Case 1:22-cv-01117-UNA Document 1 Filed 08/24/22 Page 1 of 84 PageID #: 1
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`IN THE UNITED STATES DISTRICT COURT
`FOR THE DISTRICT OF DELAWARE
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`C.A. No. __________
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`DEMAND FOR JURY TRIAL
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`COMPLAINT FOR PATENT INFRINGEMENT AND
`DECLARATORY JUDGMENT FOR PATENT INFRINGEMENT
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`Plaintiff 10x Genomics, Inc. (“10x” or “Plaintiff”) for its Complaint against Defendant
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`Parse Biosciences, Inc. (“Parse”), alleges as follows:
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`NATURE OF THE ACTION
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`1.
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`This is an action for infringement of United States Patent Nos. 10,155,981 (“the
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`’981 Patent”), 10,697,013 (“the ’013 Patent”), 10,240,197 (“the ’197 Patent”), 10,150,995 (“the
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`’995 Patent”), 10,619,207 (“the ’207 Patent”), and 10,738,357 (“the ’357 Patent”) (collectively,
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`the “Asserted Patents”). This action arises under the patent laws of the United States, Title 35,
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`United States Code, including 35 U.S.C. §271, and the Declaratory Judgment Act, Title 28, United
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`States Code, including §§ 2201, 2202.
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`
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`10X GENOMICS, INC.,
`
`
`Plaintiff,
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`
`
`v.
`
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`PARSE BIOSCIENCES, INC.,
`
`
`Defendant,
`
`
`and
`
`
`THE BOARD OF TRUSTEES OF LELAND
`STANFORD JUNIOR UNIVERSITY
`
`Nominal Defendant.
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`

