DCT

2:13-cv-00640

University Of Utah Research Foundation v. Ambry Genetics

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Key Events
Complaint

I. Executive Summary and Procedural Information

  • Parties & Counsel:
  • Case Identification: 2:13-cv-00640, D. Utah, 07/09/2013
  • Venue Allegations: Plaintiffs allege venue is proper in the District of Utah because Defendant regularly conducts business in the district, sells genetic testing products to its residents, and has attended or advertised at conferences within the jurisdiction.
  • Core Dispute: Plaintiffs allege that Defendant’s genetic testing services for the BRCA1 and BRCA2 genes infringe ten U.S. patents relating to the genes themselves, mutations therein, and methods for their detection.
  • Technical Context: The technology involves molecular diagnostic testing to identify mutations in the BRCA1 and BRCA2 genes, which are associated with a significantly increased risk of hereditary breast and ovarian cancer.
  • Key Procedural History: This complaint was filed less than one month after the U.S. Supreme Court’s decision in Association for Molecular Pathology v. Myriad Genetics, Inc. (June 13, 2013), which invalidated claims to isolated genomic DNA but held that complementary DNA (cDNA) was patent-eligible. The complaint notes that Defendant began offering its accused BRCA1 and BRCA2 analysis services on the same day the Supreme Court decision was issued, suggesting this lawsuit is a direct response to new market competition.

Case Timeline

Date Event
1994-08-12 Earliest Priority Date for ’999, ’282, and ’441 Patents
1995-12-18 Earliest Priority Date for ’492 and ’857 Patents
1996-02-12 Earliest Priority Date for ’155, ’400, ’379, and ’721 Patents
1997-08-05 U.S. Patent No. 5,654,155 Issued
1998-01-20 U.S. Patent No. 5,709,999 Issued
1998-05-05 U.S. Patent No. 5,747,282 Issued
1998-05-12 U.S. Patent No. 5,750,400 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
2002-06-07 Earliest Priority Date for ’497 Patent
2005-10-05 U.S. Patent No. 6,951,721 Issued
2007-07-31 U.S. Patent No. 7,250,497 Issued
2013-06-13 Defendant Allegedly Began Offering Accused Services
2013-07-09 Complaint Filing Date

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 addresses the need for methods to diagnose a predisposition to breast and ovarian cancer by identifying germline mutations in the BRCA1 gene, which is a tumor suppressor. (’999 Patent, col. 1:19-27).
  • The Patented Solution: The invention provides methods for detecting specific alterations in the BRCA1 gene by analyzing a nucleic acid sequence from a human sample and determining the presence or absence of a mutation. (’999 Patent, col. 1:49-62). The specification describes various techniques for this analysis, including single-strand conformation analysis (SSCA), denaturing gradient gel electrophoresis (DGGE), and chemical mismatch cleavage. (’999 Patent, col. 13:1-14:52).
  • Technical Importance: The ability to identify specific mutations linked to cancer susceptibility allowed for predictive genetic testing, enabling risk assessment and management in individuals before the onset of disease. (Compl. ¶ 14).

Key Claims at a Glance

  • The complaint asserts dependent Claim 6, which relies on independent Claim 1. (Compl. ¶ 19).
  • Independent Claim 1 contains the following essential elements:
    • A method for detecting a germline alteration in a BRCA1 gene,
    • said alteration selected from the group consisting of a 185-186delAG mutation and a 5382-5383insC mutation in a human, which comprises
    • analyzing a sequence of a BRCA1 gene or BRCA1 RNA from a human sample, or
    • summarizing the presence or absence of said alteration in said sequence.
  • Claim 6 adds the limitation that the "analyzing" step comprises amplifying all or a part of the BRCA1 gene from the sample using a primer pair. (’999 Patent, col. 162:1-5).
  • The complaint does not explicitly reserve the right to assert dependent claims.

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

The Invention Explained

  • Problem Addressed: The patent relates to the general field of human genetics and the need to isolate and detect the BRCA1 gene and mutant alleles that cause susceptibility to breast and ovarian cancer. (’282 Patent, Abstract).
  • The Patented Solution: The invention provides isolated DNA molecules encoding the BRCA1 protein, methods of using these molecules to detect mutations, and kits for performing such detection. (’282 Patent, col. 3:30-4:27). The methods include using allele-specific oligonucleotide probes to identify mutations. (’282 Patent, col. 13:39-50).
  • Technical Importance: The isolation of the BRCA1 gene sequence and the development of specific probes and primers were crucial for creating reliable and scalable diagnostic tests for hereditary cancer risk. (Compl. ¶ 14).

