Case 1:20-cv-01580-LPS Document 1-23 Filed 11/23/20 Page 1 of 13 PageID #: 642
`Case 1:20-cv-01580-LPS Document 1-23 Filed 11/23/20 Page 1 of 13 PageID #: 642
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`EXHIBIT 23
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`EXHIBIT 23
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`Case 1:17-cv-01616-LPS-CJB Document 10 Filed 02/05/18 Page 1 of 12 PageID #: 116
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`IN THE UNITED STATES DISTRICT COURT
`FOR THE DISTRICT OF DELAWARE
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`
`GUARDANT HEALTH, INC.,
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`FOUNDATION MEDICINE, INC.,
`
`
`Plaintiff
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`
`
`v.
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`
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`
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`C.A. No. 17-cv-1616-LPS-CJB
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`JURY TRIAL DEMANDED
`
`Defendant.
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`
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`FIRST AMENDED COMPLAINT
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`Plaintiff Guardant Health, Inc. (“Guardant”), for its first amended complaint against
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`Defendant Foundation Medicine, Inc. (“Foundation”) on behalf of itself, by Guardant’s attorneys,
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`hereby 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 patent infringement arising under the patent laws of the
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`United States, Title 35, United States Code, against Defendant Foundation.
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`2.
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`Guardant brings this action to halt Foundations’ infringement of Guardant’s rights
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`under the Patent Laws of the United States 35 U.S.C. § 1, et seq., which arise under U.S. Patent
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`Nos. 9,598,731 (“the ’731 patent”) (attached as Exhibit 1), 9,834,822 (“the ’822 patent”) (attached
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`as Exhibit 2), and 9,840,743 (“the ’743 patent”) (attached as Exhibit 3).
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`PARTIES
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`1.
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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 505 Penobscot Dr., Redwood City, CA 94063.
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`2.
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`Guardant was founded in 2012 by pioneers in DNA sequencing and cancer
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`diagnostics. Since its inception, Guardant has focused its expertise on the development of liquid
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`biopsy cancer assays. It was the first company to develop and commercialize a comprehensive
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`liquid biopsy assay to identify genomic biomarkers for advanced solid tumors using “cell-free
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`circulating tumor DNA,” or “ctDNA,” from simple, non-invasive blood draws.
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`3.
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`Today, Guardant markets and sells the Guardant360® ctDNA assay (“Guardant
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`360”). Guardant360 uses advanced DNA sequencing methods to identify targeted therapy
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`treatment options based on the specific changes—also known as somatic mutations—that occur
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`within the DNA of cancer cells. Guardant360 has helped thousands of oncologists find accurate
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`and actionable information about tens of thousands of cancer patients, while avoiding the high
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`costs and added risks of tissue biopsies.
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`4.
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`On information and belief, Foundation Medicine, Inc. (“Foundation”) is a
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`corporation organized and existing under the laws of the state of Delaware, having its principal
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`place of business at 150 Second Street, Cambridge, MA 02141. Foundation markets and sells a
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`liquid biopsy known as FoundationACT. On information and belief, Foundation performs
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`FoundationACT at its facility in Cambridge, MA.
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`JURISDICTION AND VENUE
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`5.
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`This action arises under the patent laws of the United States, 35 U.S.C. §§ 100, et
`
`seq., and this Court has jurisdiction over the subject matter of this action under 28 U.S.C. §§ 1331,
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`1338(a), 2201 and 2202.
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`6.
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`7.
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`Venue is proper in this Court under 28 U.S.C. §§ 1391 and 1400(b).
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`This Court has jurisdiction over Foundation because, upon information and belief,
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`Foundation Medicine is a Delaware corporation.
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`8.
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`This Court also has jurisdiction over Foundation because, upon information and
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`belief, Foundation, directly or indirectly, uses, offers for sale, and/or sells the FoundationACT
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`throughout the United States and in this judicial district.
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`9.