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`Case 1:22-cv-01117-UNA Document 1 Filed 08/24/22 Page 2 of 84 PageID #: 2
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`THE PARTIES
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`2.
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`10x is a Delaware corporation with its principal place of business at
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`6230 Stoneridge Mall Road, Pleasanton, California 94588.
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`3.
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`10x is a pioneering innovator of genomics and sequencing technologies that are
`
`providing life science researchers an unprecedented understanding of biology. By elegantly
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`combining its proprietary hardware, chemistry, and software, 10x has developed and brought to
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`market award-winning products that give single-cell and spatial views of complex biological
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`systems. 10x’s products have enabled previously infeasible forms of research in the life sciences
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`in areas of critical importance to human health, including cancer research, neuroscience,
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`immunology, infectious disease, and developmental biology. 10x is the owner of the ’981, ’013,
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`and ’197 Patents, and the exclusive licensee of the ’995, ’207, and ’357 Patents pursuant to an
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`exclusive license agreement with the Board of Trustees of Leland Stanford Junior University
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`(“Stanford University”). 10x is pursuing this action and has the right to join Stanford University,
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`the owner and licensor of the ’995, ’207, and ’357 Patents, as a party in accordance with the terms
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`of its exclusive license agreement with Stanford University.
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`4.
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`Stanford University is a trust possessing corporate powers that is organized under
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`the laws of the State of California and with its principal place of business at the Office of the
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`President, Building 10 Main Quad, Stanford, California 94305. Stanford University is owner and
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`licensor of the ’995, ’207, and ’357 Patents. Stanford University is named as a nominal defendant
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`in this action for purposes of subject matter jurisdiction only and pursuant to the United States
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`Supreme Court’s holding in Independent Wireless Telegraph Co. v. Radio Corp. of America, 269
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`U.S. 459, 468 (1926), that “[i]f the owner of a patent, being within the jurisdiction, refuses or is
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`unable to join an exclusive licensee as coplaintiff, the licensee may make him a party defendant
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`by process, and he will be lined up by the court in the party character which he should assume.”
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`2
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`Case 1:22-cv-01117-UNA Document 1 Filed 08/24/22 Page 3 of 84 PageID #: 3
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`10x requested that Stanford University join as a party in this action, but Stanford University has
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`thus far not agreed to do so. Although Stanford University is named as a nominal defendant, 10x
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`seeks relief realigning Stanford University as a plaintiff.
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`5.
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`On information and belief, Parse is a Delaware corporation with its principal place
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`of business at 201 Elliott Avenue W, Suite 290, Seattle, Washington 98119.
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`6.
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`Parse is infringing and will infringe the patents asserted in this action by its
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`manufacture, use, sale, offer to sell, sale, and/or importation into the United States of products,
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`services, and components that are and/or will be used by Parse and its customers to infringe at least
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`Claim 1 of each of the ’981, ’013, ’197, ’995, and ’207 Patents and Claim 16 of the ’357 Patent.
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`JURISDICTION AND VENUE
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`7.
`
`8.
`
`10x incorporates and realleges paragraphs 1 to 6 above as if fully set forth herein.
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`This civil action for patent infringement arises under the patent laws of the United
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`States, 35 U.S.C § 1 et seq., including in particular under 35 U.S.C. § 271. This Court has subject
`
`matter jurisdiction pursuant to 28 U.S.C. §§ 1331, 1338(a).
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`9.
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`This Court has personal jurisdiction over Parse, and venue is proper in this district
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`pursuant to 28 U.S.C. § 1400(b), because Parse is a Delaware corporation and thus resides in this
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`district.
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`10.
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`This Court has personal jurisdiction over nominal defendant Stanford University
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`because Stanford University has substantial contacts with the forum as a consequence of
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`conducting business and activities in Delaware, including having filed lawsuits in this forum.
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`3
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`Case 1:22-cv-01117-UNA Document 1 Filed 08/24/22 Page 4 of 84 PageID #: 4
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`BACKGROUND
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`11.
`
`A.
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`12.
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`10x incorporates and realleges paragraphs 1 to 10 above as if fully set forth herein.
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`10x’s Groundbreaking Single-Cell Technologies
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`10x is a life sciences technology company founded in 2012 in Pleasanton,
`
`California by Drs. Serge Saxonov and Benjamin Hindson. Since its inception, 10x has focused on
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`building new technologies to enable breakthrough discoveries and accelerate the understanding of
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`biology. To date, 10x has invested hundreds of thousands of hours and over $1 billion in research
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`and development to invent, design, and develop its proprietary line of products for understanding
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`biology at unprecedented resolution and scale. 10x continues to invest significant time and money
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`to further innovate and bring groundbreaking new products and capabilities to market.
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`13.
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`10x is a worldwide leader in genomics, the comprehensive study of biological
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`systems at a molecular and cellular level. 10x provides end-to-end solutions for genomic analysis,
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`including instruments, reagent kits, and analysis software that enable researchers to obtain and
`
`interpret vast quantities of complex biological data. Since 10x’s first commercial launch in 2015,
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`10x’s expanding suite of products has fueled a revolution in genomics, winning wide acclaim and
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`commercial success. 10x has sold more than 3,500 instruments around the world, including at all
`
`of the top 100 global research institutions and all of the top 20 global biopharmaceutical
`
`companies. In 2021, annual sales of 10x products exceeded $490 million.
`
`14.
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`Over 3,800 scientific articles have been published based on data generated from
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`10x products, including hundreds of articles in top journals such as Cell, Science, and Nature. This
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`scientific work details the use of 10x products to discover, for example: molecular mechanisms
`
`that lead to brain, breast, and lung cancers; how the immune system reacts to COVID-19 infection;
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`and a new type of lung cell that causes cystic fibrosis. The paradigm-changing nature of 10x’s
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`4
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`

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`Case 1:22-cv-01117-UNA Document 1 Filed 08/24/22 Page 5 of 84 PageID #: 5
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`products has led to numerous accolades, including seven 10x products being named to The
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`Scientist magazine’s Top 10 Innovations list between 2015 and 2021.
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`15.
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`10x’s Chromium platform has been essential to enabling single-cell genomics—the
`
`study of biology at a cell-by-cell resolution and at a massive, system-wide scale, ushering in a
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`single-cell revolution hailed by Science magazine as the 2018 “Breakthrough of the Year.”
`
`Whereas traditional biology relies on “bulk analysis” in which tissue is analyzed as averages across
`
`the sample, 10x’s breakthrough single-cell products enable researchers to analyze samples on a
`
`single cell basis—for millions of cells per experiment—thereby preserving information that is
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`specific to each cell in the sample. 10x’s single-cell products do this by “tagging” the molecules
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`of each single cell with a unique nucleic acid barcode, which can then be analyzed to trace the
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`molecule’s cellular origin. The Chromium X instrument, which launched in July 2021 and
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`facilitates cost-effective million-cell experiments, is the latest addition to 10x’s award-winning
`
`platform and was named a Top 10 Innovation in 2021 by The Scientist magazine, https://www.the-
`
`scientist.com/features/2021-top-10-innovations-69438.
`
`16.
`
`A key strength of 10x’s Chromium platform lies in its suite of products that use
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`10x’s proprietary molecular assays to probe the various essential constituents of biology—e.g.,
`
`DNA, RNA, protein, and epigenetics—within a given sample. 10x launched its flagship single-
`
`cell product, Chromium Single Cell Gene Expression, in 2016. In addition to providing
`
`researchers with the ability to measure gene activity from RNA on a cell-by-cell basis, Single Cell
`
`Gene Expression is a versatile product that utilizes 10x’s Feature Barcoding technology to enable
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`single-cell protein analysis and single-cell CRISPR screening. 10x’s Chromium Single Cell
`
`Immune Profiling product, launched in 2017, enables researchers to unravel the vast complexity
`
`of adaptive immunity by examining T-cells and B-cells at single cell resolution. 10x’s Chromium
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`
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`5
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`

