Case 1:24-cv-00687-RGA Document 1 Filed 06/11/24 Page 1 of 22 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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`JURY TRIAL DEMANDED
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`)))))))))
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`
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`GUARDANT HEALTH, INC.,
`
`Plaintiff,
`
`v.
`
`TEMPUS AI, INC.,
`
`Defendant.
`
`COMPLAINT FOR PATENT INFRINGEMENT
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`Plaintiff Guardant Health, Inc. (“Guardant”) files this Complaint for Patent Infringement
`
`against Defendant Tempus AI, Inc. (“Tempus”) and alleges as follows:
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`OVERVIEW OF THE ACTION
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`1.
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`This action is necessitated by Tempus’s unauthorized use of Guardant’s
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`groundbreaking, patented innovations in the field of cancer diagnostics. Specifically, this is an
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`action against Tempus for infringement of Guardant’s U.S. Patent Nos. 11,149,306 (the “’306
`
`Patent”), 9,902,992 (the “’992 Patent”), 10,501,810 (the “’810 Patent”), 10,793,916 (the “’916
`
`Patent”), and 11,643,693 (the “’693 Patent”) (collectively, the “Patents-in-Suit”). Tempus’s
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`infringement of the Patents-In-Suit has caused and is causing ongoing harm to Guardant. Guardant
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`brings this suit to stop Tempus’s infringement and enjoin Tempus from practicing Guardant’s
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`patented inventions. And Tempus must compensate Guardant for the infringement and injury that
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`has already occurred.
`
`2.
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`Guardant is a leading precision oncology company dedicated to helping conquer
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`cancer with data obtained through its proprietary blood tests. Guardant was founded over a decade
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`ago by Helmy Eltoukhy, Ph.D., and AmirAli Talasaz, Ph.D., pioneers in DNA sequencing and
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`cancer diagnostics. Since its inception, Guardant has focused its expertise on the development of
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`Case 1:24-cv-00687-RGA Document 1 Filed 06/11/24 Page 2 of 22 PageID #: 2
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`groundbreaking liquid biopsy cancer tests, including Guardant360® CDx, the first FDA-approved
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`liquid biopsy test. To date, over 500,000 patient samples have been analyzed using Guardant’s
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`tests.
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`3.
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`A liquid biopsy is the sampling and analysis of non-solid biological tissues, such
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`as a patient’s blood. It is distinct from a conventional biopsy, which involves the removal of tissue
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`for examination and is often conducted surgically. All cells in the human body contain DNA. When
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`a person’s organ or tissues suffer from disease such as cancer, the DNA in the cells making up the
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`organ or tissue may contain biomarkers that indicate the presence of the disease. Traditionally, a
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`biopsy would need to extract cells from a particular organ or tissues of interest. The DNA from
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`those cells would then be analyzed for biomarkers.
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`4.
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`But pieces of DNA originating from cells in many different organs and tissues also
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`circulate freely in the human bloodstream. These DNA fragments circulating in the bloodstream
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`are known as “cell-free DNA” or “cfDNA.” A simple, non-invasive blood draw can capture cell-
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`free DNA originating from cells in many different organs and tissues all at once. That DNA can
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`then be analyzed for relevant biomarkers indicating the presence of disease. But using cell-free
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`DNA in the bloodstream to look for biomarkers raises substantial complexity and problems. A
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`traditional biopsy provides a very large sample of DNA from a particular type of cell. With cell-
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`free DNA, very small numbers of DNA fragments originating from the cells of interest may be
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`present, mixed in with very large numbers of DNA fragments from many other cells.
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`5.
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`Guardant is a pioneer in the field and solved many of the problems critical to
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`unlocking the use of cell-free DNA to detect cancer and other disease in the blood. For example,
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`Guardant was one of the first companies to commercialize a comprehensive liquid biopsy test to
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`identify genomic biomarkers. Guardant’s liquid biopsy technology enables patients, including
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`those who are ineligible for traditional tissue biopsies, to obtain detailed genomic information
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`about their cancer. Guardant’s technology also allows patients to be screened for a large number
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`of potential cancers or diseases that may be present in different parts of the body, all with a simple
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`blood draw.
