 Patent, col. 5:1-29).
  • Technical Importance: The isolation and sequencing of the BRCA1 gene was a critical step in translating genetic linkage studies into clinical practice, enabling direct genetic screening for one of the most significant known hereditary cancer risks.

Key Claims at a Glance

  • The complaint challenges independent claims 1 and 20 (Compl. ¶32.a, ¶32.d; Prayer for Relief ¶1.a).
  • Independent Claim 1 consists of the following essential elements:
    • An isolated DNA coding for a BRCA1 polypeptide,
    • said polypeptide having the amino acid sequence set forth in SEQ ID NO:2.
  • Independent Claim 20 is a method claim with the following essential elements:
    • A method for screening potential cancer therapeutics, comprising:
    • growing a transformed eukaryotic host cell containing an altered BRCA1 gene causing cancer in the presence of a suspected therapeutic compound,
    • growing said cell in the absence of the compound,
    • determining the rate of growth in both conditions, and
    • comparing the growth rates, wherein a slower rate of growth in the presence of the compound indicates it is a cancer therapeutic.
  • The complaint also challenges dependent claims 2, 5, 6, and 7 (Compl. ¶32.a, ¶32.b; Prayer for Relief ¶1.a).

U.S. Patent No. 5,837,492 - "Chromosome 13-Linked Breast Cancer Susceptibility Gene"

The Invention Explained

  • Problem Addressed: Following the discovery of BRCA1, researchers recognized that not all hereditary breast cancer was accounted for, indicating the existence of at least one other major susceptibility gene ('492 Patent, col. 3:51-4:48). The patent describes the effort to locate and identify this second gene, BRCA2, which was linked to a region on chromosome 13.
  • The Patented Solution: The invention provides the isolated nucleic acid sequence of the human BRCA2 gene and the amino acid sequence of the protein it encodes (SEQ ID NO:2) ('492 Patent, Abstract). This discovery allows for the development of diagnostic methods to screen individuals for mutations in BRCA2, expanding the scope of genetic testing for hereditary breast cancer beyond BRCA1 alone ('492 Patent, col. 4:49-5:55).
  • Technical Importance: The identification of BRCA2 provided another critical piece of the hereditary cancer puzzle, enabling more comprehensive genetic risk assessment for families with a history of breast and ovarian cancer.

Key Claims at a Glance

  • The complaint challenges independent claim 1 (Compl. ¶32.a; Prayer for Relief ¶1.b).
  • Independent Claim 1 consists of the following essential elements:
    • An isolated DNA molecule coding for a BRCA2 polypeptide,
    • said DNA molecule comprising a nucleic acid sequence encoding the amino acid sequence set forth in SEQ ID NO:2.
  • The complaint also challenges dependent claims 6 and 7 (Compl. ¶32.b; Prayer for Relief ¶1.b).

U.S. Patent No. 5,693,473 - "Linked Breast and Ovarian Cancer Susceptibility Gene"

  • Technology Synopsis: This patent claims specific compositions of matter related to the BRCA1 gene. It specifically claims an isolated DNA molecule that comprises an altered BRCA1 DNA sequence, where the alteration is one of several specified mutations known to correlate with a predisposition to cancer.
  • Asserted Claims: Independent claim 1 (Compl. ¶32.b; Prayer for Relief ¶1.c).
  • Accused Features: Plaintiffs' desired ability to isolate and analyze patient DNA that naturally contains one of the specified mutations covered by the claim (Compl. ¶63).

U.S. Patent No. 5,709,999 - "Linked Breast and Ovarian Cancer Susceptibility Gene"

  • Technology Synopsis: This patent claims methods for diagnosing a predisposition for breast and ovarian cancer. It covers the act of analyzing the sequence of a BRCA1 gene from a human sample and looking for the presence of specific germline alterations.
  • Asserted Claims: Independent claim 1 (Compl. ¶32.c; Prayer for Relief ¶1.d).
  • Accused Features: Plaintiffs' desired clinical and research practice of analyzing a patient's BRCA1 gene to determine if specific inherited variants are present (Compl. ¶¶ 69-70).