Key Claims at a Glance

  • The complaint asserts Claims 6, 16, and 17. (Compl. ¶ 26).
  • Independent Claim 6 recites:
    • An isolated DNA selected from the group consisting of specific nucleotide sequences set forth in the patent.
  • Independent Claim 16 contains the following essential elements:
    • A kit for detecting mutations in the BRCA1 gene resulting in a susceptibility to breast and ovarian cancers, comprising
    • at least one allele-specific oligonucleotide probe for a BRCA1 gene mutation, and
    • instructions relating to detecting mutations in the BRCA1 gene.
  • Claim 17 depends on claim 16 and adds a pair of primers for determining the nucleotide sequence of a BRCA1 gene. (’282 Patent, col. 156:13-17).
  • The complaint does not explicitly reserve the right to assert dependent claims.

Multi-Patent Capsules

  • Patent Identification: U.S. Patent No. 5,753,441, "Method for diagnosing a predisposition for breast and ovarian cancer," Issued May 19, 1998.

  • Technology Synopsis: This patent relates to methods for detecting alterations in the BRCA1 gene to diagnose a predisposition to breast and ovarian cancer. The methods involve analyzing a tissue or body fluid sample for the presence of a mutated BRCA1 gene sequence or a truncated BRCA1 polypeptide. (’441 Patent, Abstract).

  • Asserted Claims: Claims 7, 8, 12, 23, and 26. (Compl. ¶ 33).

  • Accused Features: Defendant's BRCA1 genetic testing services are accused of infringement. (Compl. ¶¶ 15-16, 33).

  • Patent Identification: U.S. Patent No. 5,837,492, "Chromosome 13-linked breast cancer susceptibility gene," Issued November 17, 1998.

  • Technology Synopsis: This patent relates to the BRCA2 gene, which is linked to breast cancer susceptibility. The invention provides methods and materials to isolate and detect the BRCA2 gene and its mutations for use in diagnosis and prognosis. (’492 Patent, Abstract).

  • Asserted Claims: Claims 29 and 30. (Compl. ¶ 40).

  • Accused Features: Defendant's BRCA2 genetic testing services are accused of infringement. (Compl. ¶¶ 15-16, 40).

  • Patent Identification: U.S. Patent No. 6,033,857, "Method of screening for alterations in a BRCA2 gene," Issued March 7, 2000.

  • Technology Synopsis: This patent relates to methods for screening for alterations in the BRCA2 gene that indicate a predisposition to cancer. The methods involve screening for mutations that result in the translation of a truncated BRCA2 protein. (’857 Patent, Abstract).

  • Asserted Claims: Claim 4. (Compl. ¶ 47).

  • Accused Features: Defendant's BRCA2 genetic testing services are accused of infringement. (Compl. ¶¶ 15-16, 47).

  • Patent Identification: U.S. Patent No. 5,654,155, "Consensus sequence of the human BRCA1 gene," Issued August 5, 1997.

  • Technology Synopsis: This patent discloses a consensus DNA sequence for the human BRCA1 gene. This consensus sequence is intended to provide greater accuracy for genetic testing by helping to differentiate true mutations from benign polymorphic variations. (’155 Patent, Abstract).

  • Asserted Claims: Claims 2, 3, and 4. (Compl. ¶ 54).

  • Accused Features: Defendant's BRCA1 genetic testing services are accused of infringement. (Compl. ¶¶ 15-16, 54).

  • Patent Identification: U.S. Patent No. 5,750,400, "Coding sequences of the human BRCA1 gene," Issued May 12, 1998.

  • Technology Synopsis: The invention is directed to three specific coding sequences of the BRCA1 gene and their frequencies of occurrence. The patent also describes a method for determining the consensus sequence for any gene and methods of identifying individuals with increased genetic susceptibility to cancer. (’400 Patent, Abstract).

  • Asserted Claims: Claims 2, 3, 4, 5, 6, and 7. (Compl. ¶ 61).

  • Accused Features: Defendant's BRCA1 genetic testing services are accused of infringement. (Compl. ¶¶ 15-16, 61).

  • Patent Identification: U.S. Patent No. 6,051,379, "Mutations in the BRCA1 gene and methods for detection thereof," Issued April 18, 2000.

  • Technology Synopsis: This patent discloses new mutations in the BRCA1 gene and provides allele-specific sequence-based assays for their detection. The methods are intended for efficient and accurate detection of mutations in a test BRCA2 gene sample. (’379 Patent, Abstract).