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`Further, the Court has jurisdiction over Foundation because, inter alia, this action
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`arises from actions of Foundation directed toward Delaware, and because Foundation has
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`purposefully availed itself of the rights and benefits of Delaware law by engaging in systematic
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`and continuous contacts with Delaware. Upon information and belief, Foundation regularly and
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`continuously transacts business within Delaware, including by selling FoundationACT in
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`Delaware, either on its own or through its affiliates. Upon information and belief, Foundation
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`derives substantial revenue from the sale of FoundationACT in Delaware and has availed itself of
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`the privilege of conducting business within Delaware.
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`10.
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`For these reasons, and for other reasons that will be presented to the Court if
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`jurisdiction is challenged, the Court has personal jurisdiction over Foundation.
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`BACKGROUND
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`11.
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`Guardant repeats and re-alleges the foregoing paragraphs as if set forth specifically
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`herein.
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`12.
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`On information and belief, in the mid-2016 time frame Foundation began
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`commercializing FoundationACT. According to a Foundation press release, FoundationACT is
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`“an analytically validated and accurate blood-based circulating tumor DNA (ctDNA) assay that
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`provides patients and oncologists with a new option for comprehensive genomic profiling when a
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`tissue biopsy is not feasible or when tissue is not available. By analyzing circulating tumor DNA
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`isolated from a patient’s blood, FoundationACT can identify clinically relevant genomic
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`alterations, and like Foundation Medicine’s tissue-based genomic profiles, FoundationOne® and
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`FoundationOne Heme®, FoundationACT delivers this comprehensive molecular information in a
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`concise report that matches the findings with potentially relevant targeted therapies and clinical
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`trials.” Exhibit 4.
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`13.
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`In February 2017, scientists affiliated with Foundation presented the poster
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`“Genomic profiling of circulating tumor DNA (ctDNA) from patients with advanced cancers of
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`the GI tract and anus” (attached hereto as Exhibit 5) at the American Society of Clinical Oncology
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`meeting. On information and belief, this poster describes the methodology that Foundation uses
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`in its FoundationACT test, an overview of which is presented in the figure below:
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`Exhibit 5.
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`14.
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`Foundation infringes, literally or under the doctrine of equivalents, Guardant’s ’731
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`patent through its activities connected to its performance of the Foundation ACT test. For instance,
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`representative claim 1 of the ’731 patent is listed below:
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`1. A method for quantifying single nucleotide variant tumor markers in cell-
`free DNA from a subject, comprising:
`(a) providing at least 10 ng of cell-free DNA obtained from a bodily sample of
`the subject;
`(b) attaching tags comprising barcodes having from 5 to 1000 distinct barcode
`sequences to said cell-free DNA obtained from said bodily sample of the
`subject, to generate non-uniquely tagged parent polynucleotides, wherein
`each barcode sequence is at least 5 nucleotides in length;
`(c) amplifying the non-uniquely tagged parent polynucleotides to produce
`amplified non-uniquely tagged progeny polynucleotides;
`(d) sequencing the amplified non-uniquely tagged progeny polynucleotides to
`produce a plurality of sequence reads from each parent polynucleotide,
`wherein each sequence read comprises a barcode sequence and a sequence
`derived from cell-free DNA;
`(e) grouping the plurality of sequence reads produced from each non-uniquely
`tagged parent polynucleotide into families based on i) the barcode
`sequence and ii) at least one of: sequence information at a beginning of the
`sequence derived from cell-free DNA, sequence information at an end of
`the sequence derived from cell-free DNA, and length of the sequence read,
`whereby each family comprises sequence reads of non-uniquely tagged
`progeny polynucleotides amplified from a unique polynucleotide among
`the non-uniquely tagged parent polynucleotides;
`(f) comparing the sequence reads grouped within each family to each other to
`determine consensus sequences for each family, wherein each of the
`consensus sequences corresponds to a unique polynucleotide among the
`non-uniquely tagged parent polynucleotides;
`(g) providing one or more reference sequences from a human genome, said one
`or more reference sequences comprising one or more loci of reported tumor
`markers, wherein each of the reported tumor markers is a single nucleotide
`variant;
`(h) identifying consensus sequences that map to a given locus of said one or
`more loci of reported tumor markers; and
`(i) calculating a number of consensus sequences that map to the given locus
`that include the single nucleotide variant thereby quantifying single
`nucleotide variant tumor markers in said cell-free DNA from said subject.