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`6.
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`For example, the Guardant360® CDx test is a liquid biopsy test that provides
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`clinically actionable information from a routine blood draw taken from cancer patients. From the
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`extracted cell-free DNA, the test sequences a panel of genes commonly mutated in cancer and
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`detects genetic aberrations such as single nucleotide variants, indels (insertions or deletions of
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`nucleotides), gene fusions, and copy number variants.
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`7.
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`In addition to the FDA-approved Guardant360® CDx test, Guardant currently
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`offers six other tests: the Guardant360® laboratory developed test (LDT), the Guardant360
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`Response™, Guardant360 TissueNext™, Guardant Infinity™, Guardant Reveal™, and Shield™
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`tests. These tests span the cancer care continuum, including early cancer screening, treatment
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`selection, and residual disease and recurrence monitoring.
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`8.
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`Guardant’s liquid biopsy technology has several additional advantages when
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`compared to traditional tissue biopsies. Traditional tumor-based genotyping tests are limited in the
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`number of genes interrogated, require invasive biopsies, and often take upwards of 15 days before
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`results are generated. Guardant’s liquid biopsies are less painful and do not require hospital
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`services. This technology is also less expensive and generates results in a shorter period of time,
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`often in less than a week. Further, cfDNA samples allow for the detection of mutations that may
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`be missed by a tissue biopsy sample.
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`9.
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`Guardant’s technology is built on a series of cutting-edge innovations that
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`Guardant’s scientists developed over many years and at great cost through an extensive research
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`and development program. Those innovations are protected by over 95 patents issued by the United
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`States Patent and Trademark Office, including the Patents-In-Suit. These patents were issued in
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`recognition of the novelty and usefulness of Guardant’s patents.
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`10.
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`Tempus was founded in 2015. Since its inception, Tempus has capitalized on
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`Guardant’s pioneering efforts to develop copy-cat cell-free DNA liquid biopsy tests. Tempus was
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`formerly known as Tempus Labs, Inc.
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`11.
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`Tempus makes, markets, and uses liquid biopsy panels in ways that practice
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`Guardant’s Patents-In-Suit. One such category of liquid biopsy panels includes products known as
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`Tempus xF, Tempus xF+, and Tempus xM Monitor. These panels, and others that may function
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`in relevantly similar ways, will be referred to as the “Accused xF Tests.” More recently, Tempus
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`has developed a second generation of liquid tests known as Tempus xM MRD. The Tempus xM
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`MRD will be referred to as the “Accused xM Tests.” Together, the Accused xF Tests and the
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`Accused xM Tests will be referred to collectively as the “Accused Tests.”
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`12.
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`On information and belief, Tempus has been monitoring Guardant’s intellectual
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`property portfolio while making the Accused Tests. For example, in Tempus’s S-1 filing dated
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`May 20, 2024,1 Tempus stated the following:
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`The intellectual property landscape in the next generation sequencing, generative
`AI, and other fields in which we operate continues to evolve in ways that may
`impact our business. For example, we are aware of patent litigation involving
`certain disciplines in which we operate, such as liquid biopsy sequencing methods
`and minimal residual disease testing methods. While we are not a party to these
`suits, many of our competitors are or have been, including Guardant Health, Inc.,
`Haystack Oncology, Inc., Invitae Corp., Illumina, Inc., Natera, Inc., NeoGenomics
`Laboratories, Inc., Personalis, Inc., TwinStrand Biosciences, Inc., and others, and,
`as a result, we have monitored and continue to monitor their developments and their
`potential impact on the Company. Given the uncertainty of outcomes of patent
`litigation disputes, we have not determined whether our products and services could
`
`1 Available at
`https://www.sec.gov/Archives/edgar/data/1717115/000119312524142956/d221145ds1.htm
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`4
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`be subject to potential claims of patent infringement based on the patents at issue
`in these or other cases, whether we may need to modify or change any existing or
`planned sequencing procedures, or whether any of the patents at issue are valid or
`enforceable against us. However, it is possible that we will be subject to claims of
`patent infringement and that we may need to either modify our existing or future
`sequencing methods or license intellectual property from third parties, both of
`which could be time consuming and expensive.
