Case 1:20-cv-01580-LPS Document 14 Filed 12/18/20 Page 1 of 94 PageID #: 2701
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`
`
` IN THE UNITED STATES DISTRICT COURT
`
`FOR THE DISTRICT OF DELAWARE
`
`GUARDANT HEALTH, INC.,
`
`
`
`Plaintiff,
`
`
`
`v.
`
`FOUNDATION MEDICINE, INC.,
`
`Defendant.
`
`
`
`
`
`C.A. No. 20-cv-1580-LPS
`
`JURY TRIAL DEMANDED
`
`FILED UNDER SEAL
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`
`
`
`
`DECLARATION OF GREGORY COOPER, PH.D.
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`
`
`
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`
`
`
`
`
`
` IN THE UNITED STATES DISTRICT COURT
`
`FOR THE DISTRICT OF DELAWARE
`
`GUARDANT HEALTH, INC.,
`
`
`
`Plaintiff,
`
`
`
`v.
`
`FOUNDATION MEDICINE, INC.,
`
`Defendant.
`
`
`
`
`
`C.A. No. 20-cv-1580-LPS
`
`JURY TRIAL DEMANDED
`
`FILED UNDER SEAL
`
`
`
`
`
`DECLARATION OF GREGORY COOPER, PH.D.
`
`
`
`
`
`
`
`
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`Case 1:20-cv-01580-LPS Document 14 Filed 12/18/20 Page 2 of 94 PageID #: 2702
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`1.
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`I, Gregory Cooper, Ph.D., have been retained by Weil, Gotshal & Manges
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`LLP, counsel for the Plaintiff Guardant Health, Inc. (“Guardant”). I understand that Plaintiff
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`has filed suit against defendant Foundation Medicine, Inc. (“FMI”) alleging infringement of
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`United States Patent Number 10,704,086 (the ’086 Patent) and United States Patent Number
`
`10,704,085 (the ’085 patent)1.
`
`I.
`
`BACKGROUND AND QUALIFICATIONS, PREVIOUS TESTIMONY, AND
`COMPENSATION
`
`
`A.
`
`
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`Background and Qualifications
`
`2.
`
`My qualifications are set forth in my C.V. in Appendix A. I am currently a
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`Faculty Investigator at the HudsonAlpha Institute for Biotechnology (“HudsonAlpha”) in
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`Huntsville, Alabama. I have held this position since 2010. HudsonAlpha, established in 2008,
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`is an independent, non-profit institution dedicated to improving human health and welfare
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`through biological research, genomic medicine, education, and economic development. Since
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`coming to HudsonAlpha, I have set up an independent human genomics research lab. My lab
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`works on projects related to the genetics of human disease, with a particular emphasis on
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`research and clinical applications of genome sequencing for diagnosing children with
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`developmental delays and intellectual disabilities. We also study the genetics and
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`biochemistry of gene expression regulation, develop new computational approaches to
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`analysis of human genomes and related datasets, and pursue other applications of genomic
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`technologies to understand human biology.
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`
`
`3.
`
`I am also concurrently an Associate Professor Adjunct in the Department of
`
`
`1 United States Patent Number 10,704,086 (the ’086 Patent) and United States Patent Number 10,704,085 (the ’085
`patent) are attached as Ex. 1 and Ex. 2 to this Declaration.
`
`
`
`2
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`
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`Case 1:20-cv-01580-LPS Document 14 Filed 12/18/20 Page 3 of 94 PageID #: 2703
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`Genetics at the University of Alabama at Birmingham (“UAB”). I have held a UAB adjunct
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`faculty position since 2010.
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`4.
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`I earned a Bachelor of Arts in Microbiology and Bachelor of Science in
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`Mathematics and Statistics, summa cum laude, from Miami University (Oxford, OH) in 2001.
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`As an undergraduate student, I performed molecular biology and genetic research in research
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`laboratories at Miami University, the University of Illinois at Urbana-Champaign, and the
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`University of Cincinnati.
`
`5.
