DCT
5:23-cv-04823
IN RE: ChromaCode LITIGATION
I. Executive Summary and Procedural Information
- Parties & Counsel:
- Plaintiff: ChromaCode, Inc. (Delaware)
- Defendant: Bio-Rad Laboratories, Inc. (Delaware)
- Plaintiff’s Counsel: Wilson Sonsini Goodrich & Rosati, P.C.
- Case Identification: 5:23-cv-04823, N.D. Cal., 09/20/2023
- Venue Allegations: Venue is asserted on the basis that Defendant Bio-Rad Laboratories, Inc. resides in the Northern District of California, with its headquarters located in Hercules, California.
- Core Dispute: Plaintiff seeks a declaratory judgment that its High-Definition PCR (HDPCR) Assays do not infringe two of Defendant's patents related to methods for multiplexed digital assays.
- Technical Context: The technology at issue involves digital polymerase chain reaction (dPCR) methods for simultaneously detecting multiple genetic targets (multiplexing) in a biological sample.
- Key Procedural History: The complaint was filed in response to a September 6, 2023, letter from Defendant Bio-Rad to Plaintiff ChromaCode, which accused ChromaCode's HDPCR Assays of infringing the patents-in-suit and included exemplary infringement claim charts.
Case Timeline
| Date | Event |
|---|---|
| 2011-03-18 | Priority Date for U.S. Patent No. 9,222,128 |
| 2011-03-18 | Priority Date for U.S. Patent No. 9,921,154 |
| 2015-12-29 | U.S. Patent No. 9,222,128 Issues |
| 2018-03-20 | U.S. Patent No. 9,921,154 Issues |
| 2023-09-06 | Bio-Rad sends Infringement Letter to ChromaCode |
| 2023-09-20 | Complaint for Declaratory Judgment Filed |
II. Technology and Patent(s)-in-Suit Analysis
U.S. Patent No. 9,222,128, "Multiplexed digital assays with combinatorial use of signals," Issued December 29, 2015
The Invention Explained
- Problem Addressed: The patent describes a limitation in conventional multiplexed digital PCR assays where the number of targets that can be simultaneously measured is restricted by the number of distinct fluorescent dyes (or "colors") a detection instrument can distinguish. Increasing the number of detection channels to read more colors is described as expensive and impractical beyond a certain point (’128 Patent, col. 1:4-24).
- The Patented Solution: The invention proposes a method to assay more targets than there are available detection channels (i.e., assay more than R targets using R signals). This is achieved through a "combinatorial use of signals," where each signal can be a composite representing a unique combination of multiple targets present in a single partition (e.g., a droplet). The system then calculates the level of each individual target by analyzing the R signals together and mathematically accounting for the probability of multiple different targets coinciding in the same partition (’128 Patent, Abstract; col. 6:43-54).
- Technical Importance: This approach allows for a higher degree of multiplexing without requiring more complex and expensive hardware, increasing the efficiency and lowering the cost of analyzing samples with limited volumes (’128 Patent, col. 1:19-24).
Key Claims at a Glance
- The complaint identifies independent claim 1 as a subject of Defendant's infringement allegations (Compl. ¶15).
- The essential elements of claim 1 are:
- amplifying more than R targets in partitions;
- creating R signals representative of light detected in R different wavelength regimes from the partitions, where R≥2;
- calculating an average level of each target in the partitions based on the R signals,
- wherein the level calculated accounts for a coincidence of all possible combinations of the more than R targets in the same individual partitions.
- The complaint seeks a judgment of non-infringement for any claim of the patent (Compl. ¶31).
U.S. Patent No. 9,921,154, "Multiplexed digital assays," Issued March 20, 2018
The Invention Explained
- Problem Addressed: Like the ’128 Patent, this patent addresses the challenge of increasing the number of targets in a digital assay beyond the number of available optical channels in the detection hardware (’154 Patent, col. 2:11-21).
- The Patented Solution: The invention describes a system for multiplexed detection of signals from reporters for two or more distinct targets within a "common or shared channel." The system distinguishes between targets in the same channel by creating assays where each target produces a signal of a different, resolvable intensity level. This allows multiple targets to be identified and quantified using a single optical channel, thereby expanding the multiplexing capacity (’154 Patent, col. 5:55-67; col. 6:49-56).
- Technical Importance: This intensity-based multiplexing technique enables more targets to be analyzed than available optical channels, increasing the data output from a single experiment on standard dPCR instrumentation (’154 Patent, col. 5:8-13).
