DCT

3:20-cv-01465

Illumina Inc v. BGI Genomics Co Ltd

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I. Executive Summary and Procedural Information

  • Parties & Counsel:
  • Case Identification: 3:20-cv-01465, N.D. Cal., 02/27/2020
  • Venue Allegations: Venue is alleged to be proper in the Northern District of California because multiple defendants maintain principal places of business in San Jose, California, and have established physical places of business, including laboratory and R&D facilities, within the district.
  • Core Dispute: Plaintiff alleges that Defendant’s DNBSEQ line of DNA sequencing instruments, related reagent kits, and associated services infringe three U.S. patents directed to modified nucleotides used in sequencing-by-synthesis technology.
  • Technical Context: The technology at issue involves chemically modified nucleotides with reversible blocking groups, a foundational component of modern high-throughput "sequencing-by-synthesis" (SBS) methods that enable rapid and large-scale genomic analysis.
  • Key Procedural History: The complaint references a pending related case between the same parties in the same district involving other patents from the same family (Illumina, Inc. v. BGI Genomics Co., 19-cv-03770). It also notes that Defendant Complete Genomics Inc. previously filed unsuccessful inter partes review (IPR) petitions against a related patent, U.S. Patent No. 7,566,537.

Case Timeline

Date Event
2002-08-23 Priority Date for ’973, ’444, and ’025 Patents
2009-06-02 U.S. Patent No. 7,541,444 Issues
2010-08-10 U.S. Patent No. 7,771,973 Issues
2015-10-01 Accused Product Launch (BGISEQ-500)
2016-11-01 Accused Product Launch (BGISEQ-50)
2017-10-01 Accused Product Launch (MGISEQ-200/2000)
2017-10-05 CGI files IPR against related ’537 Patent
2018-10-01 Accused Product Launch (MGISEQ-T7)
2019-11-19 U.S. Patent No. 10,480,025 Issues
2020-02-27 Complaint Filing Date

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

U.S. Patent No. 7,771,973 - “Modified Nucleotides,” issued August 10, 2010

The Invention Explained

  • Problem Addressed: In "sequencing-by-synthesis" methods, a DNA polymerase adds nucleotides one at a time to a growing DNA strand. To ensure only a single nucleotide is added per cycle, a "blocking group" is needed on the 3'-hydroxyl (3'-OH) position of the sugar. The technical challenge is creating a blocking group that is robust enough to prevent multiple additions but can be easily and cleanly removed under mild conditions that do not damage the DNA, allowing the next sequencing cycle to begin (’973 Patent, col. 1:44-64).
  • The Patented Solution: The invention discloses modified nucleotides where the 3'-OH group is blocked by a specific chemical moiety, an azidomethyl group (-O-CH₂N₃). This group effectively terminates the polymerase reaction but can be removed using a mild reducing agent, such as Tris(2-carboxyethyl)phosphine (TCEP), to regenerate the 3'-OH group for the next nucleotide addition, enabling a reliable, cyclical sequencing process (’973 Patent, Abstract; col. 4:1-12).
  • Technical Importance: The development of a reliable and reversible 3'-OH blocking group was a critical step in making sequencing-by-synthesis commercially viable for high-throughput applications by enabling controlled, stepwise nucleotide incorporation (’973 Patent, col. 2:1-14).

Key Claims at a Glance

  • The complaint asserts at least independent claim 13 (Compl. ¶65).
  • Essential elements of Claim 13 (a method claim) include:
    • Providing a plurality of nucleotides where each has a base, sugar, phosphate group, and a removable 3'-OH blocking group which is an azidomethyl group.
    • Incorporating one of the nucleotides into a nucleic acid strand.
    • Detecting the incorporated nucleotide.
    • Removing the azidomethyl blocking group from the incorporated nucleotide.
  • The complaint states it reserves the right to assert additional claims (Compl. ¶65).

U.S. Patent No. 7,541,444 - “Modified Nucleotides,” issued June 2, 2009

The Invention Explained

  • Problem Addressed: As with the ’973 Patent, the technology addresses the need for a chemically stable yet reversibly cleavable blocking group at the 3'-OH position of a nucleotide for use in sequencing-by-synthesis (’444 Patent, col. 1:44-64).
  • The Patented Solution: The patent claims the chemical compound itself: a modified nucleotide featuring an azidomethyl group (-O-CH₂N₃) as the removable 3'-OH blocking group. This provides the specific chemical tool needed to execute the sequencing method described in related patents (’444 Patent, Abstract; col. 3:6-24).
  • Technical Importance: By defining the specific chemical structure of the nucleotide, this patent provides composition of matter protection for a key reagent in the sequencing-by-synthesis workflow (’444 Patent, col. 1:15-18).