U.S. Patent No. 5,710,001 - "17Q-Linked Breast and Ovarian Cancer Susceptibility Gene"

  • Technology Synopsis: This patent claims a method for screening for alterations in the BRCA1 gene. The claimed method involves comparing the BRCA1 gene sequence from a tumor sample with the sequence from a non-tumor sample from the same individual to identify somatic mutations.
  • Asserted Claims: Independent claim 1 (Compl. ¶32.d; Prayer for Relief ¶1.e).
  • Accused Features: The act of comparing two BRCA1 gene sequences from the same person and the "abstract idea that nature has made the two forms of the BRCA1 genes different" (Compl. ¶72).

U.S. Patent No. 5,753,441 - "17Q-Linked Breast and Ovarian Cancer Susceptibility Gene"

  • Technology Synopsis: This patent claims a method for screening for alterations in the BRCA1 gene by comparing a sequence from a tissue sample to the wild-type BRCA1 sequence.
  • Asserted Claims: Independent claim 1 (Compl. ¶32.d; Prayer for Relief ¶1.f).
  • Accused Features: The act of comparing a patient's BRCA1 gene sequence to a reference "wild-type" sequence and the "abstract idea that nature has made the two BRCA1 genes different" (Compl. ¶73).

U.S. Patent No. 6,033,857 - "Chromosome 13-Linked Breast Cancer Susceptibility Gene"

  • Technology Synopsis: This patent claims methods for identifying a predisposition for breast cancer by comparing a patient's BRCA2 gene sequence with a wild-type BRCA2 sequence to detect alterations.
  • Asserted Claims: Independent claims 1 and 2 (Compl. ¶32.d; Prayer for Relief ¶1.g).
  • Accused Features: The act of comparing two BRCA2 gene sequences and concluding that differences indicate a predisposition to cancer, which the complaint frames as an "abstract idea" (Compl. ¶¶ 74-75).

III. The Accused Instrumentality

Product Identification

  • The complaint does not accuse a product of infringement but rather challenges the validity of the patents-in-suit. The instrumentality at issue is Defendant Myriad's exclusive control over genetic testing for BRCA1 and BRCA2, which is commercialized as services including the "Comprehensive BRACAnalysis" and "BRACAnalysis Rearrangement Test (BART)" (Compl. ¶¶ 28, 92, 94).

Functionality and Market Context

  • Myriad's services involve sequencing a person's BRCA1 and BRCA2 genes to determine if mutations correlated with an increased risk of breast and/or ovarian cancer are present (Compl. ¶81). The complaint alleges that due to its exclusive license to the patents-in-suit, Myriad is the "sole clinical provider of full sequencing of the BRCA1 and BRCA2 genes in the United States" (Compl. ¶28).
  • This alleged monopoly prevents other laboratories and researchers, including the plaintiffs, from offering clinical BRCA testing, conducting research on the genes, or providing second opinions on test results (Compl. ¶¶ 2, 84, 90). The complaint further alleges that this control has led to high costs (over $3,000 per test), lack of insurance acceptance, and disparities in the availability of genetic information, thereby restricting patient access to crucial health information (Compl. ¶¶ 2, 87, 92, 93).

IV. Analysis of Infringement Allegations

No probative visual evidence provided in complaint.

The complaint seeks a declaratory judgment that the patents are invalid and unenforceable. The infringement analysis is therefore prospective, concerning activities the plaintiffs wish to perform but are prevented from doing by the patents.

U.S. Patent No. 5,747,282 - Infringement Allegations

Claim Element (from Independent Claim 1) Alleged Infringing Functionality Complaint Citation Patent Citation
An isolated DNA The clinical and research activities plaintiffs desire to perform, which involve extracting a patient's DNA from their cells to analyze the BRCA1 gene. The complaint alleges this act of removal constitutes "isolation." ¶51, ¶82, ¶84 col. 19:6-14
coding for a BRCA1 polypeptide, said polypeptide having the amino acid sequence set forth in SEQ ID NO:2. The act of looking at the human BRCA1 gene sequence in its "wild-type" or non-mutated form, which is naturally present in every person and codes for the specified polypeptide. ¶55, ¶56 col. 19:15-32

Identified Points of Contention

  • Scope Questions: A central question is whether the claim term "isolated DNA" can be validly construed to cover DNA sequences that are merely separated from their natural cellular environment but are otherwise identical in informational content to naturally occurring genes. The complaint argues that such a construction impermissibly covers a product of nature (Compl. ¶¶ 51-52).
  • Technical Questions: Does the act of separating a DNA molecule from its native chromosome and associated proteins create a new composition of matter with "markedly different characteristics," or does it remain, as the complaint alleges, a natural product that simply conveys the same genetic information as it does inside the body? (Compl. ¶51).

