DCT
1:25-cv-00683
Research Institute At Nationwide Children's Hospital v. Illumina Inc
I. Executive Summary and Procedural Information
- Parties & Counsel:
- Plaintiff: The Research Institute at Nationwide Children's Hospital (Ohio)
- Defendant: Illumina, Inc. (Delaware)
- Plaintiff’s Counsel: Morris, Nichols, Arsht & Tunnell LLP; King & Spalding LLP
- Case Identification: 1:25-cv-00683, D. Del., 06/03/2025
- Venue Allegations: Venue is alleged to be proper in the District of Delaware because Illumina is a Delaware corporation and therefore resides in the district for purposes of patent venue.
- Core Dispute: Plaintiff alleges that Defendant’s DRAGEN Bio-IT software infringes a patent related to methods for improving the computational efficiency of analyzing large-scale genetic sequence data.
- Technical Context: The case concerns bioinformatics pipelines for next-generation sequencing (NGS), a field where the exponential growth of data has created significant computational bottlenecks, limiting the speed of research and clinical diagnostics.
- Key Procedural History: The complaint alleges that the USPTO, during prosecution, explicitly recognized the invention as a patent-eligible improvement to bioinformatics technology. It also details extensive pre-suit history, including a 2019 presentation by Plaintiff to Defendant identifying the patent-in-suit and its relevance to the accused product, which was followed by Defendant's decision not to take a license. Further, the complaint notes that a company acquired by Defendant had previously cited the patent’s application during its own patent prosecution, and it documents a formal notice letter exchange between the parties in late 2023 and early 2024.
Case Timeline
| Date | Event |
|---|---|
| 2012-03-16 | U.S. Provisional Application 61/611,960 Priority Date |
| 2013-11-21 | '458 Patent application published as the '106 Publication |
| 2014-12-02 | Edico (later acquired by Illumina) cites '106 Publication in an IDS |
| 2017-01-24 | U.S. Patent No. 9,552,458 Issues |
| 2018-01-01 | Illumina acquires Edico Genome, developer of DRAGEN (approx. date) |
| 2018-11-13 | Prior licensee allegedly presents to Illumina on '458 Patent |
| 2019-09-10 | Plaintiff presents to Illumina regarding '458 Patent and DRAGEN |
| 2019-10-24 | Illumina declines to license '458 Patent |
| 2023-11-08 | Plaintiff sends notice letter to Illumina |
| 2023-11-14 | Illumina acknowledges receipt of notice letter |
| 2024-02-23 | Illumina responds to Plaintiff, denying infringement and invalidity |
| 2025-06-03 | Complaint Filed |
II. Technology and Patent(s)-in-Suit Analysis
U.S. Patent No. 9,552,458 - Comprehensive Analysis Pipeline for Discovery of Human Genetic Variation
The Invention Explained
- Problem Addressed: The patent addresses the "computational bottleneck" created by the vast amounts of data generated by next-generation sequencing (NGS) technologies (Compl. ¶22; ’458 Patent, col. 1:34-41). Prior methods for parallelizing the analysis, such as splitting data by chromosome, were inefficient due to the differing sizes of chromosomes, leading to uneven computational loads and challenges in accurately processing "inter-chromosomal reads" (reads that span different chromosomes) (Compl. ¶29).
- The Patented Solution: The invention claims a method to improve processing efficiency by splitting genetic data into subsets corresponding to chromosomes and defining a separate "inter-subset" specifically for read pairs where the mates map to different subsets ('458 Patent, Abstract). This structure allows for the parallel processing of both the chromosomal subsets and the inter-subset reads, which the patent asserts overcomes the accuracy and speed limitations of prior art systems that either discarded such reads or processed them inefficiently ('458 Patent, col. 3:25-42; Compl. ¶30). The complaint highlights data from the patent's Figure 9, which it asserts demonstrates the invention's superior speed over competing approaches (Compl. ¶32).
- Technical Importance: This approach allegedly enabled faster, more accurate, and deterministic analysis of genomic data, making real-time personalized genetic screening computationally feasible (Compl. ¶¶ 35-36).
Key Claims at a Glance
- The complaint asserts independent claim 1 and dependent claims 2-4 and 6 (Compl. ¶42).