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`Case 1:22-cv-01117-UNA Document 1 Filed 08/24/22 Page 6 of 84 PageID #: 6
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`Single Cell ATAC and Single Cell Multiome products, launched in 2018 and 2020, respectively,
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`complement RNA measurements by examining DNA chromatin structure and its relation to gene
`
`regulation. 10x recently introduced its Chromium Fixed RNA Profiling product, allowing fragile
`
`samples to be fixed at the point of sample collection to lock in cell states and vastly increase the
`
`number of samples that can be analyzed. Collectively, 10x’s suite of products provide researchers
`
`with an arsenal of tools to assemble a complete, multi-omic picture of biological systems.
`
`17.
`
`10x’s Chromium Single Cell ATAC and Chromium Single Cell Multiome ATAC
`
`+ Gene Expression products have facilitated significant advancements in genomic research.
`
`“ATAC” is an acronym that stands for assay for transposase-accessible chromatin, and was
`
`invented by Stanford University researchers to identify transposase-accessible chromatin in a way
`
`that allowed for the simultaneous, high-throughput identification of open chromatin regions,
`
`nucleosome positioning, and regulatory motifs using sequencing technology. 10x integrated
`
`ATAC-seq into its Chromium platform to create its award-winning single cell epigenetics
`
`products. The Chromium Single Cell ATAC products allow for evaluation of chromatin
`
`accessibility within genomes at a single cell level. The Chromium Single Cell Multiome ATAC
`
`+ Gene Expression solution allows for the simultaneous profiling of gene expression and open
`
`chromatin from the same cell (rather than on different cells within a sample), providing cell-by-
`
`cell understanding of transcriptional profiles along with their corresponding gene regulatory
`
`environment. Each of 10x’s ATAC-seq products have been named a Top 10 Innovation by The
`
`Scientist magazine, with 10x’s Chromium Single Cell ATAC solution making the list in 2019, and
`
`the Chromium Single Cell Multiome ATAC + Gene Expression in 2020. Cision PR Newswire,
`
`10x Genomics Recognized on The Scientist’s Top 10 Innovations List for Fifth Consecutive Year
`
`
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`6
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`