`
`13.
`
`As shown above, Tempus “monitored and continue[s] to monitor” patent litigation
`
`involving Guardant and the potential impact of Guardant’s patents on Tempus. Tempus also
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`understands that because of Guardant’s intellectual property, Tempus may need to “modify [its]
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`existing or future sequencing methods.”
`
`14.
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`Tempus has achieved market success with its Accused Tests. But, as described
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`below, that success derives from Tempus’s unauthorized use of Guardant’s pioneering inventions.
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`THE PARTIES
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`15.
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`Guardant is a corporation organized and existing under the laws of the state of
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`Delaware, having its principal place of business at 3100 Hanover Street, Palo Alto, CA 94034.
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`16.
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`Tempus is a corporation organized and existing under the laws of the state of
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`Delaware. Its principal place of business is 600 West Chicago Avenue, Suite 510, Chicago, Illinois
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`60654.
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`JURISDICTION AND VENUE
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`17.
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`This civil action arises under the patent laws of the United States, 35 U.S.C. § 1 et
`
`seq., including without limitation 35 U.S.C. §§ 271, 281, 283, 284, and 285. Accordingly, this
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`Court has subject matter jurisdiction under, inter alia, 28 U.S.C. §§ 1331, 1338(a), 2201 and 2202.
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`This Court has personal jurisdiction over Tempus because Tempus is subject to general and
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`specific jurisdiction in the state of Delaware. Tempus is subject to personal jurisdiction at least
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`because Tempus is a Delaware corporation and resides in this District. Tempus has made certain
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`minimum contacts with Delaware such that the maintenance of this suit does not offend traditional
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`notions of fair play and substantial justice.
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`18.
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`The exercise of personal jurisdiction comports with Tempus’s right to due process
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`because, as described above, Tempus has purposefully availed itself of the privilege of Delaware
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`corporate laws such that it should reasonably anticipate being haled into court here.
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`19.
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`Venue is proper in this District pursuant to 28 U.S.C. §§ 1391 and 1400(b) because,
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`among other things, Tempus is incorporated in Delaware.
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`THE GUARDANT PATENTS-IN-SUIT
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`20.
`
`On October 19, 2021, the United States Patent and Trademark Office lawfully
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`issued U.S. Patent No. 11,149,306, entitled “Methods and systems for detecting genetic variants.”
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`A true and correct copy of the patent is attached hereto as Exhibit A. Guardant is the owner and
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`assignee of all right, title, and interest in and to the ’306 Patent, including the right to assert all
`
`causes of action arising under the ’306 Patent and the right to sue and obtain any remedies for past,
`
`present, or future infringement.
`
`21.
`
`On February 27, 2018, the United States Patent and Trademark Office lawfully
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`issued U.S. Patent No. 9,902,992, entitled “Systems and methods to detect rare mutations and copy
`
`number variation.” A true and correct copy of the patent is attached hereto as Exhibit B. Guardant
`
`is the owner and assignee of all right, title, and interest in and to the ’992 Patent, including the
`
`right to assert all causes of action arising under the ’992 Patent and the right to sue and obtain any
`
`remedies for past, present, or future infringement.
`
`22.
`
`On December 10, 2019, the United States Patent and Trademark Office lawfully
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`issued U.S. Patent No. 10,501,810, entitled “Systems and methods to detect rare mutations and
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`copy number variation.” A true and correct copy of the patent is attached hereto as Exhibit C.
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`Guardant is the owner and assignee of all right, title, and interest in and to the ’810 Patent,
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`6
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`including the right to assert all causes of action arising under the ’810 Patent and the right to sue
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`and obtain any remedies for past, present, or future infringement.