- Independent Claim 1 recites the following essential elements:
- receiving, by a computer system, genetic sequence data specifying a plurality of chromosomes and mitochondrial DNA;
- splitting the genetic sequence data into a plurality of subsets, with each subset corresponding to either one chromosome or the mitochondrial DNA;
- defining an inter-subset of the genetic sequence data for read pairs with both mates mapped to different subsets; and
- analyzing the data by dividing processing steps among a plurality of parallel processing paths, with each path corresponding to one of the subsets.
- The complaint reserves the right to assert other claims (Compl. ¶51).
III. The Accused Instrumentality
Product Identification
The accused instrumentality is Illumina’s DRAGEN™ Bio-IT software suite ("DRAGEN") (Compl. ¶41).
Functionality and Market Context
- DRAGEN is a software suite used for secondary analysis of sequencing data, processing inputs like FASTQ and BAM/CRAM files which contain genomic data (Compl. ¶¶ 41, 44). The complaint alleges that DRAGEN is used in urgent clinical care for rapid identification of genetic variants (Compl. ¶43).
- The complaint alleges, on information and belief, that DRAGEN's architecture uses a plurality of parallel processing paths corresponding to the number of processor cores to analyze chromosomal and mitochondrial DNA, thereby reducing analysis time (Compl. ¶¶ 45-46). An image included in the complaint shows a bar chart from the '458 patent that compares the processing time of the patented method against other approaches, which the complaint uses to frame the performance benefits of the allegedly infringing system (Compl. p. 10, Fig. 9).
IV. Analysis of Infringement Allegations
The complaint does not provide the referenced claim chart exhibit (Exhibit 8). The following table summarizes the infringement theory for claim 1 based on the narrative allegations.
’458 Patent Infringement Allegations
| Claim Element (from Independent Claim 1) | Alleged Infringing Functionality | Complaint Citation | Patent Citation |
|---|---|---|---|
| A method for improving the utilization of processing capability of a computing system analyzing genetic sequence data associated with a subject, the method comprising: | DRAGEN is alleged to be a method for improving processing capability by performing secondary data analysis used in contexts like urgent clinical care (Compl. ¶43). | ¶43 | col. 20:30-34 |
| receiving, by the computer system, the genetic sequence data associated with the subject, the genetic sequence data specifying a plurality of chromosomes and mitochondrial DNA; | DRAGEN is alleged to obtain genetic sequence data from a subject by using FASTQ and BAM/CRAM files as inputs, which contain genomic data (Compl. ¶44). | ¶44 | col. 20:35-39 |
| splitting the genetic sequence data into a plurality of subsets, each subset corresponding to either one chromosome of the plurality of chromosomes or the mitochondria DNA; | DRAGEN is alleged, on information and belief, to receive and split a patient's genetic information (including chromosomal and mitochondrial DNA) into subsets and use parallel processing (Compl. ¶45). | ¶45 | col. 20:40-44 |
| defining an inter-subset of the genetic sequence data for read pairs with both mates mapped to different subsets of the plurality of subsets; and | The complaint alleges DRAGEN implements the patented method, which includes overcoming prior art deficiencies by defining an inter-subset for reads spanning two subsets, to enable parallel processing of those reads (Compl. ¶30). The complaint does not specify how DRAGEN itself performs this step. | ¶30 | col. 20:45-49 |
| analyzing the obtained genetic sequence data by the computer system by dividing one or more processing steps in the analysis among a plurality of parallel processing paths... | DRAGEN is alleged to use a plurality of parallel processing paths corresponding to the number of processor cores to analyze chromosomal and mitochondrial DNA in parallel, reducing analysis time (Compl. ¶¶ 45-46). A line graph from the patent is included to show the scalability benefits (Compl. p. 11, Fig. 10). | ¶46 | col. 20:50-54 |
Identified Points of Contention
- Scope Questions: Claim 1 recites splitting data into subsets where "each subset correspond[s] to either one chromosome...or the mitochondria DNA." A primary dispute may arise over whether this language is limited to a strict one-subset-per-chromosome division. The patent's specification extols the virtues of a more granular, sub-chromosomal splitting approach to achieve better load balancing ('458 Patent, col. 13:30-44). The infringement analysis raises the question of whether the accused DRAGEN software, if it uses sub-chromosomal splitting, would fall outside the literal scope of this claim language.
- Technical Questions: The complaint alleges that the invention involves "defining an inter-subset for reads that spanned two subsets" (Compl. ¶30) but does not provide specific factual allegations about how the accused DRAGEN software performs this function. A key evidentiary question will be what proof exists that DRAGEN's method for handling reads that span processing boundaries meets the specific "defining an inter-subset" limitation required by the claim.
