DCT
1:25-cv-01287
10X Genomics Inc v. Illumina Inc
Key Events
Complaint
I. Executive Summary and Procedural Information
- Parties & Counsel:
- Plaintiff: 10x Genomics, Inc. (Delaware) and Roche Sequencing Solutions, Inc. (Delaware)
- Defendant: Illumina, Inc. (Delaware)
- Plaintiff’s Counsel: Shaw Keller LLP; Tensegrity Law Group LLP; Wilmer Cutler Pickering Hale & Dorr LLP
- Case Identification: 1:25-cv-01287, D. Del., 10/21/2025
- Venue Allegations: Venue is alleged to be proper in the District of Delaware because Defendant Illumina is a Delaware corporation and therefore resides in the district.
- Core Dispute: Plaintiffs allege that Defendant’s single-cell RNA preparation kits, utilizing technology acquired from Fluent BioSciences, infringe five patents related to methods for creating barcoded beads and for analyzing nucleic acids in partitioned droplets.
- Technical Context: The technology at issue is single-cell genomics, a field that enables the high-resolution study of gene expression and other molecular information on a cell-by-cell basis, which is critical for research in areas such as oncology, immunology, and neuroscience.
- Key Procedural History: The complaint alleges that Defendant Illumina acquired the accused technology through its acquisition of Fluent BioSciences on July 9, 2024. Plaintiffs also allege pre-suit knowledge of the patents, based on a notice letter dated October 20, 2025, and on Defendant's alleged monitoring and citation of the asserted patent families during prosecution of its own patent applications.
Case Timeline
| Date | Event |
|---|---|
| 2011-01-31 | Priority Date for ’214 and ’902 Patents |
| 2019-02-12 | Priority Date for ’993, ’239, and ’102 Patents |
| 2023-03-01 | Fluent BioSciences began marketing its single-cell technology (approx.) |
| 2023-07-04 | U.S. Patent No. 11,692,214 Issues |
| 2024-03-19 | U.S. Patent No. 11,932,902 Issues |
| 2024-07-09 | Illumina acquires Fluent BioSciences |
| 2025-04-15 | U.S. Patent No. 12,275,993 Issues |
| 2025-05-20 | U.S. Patent No. 12,305,239 Issues |
| 2025-09-16 | U.S. Patent No. 12,416,102 Issues |
| 2025-10-21 | Complaint Filed |
II. Technology and Patent(s)-in-Suit Analysis
U.S. Patent No. 11,692,214 - Barcoded beads and method for making the same by split-pool synthesis (Issued Jul. 4, 2023)
- The Invention Explained:
- Problem Addressed: The patent describes prior art methods for analyzing biological samples as insufficient because they "require significant amounts of biological samples or will not provide cell specific information," with multiplexed protein measurement presenting particular challenges (’214 Patent, col. 1:47-52).
- The Patented Solution: The invention provides a method to create a large population of beads, each with a unique nucleic acid tag. This tag allows a researcher to simultaneously determine the identity of a biological target (e.g., a protein) and the unique cell from which it originated (’214 Patent, col. 1:40-45). This is achieved by building a "cell origination barcode" on the beads through a "split-pool" synthesis process, where beads are repeatedly split into different reaction vessels, tagged with a piece of a barcode, and then pooled back together (’214 Patent, col. 8:45-54). The nucleic acid tag also includes a "degenerate sequence."
- Technical Importance: This approach enables high-throughput, single-cell analysis of complex and heterogeneous biological samples, such as tumors, which was not feasible with older, bulk-analysis techniques (Compl. ¶11).
- Key Claims at a Glance:
- The complaint asserts independent claims 1 and 11 (Compl. ¶23).
- Independent Claim 1 (Composition): A population of beads comprising:
- A first bead with a first nucleic acid tag, which comprises (i) a first cell origination barcode and (ii) a degenerate sequence.
- A second bead with a second nucleic acid tag, which comprises (i) a second cell origination barcode and (ii) a degenerate sequence.
- The first and second cell origination barcodes are different.
- Independent Claim 11 (Method): A method for making a population of barcoded beads, comprising:
- Adding nucleic acid tags that comprise a cell origination barcode and a degenerate sequence onto beads by a split-pool barcoding process.