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`23.
`
`On October 6, 2020, the United States Patent and Trademark Office lawfully issued
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`U.S. Patent No. 10,793,916, entitled “Methods and systems for detecting genetic variants.” A true
`
`and correct copy of the patent is attached hereto as Exhibit D. Guardant is the owner and assignee
`
`of all right, title, and interest in and to the ’916 Patent, including the right to assert all causes of
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`action arising under the ’916 Patent and the right to sue and obtain any remedies for past, present,
`
`or future infringement.
`
`24.
`
`On May 9, 2023, the United States Patent and Trademark Office lawfully issued
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`U.S. Patent No. 11,643,693, entitled “Compositions and methods for isolating cell-free DNA.” A
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`true and correct copy of the patent is attached hereto as Exhibit E. Guardant is the owner and
`
`assignee of all right, title, and interest in and to the ’693 Patent, including the right to assert all
`
`causes of action arising under the ’693 Patent and the right to sue and obtain any remedies for past,
`
`present, or future infringement.
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`TEMPUS’S INFRINGEMENT OF GUARDANT’S PATENTS-IN-SUIT
`
`25.
`
`In or around September 14, 2018, Tempus announced the release of its Tempus xF
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`liquid biopsy test, describing it as “a non-invasive genomic sequencing panel” that “analyzes 77
`
`genes.”
`
`(https://www.tempus.com/news/pr/tempus-adds-tempus-xf-a-liquid-biopsy-assay-to-
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`sequencing-capabilities/). On or around July 12, 2021, Tempus published a press release
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`announcing the results of a validation study purporting to demonstrate “the reliable analytical
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`performance of the Tempus xF liquid biopsy.” (https://www.tempus.com/news/pr/tempus-xf-
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`liquid-biopsy-assay-demonstrates-extensive-analytical-and-clinical-validity-in-npj-precision-
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`oncology-study/).
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`26.
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`The validation study for Tempus xF was authored by scientists affiliated with
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`Tempus, including J. Finkle, and is titled “Validation of a liquid biopsy assay with molecular and
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`clinical profiling of circulating tumor DNA.” It was published in the Journal of Precision Oncology
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`on July 2, 2021. On information and belief, this paper describes the methodology that Tempus uses
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`in its Tempus xF liquid biopsy test. This paper will be referred to as “Finkle” and attached as
`
`Exhibit F.
`
`27.
`
`On or around June 3, 2022, Tempus published a press release announcing the
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`launch of Tempus xF+, which it described as “a new non-invasive, liquid biopsy panel of 523
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`genes,
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`focused
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`on
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`pathogenic mutations
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`in
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`cell-free DNA
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`(cfDNA).”
`
`(https://www.tempus.com/news/pr/tempus-to-launch-largest-clinically-available-liquid-biopsy-
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`panel-xf/). In this same press release, Tempus stated that it “expects that the xF+ panel will be the
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`largest clinically available liquid biopsy panel on the market, covering more genes with single
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`nucleotide variants and indels reported in all genes, plus expanded coverage of translocations/gene
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`rearrangements, and copy number variants.” On information and belief, Tempus xF+ and Tempus
`
`xF operate in a substantially similar manner, with the largest difference being the number of genes
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`targeted by each product.
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`28.
`
`Tempus’s xF liquid biopsy test detects cell-free DNA in blood specimens of
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`patients with advanced solid tumors. The test is capable of detecting mutations in 105 genes,
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`including Single Nucleotide Variants (SNVs) and insertions and deletions (INDELs), as well as
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`Copy Number Gains (CNGs) in 6 genes, and gene rearrangements in 7 genes. The test covers
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`recurrent hotspot mutations in 70 genes. Microsatellite Instability High (MSI-H) status is also
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`reported when detected. Blood Tumor Mutational Burden (bTMB) status is also reported when
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`detected. (https://www.tempus.com/wp-content/uploads/2024/03/Tempus-xF_Validation.pdf).
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`29.