`
`I earned a Ph.D. in Genetics from Stanford University in 2006 under the
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`mentorship of Professor Arend Sidow, Ph.D. My thesis work was mainly comprised of
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`computational biology work, with a focus on evolutionary comparisons of mammalian
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`genome assemblies to better annotate functional elements in human genomes and assess
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`whether mutations in those elements might contribute to disease. While there, I worked and/or
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`received training in areas including: theoretical and applied human genetics, molecular
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`evolution,
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`functional genomics, developmental biology, bioinformatics, genomic
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`technologies, and analysis of datasets produced by high throughput experimental platforms,
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`especially DNA sequencers.
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`6.
`
`Beginning in 2006, I was a Senior Fellow in the Department of Genome
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`Sciences at the University of Washington working with Professors Evan Eichler, Ph.D., and
`
`Deborah Nickerson, Ph.D. While there, I conducted my postdoctoral research. I was primarily
`
`interested in applying genomic technologies to better understand the genetic basis for human
`
`disease. One series of projects centered on analytical and algorithmic developments to identify
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`large deletion and duplication events, also known as “copy-number variants” (“CNVs”), from
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`microarray data generated to perform Single Nucleotide Polymorphism (“SNP”) genotyping.
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`
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`3
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`Case 1:20-cv-01580-LPS Document 14 Filed 12/18/20 Page 4 of 94 PageID #: 2704
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`This process involved extensive processing, normalization, and analysis of Illumina SNP
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`array data. I was further a key developer of a customized CNV genotyping assay using
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`Illumina’s BeadXpress platform. A second series of projects was aimed at better
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`understanding the genetic basis for a variety of complex traits. These included genetic
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`analyses of transcript levels, for example, and also a genome-wide association study of patient
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`response to the commonly prescribed anticoagulant warfarin. Finally, another series of
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`projects focused on analysis of high-throughput DNA-sequencing data, in particular the
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`locations of genetic variants, from individuals with Mendelian diseases. I completed my
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`postdoctoral studies in 2009.
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`7.
`
`From 2009 to 2010, I was Acting Assistant Professor in the Department of
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`Genome Sciences at the University of Washington.
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`8.
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`I am an author or contributor to more than 90 publications in the areas of
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`human genetics and genomics, including functional and evolutionary annotations of
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`mammalian genomes, DNA sequencing and DNA analysis, and the genetics of human
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`diseases, especially, but not exclusively, intellectual disabilities and other developmental
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`issues. As of November 2020, these publications have been collectively cited more than
`
`33,000 times, according to Google Scholar estimates.
`
`9.
`
`Among the awards and honors I have earned are: Harrison Scholar, Miami
`
`University (Oxford, OH) (1997-2001), Goldwater Scholar (1999-2001), Howard Hughes
`
`Medical Institute Doctoral Fellowship (2001-2006), and a Merck, Jane Coffin Childs
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`Memorial Fund Postdoctoral Fellowship (2007-2010).
`
`10.
`
`I am a Principal Investigator (“PI”) on two current human genomic research
`
`projects funded by the National Institutes of Health (“NIH”) and a PI or co-Investigator on
`
`
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`4
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`Case 1:20-cv-01580-LPS Document 14 Filed 12/18/20 Page 5 of 94 PageID #: 2705
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`several additional projects funded by non-NIH sources, including both governmental and
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`philanthropic sources. I have also been a PI or co-Investigator on multiple additional grants
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`related to human genetics and genomics, from NIH and elsewhere, that have been completed.
`
`11.
`
`In general, I have knowledge and experience with both the general scientific
`
`contexts relevant to these litigation proceedings and specific details of the technologies
`
`employed. For example, I have extensive experience with analyzing massively parallel
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`sequence datasets from human samples, including targeted sequencing, whole-genome
`
`sequencing, functional genomics in which loci with particular properties or sequence elements
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`are enriched through various experimental means, transcriptional genomics, and other related
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`types of experiments. Of particular relevance to these proceedings, I have extensive
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`experience with computational pipelines to detect genetic variants (“mutations”) within
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`collections of sequence reads.
`
`12.