V. Key Claim Terms for Construction
"splitting the genetic sequence data into a plurality of subsets, each subset corresponding to either one chromosome of the plurality of chromosomes or the mitochondria DNA"
- Context and Importance: This term is central because it defines the foundational parallelization strategy of the claim. The case may turn on whether this is construed narrowly as a strict one-to-one mapping of subsets to whole chromosomes, or more broadly to encompass other divisions of genomic data, such as the sub-chromosomal splits described as an improvement in the patent's own specification. Practitioners may focus on this term due to the potential tension between the claim's plain language and the specification's description of a technically superior embodiment.
- Intrinsic Evidence for Interpretation:
- Evidence for a Broader Interpretation: The patent’s overall objective is to enable scalable parallel processing ('458 Patent, col. 4:5-8). A party might argue that "corresponding to" should be interpreted functionally to achieve this objective, allowing for divisions other than strictly one chromosome per subset.
- Evidence for a Narrower Interpretation: The claim language recites "each subset corresponding to either one chromosome... or the mitochondria DNA," which suggests a one-to-one relationship ('458 Patent, col. 20:41-44). This interpretation is reinforced by the specification's description of the "Churchill" embodiment, which starts with a "Split by Chromosome" step that results in "25 files (chr1.bam, chr2.bam, ... chrM.bam)" ('458 Patent, col. 10:29-34).
"defining an inter-subset"
- Context and Importance: This limitation appears to capture a key point of novelty over prior art systems that allegedly mishandled reads spanning across different chromosomes or regions. Infringement will depend on whether DRAGEN's method for handling such reads is found to be equivalent to "defining an inter-subset."
- Intrinsic Evidence for Interpretation:
- Evidence for a Broader Interpretation: The specification describes this functionally, stating that "read pairs with both mates mapped to different segments, are saved into at least a second BAM file" ('458 Patent, col. 3:34-37). This could support an interpretation where any process that segregates and tracks these specific reads for later processing meets the limitation.
- Evidence for a Narrower Interpretation: The use of the term "defining" could imply a more formal, discrete step of creating a specific data set or file structure identified as the "inter-subset," as opposed to a more transient or integrated handling of such reads. The patent describes saving these reads in a "separate BAM file, identified... by inter-chr.bam" ('458 Patent, col. 10:35-39), which may support a narrower construction.
VI. Other Allegations
- Indirect Infringement: The complaint alleges inducement by asserting that Illumina supplies DRAGEN with the knowledge and intent that its users will infringe, and facilitates this infringement through the dissemination of "supporting materials, instructions, product manuals, and/or technical information" (Compl. ¶¶ 53-54).
- Willful Infringement: The complaint alleges that Illumina's infringement has been willful based on both pre- and post-suit knowledge. The allegations of pre-suit knowledge are based on: (1) a 2018 presentation to Illumina by a prior patent licensee; (2) a September 2019 presentation from Plaintiff to Illumina that "specifically identified the ’458 Patent, including the language of claim 1, and its coverage" and relevance to DRAGEN, after which Illumina declined a license; and (3) Illumina's 2018 acquisition of Edico, which had cited the '458 patent's publication in a 2014 IDS during prosecution of its own patents (Compl. ¶¶ 55-56, 60). Post-suit knowledge is alleged based on a notice letter sent in November 2023, which the complaint supports with an image of Illumina's letter acknowledging its receipt and review of the patent (Compl. ¶¶ 57-58; p. 17).
VII. Analyst’s Conclusion: Key Questions for the Case
- A core issue will be one of claim scope vs. patented improvement: can the claim language, which recites a data-splitting method based on "one chromosome" per subset, be construed to cover the more advanced sub-chromosomal splitting technique that the patent’s own specification describes as a key improvement over prior art? The resolution of this tension between the claim text and the detailed description will be critical for the infringement analysis.
- An essential evidentiary question will be one of technical proof: what evidence will emerge from discovery to show that the accused DRAGEN software performs the specific, claimed step of "defining an inter-subset" for reads that span processing boundaries, or does it employ a fundamentally different, non-infringing mechanism to manage such reads?
- Finally, the case will likely feature a significant dispute over willfulness: given the detailed allegations of pre-suit notice, including specific presentations about the patent's relevance to DRAGEN and a rejected license offer, a key question will be whether Illumina can establish that it had a good-faith belief of non-infringement or invalidity, or if its conduct will be deemed egregious.