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`Tempus’s xF+ test covers clinically relevant exons and select non-coding regions
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`in 523 genes and is capable of detecting mutations in four variant classes: single nucleotide variants
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`(SNVs) and insertion-deletions (INDELs) in 523 genes; copy number gains (CNGs) in 7 genes;
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`and gene rearrangements in 10 genes. Blood Tumor Mutational Burden (bTMB) as well as detected
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`Microsatellite Instability High (MSI-H) will be reported by the test. (https://www.tempus.com/wp-
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`content/uploads/2024/02/Tempus-xFPlus_Validation.pdf).
`
`30.
`
`On or around November 3, 2023, Tempus published a press release announcing the
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`launch of Tempus xM Monitor (formerly xF Monitor), which it described as “detect[ing] and
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`monitor[ing] changes in circulating tumor fraction to determine early response to immunotherapy
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`for patients with advanced cancers.” (https://www.tempus.com/news/tempus-announces-new-
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`ctdna-assay-xm-monitor/). In this same press release, Tempus stated that “xM Monitor is now
`
`available for research use only for both Tempus’ 105-gene liquid test, xF, and Tempus’ 523-gene
`
`liquid assay, xF+.” The Tempus xM Monitor uses the Tempus xF+ and Tempus xF Tests as inputs.
`
`31.
`
`On information and belief, Tempus performs the xF and xF+ tests at facilities in
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`the
`
`United
`
`States
`
`on
`
`a
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`regular
`
`basis.
`
`(https://www.tempus.com/wp-
`
`content/uploads/2024/03/Tempus-xF_Validation.pdf). When using the Accused xF Tests, Tempus
`
`obtains samples of cell-free DNA from subjects. The cell-free DNA is ligated to adapters,
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`including ligating unique molecular identifiers (UMIs) to the ends of each cell-free DNA fragment,
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`with these UMIs including 96 different pairs of barcodes. On information and belief, Tempus uses
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`a quantity of adapters having a number of moles more than ten times the number of moles of cell-
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`free DNA in the sample, and these adapters are ligated to the cell-free DNA with an efficiency of
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`20 percent or more.
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`32.
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`Subsequent to ligating the adapters to a cell-free DNA sample, Tempus amplifies
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`and sequences the ligated cell-free DNA to generate sequence reads. Tempus maps the sequence
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`reads to a reference sequence. Tempus groups these reads into families based on the barcodes
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`(UMIs) as well as the alignment of the sequence reads to the reference sequence. Families are then
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`collapsed into consensus sequences, each representing a unique sequence read corresponding to
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`the sequence of an original cell-free DNA fragment. Reads failing to meet a set accuracy, quality
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`score, or mapping score threshold are filtered out.
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`33.
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`The consensus sequence reads are then used to determine the presence of genetic
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`variants including copy number variations (CNVs), rearrangements, insertions, deletions,
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`microsatellite instabilities (MSIs), single nucleotide variations (SNV), and gene fusions.
`
`34.
`
`On or around January 18, 2024, Tempus published a press release announcing the
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`launch of Tempus xM MRD, which it described as a process to “Assess Minimal Residual
`
`Disease.”
`
`(https://www.tempus.com/news/tempus-introduces-xm-to-assess-minimal-residual-
`
`disease-mrd-in-patients-with-colorectal-cancer-crc-for-research-use-only/). In this same press
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`release, Tempus stated that the xM MRD “assay delivers a binary MRD assessment based on both
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`methylation and genomic variant MRD classifiers+.” On information and belief, Tempus performs
`
`the xM MRD tests at facilities in the United States on a regular basis. On information and belief,
`
`when using the xM MRD Test, Tempus performs steps substantially similar to the steps performed
`
`with the tests used in the Tempus xF+ and Tempus xF Tests, and Tempus also analyses consensus
`
`sequences generated from the test to detect methylation profiles including at least the detection of
`
`methylation.
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`FIRST COUNT
`(Infringement of ’306 Patent) (All Accused Tests)
`
`35.
