DCT
1:19-cv-02341
Biofire Defense v. Fluidigm Corp
Key Events
Complaint
I. Executive Summary and Procedural Information
- Parties & Counsel:
- Plaintiff: BioFire Defense, LLC (Delaware) and University of Utah Research Foundation (Utah)
- Defendant: Fluidigm Corporation (Delaware)
- Plaintiff’s Counsel: Thorpe, North & Western, LLP
- Case Identification: 2:16-cv-00430, D. Utah, 05/23/2016
- Venue Allegations: Plaintiff alleges venue is proper in the District of Utah because Defendant conducts business in the district directly related to the patents-in-suit, thereby causing harm to Plaintiffs in the district.
- Core Dispute: Plaintiff alleges that Defendant’s BioMark system infringes two patents related to methods and systems for monitoring DNA amplification during Polymerase Chain Reaction (PCR) using fluorescence.
- Technical Context: The technology at issue is real-time, or quantitative, Polymerase Chain Reaction (qPCR), a foundational technique in molecular biology for rapidly amplifying and quantifying DNA for research and diagnostic purposes.
- Key Procedural History: The complaint notes that a reexamination certificate was issued for U.S. Patent No. 7,670,832 on September 21, 2015. This event, occurring prior to the complaint's filing, suggests that the patent's claims survived a validity challenge at the U.S. Patent and Trademark Office, a fact that may be raised in response to potential invalidity defenses.
Case Timeline
| Date | Event |
|---|---|
| 1996-06-04 | Earliest Priority Date for ’670 and ’832 Patents |
| 2001-01-16 | U.S. Patent No. 6,174,670 Issues |
| 2010-03-02 | U.S. Patent No. 7,670,832 Issues |
| 2015-09-21 | Reexamination Certificate for U.S. Patent No. 7,670,832 Issues |
| 2016-05-23 | Complaint Filed |
II. Technology and Patent(s)-in-Suit Analysis
U.S. Patent No. 6,174,670 - “Monitoring Amplification of DNA During PCR,” Issued Jan. 16, 2001
The Invention Explained
- Problem Addressed: Conventional Polymerase Chain Reaction (PCR) required time-consuming, post-amplification analysis steps, such as gel electrophoresis, to visualize and quantify the resulting DNA product, a process that is slow and introduces risks of sample contamination (’670 Patent, col. 2:14-21).
- The Patented Solution: The patent discloses methods to monitor the progress of a PCR amplification in "real time" by measuring fluorescence within the reaction vessel during the thermal cycling process. This is accomplished by including a fluorescent entity, such as a dye that binds to double-stranded DNA, in the reaction mixture and continuously measuring its signal as the amount of amplified DNA increases with each cycle (’670 Patent, Abstract; col. 1:15-24). This allows for product identification and quantification without subsequent processing steps.
- Technical Importance: This approach enabled quantitative PCR (qPCR), transforming the technique from a purely qualitative tool for DNA detection into a precise method for quantifying the amount of starting nucleic acid in a sample (Compl. ¶¶13-14).
Key Claims at a Glance
- The complaint asserts independent claim 76 (’670 Patent, col. 73:70-74; Compl. ¶26). The essential elements are:
- A method of analyzing nucleic acid hybridization comprising the steps of: (a) providing a mixture comprising a nucleic acid sample to be analyzed and a nucleic acid binding fluorescent entity; and
- (b) monitoring fluorescence while changing temperature at a rate of ≥0.1° C./second.
U.S. Patent No. 7,670,832 - “System For Fluorescence Monitoring,” Issued Mar. 2, 2010
The Invention Explained
- Problem Addressed: The practical implementation of real-time PCR methods requires specialized instrumentation capable of performing both rapid, precise thermal cycling and sensitive fluorescence detection in the same device (’832 Patent, col. 1:28-44).
- The Patented Solution: The patent describes a system specifically designed for fluorescence monitoring during PCR. The claimed device integrates a heat exchange component for thermal cycling, a control device to manage the temperature cycles, an optical system with an excitation source and a photodetector to measure fluorescence, and a processor programmed to analyze the resulting data, including the generation of a "melting curve" to characterize the amplified DNA product (’832 Patent, Abstract; Fig. 51).