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`Case 1:22-cv-01117-UNA Document 1 Filed 08/24/22 Page 7 of 84 PageID #: 7
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`(Dec. 1, 2021), https://www.prnewswire.com/news-releases/10x-genomics-recognized-on-the-
`
`scientists-top-10-innovations-list-for-fifth-consecutive-year-301435676.html.
`
`B.
`
`18.
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`Parse’s Infringing Evercode Whole Transcriptome (“WT”) Products
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`Parse is a single-cell genomics company that has made clear that it intends nothing
`
`less than to copy 10x’s complete lineup of single-cell products wholesale. Parse currently sells a
`
`single-cell gene expression product called Evercode Whole Transcriptome (“WT”). In April 2022,
`
`Parse opened up early access programs for two new assays: a targeted single-cell RNA sequencing
`
`product and a single-cell CRISPR product. Parse further announced that it plans to launch in the
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`second half of this year early access to a single-cell ATAC-seq product (“Parse Single-Cell ATAC-
`
`Seq Product”). See Andrew P. Han, Parse Biosciences Expands Single-Cell Product Line, Global
`
`Reach (Apr. 14, 2022), https://www.genomeweb.com/sequencing/parse-biosciences-expands-
`
`single-cell-product-line-global-reach. GenomeWeb noted that these new products “will help Parse
`
`compete with 10x Genomics, which already offers solutions for all of the applications Parse is
`
`pursuing.” Id.; see also Rosenberg et al., Single-Cell Profiling of the Developing Mouse Brain
`
`and Spinal Cord with Split-Pool Barcoding, 360 Science 176 & Suppl. Materials (Apr. 13, 2018)
`
`(referencing comparison of Parse’s SPLiT-seq method to “droplet-based scRNA-seq methods” and
`
`using 10x’s Chromium v2 as a comparator in Fig. S3); but see Fred Hutch Innovation Lab, Twitter,
`
`https://twitter.com/hutchinnovation/status/1484326929482219520 (last visited Aug. 24, 2022)
`
`(comparing Parse’s products to 10x’s and noting that Parse’s “[c]ell recovery was ~20% compared
`
`to 10x’s 50-60%,” and that Parse’s process as “more cumbersome” than 10x as it required “at least
`
`2 full days and a lot of pipetting.”).
`
`19.
`
`On information and belief, Parse copied 10x’s single-cell dual-tagging technology
`
`to identify the cell and the polynucleotide within that cell despite knowing of the existence of 10x’s
`
`patents that cover 10x’s single-cell dual-tagging technologies, including the ’981, ’013, and ’197
`
`
`
`7
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`

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`Case 1:22-cv-01117-UNA Document 1 Filed 08/24/22 Page 8 of 84 PageID #: 8
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`Patents, or deliberately not finding out which of 10x’s patents covered 10x’s single-cell dual-
`
`tagging technologies.
`
`20.
`
`On information and belief, Parse provides its Evercode WT kits—including
`
`reagents, other consumables, and data analysis software—to its customers. Parse asserts in its
`
`publications that its technology is based on a split-pool combinatorial barcoding method called
`
`SPLiT-Seq. Parse Biosciences, Technology, https://www.parsebiosciences.com/technology
`
`(citing Rosenberg et al., Single-Cell Profiling of the Developing Mouse Brain and Spinal Cord
`
`with Split-Pool Barcoding, 360 Science 176 (Apr. 13, 2018)). The first kit launched by Parse
`
`purports to enable users to process up to 100,000 single cells and 48 samples. See Parse
`
`Biosciences,
`
`EvercodeTM Whole
`
`Transcriptome
`
`Single Cell
`
`for Any
`
`Lab,
`
`https://www.parsebiosciences.com/products/evercode-whole-transcriptome (last visited Aug. 24,
`
`2022). In late 2021, Parse began offering its Evercode WT Mini kit that purports to enable users
`
`to process up to 10,000 single cells and its Evercode WT Mega kit that purports to enable users to
`
`process up to one million single cells. See Parse Biosciences, Explore Single Cell,
`
`https://www.parsebiosciences.com/products/evercode-whole-transcriptome-mini
`
`(last visited
`
`Aug. 24, 2022); Parse Biosciences, EvercodeTM Whole Transcriptome Mega 1 Million Cells for
`
`Your Lab Today, https://www.parsebiosciences.com/products/evercode-whole-transcriptome-
`
`mega (last visited Aug. 24, 2022). Each of Parse’s Evercode WT Products purportedly enable
`
`users to analyze molecular signatures at the single-cell level. See, e.g., Parse Biosciences,
`
`https://www.parsebiosciences.com (“Single cell insights are accessible to biological researchers in
`
`any lab with the Evercode™ combinatorial barcoding approach.”) (last visited Aug. 24, 2022).
`
`21.
`
`On information and belief, Parse purports that its Evercode WT Products are used
`
`to convert single cells of nuclei into individualized reaction compartments and that the cells or
`
`
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`8
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`