`
`I have previously served as an expert witness in three patent infringement
`
`proceedings. First, I worked on behalf of Illumina in a lawsuit against Ariosa (now owned by
`
`Roche), case number 3:12-cv-05501-SI (N.D. Ca.), which centered on non-invasive prenatal
`
`diagnostic technologies based on cell-free DNA testing. I was deposed in that proceeding and
`
`also testified at trial. Additionally, I have previously worked as an expert on Guardant’s
`
`behalf in two lawsuits directly related to this one, including infringement cases against
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`Personal Genome Diagnostics (PGDX) and Foundation Medicine (FMI), case numbers 17-
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`cv-1623-LPS-CJB (D. Del.) and 17-cv-1616-LPS-CJB (D. Del.) I was deposed in both of
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`those cases; the former has been settled and a trial date for the latter has been delayed to an
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`as-yet undetermined date.
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`13.
`
`Based upon my experience, qualifications and expertise, I am qualified as an
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`
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`5
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`Case 1:20-cv-01580-LPS Document 14 Filed 12/18/20 Page 6 of 94 PageID #: 2706
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`expert in the fields of DNA sequencing and nucleic-acid based assays and the technologies
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`relating to the ’086 Patent. Furthermore, I believe that I am qualified to opine as to the
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`presence and extent of potential patent infringement within this scientific and technological
`
`area.
`
`B.
`
`Compensation
`
`14.
`
`I am being compensated for my time at a rate of
`
` per hour. My
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`compensation is not dependent in any way upon the outcome of this proceeding.
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`15.
`
`Beyond having general and specific expertise from my educational
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`background and work, I have also performed a careful and extensive review of documents
`
`and evidence specific to this litigation, including, but not necessarily limited to:
`
`
`
`
`
`the ’086 Patent and the ’085 Patent
`
`relevant scientific publications, including those published by FMI employees and
`
`other scientists not associated with the parties of this litigation; and
`
` publicly available information on Foundation’s websites.
`
`16.
`
`A full list of the documents, products, and information I have reviewed is listed
`
`in Appendix B. To the extent not identified in Appendix B, I have also considered each of the
`
`documents cited in this report.
`
`17.
`
`Based on my review of the foregoing materials, it is my opinion that FMI
`
`infringes claim 1 of the ’085 Patent and claim 1 of the ’086 Patent.
`
`II.
`
`LEGAL STANDARDS
`
`18.
`
`I am not a patent attorney nor have I independently researched the law on
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`infringement. However, I have been informed by counsel of the various legal standards that
`
`apply to the pertinent technical issues, and I have applied those standards in arriving at my
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`conclusions expressed in this Report.
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`
`
`6
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`Case 1:20-cv-01580-LPS Document 14 Filed 12/18/20 Page 7 of 94 PageID #: 2707
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`19.
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`I have been informed that the “specification” of a patent includes the written
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`description of one or more preferred embodiments of the invention, any drawings or figures,
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`and one or more claims that point out and distinctly claim the subject matter of the invention.
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`It is the claims that define the scope of the patent. A separate invention is defined by each
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`claim.
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`20.
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`I am informed that a dependent claim incorporates each and every element of
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`the claim from which it depends.
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`21. My understanding of is that an accused method infringes a claim if it performs
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`all the elements of that claim, regardless of whether or not there are other additional steps in
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`the accused method.
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`22. While literal infringement requires each step to be literally performed in the
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`accused method, infringement under the doctrine of equivalents can be found when every
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`claim element that is not literally present is nonetheless equivalently performed.
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`23.
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`I am informed that, under the doctrine of equivalents, even if an accused
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`method does not literally perform one or more limitations of a claim of a patent, the accused
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`method may still infringe that claim if the differences between the accused method and the
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`limitation of the claimed method are insubstantial.
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`24.
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`I am further informed that one test for the applicability of the doctrine of
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`equivalents is that the accused method performs substantially the same function in
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`substantially the same way to achieve substantially the same result as the claimed method.
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`25.
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`I have been informed that the burden of proof for proving patent infringement
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`is by a preponderance of the evidence, which means that the accused device is more likely to
`
`infringe than not to infringe a claim of the patents-in-suit.
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`
`
`7
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`Case 1:20-cv-01580-LPS Document 14 Filed 12/18/20 Page 8 of 94 PageID #: 2708
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`III.
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`SUMMARY OF THE TECHNOLOGY
`A.
`
`DNA
`
`26.