- Technical Importance: This invention claims the physical apparatus that makes real-time, quantitative PCR a practical and automated laboratory technique, combining the previously separate steps of amplification and analysis into a single, closed-tube process (Compl. ¶¶10, 13-14).
Key Claims at a Glance
- The complaint asserts independent claims 1, 11, 14, and 17 (’832 Patent, col. 63:47-64:67; Compl. ¶29). The essential elements of representative system claim 1 are:
- A device for performing PCR and monitoring the reaction of a sample comprising a nucleic acid and a fluorescent dye, comprising: a reaction vessel;
- a heat exchange component for heating and cooling the sample;
- a control device programmed for repeatedly operating the heat exchange component to subject the sample to thermal cycling;
- an excitation source for optically exciting the sample;
- a photodetector for detecting temperature-dependent fluorescence levels; and
- a processor programmed to generate a melting curve of the amplification product.
III. The Accused Instrumentality
Product Identification
- Defendant’s system called BioMark (the "Infringing System") (Compl. ¶18).
Functionality and Market Context
- The complaint alleges the BioMark system is intended for the life science market and uses PCR (Compl. ¶17). Its accused functionality includes monitoring mixtures of nucleic acid samples and fluorescent entities, analyzing nucleic acid hybridization by monitoring fluorescence while changing temperature, and generating melting curves (Compl. ¶¶24, 25, 30). The complaint further alleges that the BioMark system comprises a heat exchange component, a control device, an excitation source, a detector, and a processor, mapping its architecture directly onto the elements of claim 1 of the ’832 Patent (Compl. ¶31).
IV. Analysis of Infringement Allegations
’670 Patent Infringement Allegations
| Claim Element (from Independent Claim 76) | Alleged Infringing Functionality | Complaint Citation | Patent Citation |
|---|---|---|---|
| A method of analyzing nucleic acid hybridization comprising the steps of: (a) providing a mixture comprising a nucleic acid sample to be analyzed and a nucleic acid binding fluorescent entity; | Defendant has allegedly used the Infringing System to monitor mixtures comprising a nucleic acid sample and a nucleic acid binding fluorescent entity. | ¶24 | col. 15:20-25 |
| and (b) monitoring fluorescence while changing temperature at a rate of ≥0.1° C./second. | Defendant has allegedly used the Infringing System to analyze nucleic acid hybridization by monitoring fluorescence while changing temperature at a rate equal to or greater than 0.1° C. | ¶25 | col. 38:25-29 |
’832 Patent Infringement Allegations
| Claim Element (from Independent Claim 1) | Alleged Infringing Functionality | Complaint Citation | Patent Citation |
|---|---|---|---|
| A device for performing PCR and monitoring the reaction of a sample comprising a nucleic acid and a fluorescent dye comprising: a reaction vessel... a heat exchange component... | The Infringing System is alleged to comprise a heat exchange component. | ¶31 | col. 2:4-11 |
| a control device programmed for repeatedly operating the heat exchange component to subject the sample to thermal cycling... | The Infringing System is alleged to comprise a control device used to operate the heat exchange component for thermal cycling. | ¶31 | col. 2:4-11 |
| an excitation source for optically exciting the sample... | The Infringing System is alleged to comprise an excitation source for optically exciting the sample. | ¶31 | col. 2:4-11 |
| a photodetector for detecting temperature-dependent fluorescence levels... | The Infringing System is alleged to comprise a detector for detecting fluorescence. | ¶31 | col. 2:4-11 |
| and a processor programmed to generate a melting curve of the amplification product... | The Infringing System is alleged to comprise a processor programmed to generate a melting curve. | ¶31 | col. 2:4-11 |
- Identified Points of Contention:
- Evidentiary Questions: For the ’670 Patent, a central question may be evidentiary. The complaint alleges the accused system operates at the specific temperature change rate of ≥0.1° C./second, but does not provide supporting documentation (such as technical specifications or user manuals) to substantiate this factual allegation (Compl. ¶25). The defense may challenge the factual basis for this claimed operational parameter.