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`Case 1:22-cv-01117-UNA Document 1 Filed 08/24/22 Page 9 of 84 PageID #: 9
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`nuclei can be paired with unique cellular barcodes and unique molecular indices through a non-
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`automated, labor-intensive manual method of pooling, tagging, re-pooling, re-tagging, etc. See,
`
`e.g., Parse Biosciences, Technology, https://www.parsebiosciences.com/technology (last visited
`
`Aug. 24, 2022); Rosenberg et al., Single-Cell Profiling of the Developing Mouse Brain and Spinal
`
`Cord with Split-Pool Barcoding, 360 Science 176, 177, Suppl. Materials Fig. S1 (Apr. 13, 2018).
`
`
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`9
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`22.
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`On information and belief, Parse claims that its products’ barcode tagging allow the
`
`user to track a molecule of interest and the cell of origin of that molecule, and as a result detect
`
`and quantify the level of the molecule of interest by sequencing:
`
`
`
`Decode Science, Parse Biosciences Introduces Single Cell 3.0, YouTube (Nov. 17, 2021),
`
`https://www.youtube.com/watch?v=GP3zx0-D_Yg at 6:33; see also Rosenberg et al., Single-Cell
`
`Profiling of the Developing Mouse Brain and Spinal Cord with Split-Pool Barcoding, 360 Science
`
`176,
`
`177
`
`(Apr.
`
`13,
`
`2018);
`
`Parse
`
`Biosciences,
`
`Technology,
`
`https://www.parsebiosciences.com/technology (last visited Aug. 24, 2022).
`
`23.
`
`The “Evercode WT Products” are all products or components that are and/or will
`
`be made, used, offered for sale, sold, and/or imported into the United States by or on behalf of
`
`Parse in connection with Parse’s Evercode WT Products and workflows. The Evercode WT
`
`Products include, for example and without limitation, reagents, other consumables, and data
`
`analysis software used or provided by Parse in connection with its kits, along with instruction
`
`manuals for how to use the Evercode WT Products.
`
`24.
`
`On information and belief, the Evercode WT Products are and/or will be, marketed,
`
`offered for sale, and sold by Parse to potential and actual customers with material including
`
`technical brochures, instructional information, dataset examples, tutorials, and support suite
`
`
`
`10
`
`

`

`Case 1:22-cv-01117-UNA Document 1 Filed 08/24/22 Page 11 of 84 PageID #: 11
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`information (collectively, “Parse Instructional Materials”). Such materials can be found for
`
`example
`
`on Parse’s website
`
`(parsebiosciences.com), Parse’s YouTube
`
`channel
`
`(https://www.youtube.com/channel/UCnV6KzlTvt8JYX2idK7nY1A/videos), and Parse’s Vimeo
`
`channel (https://vimeo.com/504880645). On information and belief, the Parse Instructional
`
`Materials provide instructions, recommendations, and suggestions to customers on how to use
`
`Parse’s Evercode WT Products.
`
`25.
`
`On information and belief, Evercode WT Products are and/or will be, presented by
`
`Parse to potential and actual customers at seminars, conferences, and meetings (collectively,
`
`“Parse Instructional Presentations,” and together with “Parse Instructional Materials,” “Parse
`
`Instructional Materials and Presentations”). On information and belief, the Parse Instructional
`
`Presentations provide instructions, recommendations, and suggestions to customers on how to use
`
`Parse’s Evercode WT Products.
`
`26.
`
`In addition, on information and belief, Parse copied 10x’s ATAC-seq technologies
`
`despite knowing of the existence of 10x’s patents that cover 10x’s ATAC-seq technologies,
`
`including the ’995, ’207, and ’357 Patents, or deliberately not finding out which of 10x’s patents
`
`covered 10x’s ATAC-seq technologies.
`
`27.
`
`On information and belief, in or around April 2022, Parse announced its plans to
`
`launch, in the second half of 2022, the Parse Single-Cell ATAC-Seq Product (as in the case of the
`
`10x technology described in paragraph 17 above, “ATAC-seq” is an acronym that stands for assay
`
`for transposase-accessible chromatin by sequencing). See Andrew P. Han, Parse Biosciences
`
`Expands
`
`Single-Cell
`
`Product
`
`Line,
`
`Global
`
`Reach
`
`(Apr.
`
`14,
`
`2022)
`
`https://www.genomeweb.com/sequencing/parse-biosciences-expands-single-cell-product-line-
`
`global-reach#.YuvXJbfMKUk. On information and belief, Parse announced on Twitter, “A big
`
`
`
`11
`
`

