DCT

1:22-cv-01117

10X Genomics Inc v. Parse Biosciences Inc

Log In

I. Executive Summary and Procedural Information

  • Parties & Counsel:
  • Case Identification: 1:22-cv-01117, D. Del., 08/24/2022
  • Venue Allegations: Venue is alleged as proper in the District of Delaware because the Defendant is a Delaware corporation.
  • Core Dispute: Plaintiff alleges that Defendant’s single-cell gene expression and chromatin analysis products infringe six patents related to methods for barcoding and analyzing nucleic acids from single cells.
  • Technical Context: Single-cell genomics provides high-resolution biological data by analyzing individual cells, a significant advance over traditional "bulk" methods that average results across entire tissue samples.
  • Key Procedural History: Plaintiff 10x Genomics owns three of the asserted patents and is the exclusive licensee of the other three from The Board of Trustees of Leland Stanford Junior University, which is named as a nominal defendant. The complaint alleges that Defendant had knowledge of the asserted patents at least as of a notice letter sent one day prior to the filing of the suit.

Case Timeline

Date Event
2009-08-20 Priority Date for ’981, ’013, ’197 Patents
2013-05-23 Priority Date for ’995, ’207, ’357 Patents
2018-12-11 ’995 Patent Issued
2018-12-18 ’981 Patent Issued
2019-03-26 ’197 Patent Issued
2020-04-14 ’207 Patent Issued
2020-06-30 ’013 Patent Issued
2020-08-11 ’357 Patent Issued
Late 2021 Defendant launched Evercode WT Mini and Mega kits
2022-04-14 Defendant announced plans to launch Single-Cell ATAC-Seq Product
2022-08-24 Complaint Filed

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

U.S. Patent No. 10,155,981 - "Methods for analyzing nucleic acids from single cells," Issued December 18, 2018

The Invention Explained

  • Problem Addressed: Traditional biological analysis techniques average molecular information across large populations of cells, obscuring critical differences between individual cells (Compl. ¶15). The patent addresses the need for methods that can analyze nucleic acids on a single-cell basis at a massive scale.
  • The Patented Solution: The invention describes a method for uniquely "dual-tagging" nucleic acids from a plurality of single cells. Each resulting tagged molecule contains a multiplex identifier (MID) sequence that comprises two parts: a "first tag sequence" that identifies the cell from which the molecule originated, and a "second tag sequence" that distinguishes that specific molecule from other molecules within the same cell. This dual-labeling system allows nucleic acids from many thousands or millions of cells to be pooled, sequenced together, and then bioinformatically traced back to their single-cell and single-molecule origin (Compl. ¶¶15, 44; ’981 Patent, Abstract, col. 20:5-25).
  • Technical Importance: This dual-tagging approach enables the "unprecedented resolution and scale" required for modern single-cell genomics, forming a basis for high-throughput analysis of complex biological systems (Compl. ¶12).

Key Claims at a Glance

  • The complaint asserts independent Claim 1 (Compl. ¶42).
  • Essential elements of Claim 1 include:
    • Providing a sample comprising a plurality of single cells, each containing sample polynucleotides.
    • Generating tagged polynucleotides, where each tagged polynucleotide comprises (i) a sequence from a sample polynucleotide and (ii) a multiplex identifier (MID) sequence.
    • The MID sequence itself comprises: (I) a first tag sequence associated with the single cell of origin, which is different for different cells, and (II) a second tag sequence distinguishing the sample polynucleotide from others derived from the same cell.
    • Sequencing the tagged polynucleotides.
    • Using the first tag sequence to correlate the result to the cell of origin.
    • Using the second tag sequence to correlate the result to the specific sample polynucleotide.
  • The complaint does not explicitly reserve the right to assert dependent claims for this patent.