`
`Guardant repeats and re-alleges the foregoing paragraphs as if set forth specifically
`
`herein.
`
`36.
`
`37.
`
`The claims of the ’306 Patent are valid and enforceable.
`
`The claims of the ’306 Patent are directed to patentable subject matter. The ’306
`
`Patent is directed to innovations that provides for a method for reducing or tracking redundancy
`
`of sequence reads.
`
`38.
`
`Each of the Accused Tests, and Tempus’s use of each of the Accused Tests,
`
`practices steps that are identical or equivalent to each claimed element of the patented invention
`
`pointed out by at least Claim 1 of the ’306 Patent.
`
`39.
`
`Claim 1 of the ’306 Patent recites:
`
`1. A method, comprising:
`
`(a) providing a population of cell-free deoxyribonucleic acid
`(cfDNA) molecules having first and second complementary
`strands;
`
`(b) tagging a plurality of the cfDNA molecules in the population
`with duplex tags comprising molecular barcodes to produce tagged
`parent polynucleotides, wherein the duplex tags are attached to
`both ends of a molecule of the plurality of the cfDNA molecules,
`wherein the plurality of the cfDNA molecules are tagged with n
`different combinations of molecular barcodes, wherein n is at least
`2 and no more than 100,000*z, wherein z is a mean of an expected
`number of duplicate molecules in the population of cfDNA
`molecules that map to identical start and stop positions on a
`reference sequence;
`
`(c) amplifying a plurality of the tagged parent polynucleotides to
`produce amplified progeny polynucleotides;
`
`(d) sequencing at least a subset of the amplified progeny
`polynucleotides to produce a set of sequence reads; and
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`(e) reducing or tracking redundancy of a plurality of sequence
`reads from the set of sequence reads using at least sequencing
`information from the molecular barcodes of the duplex tags to
`determine distinct cfDNA molecules from among the tagged parent
`polynucleotides, wherein the distinct cfDNA molecules are
`determined based on (i) paired reads corresponding to sequence
`reads generated from a first tagged strand and a second tagged
`complementary strand derived from cfDNA molecules from
`among the tagged parent polynucleotides, or (ii) unpaired reads
`corresponding to sequence reads generated from a first tagged
`strand having no second tagged complementary strand derived
`from cfDNA molecules from among the tagged parent
`polynucleotides, wherein reducing or tracking the redundancy of
`the plurality of sequence reads comprises mapping at least a subset
`of the plurality of sequence reads to the reference sequence.
`
`40.
`
`Tempus is not licensed or otherwise authorized to practice the claims of the ’306
`
`Patent.
`
`41.
`
`On information and belief, Tempus has infringed and continues to infringe one or
`
`more claims of the ’306 patent pursuant to 35 U.S.C. § 271(a), including at least claim 1, literally
`
`or under the doctrine of equivalents, by its use of the Accused Tests within the United States,
`
`without authority. As an example, attached as Exhibit G is a preliminary and exemplary claim
`
`chart illustrating one way in which Tempus infringes claim 1 of the ’306 patent.
`
`42.
`
`Thus, by its acts, Tempus has injured Guardant and is liable to Guardant for directly
`
`infringing one or more claims of the ’306 Patent, whether literally or under the doctrine of
`
`equivalents.
`
`43.
`
`As a result of Tempus’s infringement of the ’306 Patent, Guardant has suffered
`
`monetary damages, and seeks recovery, in an amount to be proven at trial, adequate to compensate
`
`for Tempus’s infringement, but in no event less than a reasonable royalty with interest and costs.
`
`44.
`
`On information and belief, Tempus will continue to infringe the ’306 Patent unless
`
`enjoined by this Court. Tempus’s infringement of Guardant’s rights under the ’306 Patent will
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`continue to damage Guardant, causing irreparable harm for which there is no adequate remedy at
`
`law, unless enjoined by this Court.
`
`SECOND COUNT
`(Infringement of ’992 Patent) (All Accused Tests)
`
`45.