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`Case 1:22-cv-01117-UNA Document 1 Filed 08/24/22 Page 12 of 84 PageID #: 12
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`thank you to @genomeweb and @HanAndrewP for covering our new product line, which includes
`
`a targeted scRNAseq assay, scCRISPR screen kit, scATAC-seq kit, and an immune profiling kit.
`
`Follow us for updates! #scRNAseq #CRISPR #ATACseq #immuneprofiling.” Parse Biosciences,
`
`Twitter (Apr. 15, 2022), https://twitter.com/ParseBio?ref_src=twsrc%5Egoogle%7Ctwcamp%
`
`5Eserp%7Ctwgr%5Eauthor. On information and belief, the Single-Cell ATAC-Seq Product will
`
`be an add-on to the Evercode WT Products. See Andrew P. Han, Parse Biosciences Expands
`
`Single-Cell
`
`Product
`
`Line,
`
`Global
`
`Reach
`
`(Apr.
`
`14,
`
`2022)
`
`https://www.genomeweb.com/sequencing/parse-biosciences-expands-single-cell-product-line-
`
`global-reach#.YuvXJbfMKUk.
`
`28. Moreover, on information and belief, Parse’s Single Cell ATAC-Seq Product is or
`
`will be used by Parse and will be used by its customers to perform the ATAC-seq method, namely
`
`generating a library of tagged fragments from open chromatin in the nucleus of a cell and
`
`sequencing those tagged fragments to obtain a sequencing library of the regions of open chromatin:
`
`
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`12
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`

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`
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`ATAC-seq is a probe of open chromatin state. (A) ATAC-seq library
`preparation schematic: An insertional enzyme complex, such as Tn5 transposase
`(green) loaded with sequence adaptors (red and blue), inserts only in regions of
`open chromatin (nucleosomes in gray) and generates a library of fragments that can
`be PCR amplified and sequenced. (B) During PCR amplification, additional
`sequences are incorporated into the adaptors, which include common sequencing
`ends and a sequencing barcode.
`
`Buenrostro et al., ATAC-Seq: A Method for Assaying Chromatin Accessibility Genome Wide, 109
`
`Current Protocols in Molecular Biology 21.29.1, 21.29.2 (Jan. 2015); Buenrostro et al.,
`
`Transposition of Native Chromatin for Multimodal Regulatory Analysis and Personal
`
`
`
`13
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`

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`Case 1:22-cv-01117-UNA Document 1 Filed 08/24/22 Page 14 of 84 PageID #: 14
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`Epigenomics, 10(12) Nature Methods 1213 (2013); see also Klemm, Shipony, & Greenleaf,
`
`Chromatin accessibility and the regulatory epigenome, 20 Nature Reviews 207, 208–210 (Apr.
`
`2019); Wikipedia, ATAC-seq, https://en.wikipedia.org/wiki/ATAC-seq (last visited Aug. 24,
`
`2022).
`
`29.
`
`The Parse Single-Cell ATAC-Seq Product are all products or components that have
`
`been, are and will be made, used, sold, offered for sale, and/or imported into the United States by
`
`or on behalf of Parse in connection with the Parse Single-Cell ATAC-Seq Product kit and
`
`workflows. The Parse Single-Cell ATAC-Seq Product includes, for example and without
`
`limitation, reagents, other consumables, and data analysis software used or provided by Parse in
`
`connection with its kits, along with instruction manuals for how to use the Parse Single-Cell
`
`ATAC-Seq Product.
`
`30.
`
`On information and belief, the Parse Single-Cell ATAC-Seq Product will be
`
`marketed, offered for sale, and sold by Parse to potential and actual customers with material
`
`including technical brochures, instructional information, dataset examples, tutorials, and support
`
`suite information (collectively, “Parse ATAC-Seq Instructional Materials”). On information and
`
`belief, the Parse ATAC-Seq Instructional Materials will provide instructions, recommendations,
`
`and suggestions to customers on how to use Parse Single-Cell ATAC-Seq Product.
`
`31.
`
`On information and belief, the Parse Single-Cell ATAC-Seq Product will be
`
`presented by Parse to potential and actual customers at seminars, conferences, and meetings
`
`(collectively, “Parse ATAC-Seq Instructional Presentations,” and together with Parse ATAC-Seq
`
`Instructional Materials, “Parse ATAC-Seq Instructional Materials and Presentations”). On
`
`information and belief, the Parse ATAC-Seq Instructional Presentations provide instructions,
`
`
`
`14
`
`

