California Institute Of Technology v. Bio Rad Laboratories Inc

I. Executive Summary and Procedural Information

• Parties & Counsel:
  • Plaintiff: California Institute of Technology (California)
  • Defendant: Bio-Rad Laboratories, Inc. (Delaware)
  • Plaintiff’s Counsel: Sheppard, Mullin, Richter & Hampton LLP
• Case Identification: 5:25-cv-01701, N.D. Cal., 02/18/2025
• Venue Allegations: Venue is alleged to be proper in the Northern District of California because Defendant is headquartered in the district, maintains a regular and established place of business there, and has previously conceded that jurisdiction and venue are proper in the district in related litigation.
• Core Dispute: Plaintiff alleges that Defendant’s QX600 and QX ONE Droplet Digital PCR systems, which are capable of detecting more genetic targets than available fluorescence colors, infringe a patent related to multiplexed biochemical detection.
• Technical Context: The technology concerns high-definition multiplexed Polymerase Chain Reaction (PCR), a technique that significantly increases the number of distinct analytes detectable in a single biological sample, which is critical for efficiency and cost-effectiveness in molecular diagnostics.
• Key Procedural History: The complaint notes that this lawsuit follows extensive, ongoing litigation between Defendant and Plaintiff’s licensee, ChromaCode, Inc., over competing multiplexing technologies, including a consolidated case, In re ChromaCode Litigation, in the same district. The patent-in-suit issued on December 17, 2024, and was produced to Defendant in that litigation four days later, forming the basis for the willfulness allegation.

Case Timeline

Date	Event
2012-02-03	Priority Date for U.S. Patent No. 12,168,797
2022-12-14	Alleged first offer for sale of Accused Bio-Rad QX600 System
2023-09-20	Related litigation (ChromaCode I) filed against Bio-Rad in N.D. Cal.
2023-10-05	Related litigation (ChromaCode II) filed against Bio-Rad in C.D. Cal.
2024-08-14	ChromaCode I and II consolidated into In re ChromaCode Litigation
2024-12-12	Markman hearing held in the In re ChromaCode Litigation
2024-12-17	U.S. Patent No. 12,168,797 issues
2024-12-21	'797 Patent produced to Defendant in the In re ChromaCode Litigation
2025-02-18	Complaint filed

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

U.S. Patent No. 12,168,797 - "Signal Encoding and Decoding in Multiplexed Biochemical Assays"

• Patent Identification: U.S. Patent No. 12,168,797, "Signal Encoding and Decoding in Multiplexed Biochemical Assays," issued December 17, 2024. (Compl. ¶32; ’797 Patent, (45), (54)).

The Invention Explained

• Problem Addressed: The patent addresses the limitations of traditional fluorescence-based biochemical assays, such as PCR. These methods are constrained by the number of available, spectrally distinct fluorophores, which limits the number of targets that can be detected simultaneously in one sample (Compl. ¶¶2, 16, 23). This "one-target-per-color" system also suffers from "degeneracy," where using the same color for different targets can lead to ambiguous results that do not uniquely identify the analytes present (Compl. ¶¶3, 24; ’797 Patent, col. 1:41-50).
• The Patented Solution: The invention claims to solve this problem by encoding and decoding signals using not just the color (wavelength) of a fluorescent signal, but also its intensity level. By associating each target analyte with a unique combination of color and intensity, the system can unambiguously identify more targets than there are available color channels (Compl. ¶¶4, 27). A processor-controlled analyzer applies a "decoding matrix" to the cumulative signal from all fluorophores to determine which specific analytes are present in the sample, even when multiple targets share the same fluorophore (’797 Patent, Abstract; col. 2:1-17).
• Technical Importance: This technology, referred to in the complaint as HDPCR, enables a significant expansion of multiplexing capabilities, which is critical for developing faster, more cost-effective, and high-throughput molecular diagnostic assays (Compl. ¶28).