  • Accused Features: The complaint does not specify the gene, but the patent title refers to BRCA1. The abstract refers to BRCA2. The accused features are Defendant's BRCA1 and BRCA2 genetic testing services. (Compl. ¶¶ 15-16, 68).

  • Asserted Claims: Claims 32 and 33. (Compl. ¶ 68).

  • Patent Identification: U.S. Patent No. 6,951,721, "Method of determining the haplotype of a human BRCA1 gene," Issued October 5, 2005.

  • Technology Synopsis: This patent discloses methods for identifying functional allele profiles, or haplotypes, of a given gene. The methods are intended for use in the treatment and diagnosis of diseases and for genetic and pharmacogenetic applications. (’721 Patent, Abstract).

  • Asserted Claims: Claim 5. (Compl. ¶ 75).

  • Accused Features: Defendant's BRCA1 genetic testing services are accused of infringement. (Compl. ¶¶ 15-16, 75).

  • Patent Identification: U.S. Patent No. 7,250,497, "Large deletions in human BRCA1 gene and use thereof," Issued July 31, 2007.

  • Technology Synopsis: This patent discloses the identification of large deletions in the BRCA1 gene in patients. These deletions are described as predisposing patients to breast and ovarian cancer and are presented as useful markers for detecting such predisposition. (’497 Patent, Abstract).

  • Asserted Claims: Claims 3, 4, 5, 6, 7, 8, 11, 14, 17, 18, and 19. (Compl. ¶ 82).

  • Accused Features: Defendant's BRCA1 genetic testing services, specifically including deletion/duplication analyses, are accused of infringement. (Compl. ¶¶ 16, 82).

III. The Accused Instrumentality

Product Identification

  • The accused instrumentalities are Defendant’s laboratory services, including those marketed as BRCA1, BRCA2, BRCAPlus, BreastNext, OvaNext, and CancerNext. (Compl. ¶¶ 15, 19).

Functionality and Market Context

  • The complaint alleges that Defendant offers clinical diagnostic and genomic services which include the testing and analysis of BRCA1 and BRCA2 genes. (Compl. ¶ 15). These services allegedly comprise "full gene sequencing and deletion/duplication analyses" for these genes and utilize "next-generation sequencing technology." (Compl. ¶ 16).
  • The complaint alleges that Defendant began offering these services on June 13, 2013. (Compl. ¶ 16). This date corresponds with the U.S. Supreme Court's decision in Association for Molecular Pathology v. Myriad Genetics, Inc., which altered the patent-eligibility landscape for gene patents. The timing suggests the accused services were launched to compete directly with Plaintiff Myriad's established testing services. (Compl. ¶¶ 11-14).
  • No probative visual evidence provided in complaint.

IV. Analysis of Infringement Allegations

The complaint does not provide sufficient detail for analysis of how the accused services meet each specific claim limitation. The following tables summarize the infringement theory based on the general descriptions provided.

  • 5,709,999 Infringement Allegations
Claim Element (from Independent Claim 1) Alleged Infringing Functionality Complaint Citation Patent Citation
A method for detecting a germline alteration in a BRCA1 gene, said alteration selected from the group consisting of a 185-186delAG mutation and a 5382-5383insC mutation in a human which comprises analyzing a sequence of a BRCA1 gene... Defendant offers services that include "testing and analysis of BRCA1 and BRCA2 genes" and "full gene sequencing and deletion/duplication analyses for the BRCA 1 and BRCA 2 genes." ¶15, ¶16, ¶19 col. 13:1-14:52
...from a human sample... The complaint does not specify the source of the sample, but clinical genetic testing typically uses blood or saliva samples. ¶15 col. 13:4-6
  • 5,747,282 Infringement Allegations
Claim Element (from Independent Claim 16) Alleged Infringing Functionality Complaint Citation Patent Citation
A kit for detecting mutations in the BRCA1 gene... The complaint alleges Defendant is "making, manufacturing, promoting... and selling" products which infringe, which Plaintiffs may argue constitutes the provision of a "kit," even if used internally for a testing service. ¶26 col. 6:21-31
...comprising at least one allele-specific oligonucleotide probe for a BRCA1 gene mutation... Defendant's alleged "full gene sequencing" services would necessarily use oligonucleotide probes or primers to identify sequences. ¶16, ¶26 col. 15:23-45
...and instructions relating to detecting mutations in the BRCA1 gene. The complaint does not provide sufficient detail for analysis of this element. ¶26 col. 6:21-31
  • Identified Points of Contention:
    • Scope Questions: A primary question for the ’999 Patent will be whether Defendant’s "full gene sequencing" service meets the claim limitation of "analyzing a sequence" for the specific mutations (185-186delAG and 5382-5383insC) recited in Claim 1. A court may need to determine if a general sequencing of the entire gene inherently performs the claimed step of detecting those particular alterations.
    • Technical Questions: For the ’282 Patent, a key legal and factual question is whether Defendant’s internal laboratory testing service constitutes a "kit" as required by Claim 16. Practitioners may dispute whether reagents assembled and used internally for a service, rather than packaged for sale to a third party, fall within the scope of the term "kit."