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`Case 1:22-cv-01117-UNA Document 1 Filed 08/24/22 Page 15 of 84 PageID #: 15
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`recommendations, and suggestions to customers on how to use the Parse Single-Cell ATAC-Seq
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`Product.
`
`THE PATENTS-IN-SUIT
`
`32.
`
`10x incorporates and realleges paragraphs 1 to 31 above as if fully set forth herein.
`
`33.
`By its manufacture, use, offer for sale, sale, and/or importation into the United
`States of the Evercode WT Products, Parse is infringing and will infringe the ’981, ’013, and ’197
`Patents. By its manufacture, use, offer for sale, sale, and/or importation into the United States of
`the Parse Single-Cell ATAC-Seq Product (together with Evercode WT Products, the “Accused
`Instrumentalities”), Parse is infringing and will infringe the ’995, ’207, and ’357 Patents.
`a.
`The ’981 Patent, entitled “Methods for analyzing nucleic acids from single
`
`cells,” is attached as Exhibit 1;
`
`b.
`
`The ’013 Patent, entitled “Methods for analyzing nucleic acids from single
`
`cells,” is attached as Exhibit 2;
`
`c.
`
`The ’197 Patent, entitled “Methods for analyzing nucleic acids from single
`
`cells,” is attached as Exhibit 3;
`
`d.
`
`The ’995 Patent, entitled “Transposition of Native Chromatin for Personal
`
`Epigenomics,” is attached as Exhibit 4;
`
`e.
`
`The ’207 Patent, entitled “Transposition of Native Chromatin for Personal
`
`Epigenomics,” is attached as Exhibit 5; and
`
`f.
`
`The ’357 Patent, entitled “Transposition of Native Chromatin for Personal
`
`Epigenomics,” is attached as Exhibit 6.
`
`The ‘981, ’013, ’197, ’995, ’207, and ’357 Patents are referred to collectively as “the Asserted
`
`Patents.”
`
`
`
`15
`
`

`

`Case 1:22-cv-01117-UNA Document 1 Filed 08/24/22 Page 16 of 84 PageID #: 16
`
`34.
`
`The ’981 Patent was duly and legally issued on December 18, 2018, by the United
`
`States Patent and Trademark Office. U.S. Application No. 15/677,957, which issued as the ’981
`
`Patent, claims the benefit of Provisional Application Nos. 61/288,792, filed on December 21, 2009,
`
`and 61/235,595, filed on August 20, 2009. Sydney Brenner, Gi Mikawa, Robert Osborne, and
`
`Andrew Slatter are the named inventors of the ’981 Patent. 10x is the sole legal owner of the ’981
`
`Patent. The assignment abstract and record for the ’981 Patent is attached as Exhibit 7.
`
`35.
`
`The ’013 Patent was duly and legally issued on June 30, 2020, by the United States
`
`Patent and Trademark Office. U.S. Application No. 16/817,461, which issued as the ’013 Patent,
`
`claims the benefit of Provisional Application Nos. 61/288,792, filed on December 21, 2009, and
`
`61/235,595, filed on August 20, 2009. Sydney Brenner, Gi Mikawa, Robert Osborne, and Andrew
`
`Slatter are the named inventors of the ’013 Patent. 10x is the sole legal owner of the ’013 Patent.
`
`The assignment abstract and record for the ’013 Patent is attached as Exhibit 8.
`
`36.
`
`The ’197 Patent was duly and legally issued on March 26, 2019, by the United
`
`States Patent and Trademark Office. U.S. Application No. 16/194,047, which issued as the ’197
`
`Patent, claims the benefit of Provisional Application No. 61/288,792, filed on December 21, 2009,
`
`and Provisional Application No. 61/235,595, filed on August 20, 2009. Sydney Brenner, Gi
`
`Mikawa, Robert Osborne, and Andrew Slatter are the named inventors of the ’197 Patent. 10x is
`
`the sole legal owner of the ’197 Patent. The assignment abstract and record for the ’197 Patent is
`
`attached as Exhibit 9.
`
`37.
`
`The ’995 Patent was duly and legally issued on December 11, 2018, by the United
`
`States Patent and Trademark Office. U.S. Application No. 16/043,874, which issued as the ’995
`
`Patent, claims the benefit of Provisional Application No. 61/826,728, filed on May 23, 2013. Paul
`
`Giresi, Jason D. Buenrostro, Howard Y. Chang, and William J. Greenleaf are the named inventors
`
`
`
`16
`
`