Key Claims at a Glance

• The complaint asserts independent claims 1, 19, 22, and 30 (Compl. ¶34). Claims 1 and 19 are directed to systems, Claim 22 to a reaction mixture, and Claim 30 to a kit.
• Independent Claim 1: Recites a system comprising:
  • A sample chamber configured to house a sample, analyte-specific hybridization probes, and multiple fluorophores.
  • A multi-channel detector for detecting first, second, third, and fourth electromagnetic signals at distinct wavelengths generated by excitement of four corresponding fluorophores.
  • A processor-controlled analyzer that receives a cumulative signal and applies a "decoding matrix" to "unambiguously detect" M analytes by associating each with a first value (intensity) and a second value (wavelength).
  • The system operates without immobilization, mass spectrometry, or melting curve analysis.
  • A mathematical relationship where M (number of analytes) is greater than C (number of channels/colors), and M is defined by the formula M=C*log₂(F+1).
• Independent Claim 19: Recites a system comprising a processor, display, and non-transitory computer-readable medium with instructions for the processor to:
  • Obtain "cumulative signal data" from a digital PCR instrument.
  • Apply a "decoding matrix" to this data to "unambiguously determine" the presence or absence of M analytes.
  • Plot a representation of the intensity and wavelength values on the display.
• The complaint does not explicitly reserve the right to assert dependent claims, but infringement allegations are made generally against the patent.

III. The Accused Instrumentality

Product Identification

• The accused instrumentalities are Defendant’s "QX600 Droplet Digital PCR System" and "QX ONE Droplet Digital PCR System," along with associated components and assays (collectively, the "Accused Products") (Compl. ¶¶42, 50, 57).

Functionality and Market Context

• The complaint alleges the Accused Products perform "advanced... multiplexing," enabling the detection of more targets than available color channels (Compl. ¶¶10, 51). Specifically, the QX600 System is advertised as having "six color detection capable of quantifying 12 targets per well" (Compl. ¶42). The QX ONE System is alleged to use four color channels to detect up to eight targets (Compl. ¶51).
• This enhanced capability is allegedly achieved through a feature Defendant calls "Amplitude multiplex," which the complaint describes as a "Method to increase multiplexing up to twelve targets per well, with one or two targets detected per [color]" (Compl. ¶46).
• A promotional bulletin for the QX600 system, included in the complaint, depicts 2-D fluorescence plots showing the detection of 12 targets using six channels, with distinct data clusters separated by amplitude within a single channel (Compl. p. 18, ¶47). A similar bulletin for the QX ONE system shows the detection of eight targets using four color channels, also demonstrating separation by amplitude (Compl. p. 20, ¶51).
• The complaint positions the Accused Products as commercially important advancements in the life science research and clinical diagnostics markets, leveraging Defendant's established ddPCR technology platform (Compl. ¶¶19, 42).

IV. Analysis of Infringement Allegations

• Claim Chart Summary: The complaint provides a narrative infringement theory for Claim 1 (Compl. ¶57).

U.S. Patent No. 12,168,797 Infringement Allegations

Claim Element (from Independent Claim 1)	Alleged Infringing Functionality	Complaint Citation	Patent Citation
a sample chamber configured to house a sample and analyte-specific reagent mixtures...	The Accused Products include a sample chamber (e.g., wells for droplet generation) for housing samples and reagent mixtures.	¶57	col. 11:25-27
a multi-channel detector to detect... a fourth electromagnetic signal at a fourth wavelength...	The QX600 system has a six-color detector and the QX ONE has a four-color detector, both capable of detecting signals at multiple wavelengths.	¶¶42, 51, 57	col. 11:28-12:7
a processor controlled analyzer to receive... a cumulative signal... and apply a decoding matrix to the cumulative signal to unambiguously detect the presence or absence of at least each of M analytes...	The Accused Products allegedly use a processor-controlled analyzer that applies a "mathematical model or equivalent decoding matrix" to process cumulative fluorescence signals from multiple fluorophores. This is allegedly performed via Defendant's "Amplitude multiplex" feature.	¶¶46, 57	col. 12:8-14
wherein M is greater than the number of the second values used to encode the analytes (C)...	The QX600 system allegedly detects 12 targets (M) using 6 colors (C), and the QX ONE system detects 8 targets using 4 colors, thereby meeting the M > C limitation.	¶¶42, 51	col. 12:18-20