V. Key Claim Terms for Construction

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

  • Context and Importance: The definition of this term is critical because the claim is directed to detecting a specific, narrow group of mutations. The case may turn on whether "analyzing" requires a targeted search for those mutations or if the term is met by a comprehensive sequencing of the gene that would incidentally reveal their presence or absence.

  • Intrinsic Evidence for Interpretation:

    • Evidence for a Broader Interpretation: The detailed description of the invention discusses a wide array of general DNA analysis methods, such as SSCA, DGGE, and direct DNA sequencing, which are not limited to detecting only the two mutations specified in the claim. (’999 Patent, col. 13:1-14:52).
    • Evidence for a Narrower Interpretation: The claim preamble states the method is "for detecting a germline alteration," and the body of the claim explicitly limits this alteration to being "selected from the group consisting of a 185-186delAG mutation and a 5382-5383insC mutation." This language may support an interpretation that "analyzing" is tied to the specific purpose of finding those particular mutations. (’999 Patent, col. 161:62-67).

  • The Term: "kit" (’282 Patent, Claim 16)

  • Context and Importance: Infringement of Claim 16 hinges on whether Defendant's internal laboratory service constitutes the provision of a "kit." Practitioners may focus on this term because if it is construed to require components packaged together for sale or distribution to an end-user, an internal testing service may not infringe.

  • Intrinsic Evidence for Interpretation:

    • Evidence for a Broader Interpretation: The specification describes "kits for detecting in an analyte a polynucleotide comprising a portion of the BRCA1 locus" without explicitly limiting them to external sale, potentially encompassing reagents assembled for internal diagnostic use. (’282 Patent, col. 6:21-31).
    • Evidence for a Narrower Interpretation: The claim requires the kit to comprise a probe "and instructions." The inclusion of "instructions" may suggest a product intended for use by a third party, which would support a narrower definition that excludes reagents used internally by the service provider itself. (’282 Patent, col. 156:13-17).

VI. Other Allegations

  • Indirect Infringement: The complaint makes conclusory allegations of induced and contributory infringement for each asserted patent. (Compl. ¶¶ 19, 26, 33, 40, 47, 54, 61, 68, 75, 82). However, it does not plead specific facts to support the knowledge and intent elements required for such claims, such as alleging that Defendant provides instructions or materials that encourage its customers or third parties to perform infringing acts.
  • Willful Infringement: The complaint alleges that Defendant has willfully infringed each of the asserted patents. (Compl. ¶¶ 22, 29, 36, 43, 50, 57, 64, 71, 78, 85). The complaint does not allege any pre-suit knowledge, such as a cease-and-desist letter. The basis for willfulness appears to be grounded in the allegation that infringement is ongoing after the filing of the complaint.

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

  • A central issue will be one of patent eligibility: In the wake of the Supreme Court's decision limiting the patentability of isolated DNA, a key question will be whether the asserted method claims, which recite steps of "analyzing" and "comparing" genetic sequences, and composition claims directed to short oligonucleotide primers, are directed to patent-eligible subject matter or are instead impermissible attempts to claim natural phenomena and laws of nature.
  • A key threshold question will be one of claim scope: Can Plaintiffs establish that Defendant’s services, which are alleged to use "next-generation sequencing technology" to analyze entire genes, meet the specific limitations of the asserted claims, such as the requirement in the '999 patent of analyzing for a narrowly defined group of mutations, or the requirement in the '282 patent for the provision of a "kit"?
  • An underlying evidentiary question will be one of factual proof: Given the complaint's lack of specific technical details, a core challenge for Plaintiffs will be to adduce evidence through discovery that demonstrates precisely how Defendant's internal laboratory processes and technologies map onto the elements of the asserted claims.