`

`Case 1:22-cv-01117-UNA Document 1 Filed 08/24/22 Page 17 of 84 PageID #: 17
`
`of the ’995 Patent. Stanford University is the sole legal owner of the ’995 Patent. The assignment
`
`abstract and record for the ’995 Patent is attached as Exhibit 10. 10x is the exclusive licensee of
`
`the ’995 Patent, including the right to sue for acts of infringement and to recover damages.
`
`38.
`
`The ’207 Patent was duly and legally issued on April 14, 2020, by the United States
`
`Patent and Trademark Office. U.S. Application No. 16/418,889, which issued as the ’207 Patent,
`
`claims the benefit of Provisional Application No. 61/826,728, filed on May 23, 2013. Paul Giresi,
`
`Jason D. Buenrostro, Howard Y. Chang, and William J. Greenleaf are the named inventors of the
`
`’207 Patent. Stanford University is the sole legal owner of the ’207 Patent. The assignment
`
`abstract and record for the ’207 Patent is attached as Exhibit 11. 10x is the exclusive licensee of
`
`the ’207 Patent, including the right to sue for acts of infringement and to recover damages.
`
`39.
`
`The ’357 Patent was duly and legally issued on August 11, 2020, by the United
`
`States Patent and Trademark Office. U.S. Application No. 16/418,796, which issued as the ’357
`
`Patent, claims the benefit of Provisional Application No. 61/826,728, filed on May 23, 2013. Paul
`
`Giresi, Jason D. Buenrostro, Howard Y. Chang, and William J. Greenleaf are the named inventors
`
`of the ’357 Patent. Stanford University is the sole legal owner of the ’357 Patent. The assignment
`
`abstract and record for the ’357 Patent is attached as Exhibit 12. 10x is the exclusive licensee of
`
`the ’357 Patent, including the right to sue for acts of infringement and to recover damages.
`
`40.
`
`The Asserted Patents describe specific steps and materials—as opposed to the
`
`countless other ways one could try to develop a method for nucleic acid analysis, including
`
`chromatin analysis—and are neither abstract, nor in any way preempt the field of single-cell
`
`nucleic acid analysis or chromatin analysis. The patented subject matter covers specific and
`
`concrete methods that remove limitations imposed by older sequencing technologies and are useful
`
`in a number of other nucleic acid analyses.
`
`
`
`17
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`

`Case 1:22-cv-01117-UNA Document 1 Filed 08/24/22 Page 18 of 84 PageID #: 18
`
`FIRST CAUSE OF ACTION
`(INFRINGEMENT OF U.S. PATENT NO. 10,155,981)
`
`41.
`
`42.
`
`10x incorporates and realleges paragraphs 1 to 40 above as if fully set forth herein.
`
`Parse’s manufacture, use, offer for sale, sale, and/or importation into the United
`
`States of its Evercode WT Products directly infringes at least Claim 1 of the ’981 Patent, literally
`
`or by equivalents, under 35 U.S.C. §§ 271(a), (f), (g).
`
`43.
`
`Parse’s manufacture, use, offer for sale, sale, and/or importation into the United
`
`States of its Evercode WT Products indirectly infringes at least Claim 1 of the ’981 Patent, literally
`
`or by equivalents, under 35 U.S.C. §§ 271(b), (c) based on an underlying act of direct infringement
`
`by Parse’s customers.
`
`44.
`
`Claim 1 of the ’981 Patent recites:
`
`A method of analyzing nucleic acids from a plurality of single cells, the method
`comprising:
`
`(a) providing a sample comprising a plurality of single cells, wherein each
`single cell of the plurality of single cells comprises a plurality of sample
`polynucleotides;
`
`(b) generating a plurality of tagged polynucleotides from the plurality of sample
`polynucleotides, wherein each tagged polynucleotide comprises:
`
`(i) a sequence from a sample polynucleotide of the plurality of sample
`polynucleotides; and
`
`(ii) a multiplex identifier (MID) sequence comprising:
`
`I. a first tag sequence associated with the single cell from which the
`sample polynucleotide is derived, wherein the first tag sequence is a
`different sequence for different single cells in the plurality of single
`cells; and
`
`II. a second tag sequence distinguishing the sample polynucleotide from
`other sample polynucleotides derived from the same single cell;
`
`
`
`18
`
`

`

`Case 1:22-cv-01117-UNA Document 1 Filed 08/24/22 Page 19 of 84 PageID #: 19
`
`(c) sequencing the plurality of tagged polynucleotides to obtain a plurality of
`identified polynucleotide sequences;
`
`(d) using the first tag sequenc