- The complaint notes that it may also assert dependent claims directed to specific improvements, such as population size and multiple rounds of barcoding (Compl. ¶27).
U.S. Patent No. 11,932,902 - Barcoded beads and method for making the same by split-pool synthesis (Issued Mar. 19, 2024)
- The Invention Explained:
- Problem Addressed: The patent addresses the same problem as the ’214 Patent: prior methods for analyzing biological samples lacked the ability to provide cell-specific information, especially for multiplexed protein measurements (’902 Patent, col. 1:51-56, as quoted in Compl. ¶30).
- The Patented Solution: The invention claims a method for creating cell origination barcodes on beads through an iterative "split-pool" process. This involves physically splitting a pool of beads into multiple reaction volumes, appending pre-made oligonucleotide sequences to the beads in each volume, and then pooling the beads back together. By repeating this process, a unique, ordered sequence of oligonucleotides is built up to form the final barcode on each bead (’902 Patent, Abstract, as quoted in Compl. ¶30).
- Technical Importance: The iterative split-pool synthesis process allows for the combinatorial creation of an exponentially large library of unique barcodes, enabling the analysis of millions of individual cells in a single experiment (Compl. ¶11).
- Key Claims at a Glance:
- The complaint asserts independent claims 1, 17, and 23 (Compl. ¶28).
- Independent Claim 1 (Method): A method for adding cell origination barcodes onto beads, comprising the steps of (a) splitting a pool of beads, (b) appending different pre-made oligonucleotides in the separate volumes, (c) pooling the beads, and (d) repeating steps (a)-(c) one or more times, where oligonucleotides are added to previously appended ones.
- Independent Claim 17 (Method): A method of adding barcodes via a split-pool process comprising multiple rounds of (i) splitting, (ii) adding pre-made oligonucleotides, and (iii) pooling the beads.
- Independent Claim 23 (Composition): A population of beads where a first bead has a first cell origination barcode comprising a first plurality of ordered oligonucleotides, and a second bead has a different, second cell origination barcode comprising a second plurality of ordered oligonucleotides.
- The complaint reserves the right to assert dependent claims related to multiple rounds of barcoding and specific bead choices (Compl. ¶32).
U.S. Patent No. 12,275,993 - Analysis of nucleic acid sequences
- Patent Identification: U.S. Patent No. 12,275,993, "Analysis of nucleic acid sequences," issued April 15, 2025 (Compl. ¶33).
- Technology Synopsis: The patent addresses the technical challenge of altering the concentration of a reagent within a pre-formed droplet (’993 Patent, col. 1:41-43, as quoted in Compl. ¶37). The patented solution is a method that uses two separate emulsions: a first containing droplets with a lysis reagent, and a second containing droplets with a cell and barcoded particles. The method transfers the lysis reagent from the first emulsion to the second via micelles to lyse the cell (Compl. ¶36).
- Asserted Claims: Independent claims 1 and 25 (Compl. ¶36).
- Accused Features: The complaint alleges that the accused workflow, which uses two emulsions and micellar transport to deliver a lysis reagent to cell-containing droplets, infringes the ’993 Patent (Compl. ¶¶16, 73).
U.S. Patent No. 12,305,239 - Analysis of nucleic acid sequences
- Patent Identification: U.S. Patent No. 12,305,239, "Analysis of nucleic acid sequences," issued May 20, 2025 (Compl. ¶34).
- Technology Synopsis: This patent also addresses the difficulty of changing reagent amounts in existing droplets (’239 Patent, col. 1:41-43, as quoted in Compl. ¶42). The claimed solution involves generating a "micellized lysis agent" from a first set of droplets and delivering it to a second set of droplets containing cells and barcoded particles, thereby lysing the cells and enabling the barcoding of their mRNA (Compl. ¶41).
- Asserted Claims: Independent claims 1 and 29 (Compl. ¶41).
- Accused Features: The accused workflow is alleged to infringe by generating and delivering a "micellized lysis agent" between droplets to lyse cells (Compl. ¶¶16, 81).
U.S. Patent No. 12,416,102 - Systems and methods for transfer of reagents between droplets
- Patent Identification: U.S. Patent No. 12,416,102, "Systems and methods for transfer of reagents between droplets," issued September 16, 2025 (Compl. ¶35).