U.S. Patent No. 10,697,013 - "A method for multiplexed analysis of nucleic acids from single cells," Issued June 30, 2020

The Invention Explained

  • Problem Addressed: The patent addresses the challenge of performing high-throughput, multiplexed analysis of nucleic acids from single cells, which requires a robust method to uniquely label molecules from a large number of individual cells in a pooled sample (Compl. ¶15).
  • The Patented Solution: The invention claims a method of "combinatorial tagging" to generate tagged polynucleotides. The process involves two distinct molecular biology steps: first, providing an extension product by using a "first oligonucleotide tag" in a primer extension reaction, and second, "ligating a second oligonucleotide tag" to that extension product. This creates a tagged molecule with a first tag sequence to distinguish it from molecules in other cells and a second tag sequence to distinguish it from other molecules within the same cell, enabling subsequent amplification, sequencing, and counting on a single-cell basis (’013 Patent, Abstract, col. 32:17-33:5).
  • Technical Importance: This method provides a specific biochemical pathway—combining primer extension and ligation—to achieve the combinatorial barcoding necessary for large-scale single-cell experiments (Compl. ¶¶15, 63).

Key Claims at a Glance

  • The complaint asserts independent Claim 1 (Compl. ¶61).
  • Essential elements of Claim 1 include:
    • Providing a sample of cells, each with sample polynucleotides.
    • Performing combinatorial tagging to generate tagged polynucleotides from the sample polynucleotides and oligonucleotide tags.
    • The generation step includes: (A) providing an extension product via primer extension using a first oligonucleotide tag, and (B) ligating a second oligonucleotide tag to that extension product.
    • The resulting tagged polynucleotide comprises: (i) the sample sequence, (ii) a first tag sequence distinguishing the molecule from those in other cells, and (iii) a second tag sequence distinguishing the molecule from others in the same cell.
    • Amplifying and sequencing the tagged polynucleotides.
    • Using the determined sequences to count sample polynucleotides for different molecules across different single cells.
  • The complaint does not explicitly reserve the right to assert dependent claims for this patent.

Multi-Patent Capsule: U.S. Patent No. 10,240,197 - "Methods of counting nucleic acids in a sample," Issued March 26, 2019

  • Technology Synopsis: This patent is from the same family as the ’981 and ’013 patents and relates to single-cell nucleic acid analysis. It describes a method for counting nucleic acids by generating tagged polynucleotides comprising a "first tag sequence" to distinguish the cell of origin and a "second tag sequence" to distinguish the molecule within that cell, followed by sequencing to determine these tags and the sample sequence (Compl. ¶83).
  • Asserted Claims: The complaint asserts independent Claim 1 (Compl. ¶81).
  • Accused Features: The accused features are part of the Defendant’s Evercode WT Products, which allegedly perform a method of counting nucleic acids using a dual-tagging approach (Compl. ¶81, 84).

Multi-Patent Capsule: U.S. Patent No. 10,150,995 - "Transposition of Native Chromatin for Personal Epigenomics," Issued December 11, 2018

  • Technology Synopsis: This patent relates to the field of epigenomics, specifically the analysis of chromatin accessibility via a technique known as ATAC-seq (Assay for Transposase-Accessible Chromatin with sequencing). The invention describes a method where an "insertional enzyme complex," such as a transposase, is used to insert tags into accessible or "open" regions of chromatin without the use of an antibody. These tagged fragments are then analyzed, for example by sequencing, to map regions of chromatin accessibility (’995 Patent, Abstract, col. 1:44-51; Compl. ¶¶17, 104).
  • Asserted Claims: The complaint asserts independent Claim 1 (Compl. ¶101).
  • Accused Features: The accused features are embodied in the Defendant’s Parse Single-Cell ATAC-Seq Product, which is alleged to use an insertional enzyme to tag and fragment open chromatin for sequencing (Compl. ¶¶101, 108).

Multi-Patent Capsule: U.S. Patent No. 10,619,207 - "Transposition of Native Chromatin for Personal Epigenomics," Issued April 14, 2020

  • Technology Synopsis: This patent is from the same family as the ’995 patent and also covers ATAC-seq technology. The claimed method involves lysing cells to provide cell nuclei, contacting the nuclei with a transposase complex to "tagment" (tag and fragment) open chromatin regions, and then performing subsequent reactions to create a sequencing library (Compl. ¶¶17, 124).
  • Asserted Claims: The complaint asserts independent Claim 1 (Compl. ¶121).
  • Accused Features: The infringement allegations are directed at the Defendant’s Parse Single-Cell ATAC-Seq Product, which is alleged to perform the claimed method of lysing cells and using a transposase complex to generate a sequencing library from open chromatin (Compl. ¶¶121, 128-130).