• Identified Points of Contention:
  • Scope Questions: A central dispute may arise over the meaning of "decoding matrix." The complaint alleges Defendant's "Amplitude multiplex" functionality and "mathematical model" are equivalent to a "decoding matrix" (Compl. ¶57). The defense may argue that "amplitude multiplexing" is a distinct technology that does not meet the specific structural or functional requirements of the claimed "decoding matrix" as defined and enabled by the patent specification.
  • Technical Questions: The complaint alleges infringement of claims containing the formula M=C*log₂(F+1) but does not provide a factual basis showing how the Accused Products' operation maps to this specific equation. A key evidentiary question will be whether Plaintiff can demonstrate that the relationship between targets, colors, and intensity levels in the Accused Products satisfies this mathematical limitation, either literally or equivalently. The visual evidence in the complaint shows clustered data points rather than discrete integer-based intensity levels, which may raise questions about a technical mismatch with the patent's specific embodiments (Compl. p. 18; '797 Patent, Tbl. 3).

V. Key Claim Terms for Construction

• The Term: "decoding matrix"

• Context and Importance: This term is at the core of the patented invention and the infringement allegations. The case will likely depend on whether Defendant's "Amplitude multiplex" software and data analysis methods fall within the scope of this term. Practitioners may focus on this term because its construction will determine whether a system that distinguishes targets by signal strength performs the same function as the claimed invention.

• Intrinsic Evidence for Interpretation:

  • Evidence for a Broader Interpretation: The patent specification provides a broad, functional definition, stating a decoding matrix "enables the conversion of a cumulative signal to information concerning the presence or absence of one or more analytes" (’797 Patent, col. 10:21-25).
  • Evidence for a Narrower Interpretation: The specification provides detailed examples of decoding matrices in tabular form (e.g., ’797 Patent, Tbl. 4) based on discrete, additive integer intensity values. A party could argue the term should be limited to these specific disclosed embodiments, especially if they are presented as the solution to the degeneracy problem.

• The Term: "cumulative signal"

• Context and Importance: This term is critical for defining the input to the "decoding matrix." How this signal is formed and what it represents will be key to the infringement analysis. The dispute may turn on whether the signal measured by the Accused Products is "cumulative" in the manner required by the claims.

• Intrinsic Evidence for Interpretation:

  • Evidence for a Broader Interpretation: Claim 1 describes it generally as a signal "based on the first, second, third, and fourth electromagnetic signals" (’797 Patent, col. 12:9-11), suggesting any combined or aggregate signal could qualify.
  • Evidence for a Narrower Interpretation: The patent’s examples consistently illustrate the cumulative signal as an additive sum of integer-based intensity levels for each color channel (’797 Patent, Tbl. 3; col. 13:11-14). This could support an argument that the term requires a specific type of digital, additive signal, potentially excluding other forms of analog signal aggregation.

VI. Other Allegations

• Indirect Infringement: The complaint alleges both induced and contributory infringement. The inducement allegation is based on Defendant's "QX600 System User Guide," which allegedly instructs and encourages customers to use the infringing "Amplitude multiplex" feature (Compl. ¶58). The contributory infringement allegation is based on the sale of the Accused Products and associated assays that are alleged to be especially made for the infringing use and not a staple article of commerce (Compl. ¶¶59-60).
• Willful Infringement: Willfulness is alleged based on Defendant’s knowledge of the ’797 Patent as of December 21, 2024, when Plaintiff produced it to Defendant in the context of the separate but related In re ChromaCode Litigation (Compl. ¶¶19, 48). The complaint alleges that Defendant’s continued sale of the Accused Products after receiving notice constitutes willful, wanton, and egregious infringement (Compl. ¶62).

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

• A core issue will be one of claim scope and technical equivalence: Will the court construe the term "decoding matrix" broadly to encompass any algorithm that resolves signal intensity levels, as Plaintiff alleges, or will it be limited to the specific, integer-based tabular structures disclosed in the patent? The resolution of this question will likely determine whether Defendant's "amplitude multiplexing" technology infringes.
• A key evidentiary question will be one of mathematical proof: Can Plaintiff provide evidence that the operation of the Accused Products meets the specific mathematical formula "M=C*log₂(F+1)" recited in the asserted claims? The complaint asserts this is met but provides no analysis, making it a central point that will require technical expert testimony to resolve.
• A third significant question will concern willfulness and damages: Given the extensive pre-existing litigation between Defendant and Plaintiff's licensee, and the allegation that Plaintiff provided the patent to Defendant just four days after its issuance, a court will likely scrutinize Defendant’s conduct for evidence of objective recklessness to determine willfulness.