`
`Guardant repeats and re-alleges the foregoing paragraphs as if set forth specifically
`
`herein.
`
`46.
`
`47.
`
`The claims of the ’992 Patent are valid and enforceable.
`
`The claims of the ’992 Patent are directed to patentable subject matter. The ’992
`
`Patent is directed to innovations that detect genetic aberrations in cell-free DNA.
`
`48.
`
`Each of the Accused Tests, and Tempus’s use of each of the Accused Tests,
`
`practices steps that are identical or equivalent to each claimed element of the patented invention
`
`pointed out by at least Claim 1 of the ’992 Patent.
`
`49.
`
`Claim 1 of the ’992 Patent recites:
`
`1. A method for detecting genetic aberrations in cell-free DNA
`(“cfDNA”) molecules from a subject, comprising:
`
`a) providing cfDNA molecules obtained from a bodily sample of
`the subject;
`
`b) attaching tags comprising barcodes having a plurality of
`different barcode sequences to the cfDNA molecules to tag at least
`20% of the cfDNA molecules, which attaching comprises ligating
`adaptors comprising the barcodes to both ends of the cfDNA
`molecules, wherein ligating comprises using more than 10× molar
`excess of the adaptors as compared to the cfDNA molecules,
`thereby generating tagged parent polynucleotides;
`
`c) amplifying the tagged parent polynucleotides to produce
`amplified tagged progeny polynucleotides;
`
`d) sequencing the amplified tagged progeny polynucleotides to
`produce a plurality of sequence reads from each of the tagged
`parent polynucleotides, wherein each sequence read of the plurality
`of sequence reads comprises a barcode sequence and a sequence
`derived from a cfDNA molecule of the cfDNA molecules;
`
`13
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`Case 1:24-cv-00687-RGA Document 1 Filed 06/11/24 Page 14 of 22 PageID #: 14
`
`e) mapping sequence reads of the plurality of sequence reads to
`one or more reference sequences from a human genome;
`
`f) grouping the sequence reads mapped in e) into families based at
`least on barcode sequences of the sequence reads, each of the
`families comprising sequence reads comprising the same barcode
`sequence, whereby each of the families comprises sequence reads
`amplified from the same tagged parent polynucleotide;
`
`g) at each of a plurality of genetic loci in the one or more reference
`sequences, collapsing sequence reads in each family to yield a base
`call for each family at the genetic locus; and
`
`h) detecting, at one or more genetic loci, a plurality of genetic
`aberrations, wherein the plurality of genetic aberrations comprises
`two or more different members selected from the group of
`members consisting of a single base substitution, a copy number
`variation (CNV), an insertion or deletion (indel), and a gene
`fusion.
`
`50.
`
`Tempus is not licensed or otherwise authorized to practice the claims of the ’992
`
`Patent.
`
`51.
`
`On information and belief, Tempus has infringed and continues to infringe at least
`
`claim 1 of the ’992 patent pursuant to 35 U.S.C. § 271(a), literally or under the doctrine of
`
`equivalents, by its use of the Accused Tests within the United States, without authority. As an
`
`example, attached as Exhibit H is a preliminary and exemplary claim chart illustrating one way in
`
`which Tempus infringes claim 1 of the ’992 patent.
`
`52.
`
`Thus, by its acts, Tempus has injured Guardant and is liable to Guardant for directly
`
`infringing one or more claims of the ’992 Patent, whether literally or under the doctrine of
`
`equivalents.
`
`53.
`
`On information and belief, Tempus will continue to infringe the ’992 Patent unless
`
`enjoined by this Court. Tempus’s infringement of Guardant’s rights under the ’992 Patent will
`
`14
`
`

`

`Case 1:24-cv-00687-RGA Document 1 Filed 06/11/24 Page 15 of 22 PageID #: 15
`
`continue to damage Guardant, causing irreparable harm for which there is no adequate remedy at
`
`law, unless enjoined by this Court.
`
`THIRD COUNT
`(Infringement of ’810 Patent) (All Accused Tests)
`
`54.