Multi-Patent Capsule: U.S. Patent No. 10,738,357 - "Transposition of Native Chromatin for Personal Epigenomics," Issued August 11, 2020

  • Technology Synopsis: This patent, also from the same family as the ’995 and ’207 patents, claims a composition rather than a method. The claimed composition comprises a permeabilized cell nucleus which itself contains an insertional enzyme complex (e.g., transposase) and a plurality of tagged nucleic acid fragments derived from regions of open chromatin (Compl. ¶145). This represents an intermediate state in the ATAC-seq process.
  • Asserted Claims: The complaint asserts independent Claim 16 (Compl. ¶143).
  • Accused Features: Infringement is alleged against the Parse Single-Cell ATAC-Seq Product, which allegedly creates the claimed composition during its workflow (Compl. ¶¶142, 146).

III. The Accused Instrumentality

Product Identification

  • The complaint identifies two lines of accused instrumentalities: (1) the "Evercode WT Products" (including Evercode WT, Mini, and Mega kits) and (2) the "Parse Single-Cell ATAC-Seq Product" (Compl. ¶¶18, 20, 27, 33).

Functionality and Market Context

  • The Evercode WT Products are kits that enable single-cell gene expression analysis using a technique called "split-pool combinatorial barcoding" or "SPLiT-Seq" (Compl. ¶20). This process involves physically separating cells into different wells, applying a first set of barcodes via an in-cell reverse transcription reaction, pooling the cells, re-distributing them into new wells, and applying a second set of barcodes via ligation (Compl. ¶¶21-22, 49). The complaint includes a diagram illustrating this multi-round split-and-pool process (Compl. p. 9, Figure entitled "Reverse transcription... Ligation... Lysis + PCR... Library Prep"). This process allegedly results in each cell's transcriptome being labeled with a unique combination of barcodes that allows its molecular contents to be traced after sequencing (Compl. ¶¶22, 49).
  • The Parse Single-Cell ATAC-Seq Product is a kit designed to perform an "assay for transposase-accessible chromatin by sequencing" (Compl. ¶27). This method is alleged to generate a library of tagged DNA fragments from "open chromatin" within the cell nucleus, which can then be sequenced to map gene regulatory regions (Compl. ¶28). The complaint includes a diagram illustrating how an insertional enzyme complex, such as Tn5 transposase, inserts sequence adaptors only into open regions of chromatin to generate amplifiable fragments (Compl. p. 13, Figure "ATAC-seq is a probe of open chromatin state").
  • The complaint alleges that the Defendant intends to "copy 10x's complete lineup of single-cell products wholesale" and that the accused products compete directly with the Plaintiff's offerings (Compl. ¶18).

IV. Analysis of Infringement Allegations

’981 Patent Infringement Allegations

Claim Element (from Independent Claim 1) Alleged Infringing Functionality Complaint Citation Patent Citation
(a) providing a sample comprising a plurality of single cells, wherein each single cell...comprises a plurality of sample polynucleotides; The accused Evercode WT Products are used with a sample of single cells or nuclei, each containing polynucleotides (transcripts) (Compl. p. 22). ¶48 col. 19:1-4
(b) generating a plurality of tagged polynucleotides...wherein each tagged polynucleotide comprises: (i) a sequence from a sample polynucleotide...and (ii) a multiplex identifier (MID) sequence comprising: The products generate tagged polynucleotides through a multi-round barcoding process where transcripts are labeled with barcodes (Compl. p. 24). ¶49 col. 20:5-9
I. a first tag sequence associated with the single cell...wherein the first tag sequence is a different sequence for different single cells...; and The combination of barcodes applied during four rounds of split-pool barcoding allegedly creates a unique cell-specific identifier, which functions as the "first tag sequence" (Compl. p. 24). ¶49 col. 20:12-16
II. a second tag sequence distinguishing the sample polynucleotide from other sample polynucleotides derived from the same single cell; A unique molecular identifier (UMI) is allegedly incorporated into the barcode, which serves to distinguish individual transcript molecules originating from the same cell (Compl. p. 24, Figure "Labeling transcriptomes with split-pool barcoding"). ¶49 col. 20:17-20
(c) sequencing the plurality of tagged polynucleotides to obtain a plurality of identified polynucleotide sequences; The instructional materials for the accused products direct users to sequence the resulting barcoded libraries using next-generation sequencing (NGS). ¶50 col. 20:21-23
(d) using the first tag sequence to correlate the identified polynucleotide sequence with the single cell from which the identified polynucleotide sequence is derived; and The data analysis pipeline allegedly uses the unique four-barcode combination to assemble each transcriptome and associate it with its cell of origin. ¶51 col. 20:24-27
(e) using the second tag sequence to correlate the identified polynucleotide sequence with the sample polynucleotide from which the identified polynucleotide sequence is derived. The data analysis allegedly uses the UMI sequence to identify and count individual transcript molecules. ¶51 col. 20:28-31