`Performance of Foundation’s FoundationACT test leads to infringement of this
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`15.
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`claim in the following way. First, in FoundationACT, more than 10 ng of cell free DNA is obtained
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`from a patient blood draw (step a). Tags comprising barcodes are then attached to both ends of
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`the DNA fragments that are present in the sample of cell free DNA (step b). The tagged DNA
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`sample is then subject to PCR amplification (step c). The amplified DNA is then subject to
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`sequencing on the Illumina sequencing platform, resulting in sequence reads that consist of a
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`barcode sequence and a sequence present in the cell free DNA (step d). The sequence reads are
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`(i) grouped into families based on the barcode and additional sequence information, allowing one
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`to collect sequence information that arises from the same DNA molecule (step e), (ii) compared to
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`one another to arrive at a “consensus sequence” that represents a more accurate determination of
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`the sequence of the molecule in question (step f), and (iii) mapped to a reference genome to identify
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`sequences that map to regions of the genome associated with cancer tumor markers (steps f-h).
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`Finally, the number of tumor markers present in the original sample are quantified (step i).
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`16.
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`As an example, attached hereto as Exhibit 6 is a preliminary and exemplary claim
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`chart detailing Foundation’s infringement of multiple claims of the ’731 patent. This chart is not
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`intended to limit Guardant’s right to modify this chart or any other claim chart or allege that other
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`activities of Foundation infringe the identified claims or any other claims of the ’731 patent or any
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`other patents.
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`17.
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`Foundation infringes, literally or under the doctrine of equivalents, Guardant’s ’822
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`patent through its activities connected to its performance of the Foundation ACT test. For instance,
`
`representative claim 1 of the ’822 patent is listed below:
`
`1. A method, comprising:
`(a) providing a population of cell free DNA (“cfDNA”) molecules obtained
`from a bodily sample from a subject;
`(b) converting the population of cfDNA molecules into a population of non-
`uniquely tagged parent polynucleotides, wherein each of the non-uniquely
`tagged parent polynucleotides comprises (i) a sequence from a cfDNA
`molecule of the population of cfDNA molecules, and (ii) an identifier
`sequence comprising one or more polynucleotide barcodes;
`(c) amplifying the population of non-uniquely tagged parent polynucleotides
`to produce a corresponding population of amplified progeny
`polynucleotides;
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`(d) sequencing the population of amplified progeny polynucleotides to produce
`a set of sequence reads;
`(e) mapping sequence reads of the set of sequence reads to one or more
`reference sequences from a human genome;
`(f) grouping the sequence reads into families, each of the families comprising
`sequence reads comprising the same identifier sequence and having the
`same start and stop positions, whereby each of the families comprises
`sequence reads amplified from the same tagged parent polynucleotide;
`(g) at each genetic locus 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) determining a frequency of one or more bases called at the locus from
`among the families.
`Performance of Foundation’s FoundationACT test leads to infringement of this
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`18.
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`claim in the following way. First, in FoundationACT, cell free DNA is obtained from a patient
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`blood draw (step a). Tags comprising barcodes are then attached to both ends of the population of
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`DNA fragments that are present in the sample of cell free DNA (step b). The tagged DNA sample
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`is then subject to PCR amplification (step c). The amplified DNA is then subject to sequencing
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`on the Illumina sequencing platform, resulting in sequence reads that consist of a barcode sequence
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`and a sequence present in the cell free DNA (step d). Sequence reads are (i) compared to reference
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`sequences from databases such as the COSMIC database (step e), (ii) grouped into families based
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`on the barcode and additional sequence information, allowing one to collect sequence information
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`that arises from the same DNA molecule (step f), and (iii) compared to one another to arrive at a
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`“consensus sequence” that yields a consensus base call at any position in the sequence (step g).
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`Finally, the frequency of specific bases in the form of tumor markers present in the original sample
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`are quantified (step h).
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`19.