`
`DNA is the molecule that stores genetic information in living organisms,
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`including in cancer-causing tumor cells. DNA is a chain of four basic building blocks, known
`
`as nucleotides. The four different kinds of nucleotides are Thymine (T), Cytosine (C),
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`Adenine (A), and Guanine (G). The order of these nucleotides encodes genetic information in
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`living organisms. See Recombinant DNA: Genes and Genomes – A Short Course, 3rd Ed by
`
`James D. Watson, et al.
`
`27.
`
`The human genetic code contains ~3 billion nucleotides spread out over 23
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`chromosomes. A complete sequence of these nucleotides is referred to as a “human genome”.
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`There is, on average, an ~99.9% similarity between any given stretch of DNA sequence in
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`one person versus another; that is to say, that, there is a “point substitution” approximately 1
`
`in every 1,000 nucleotides of genomic sequence (e.g., Ex. 3 [A map of human genome
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`variation from population-scale sequencing]). Other types of variation, such as insertions and
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`deletions (“indels”), copy-number variants (“CNVs”), and rearrangements, can also be
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`observed between any two individuals. Further, humans are “diploid”, which is to say that
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`they inherit one set of chromosomes from their mother and one from their father. The
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`similarity between these individual genomic copies, sometimes referred to as “haploid
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`genomes”, also tends to be ~99.9% in any given stretch of sequence. Additionally, as for
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`differences between two people, other types of variation, such as indels, CNVs, and
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`rearrangements, can also exist between the two haploid genomes within one person. In
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`general, variations in only a small fraction of the 3 billion nucleotides in the human genome
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`– as stated previously, for example, point substitutions tend to occur at only ~0.1% of all
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`positions -- are responsible for wide variations among human beings.
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`
`
`8
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`Case 1:20-cv-01580-LPS Document 14 Filed 12/18/20 Page 9 of 94 PageID #: 2709
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`Fig. 12
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`28.
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`Another aspect of human genetics important to these proceedings is genetic
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`variation among cells in a person. In particular, nearly all cells, with a few exceptions such as
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`red blood cells and gametes, are diploid and contain nearly the same two haploid genomes,
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`one that was inherited from a person’s mother and one from their father. However, differences
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`can also arise within a given cell or subset of cells inside a given person. This phenomenon is
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`sometimes termed “somatic” variation. In some cases, a genetic variant arises in a cell that
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`can alter the rate at which it grows, behaves, or divides. The “daughter” cells that emerge arise
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`when that cell divides will inherit that variant. If that cell divides too rapidly, or causes other
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`cells to divide too rapidly, it can lead to cancer.
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`29.
`
`It is also important to note that DNA can also be found outside of cells in the
`
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`2 From Guardant Health, Inc.’s Technology Tutorial from Case Nos. 1:17-cv-01616 (D.I. 52) and 1:17-cv-01623 (D.I.
`58).
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`
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`9
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`Case 1:20-cv-01580-LPS Document 14 Filed 12/18/20 Page 10 of 94 PageID #: 2710
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`body. When cells die, for example, they may burst open and release their contents into the
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`surrounding “extracellular” space nearby; the genomic DNA present in these cells thus
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`becomes “cell-free DNA”. While much of this cell-free DNA is quickly degraded, it can
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`sometimes remain stable and intact and enter the bloodstream, a basic phenomenon which
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`was discovered many decades ago (Mandel and Metais 1948). As technologies matured,
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`scientists and clinicians began to recognize that analyses of cell-free DNA in people may
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`provide clues about their health. For example, in 1997 Dennis Lo and colleagues showed that
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`fetal DNA could be detected in plasma, which is a cell-free component of blood, of pregnant
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`women (Ex. 5 [Presence of fetal DNA in maternal plasma and serum]). Similarly, it was also
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`found that cell-free DNA levels in the plasma could be altered by cancer (e.g., by Leon in
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`1977) and that cell-free DNA that was specific to tumor cells could also be detected (e.g., by
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`Stroun in 1989).
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`B.
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`Sequencing
`
`30.
`
`One can make a determination of the sequence of an individual’s DNA using
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`machines known as sequencers. Specifically, below is an Illumina Next-Generation
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`Sequencing (NGS) machine, which is widely used by both academic researchers and
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`diagnostics companies for “high-throughput DNA sequencing.”
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`31.