Identified Points of Contention

  • Scope Questions: The complaint alleges that the unique barcode combination generated by four separate split-pool steps collectively constitutes the claimed "first tag sequence" (Compl. ¶49). A potential point of contention is whether this combinatorial, multi-part identifier, assembled in situ, meets the definition of "a first tag sequence" as understood in the context of the ’981 Patent, which might be argued to describe a more discrete, pre-defined tag structure.
  • Technical Questions: Claim 1 recites a "multiplex identifier (MID) sequence" that comprises a first and second tag sequence. The complaint presents a diagram showing a final barcoded cDNA molecule where the barcodes and UMI are distinct parts of a larger construct (Compl. p. 24, Figure "Labeling transcriptomes..."). What evidence does the complaint provide that the UMI ("second tag") and the combinatorial cell barcode ("first tag") are structurally part of a single, cohesive "multiplex identifier (MID) sequence" as required by the claim?

’013 Patent Infringement Allegations

Claim Element (from Independent Claim 1) Alleged Infringing Functionality Complaint Citation Patent Citation
(b) performing combinatorial tagging to generate a plurality of tagged polynucleotides...wherein a tagged polynucleotide...is generated by: The accused products' "split-pool combinatorial barcoding" method is alleged to be a form of "combinatorial tagging" (Compl. p. 36). ¶67 col. 32:23-26
(A) providing an extension product by primer extension using a first oligonucleotide tag and a sample polynucleotide... and The first round of barcoding in the accused process allegedly involves an in-cell reverse transcription (RT) reaction using well-specific barcoded primers, which is a form of primer extension using a first tag (Compl. p. 38, Figure "Labeling transcriptomes..."). ¶68 col. 32:28-32
(B) ligating a second oligonucleotide tag to said extension product... The second and third rounds of barcoding in the accused process allegedly involve appending additional well-specific barcodes to the cDNA through in-cell ligation (Compl. p. 38, Figure "Labeling transcriptomes..."). ¶68 col. 32:33-34
wherein said tagged polynucleotide...comprises... (ii) a first tag sequence distinguishing said sample polynucleotide from sample polynucleotides from other cells; and The unique combination of barcodes applied across the multiple rounds allegedly serves as the cell-distinguishing "first tag sequence". ¶68 col. 33:10-12
(iii) a second tag sequence distinguishing said sample polynucleotide from other sample polynucleotides from said cell; The unique molecular identifier (UMI), allegedly incorporated in the third-round barcode, serves as the molecule-distinguishing "second tag sequence". ¶68 col. 33:13-15
(c) amplifying said tagged polynucleotide... The accused process includes a final polymerase chain reaction (PCR) step to amplify the fully barcoded library for sequencing (Compl. p. 40, Figure "Lysis + PCR"). ¶69 col. 33:16-19
(d) sequencing said plurality of amplified polynucleotides... Users are instructed to sequence the resulting libraries using NGS platforms. ¶70 col. 33:20-26
(e) using the sequences determined in step (d) to count sample polynucleotides for multiple different...cells... The data analysis pipeline allegedly assembles each transcriptome by combining reads with the same barcode combination, which allows for counting molecules from different cells. ¶71 col. 33:27-31

Identified Points of Contention

  • Scope Questions: Claim 1(b) recites generating the tag by "(A) providing an extension product by primer extension using a first oligonucleotide tag" and "(B) ligating a second oligonucleotide tag." The accused process involves one primer extension step followed by multiple subsequent ligation steps to add more barcodes (Compl. ¶68, citing p. 38 figure). This raises the question of whether the combination of tags added via ligation can collectively be considered the "second oligonucleotide tag," or if the claim requires a simpler two-tag process.
  • Technical Questions: What evidence does the complaint provide that the various barcodes applied in different rounds of ligation function together as a single "second oligonucleotide tag" as recited in the claim, rather than as a series of distinct tags applied sequentially?