Key Claims at a Glance
- The complaint identifies independent claim 1 as a subject of Defendant's infringement allegations (Compl. ¶15).
- The essential elements of claim 1 are:
- forming partitions that collectively contain R targets;
- amplifying the R targets in the partitions;
- collecting data representing amplification of each of the R targets in the partitions, with all data collected in fewer than R optical channels;
- determining a respective level of each of the R targets from the data;
- wherein each level is specific for a single target of the R targets; and
- wherein the level determined for at least one of the R targets is based in part on a partition count for a partition population positive for two of the R targets.
- The complaint seeks a judgment of non-infringement for any claim of the patent (Compl. ¶39).
III. The Accused Instrumentality
Product Identification
- Plaintiff ChromaCode’s "HDPCR Assays" (Compl. ¶7).
Functionality and Market Context
- The complaint references infringement allegations concerning ChromaCode's activities, including the making, using, offering to sell, and selling of its HDPCR Assays (Compl. ¶14). Bio-Rad's allegations, attached as Exhibit C to the complaint, describe the accused technology as a "high-definition PCR (HDPCR™) assay" for multiplexed detection of DNA and RNA variants (Compl., Ex. C, App'x 1, p. 78). The technology is alleged to enable "different variants to generate a signal at different intensity levels in single color channel, allowing for greater than N targets in N color channels." It is also described as using "resilient encoding," which "generates a signal in more than one color channel to create a form of error-detecting code" (Compl., Ex. C, App'x 1, p. 78).
IV. Analysis of Infringement Allegations
U.S. Patent No. 9,222,128 Infringement Allegations
| Claim Element (from Independent Claim 1) | Alleged Infringing Functionality | Complaint Citation | Patent Citation |
|---|---|---|---|
| amplifying more than R targets in partitions; | ChromaCode’s HDPCR assays allegedly perform multiplexed detection of numerous DNA and RNA variants, exceeding the number of available detection channels. | ¶15; Ex. C, App'x 1, p. 78 | col. 5:3-12 |
| creating R signals representative of light detected in R different wavelength regimes from the partitions, where R≥2; and | ChromaCode’s technology allegedly uses a "resilient encoding strategy" where targets are encoded in single channels or across multiple channels to create signals. A provided visual, "Figure 1. Resilient encoding strategy for molecular variants," illustrates how multiple targets are encoded in different channels (Compl., Ex. C, App'x 1, p. 78). | ¶15; Ex. C, App'x 1, p. 78 | col. 6:26-41 |
| calculating an average level of each target in the partitions based on the R signals, | The accused HDPCR technology is alleged to resolve partitions that contain single or multiple variants. | ¶15; Ex. C, App'x 1, p. 79 | col. 8:51-55 |
| wherein the level calculated accounts for a coincidence of all possible combinations of the more than R targets in the same individual partitions; | Bio-Rad alleges that ChromaCode's ability to "resolve partitions that contain both and those that contain only one" variant constitutes a calculation that accounts for the coincidence of different targets in the same partition. A provided visual, "Figure 2," illustrates experimental data allegedly showing this resolution (Compl., Ex. C, App'x 1, p. 79). | ¶15; Ex. C, App'x 1, p. 79 | col. 8:10-17 |
Identified Points of Contention
- Scope Questions: The primary dispute appears to center on the final limitation of claim 1. ChromaCode explicitly argues that its products do not perform the claimed step of "calculat[ing] an average level of each target... wherein the level calculated accounts for a coincidence of all possible combinations of the more than R targets in the same individual partitions" (Compl. ¶19). This raises the question of whether ChromaCode's proprietary data analysis method falls within the scope of this claim element.