- Technology Synopsis: This patent also addresses the challenge of modifying reagent concentrations within droplets (’102 Patent, col. 1:41-43, as quoted in Compl. ¶47). The solution is a method where droplets are generated by agitation, and a reagent is transferred from one droplet to another "via a mediator comprising an aggregate of surfactant molecules" (i.e., a micelle) to release nucleic acids from an analyte carrier (Compl. ¶46).
- Asserted Claims: Independent claim 1 (Compl. ¶46).
- Accused Features: The accused workflow is alleged to infringe by using a "mediator" comprised of surfactant molecules to transfer reagents between droplets (Compl. ¶¶16, 22, 89).
III. The Accused Instrumentality
- Product Identification: The accused instrumentalities are Illumina's Single Cell 3' RNA Prep Kits, including the T2, T10, T20, and T100 kits, and associated components, reagents, and services. These products were previously marketed by Fluent BioSciences as "Fluent PIPseq V 3' Single Cell RNA Kits" before Illumina's acquisition of Fluent (Compl. ¶¶16, 19).
- Functionality and Market Context: The complaint alleges the accused kits use a workflow called "PIPseq chemistry" to perform single-cell mRNA capture and barcoding without complex microfluidics (Compl. ¶16). The process involves emulsifying a cell suspension with template particles—hydrogel beads containing barcoded oligonucleotides—to create "particle-templated instant partitions" (PIPs). Lysis reagents from a separate emulsion are then transferred into these cell-containing PIPs "via micellar transport." This lyses the cells, releasing mRNA that is then captured by a poly(dT)V sequence on the barcoded bead and reverse transcribed into cDNA for sequencing (Compl. ¶16). Figure 2 from the complaint illustrates the accused seven-step workflow, from preparing a cell suspension to data analysis (Compl. p. 8).
IV. Analysis of Infringement Allegations
The complaint references claim chart exhibits that were not provided. The following tables are constructed based on the narrative allegations in the complaint body.
U.S. Patent No. 11,692,214 Infringement Allegations
| Claim Element (from Independent Claim 11) | Alleged Infringing Functionality | Complaint Citation | Patent Citation |
|---|---|---|---|
| adding nucleic acid tags that comprise a cell origination barcode...onto beads | The accused workflow uses beads with barcoded oligonucleotides that include "cell barcodes for identifying the PIP [particle-templated instant partitions]." | ¶16 | col. 8:45-50 |
| ...and a degenerate sequence | The barcoded oligonucleotide on the accused beads includes a "poly(dT)V capture site for 3' capture of mRNA," where 'V' represents a degenerate base (A, C, or G). | ¶16 | col. 6:20-23 |
| ...by a split-pool barcoding process. | The barcoded beads used in the accused kits are allegedly synthesized using a "split-pooling method" involving repeated steps of suspending beads in wells, attaching barcodes, and pooling. | ¶17, ¶18 | col. 8:45-54 |
U.S. Patent No. 11,932,902 Infringement Allegations
| Claim Element (from Independent Claim 1) | Alleged Infringing Functionality | Complaint Citation | Patent Citation |
|---|---|---|---|
| (a) splitting a pool of beads into a plurality of reaction volumes; | The accused synthesis method involves "suspending beads in each well of a 96-well plate," which constitutes splitting a pool into multiple reaction volumes. | ¶17 | Abstract |
| (b) appending pre-made oligonucleotides onto the beads in the plurality of reaction volumes... | The accused method involves "attaching the unique barcode" contained in each well onto the beads suspended within that well. | ¶17 | Abstract |
| (c) pooling the beads; and | The accused method involves "pooling the beads from the 96 wells" after the barcode attachment step. | ¶17 | Abstract |
| (d) repeating steps (a)-(c) one or more times to produce a pool of beads that comprise the cell origination barcodes... | The accused method involves "repeating the steps to add four (4) barcode sequences," with documentation indicating a "tiered barcode system." | ¶17, ¶18 | Abstract |
- Identified Points of Contention:
- Scope Questions: The infringement read for the ’214 Patent hinges on whether the accused product's "poly(dT)V capture site" meets the claim limitation of a "degenerate sequence." A potential dispute is whether the term "degenerate sequence," as used in the patent, can be construed to cover a sequence whose primary function is mRNA capture, or if its scope is limited by specification examples describing such sequences for functions like "tagging" or post-amplification equalization (’214 Patent, Fig. 6).