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`The Illumina sequencing platform can simultaneously sequence millions of
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`fragments of DNA at the same time, and is hence commonly referred to as a “massively
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`parallel” sequencing platform.
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`10
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`Case 1:20-cv-01580-LPS Document 14 Filed 12/18/20 Page 11 of 94 PageID #: 2711
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`Fig. 33
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`32.
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`There are four basic types of genetic mutations that can lead to cancer, shown
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`in the four figures presented below.
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`
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`Fig. 44
`
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`3 From Guardant Health, Inc.’s Technology Tutorial from Case Nos. 1:17-cv-01616 (D.I. 52) and 1:17-cv-01623 (D.I.
`58).
`
` 4
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` From Guardant Health, Inc.’s Technology Tutorial from Case Nos. 1:17-cv-01616 (D.I. 52) and 1:17-cv-01623 (D.I.
`58).
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`
`
`
`11
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`Case 1:20-cv-01580-LPS Document 14 Filed 12/18/20 Page 12 of 94 PageID #: 2712
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`33.
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`First, in the upper left, there are single nucleotide variants, where one
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`nucleotide is replaced with another. In the figure, the typical nucleotide is an A, and is replaced
`
`with a C.
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`34.
`
`Second, in the upper right, there are insertions & deletions, also known as
`
`“indels”, where a nucleotide or group of nucleotides is added or removed, respectively. In the
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`figure, the normal sequence consist of as stretch that reads T-C-A-T, but the A has been
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`deleted such that the mutated sequence reads T-C-T.
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`35.
`
`Third, in the lower left, there are gene fusions, where a DNA rearrangement
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`occurs and leads to genes being combined together or otherwise rearranged so as to lead to a
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`change in how the gene functions. In the figure, the blue and orange regions of the
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`chromosome on the left are re arranged and appear instead in the chromosome on the right.
`
`36.
`
`Finally, in the lower right, there are copy number variations (CNVs), also
`
`known as gene amplifications or deletions, where whole genes or even entire chromosomes
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`are duplicated or deleted within a cell. In the figure, two examples are shown. First, there is a
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`CNV in which a single gene is either deleted or duplicated. As an example, for the blue gene
`
`labeled C, there can be one less copy or one extra copy.
`
`37.
`
`I note that, in general, the terms “genetic variant”, “variant”, “variation”,
`
`“genetic variation”, “mutation”, “allele”, “genetic aberration”, “genetic alteration”, and
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`related terms, while not strictly identical in meaning, are similar terms and often used
`
`interchangeably and generally to refer to a change in DNA between two individuals, between
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`two copies of genetic information within an individual, or among cells within an individual.
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`Many, in fact most, “mutations” are harmless with little to no effect on a cell, tissue, or
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`organism, while some can have large effects and lead to disease, like cancer. Unless otherwise
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`
`
`12
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`Case 1:20-cv-01580-LPS Document 14 Filed 12/18/20 Page 13 of 94 PageID #: 2713
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`specified, and as a reflection of their interchangeable use amongst the various documents and
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`sources used for this report, such terms are also used interchangeably and generically below.
`
`IV.
`
`BACKGROUND OF THE INVENTION
`A.
`
`Tissue Biopsies
`
`38. Most cancer-diagnosis techniques require the use of invasive biopsies in which
`
`one uses a needle or surgical instrument to physically extract a piece of the tumor, as shown
`
`in the figure below. Tissue biopsies, however, carry many disadvantages. First, tissue biopsies
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`require invasive procedures that have a chance of medical complications. Indeed, it is by no
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`means straightforward to sample a tumor that is, for instance, present in a patient’s brain or
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`lung. Second, tissue biopsies are costly, due to the extensive imaging and surgical work that
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`is typically required to obtain one. Third, tissue biopsies require the presence of a known
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`tumor, limiting their use only to patients with more advanced stage cancers. Fourth, tissue
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`biopsies often sample only a small site in a tumor. This means that biopsy samples do not
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`accurately represent the entire tumor or set of tumors in a patient and may miss clinically
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`relevant biomarkers due to tumor heterogeneity. This could lead to a biopsy missing key
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`mutations.