Key Claims at a Glance

  • The complaint asserts at least independent claim 3 (Compl. ¶146).
  • Essential elements of Claim 3 (a composition of matter claim) include:
    • A modified nucleotide of a specific chemical formula.
    • Wherein the base is adenine.
    • The sugar moiety has an -O-(azidomethyl) group at the 3' position.
    • The sugar moiety has a triphosphate group at the 5' position.
  • The complaint states it reserves the right to assert additional claims (Compl. ¶146).

U.S. Patent No. 10,480,025 - “Labelled Nucleotides,” issued November 19, 2019

Technology Synopsis

This patent addresses the need for nucleotides used in sequencing to be attached to a detectable label (like a fluorescent dye). The invention describes nucleotides where a label is attached to the base via a "cleavable linker." This allows the label to be detected after incorporation and then chemically removed so it does not interfere with subsequent sequencing steps (’025 Patent, col. 2:24-28, 4:41-48).

Asserted Claims

Claims 1-8 are asserted, with Claim 1 being independent (Compl. ¶59).

Accused Features

The complaint alleges that Defendants' "DNBSEQ systems with standardMPS chemistry" infringe by using labeled nucleotides with cleavable linkers, as claimed in the patent (Compl. ¶¶ 235, 242, 248).

III. The Accused Instrumentality

Product Identification

The accused instrumentalities are collectively referred to as "DNBSEQ products," which include DNBSEQ sequencers (e.g., DNBSEQ-G50, DNBSEQ-G400, DNBSEQ-T7), DNBSEQ Sample Preparation Systems, and DNBSEQ reagent kits (Compl. ¶¶ 42-44).

Functionality and Market Context

  • The complaint alleges that the DNBSEQ systems are DNA sequencers that perform "stepwise sequencing-by-synthesis (SBS)" (Compl. ¶45). This process allegedly relies on the use of nucleotides that have a "3'-O-azidomethyl blocking group" supplied in the DNBSEQ reagent kits (Compl. ¶¶ 16, 24-25).
  • The complaint distinguishes between two chemistries allegedly used by Defendants: a "standardMPS" chemistry and a newer "CoolMPS™" chemistry. The CoolMPS chemistry is described as using "unlabeled 3'-blocked nucleotides," which Plaintiff alleges still infringe the patents-in-suit (Compl. ¶¶ 17, 45). The complaint includes a map from MGI Ltd.'s website identifying its "State-of-the-art technology research and development base" in Silicon Valley, California, which Plaintiff presents as evidence of MGI's role in developing this technology (Compl. ¶27b).
  • Defendants are alleged to be marketing and preparing to launch these products commercially in the United States, having already installed and operated them at a facility in San Jose, California (Compl. ¶¶ 3, 23, 48). The complaint includes a map from BGI Ltd.'s website showing its "representative offices" and "laboratories" in California to support allegations of its established presence in the market (Compl. ¶22a).

IV. Analysis of Infringement Allegations

As the complaint references claim-chart exhibits that are not provided with the filing, the infringement allegations are summarized below in prose based on the narrative theory of infringement.

’973 Patent Infringement Allegations (Method Claim 13)

The complaint alleges that Defendants directly infringe the method of claim 13 by operating the DNBSEQ sequencers in the United States, particularly at their San Jose facility (Compl. ¶¶ 51, 68). The accused method is the sequencing-by-synthesis process, which allegedly involves the claimed steps of incorporating a nucleotide with an azidomethyl blocking group, detecting it, and then chemically removing the blocking group to allow the next cycle. The complaint further alleges that Defendants induce infringement by providing customers with DNBSEQ systems, reagent kits, and instructional materials that direct them to perform this patented method (Compl. ¶¶ 52, 72-77). Contributory infringement is alleged on the basis that the supplied DNBSEQ systems and reagent kits are material components of the invention, are not staple articles of commerce, and have no substantial non-infringing use (Compl. ¶¶ 53, 80-81).