V. Key Claim Terms for Construction

For the ’981 Patent

  • The Term: "a first tag sequence associated with the single cell"
  • Context and Importance: This term's construction is critical because the accused Evercode WT products allegedly create a cell-identifying marker not with a single tag, but through a combination of barcodes applied in successive split-pool rounds (Compl. ¶49). The infringement analysis will depend on whether this combinatorial identifier can be construed as "a first tag sequence."
  • Intrinsic Evidence for Interpretation:
    • Evidence for a Broader Interpretation: The specification states that a "multiplex identifier (MID)" can be "a tag or combination of tags" and that its identity "can be used to differentiate polynucleotides in a sample" (’981 Patent, col. 6:33-36). This language may support an interpretation where a "tag sequence" can be composed of multiple, non-contiguous parts that function together as an identifier.
    • Evidence for a Narrower Interpretation: The detailed examples may describe embodiments where a single, discrete oligonucleotide containing the cell-specific barcode is introduced in one step, for example within an emulsion droplet (’981 Patent, col. 20:5-20). This could support an argument that "a first tag sequence" refers to a singular molecular entity.

For the ’013 Patent

  • The Term: "performing combinatorial tagging"
  • Context and Importance: The complaint directly maps the accused "split-pool combinatorial barcoding" method onto this claim term (Compl. ¶67). The definition of "combinatorial tagging," particularly in light of the subsequent limitations requiring a specific two-step biochemical process (primer extension then ligation), will be central to the infringement dispute.
  • Intrinsic Evidence for Interpretation:
    • Evidence for a Broader Interpretation: The patent abstract describes the invention as a "method for multiplexed analysis of nucleic acids from single cells" using "combinatorial tagging," suggesting the term is meant to capture the overall goal of the process (’013 Patent, Abstract). The specification may provide a general definition that encompasses any method of combining tags to generate unique identifiers.
    • Evidence for a Narrower Interpretation: Claim 1 explicitly defines how the "combinatorial tagging" is performed: by "(A) providing an extension product by primer extension using a first oligonucleotide tag" and "(B) ligating a second oligonucleotide tag" (’013 Patent, col. 32:23-34). This explicit two-step definition within the claim itself could be used to argue for a narrower construction that does not read on processes involving more than two tagging steps or different combinations of biochemical reactions.

VI. Other Allegations

  • Indirect Infringement: The complaint alleges inducement of infringement for all asserted patents. The basis for this allegation is that the Defendant provides customers with instructional materials, presentations, technical brochures, and online tutorials that actively instruct and encourage them to use the accused products in an infringing manner (Compl. ¶¶ 46, 55, 65, 75).
  • Willful Infringement: The complaint alleges willful infringement based on two theories. First, it alleges post-suit knowledge based on a notice letter sent to the Defendant on August 23, 2022, one day before the complaint was filed (Compl. ¶¶ 52, 72). Second, it alleges pre-suit knowledge on "information and belief" that the Defendant "set out to copy 10x products and would have been aware of 10x's patents as part of its research" (Compl. ¶¶ 52, 72).

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

  • A core issue will be one of definitional scope: can terms such as "a first tag sequence" (’981 Patent) be construed to cover a composite identifier formed by combining multiple barcodes in separate, sequential steps, as allegedly occurs in the accused split-pool barcoding method?
  • A key infringement question will be one of process mapping: does the accused multi-round tagging process—which involves one primer extension step and multiple subsequent ligation steps—map onto the specific two-step "first tag... by primer extension" and "second tag... by ligating" structure required by Claim 1 of the ’013 patent, or is there a fundamental mismatch in the claimed sequence of biochemical events?
  • A central issue for the chromatin analysis patents (’995, ’207, ’357) will be a factual and technical comparison: does the Defendant's Single-Cell ATAC-Seq Product, as it operates in practice, perform the specific steps of contacting cell nuclei with a transposase complex to tagment open chromatin, thereby creating the claimed methods and compositions?