- Technical Questions: For the ’902 Patent, Claim 1(d) requires that oligonucleotides in repeat steps are "added to previously appended oligonucleotides to form the cell origination barcodes." This language may suggest a specific chemical process, such as ligation or extension. A question for the court will be whether the accused product's method of "attaching" and "add[ing]" barcode sequences (Compl. ¶17) performs this specific step of elongating a previously attached oligonucleotide chain.
V. Key Claim Terms for Construction
The Term: "degenerate sequence" (from ’214 Patent, Claim 1)
- Context and Importance: This term's construction is critical for infringement of the ’214 Patent's composition claims. Plaintiffs' theory appears to equate the accused product's "poly(dT)V capture site" with this limitation. Practitioners may focus on this term because its definition will determine whether a feature designed for mRNA capture falls within the scope of a claim element potentially intended for molecular counting or tagging.
- Intrinsic Evidence for Interpretation:
- Evidence for a Broader Interpretation: The specification states that a "random region" can be "either a degenerate oligo or nucleotides that will allow random base matching" (’214 Patent, col. 6:20-23), suggesting the term is not limited to a single specific structure or function.
- Evidence for a Narrower Interpretation: The patent's figures and description of a "random region to 'tag' each dual bar code individually" (’214 Patent, Fig. 6) may be argued to limit the term's scope to sequences used for tagging or equalization, a different function than mRNA capture.
The Term: "appending pre-made oligonucleotides onto the beads" (from ’902 Patent, Claim 1)
- Context and Importance: The mechanism of "appending" is central to the method claims of the ’902 Patent. The dispute may turn on whether this term implies a specific chemical reaction (e.g., ligation, extension) or can broadly cover any method of attachment.
- Intrinsic Evidence for Interpretation:
- Evidence for a Broader Interpretation: The plain language of "appending" does not inherently require a specific chemical mechanism. The patent abstract, as quoted in the complaint, uses the general term "appending" without further limitation (Compl. ¶30).
- Evidence for a Narrower Interpretation: A defendant may argue that the specification's embodiments, if they only disclose specific methods like enzymatic ligation to join oligonucleotides, limit the term "appending" to those disclosed mechanisms. The patent's description of forming the barcode by adding oligonucleotides "to previously appended oligonucleotides" (Compl. ¶28) may support an interpretation requiring chain elongation.
VI. Other Allegations
- Indirect Infringement: The complaint alleges both induced and contributory infringement for all five asserted patents. The inducement allegations are based on Defendant's product documentation, user guides, data sheets, and training materials, which allegedly instruct customers to use the accused kits in a manner that directly infringes the patents (Compl. ¶¶ 55, 65, 73, 81, 89).
- Willful Infringement: Willfulness is alleged for all five patents. The complaint bases this on alleged pre-suit and post-suit knowledge. Pre-suit knowledge is alleged based on a notice letter sent by 10x on October 20, 2025, as well as on Illumina's alleged monitoring of the asserted patent families and citation of those families during the prosecution of its own patents (Compl. ¶¶ 54, 58, 64, 72, 80, 88).
VII. Analyst’s Conclusion: Key Questions for the Case
- A core issue will be one of technical operation: does the accused two-emulsion workflow, which employs "micellar transport" to deliver lysis reagents, practice the specific multi-step methods of generating and transferring reagents between droplets as claimed by the ’993, ’239, and ’102 Patents? This raises an evidentiary question of functional equivalence between the accused process and the claimed steps.
- Another central issue will be one of definitional scope: can the term "degenerate sequence" in the ’214 Patent, which the specification links to "tagging" functions, be construed to cover the "poly(dT)V capture site" in the accused product, whose primary function is capturing mRNA? The outcome of this claim construction dispute may be dispositive for infringement of that patent.
- A third key question will concern the intersection of claim scope and public knowledge: does the accused "split-pool" synthesis method, which the complaint itself links to a 2021 scientific publication (Compl. ¶17), fall within the scope of the ’214 and ’902 Patent claims, which have a 2011 priority date? The court's analysis of the technical steps of the accused process relative to both the prior art and the patent claims will be critical.