’444 Patent Infringement Allegations (Composition Claim 3)

The complaint alleges that Defendants infringe claim 3 by making, using, selling, or importing into the United States DNBSEQ reagent kits that contain the claimed modified nucleotides with a 3'-O-azidomethyl blocking group (Compl. ¶¶ 55, 149). The infringement theory centers on the chemical composition of the nucleotides within the "standardMPS" and "CoolMPS" reagent kits. The complaint alleges these reagents are used in Defendants' DNBSEQ sequencers in their San Jose facility and are being offered for sale in the U.S. (Compl. ¶¶ 23, 55). Allegations of inducement and contributory infringement follow a similar logic as for the ’973 patent, focusing on the supply of the reagent kits and systems designed to use them (Compl. ¶¶ 56-57, 153-162).

Identified Points of Contention

  • Technical Questions: A central factual dispute will likely be the chemical structure of the 3' blocking group in the nucleotides used in Defendants' "CoolMPS" chemistry. While Defendants describe it as a "new chemistry," Plaintiff alleges on information and belief that it uses "unlabeled 3'-blocked nucleotides" that infringe (Compl. ¶¶ 17, 45). The case may turn on evidence revealing the exact composition of these reagents.
  • Scope Questions: The complaint accuses a wide range of activities, including use, testing, development, and promotional activities in the U.S. (Compl. ¶¶ 51, 55). A potential point of contention may be whether these pre-commercial launch activities constitute "use" under 35 U.S.C. § 271(a) or fall within the safe harbor of § 271(e)(1), though the complaint does not suggest the latter is at issue.

V. Key Claim Terms for Construction

  • The Term: "removable 3'-OH blocking group which is an azidomethyl group" (’973 Patent, cl. 13) and "an -O-(azidomethyl) group" (’444 Patent, cl. 3).
  • Context and Importance: This term is the technological core of the asserted patents. The infringement analysis for both the method and composition claims depends entirely on whether the blocking group used in the accused DNBSEQ chemistries is an "azidomethyl group" as construed by the court. Practitioners may focus on this term because Defendants' "CoolMPS" chemistry is presented as a new technology, suggesting a potential dispute over whether it employs a chemically different, non-infringing blocking group (Compl. ¶45).
  • Intrinsic Evidence for Interpretation:
    • Evidence for a Broader Interpretation: The patent specification discusses the general requirements for a blocking group, stating it must prevent additional nucleotide incorporation while being easily removable without damaging the polynucleotide chain (’973 Patent, col. 1:47-54). A party could argue that any group functioning in this way and based on an azidomethyl-like structure falls within the spirit of the invention.
    • Evidence for a Narrower Interpretation: The specification explicitly defines the azidomethyl group as "-CH₂N₃" and details its chemical properties and specific cleavage reactions, such as using TCEP (’973 Patent, col. 4:1-12, col. 7:6-12). A party could argue this provides a precise structural definition, limiting the claim scope to this exact chemical moiety and excluding other potential blocking groups that may be functionally similar but structurally different.

VI. Other Allegations

Indirect Infringement

The complaint alleges both induced and contributory infringement for all three patents-in-suit. Inducement is primarily based on allegations that Defendants provide DNBSEQ systems with pre-programmed software, user manuals, and technical specifications that instruct and encourage customers to perform the patented sequencing methods (Compl. ¶¶ 73, 77, 106). Contributory infringement is based on the allegation that the DNBSEQ sequencers and reagent kits are specialized components that are a material part of the inventions and are not staple articles of commerce suitable for substantial non-infringing use (Compl. ¶¶ 81, 110, 141).

Willful Infringement

Willfulness is alleged for all asserted patents. The complaint bases this on alleged pre-suit knowledge, asserting that Defendants knew or should have known of the patents due to their publication dates, Plaintiff's public enforcement activities, and Defendants' own litigation activities, including CGI's IPR filings against a related patent in the same family as early as October 5, 2017 (Compl. ¶¶ 82, 95, 111).

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

  • A core issue will be one of chemical identity: what is the precise molecular structure of the 3'-OH blocking group used in the nucleotides of Defendants' "CoolMPS" chemistry? Discovery and expert testimony will be central to determining whether this "new" chemistry falls within the structural and functional scope of the claimed "azidomethyl group."
  • A key evidentiary question will be one of knowledge and intent: given the extensive and intertwined litigation history between the parties involving related patents, what evidence demonstrates that Defendants had pre-suit knowledge of the specific '973, '444, and '025 patents, and does their continued activity in the face of this alleged knowledge constitute willful infringement?
  • A secondary issue will be one of commercial use: does Defendants' alleged use of the DNBSEQ systems for research, development, and promotional activities within their U.S. facilities prior to a full commercial launch constitute direct infringement under 35 U.S.C. § 271(a)?