- Scope Questions: For the ’832 Patent, the complaint’s description of the accused system closely mirrors the language of claim 1. A potential point of contention may arise regarding the scope of "a processor programmed to generate a melting curve." The question may be whether the processor internal to the BioMark device performs this function, or if it merely acquires raw data that is then processed by an external computer, which may or may not satisfy the claim limitation as construed by the court.
No probative visual evidence provided in complaint.
V. Key Claim Terms for Construction
The Term: "nucleic acid binding fluorescent entity" (’670 Patent, claim 76)
- Context and Importance: The scope of this term is fundamental to the breadth of the asserted method claim. Its construction will determine whether the claim covers only the specific types of fluorescent dyes discussed in the patent or a wider range of fluorescence-based detection chemistries used in modern qPCR.
- Intrinsic Evidence for Interpretation:
- Evidence for a Broader Interpretation: The specification discloses various types of fluorescent entities, including both "double strand-specific" dyes and "sequence-specific" probes, suggesting the term is generic (’670 Patent, col. 21:30-34).
- Evidence for a Narrower Interpretation: The patent provides extensive detail and examples focused on the SYBR™ Green I dye, identifying it as "preferred" (’670 Patent, col. 22:11-13). A defendant might argue that this focus limits the scope of the term to this class of intercalating dyes or those with similar binding properties.
The Term: "processor programmed to generate a melting curve" (’832 Patent, claim 1)
- Context and Importance: This term defines a key functional capability of the claimed system. Practitioners may focus on this term because its construction could determine whether infringement requires the entire function to be performed by a single, integrated processor within the device itself, or if it can be met by a system where the device acquires data and an external computer generates the curve.
- Intrinsic Evidence for Interpretation:
- Evidence for a Broader Interpretation: The patent’s Figure 51 depicts a system architecture where "PC Software" and on-instrument "Board-level software" and "Controller hardware" interact (’832 Patent, Fig. 51). This could support an interpretation that the "processor" function can be distributed between the instrument and a connected computer.
- Evidence for a Narrower Interpretation: The claim recites "a processor" in the singular. A defendant may argue that this requires a single processor within the claimed "device" to perform the complete function of generating the melting curve, not merely collecting data for subsequent, external processing.
VI. Other Allegations
- Indirect Infringement: The complaint alleges both induced and contributory infringement for both patents. The inducement claims are based on allegations that Defendant's "literature" and instructions teach customers to use the BioMark system in an infringing manner (Compl. ¶¶43, 53). The contributory infringement claims are based on allegations that the BioMark system is especially made or adapted for practicing the patented methods and has no substantial non-infringing use (Compl. ¶¶76, 83).
- Willful Infringement: Willfulness is alleged for all causes of action. The complaint asserts that Defendant acted in an "objectively reckless manner" with knowledge that its acts would likely induce or contribute to infringement of a valid patent (Compl. ¶¶28, 40, 51, 82). The complaint does not plead specific facts indicating pre-suit knowledge, such as a prior notice letter.
VII. Analyst’s Conclusion: Key Questions for the Case
- A central issue will be one of evidentiary proof: For the method claims of the ’670 Patent, what factual evidence will Plaintiffs provide to demonstrate that the accused BioMark system is used in a manner that meets the specific numerical limitation of "changing temperature at a rate of ≥0.1° C./second"?
- A key question will be one of claim scope: For the system claims of the ’832 Patent, how will the court construe the term "a processor programmed to generate a melting curve"? The resolution will likely determine whether the claim is limited to a device with a fully integrated processing capability or if it can read on systems where data acquisition and data processing are performed by separate components (e.g., the instrument and an external PC).
- A third question concerns damages and intent: Given the allegations of direct, induced, and contributory infringement, along with willfulness, the development of facts around Defendant’s knowledge of the patents-in-suit and its intent will be critical, particularly in light of the pre-suit reexamination of the ’832 Patent.