`
`As an example, attached hereto as Exhibit 7 is a preliminary and exemplary claim
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`chart detailing Foundation’s infringement of multiple claims of the ’822 patent. This chart is not
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`intended to limit Guardant’s right to modify this chart or any other claim chart or allege that other
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`Case 1:17-cv-01616-LPS-CJB Document 10 Filed 02/05/18 Page 8 of 12 PageID #: 123
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`activities of Foundation infringe the identified claims or any other claims of the ’ 822 patent or
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`any other patents.
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`20.
`
`Foundation infringes, literally or under the doctrine of equivalents, Guardant’s ’743
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`patent through its activities connected to its performance of the Foundation ACT test. For instance,
`
`representative claim 1 of the ’743 patent is listed below:
`
`1. A method for detecting copy number variation, comprising:
`(a) sequencing extracellular polynucleotides from a bodily sample from a
`subject, wherein each of the extracellular polynucleotides generates a
`plurality of sequence reads;
`(b) filtering out reads that fail to meet a set accuracy, quality score, or mapping
`score threshold;
`(c) mapping the plurality of sequence reads to a reference sequence;
`(d) quantifying mapped reads or unique sequence reads in a plurality of
`predefined regions of the reference sequence; and
`(e) determining copy number variation in one or more of the plurality of
`predefined regions by: i) normalizing a number of reads in the plurality of
`predefined regions to each other, or a number of unique sequence reads in
`the plurality of predefined regions to each other; and/or ii) processing a
`number of reads in the plurality of predefined regions or a number of
`unique sequence reads in the plurality of predefined regions with numbers
`obtained from a control sample.
`Performance of Foundation’s FoundationACT test leads to infringement of claim 1
`
`21.
`
`in the following way. First, in FoundationACT, cell-free DNA is amplified and sequenced,
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`generating a plurality of reads (step a). Second, the plurality of sequences are grouped together to
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`form consensus sequences and errors in individual sequence reads are removed (step b). The
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`consensus sequence is then mapped to a reference sequence (step c) and the percentage of variants
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`such as copy number variants are quantified (steps d-e).
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`22.
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`As an example, attached hereto as Exhibit 8 is a preliminary and exemplary claim
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`chart detailing Foundation’s infringement of multiple claims of the ’743 patent. This chart is not
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`intended to limit Guardant’s right to modify this chart or any other claim chart or allege that other
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`- 8 -
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`Case 1:20-cv-01580-LPS Document 1-23 Filed 11/23/20 Page 10 of 13 PageID #: 651
`Case 1:17-cv-01616-LPS-CJB Document 10 Filed 02/05/18 Page 9 of 12 PageID #: 124
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`activities of Foundation infringe the identified claims or any other claims of the ’743 patent or any
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`other patents.
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`23.
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`herein.
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`COUNT I
`(Infringement of U.S. Patent No. 9,598,731)
`Guardant repeats and re-alleges the foregoing paragraphs as if set forth specifically
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`24.
`
`On March 21, 2017, the United States Patent and Trademark Office duly and legally
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`issued the ’731 patent, entitled “Systems and Methods to Detect Rare Mutations and Copy Number
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`Variation,” which is solely assigned to Guardant. Guardant is the owner of all rights, title to and
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`interest in the ’731 patent.
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`25.
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`On information and belief, Foundation has infringed and continues to infringe at
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`least claims 1-3, 6-9, 12 and 16-17 of the ’731 patent pursuant to 35 U.S.C. § 271(a), literally or
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`under the doctrine of equivalents, by performing within the United States without authority the
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`FoundationACT test. As an example, attached as Exhibit 6 is a preliminary and exemplary claim
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`chart detailing Foundation’s infringement of these claims of the ’731 patent. This chart is not
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`intended to limit Guardant’s right to modify the chart or allege that other activities of Guardant
`
`infringe the identified claims or any other claims of the ’731 patent or any other patents.
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`26.
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`Exhibit 6 is hereby incorporated by reference in its entirety. Each claim element in
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`Exhibit 6 that is mapped to Foundation’s FoundationACT test shall be considered an allegation
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`within the meaning of the Federal Rules of Civil Procedure and therefore a response to each
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`allegation is required.
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`COUNT II
`(Infringement of U.S. Patent No. 9,834,822)
`Guardant repeats and re-alleges the foregoing paragraphs as if set forth specifically
`
`27.
`
`herein.