U.S. Patent No. 9,921,154 Infringement Allegations
| Claim Element (from Independent Claim 1) | Alleged Infringing Functionality | Complaint Citation | Patent Citation |
|---|---|---|---|
| forming partitions that collectively contain R targets; | ChromaCode’s HDPCR assays are run on a digital PCR system, which inherently involves forming partitions containing the targets. | ¶15; Ex. C, App'x 2, p. 83 | col. 6:57-61 |
| amplifying the R targets in the partitions; | The accused HDPCR assays are described as being run on the Applied Biosystems QuantStudio Absolute Q Digital PCR system, which performs amplification. | ¶15; Ex. C, App'x 2, p. 83 | col. 7:4-7 |
| collecting data representing amplification of each of the R targets in the partitions, all of the data being collected in fewer than R optical channels; | ChromaCode’s technology is alleged to enable "different variants to generate a signal at different intensity levels in single color channel, allowing for greater than N targets in N color channels," which is alleged to satisfy the "fewer than R optical channels" limitation. | ¶15; Ex. C, App'x 2, p. 84 | col. 5:35-42 |
| determining a respective level of each of the R targets from the data, | Data analysis is allegedly performed with "proprietary analysis algorithms" to determine the presence of different variants. | ¶15; Ex. C, App'x 2, p. 85 | col. 9:46-48 |
| wherein each level is specific for a single target of the R targets, | The accused assays are for multiplexed detection of specific DNA and RNA variants. | ¶15; Ex. C, App'x 2, p. 85 | col. 10:49-54 |
| and wherein the level determined for at least one of the R targets is based in part on a partition count for a partition population positive for two of the R targets; | Bio-Rad alleges that ChromaCode’s ability to "resolve partitions that contain both [variants] and those that contain only one" is based on a partition count for a population positive for two targets. | ¶15; Ex. C, App'x 2, p. 85 | col. 12:4-14 |
Identified Points of Contention
- Technical Questions: ChromaCode contends that its products do not "determine[e] a respective level of each of the R targets from the data" as required by the claim (Compl. ¶20). It further denies that its products require "a partition count for a partition population positive for two of the R targets" (Compl. ¶20). This suggests a potential dispute over whether ChromaCode's algorithms perform the specific analytical steps recited in the claim, or if they use an alternative, un-claimed methodology to achieve a similar multiplexing result.
V. Key Claim Terms for Construction
Term from the ’128 Patent: "accounts for a coincidence of all possible combinations" (claim 1)
- Context and Importance: This term defines the core mathematical operation that enables the "combinatorial use of signals." The infringement dispute may turn on whether ChromaCode's data analysis methods meet this definition. Practitioners may focus on this term because ChromaCode's complaint specifically denies performing this function (Compl. ¶19).
- Intrinsic Evidence for Interpretation:
- Evidence for a Broader Interpretation: The specification suggests that the calculation can be performed through various means, stating that "solutions may be found by numerical analysis, also termed numerical approximation" (’128 Patent, col. 9:1-2), which may support construing the term to cover a range of algorithmic approaches.
- Evidence for a Narrower Interpretation: The detailed description provides specific examples of calculating target levels by "finding solutions to a series of simultaneous equations" and includes an exemplary MATLAB implementation (’128 Patent, col. 8:60-64; col. 15:52-col. 18:11). This could be used to argue that the term is limited to the specific mathematical models disclosed.
Term from the ’154 Patent: "level determined for at least one of the R targets is based in part on a partition count for a partition population positive for two of the R targets" (claim 1)
- Context and Importance: This limitation appears to require that the quantification of at least one target relies on identifying and counting partitions that contain at least two different targets. ChromaCode explicitly denies that its products require such a count (Compl. ¶20), making this term's construction central to the infringement analysis for the ’154 patent.
- Intrinsic Evidence for Interpretation:
- Evidence for a Broader Interpretation: The claim uses the general term "based in part on," which could suggest that any analytical reliance on a multi-target population, however indirect, would suffice.
- Evidence for a Narrower Interpretation: The patent’s detailed description and figures repeatedly illustrate the concept of identifying and counting droplets in distinct "double-positive" clusters on a scatter plot (’154 Patent, Figs. 5, 12-18; col. 15:48-col. 16:11). This may support an interpretation that the "partition count" must come from an explicitly identified and enumerated population of partitions containing two specific targets.
VI. Other Allegations
- Indirect Infringement: The complaint states that ChromaCode has not induced or contributed to any third-party product or technology that practices the patents-in-suit (Compl. ¶2, ¶18).
VII. Analyst’s Conclusion: Key Questions for the Case
The dispute appears to center on the specific data analysis methods employed by ChromaCode’s HDPCR platform. The key questions for the case will likely be:
- A core issue will be one of algorithmic scope: does ChromaCode's proprietary data analysis algorithm perform the specific mathematical step of "account[ing] for a coincidence of all possible combinations" of targets as required by claim 1 of the ’128 Patent, or does it utilize a different, non-infringing computational method to deconvolve multiplexed signals?
- A key evidentiary question will be one of functional operation: does ChromaCode's system rely on a "partition count for a partition population positive for two of the R targets" to determine target levels, as recited in claim 1 of the ’154 Patent, or does it quantify targets using an alternative analytical framework that does not require this specific step?