U.S. Patent No. 5,837,492 - Infringement Allegations

Claim Element (from Independent Claim 1) Alleged Infringing Functionality Complaint Citation Patent Citation
An isolated DNA molecule The clinical and research activities plaintiffs desire to perform, which involve extracting a patient's DNA from their cells to analyze the BRCA2 gene. ¶60, ¶82, ¶84 col. 19:10-18
coding for a BRCA2 polypeptide... said DNA molecule comprising a nucleic acid sequence encoding the amino acid sequence set forth in SEQ ID NO:2. The act of analyzing the human BRCA2 gene sequence in its "wild-type" or non-mutated form, which naturally occurs in the human body and encodes the specified polypeptide. ¶60 col. 19:19-35

Identified Points of Contention

  • Scope Questions: Similar to the '282 Patent, the dispute will focus on whether the term "isolated DNA molecule" as applied to the BRCA2 gene encompasses a patent-ineligible product of nature.
  • Technical Questions: The analysis for the ’492 Patent raises the same fundamental question as for the '282 Patent: what is the technical and legal significance of "isolating" a naturally occurring gene?

V. Key Claim Terms for Construction

  • The Term: "isolated DNA" (from Claim 1 of the '282 Patent and Claim 1 of the '492 Patent).
  • Context and Importance: The definition of this term is the central issue of the case for the composition claims. Plaintiffs' core argument is that the claimed "isolated DNA" is a natural product and therefore unpatentable under 35 U.S.C. § 101 (Compl. ¶¶ 4, 51-52). The court's construction of this term will determine whether the act of separating a gene from its native chromosomal environment renders it a patent-eligible invention.
  • Intrinsic Evidence for Interpretation:
    • Evidence for a Broader Interpretation: The patent defines "isolated" or "substantially pure" nucleic acid as one "which is substantially separated from other cellular components which naturally accompany a native human sequence" ('282 Patent, col. 19:6-9). This language may support a broad construction that includes any DNA sequence removed from the human body, which is the interpretation Plaintiffs challenge.
    • Evidence for a Narrower Interpretation: The same definition also states that the term "embraces a nucleic acid sequence or protein which has been removed from its naturally occurring environment, and includes recombinant or cloned DNA isolates and chemically synthesized analogs" ('282 Patent, col. 19:9-14). This language, particularly the reference to recombinant, cloned, and synthesized molecules (such as cDNA), could support a narrower construction limited to DNA molecules that are not simply excised from the genome but are created or manipulated in a laboratory.

VI. Other Allegations

  • Indirect Infringement: The complaint does not allege indirect infringement but rather states that plaintiff organizations, such as Breast Cancer Action, fear being accused of inducing infringement if they provide information to the public about alternative BRCA testing options offered by labs other than Myriad (Compl. ¶19).
  • Willful Infringement: Willful infringement is not alleged. The complaint does, however, establish Defendant Myriad's knowledge and enforcement of its patent rights by citing cease-and-desist letters sent to academic researchers, which serves as the basis for the plaintiffs' claim that a live controversy exists and that their desired activities are chilled (Compl. ¶¶ 11, 49).

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

This case presents foundational questions about the patentability of genetic material and diagnostic correlations, rather than a conventional infringement dispute. The central issues for the court will likely be:

  • A core issue will be one of patent eligibility for compositions of matter: is an "isolated" human DNA sequence, whose genetic information is identical to that found in nature, a patent-ineligible "product of nature," or does the act of severing it from its native chromosome create a non-naturally occurring molecule with markedly different characteristics sufficient to confer patentability under 35 U.S.C. § 101?
  • A second key issue will be one of patent eligibility for methods: do the patent claims covering the acts of "looking at," "analyzing," or "comparing" genetic sequences claim patent-ineligible "laws of nature" or "abstract ideas," or do they recite a patent-eligible application of a natural correlation?