`
`28.
`
`On December 5, 2017, the United States Patent and Trademark Office duly and
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`legally issued the ’822 patent, entitled “Systems and Methods to Detect Rare Mutations and Copy
`
`Number Variation,” which is solely assigned to Guardant. Guardant is the owner of all rights, title
`
`to and interest in the ’822 patent.
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`29.
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`On information and belief, Foundation has infringed and continues to infringe at
`
`least claims 1-3, 5-9, 11, 13, 18, and 20 of the ’822 patent pursuant to 35 U.S.C. § 271(a), literally
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`or under the doctrine of equivalents, by performing within the United States without authority the
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`FoundationACT test.
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`30.
`
`Exhibit 7 is hereby incorporated by reference in its entirety. Each claim element in
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`Exhibit 7 that is mapped to Foundation’s FoundationACT test shall be considered an allegation
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`within the meaning of the Federal Rules of Civil Procedure and therefore a response to each
`
`allegation is required.
`
`COUNT III
`(Infringement of U.S. Patent No. 9,840,743)
`Guardant repeats and re-alleges the foregoing paragraphs as if set forth specifically
`
`31.
`
`herein.
`
`32.
`
` On December 12, 2017, the United States Patent and Trademark Office duly and
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`legally issued the ’743 patent, entitled “Systems and Methods to Detect Rare Mutations and Copy
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`Number Variation,” which is solely assigned to Guardant. Guardant is the owner of all rights, title
`
`to and interest in the ’743 patent.
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`
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`33.
`
`On information and belief, Foundation has infringed and continues to infringe at
`
`least claims 1-7, 9-13, and 15-26 of the ’743 patent pursuant to 35 U.S.C. § 271(a), literally or
`
`under the doctrine of equivalents, by performing within the United States without authority the
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`FoundationACT test.
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`34.
`
`Exhibit 8 is hereby incorporated by reference in its entirety. Each claim element in
`
`Exhibit 8 that is mapped to Foundation’s FoundationACT test shall be considered an allegation
`
`within the meaning of the Federal Rules of Civil Procedure and therefore a response to each
`
`allegation is required.
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`JURY DEMAND
`
`35.
`
`Guardant demands a jury trial on all issues so triable.
`
`PRAYER FOR RELIEF
`
`WHEREFORE, Guardant prays that this Court grant the following relief:
`
`A.
`
`A judgment that Foundation has infringed the ’731 patent, the ’822 patent,
`
`and/or the ’743 patent and that the ’731 patent, the ’822 patent, and/or the ’743 patent are valid.
`
`B.
`
`Damages or other monetary relief, including, but not limited to, costs and
`
`pre- and post-judgment interest, to Guardant;
`
`C.
`
`An order enjoining Foundation and its officers, directors, agents, servants,
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`affiliates, employees, divisions, branches, subsidiaries, parents, and all others acting in active
`
`concert therewith from further infringement of the ’731 patent, the ’822 patent, and/or the ’743
`
`patent;
`
`D.
`
`Such further and other relief as this Court deems proper and just,
`
`including, but not limited to, a determination that this is an exceptional case under 35 U.S.C.
`
`§ 285 and an award of attorneys’ fees and costs to Guardant in this action.
`
`
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`Dated: February 5, 2018
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`Respectfully submitted,
`
`FARNAN LLP
`
`
`
`/s/ Michael J. Farnan
`Joseph J. Farnan, Jr. (Bar No. 100245)
`Brian E. Farnan (Bar No. 4089)
`Michael J. Farnan (Bar No. 5165)
`919 N. Market St., 12th Floor
`Wilmington, DE 19801
`Tel: (302) 777-0300
`Fax: (302) 777-0301
`farnan@farnanlaw.com
`bfarnan@farnanlaw.com
`mfarnan@farnanlaw.com
`
`Edward R. Reines (admitted pro hac vice)
`Derek Walter (admitted pro hac vice)
`WEIL, GOTSHAL &MANGES LLP
`201 Redwood Shores Parkway
`Redwood Shores, CA 94065
`(650) 802-3000
`
`Attorneys for Plaintiff Guardant Health, Inc.
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`- 12 -
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