`
`Guardant repeats and re-alleges the foregoing paragraphs as if set forth specifically
`
`herein.
`
`55.
`
`56.
`
`The claims of the ’810 Patent are valid and enforceable.
`
`The claims of the ’810 Patent are directed to patentable subject matter. The ’810810
`
`Patent is directed to innovations that detect somatic genetic variants in cell-free DNA.
`
`57.
`
`Each of the Accused Tests, and Tempus’s use of each of the Accused Tests,
`
`practices steps that are identical or equivalent to each claimed element of the patented invention
`
`pointed out by at least Claim 1 of the ’810 Patent.
`
`58.
`
`Claim 1 of the ’810 Patent recites:
`
`1. A method for detecting somatic genetic variants of cell-free
`deoxyribonucleic acid (DNA) in a human subject, the method
`comprising:
`
`a) obtaining 10 to 100 nanograms (ng) of double-stranded cell-free
`DNA from a blood sample from the human subject;
`
`b) ligating adapters comprising molecular barcodes to ends of a
`plurality of molecules of the double-stranded cell-free DNA to
`produce tagged parent polynucleotides, wherein the molecular
`barcodes together constitute a set of 5-100 molecular barcodes
`from 5-20 nucleotides in length;
`
`c) amplifying a plurality of the tagged parent polynucleotides to
`produce progeny polynucleotides with associated molecular
`barcodes;
`
`d) selectively enriching the progeny polynucleotides for target
`regions associated with cancer, whereby enriched progeny
`polynucleotides are generated;
`
`15
`
`

`

`Case 1:24-cv-00687-RGA Document 1 Filed 06/11/24 Page 16 of 22 PageID #: 16
`
`e) sequencing a portion of the enriched progeny polynucleotides to
`produce sequencing reads of the progeny polynucleotides with
`associated molecular barcodes;
`
`f) aligning mappable portions of the sequencing reads to a human
`reference genome;
`
`g) grouping a plurality of the sequencing reads into families based
`on the sequence information of the molecular barcodes and the
`beginning and end base positions of the mapped portion of the
`progeny polynucleotides; and
`
`h) detecting, from among a plurality of the families, the presence
`or absence of one or more somatic genetic variants comprising a
`single nucleotide variant (SNV), a copy number variation (CNV),
`an insertion or deletion (indel), a gene fusion, or any combination
`thereof.
`
`59.
`
`Tempus is not licensed or otherwise authorized to practice the claims of the ’810
`
`Patent.
`
`60.
`
`On information and belief, Tempus has infringed and continues to infringe at least
`
`claim 1 of the ’810 patent pursuant to 35 U.S.C. § 271(a), literally or under the doctrine of
`
`equivalents, by its use of the Accused Tests within the United States, without authority. As an
`
`example, attached as Exhibit I is a preliminary and exemplary claim chart illustrating one way in
`
`which Tempus infringes claim 1 of the ’810 patent.
`
`61.
`
`Thus, by its acts, Tempus has injured Guardant and is liable to Guardant for directly
`
`infringing one or more claims of the ’810 Patent, whether literally or under the doctrine of
`
`equivalents.
`
`62.
`
`On information and belief, Tempus will continue to infringe the ’810 Patent unless
`
`enjoined by this Court. Tempus’s infringement of Guardant’s rights under the ’810 Patent will
`
`continue to damage Guardant, causing irreparable harm for which there is no adequate remedy at
`
`law, unless enjoined by this Court.
`
`16
`
`

`

`Case 1:24-cv-00687-RGA Document 1 Filed 06/11/24 Page 17 of 22 PageID #: 17
`
`FOURTH COUNT
`(Infringement of ’916 Patent) (At Least the Accused xF Tests)
`
`63.
`
`Guardant repeats and re-alleges the foregoing paragraphs as if set forth specifically
`
`herein.
`
`64.
`
`65.
`
`The claims of the ’916 Patent are valid and enforceable.
`
`The c