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`
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`Fig. 55
`
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`5 From Guardant Health, Inc.’s Technology Tutorial from Case Nos. 1:17-cv-01616 (D.I. 52) and 1:17-cv-01623 (D.I.
`58).
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`13
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`39.
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`Cellular DNA is normally locked inside a cell within its nucleus; sometimes,
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`however, bits of DNA are released into the bloodstream. For example, when a cell dies, its
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`chromosomes are spilled into the blood stream, and are then quickly digested by the body into
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`small fragments consisting of, on average, about 170 nucleotides in length. This is known to
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`happen regularly with tumor cells, as shown in the figure below, albeit sometimes with larger
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`DNA fragments. Guardant’s technology analyzes this type of DNA, also known as “cell-free
`
`DNA” or “cfDNA.” cfDNA that originates from cancer cells is known as “circulating tumor
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`DNA” or “ctDNA.”
`
`
`
`Fig. 66
`
`B.
`
`Liquid Biopsies And The Approach Of The Patents-in-Suit
`
`40.
`
`In this section, I provide an overview of “liquid biopsies” and the approach in
`
`the Patents-in-Suit. To be clear, this section is intended to give a general overview of the
`
`patented approach, and does not capture all of the specific details recited in the various claims
`
`of the patent-in-suit.
`
`41.
`
`The ’086 and ’085 Patents are continuations of a common parent and share a
`
`common specification. The common specification describes a series of innovations in the
`
`field of “liquid biopsies.” The field of liquid biopsies is one in which cancer causing mutations
`
`
`6 From Guardant Health, Inc.’s Technology Tutorial from Case Nos. 1:17-cv-01616 (D.I. 52) and 1:17-cv-01623 (D.I.
`58).
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`
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`14
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`Case 1:20-cv-01580-LPS Document 14 Filed 12/18/20 Page 15 of 94 PageID #: 2715
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`are detected using cfDNA, extracted from a simple, non-invasive blood draw. Using cfDNA
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`overcomes many of the challenges of tissue biopsies. A simple blood draw avoids an invasive
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`biopsy, reduces cost, and increase patient safety. Further, because cfDNA is released by most
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`tumor cells and only stays in a person’s body for a limited time, this approach is able to
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`analyze an up-to-date spectrum of mutations across the entire collection of tumors in a cancer
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`patient.
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`42.
`
`One primary problem with using cfDNA to find mutations is that cfDNA is
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`present in very small quantities. And the percentage of cfDNA that contain DNA originating
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`from tumors is even lower. The percentage is often so low that the mutations are
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`indistinguishable from errors, or noise, that result from the typical DNA preparation and
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`sequencing process. Thus, detecting mutations associated with cancer becomes a problem of
`
`finding a needle in a haystack.
`
`43.
`
`The figure below is from Guardant’s publication describing their technology
`
`for detecting cancer-causing mutations in cfDNA, which is known in the industry as “digital
`
`sequencing.” In the figure below, true mutations are highlighted in red, and deviations from
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`the normal human sequence that are not real, but are nothing more than standard sequencing
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`errors, are shown by black dots. Normal human genetic variation is present in much higher
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`quantities, shown in green.
`
`44.
`
`As the figure below shows, the prevalence of true mutations that cause cancer
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`is so low that they are indistinguishable from noise.
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`
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`15
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`Case 1:20-cv-01580-LPS Document 14 Filed 12/18/20 Page 16 of 94 PageID #: 2716
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`Fig. 77
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`45.
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`As the common specification of the Patents describes, false positive mutations
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`come largely from two sources. See, e.g., Ex. 2 [’085 patent] at 31:30-37 (“Noise can be
`
`introduced through errors in copying and/or reading a polynucleotide. For example, in a
`
`sequencing process a single polynucleotide can first be subject to amplification. Amplification
`
`can introduce errors, so that a subset of the amplified polynucleotides may contain, at a
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`particular locus, a base that is not the same as the original base at that locus. Furthermore, in
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`the reading process a base at any particular locus may be read incorrectly.”). To detect
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`sequences, DNA must first be copied. Any copying process that is not 100% accurate will
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`introduce false mutations. Additionally, modern sequencing techniques may have an
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`additional error rate of 0.1 to 10%, depending upon the particular sequencing technology and
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`application. These factors generate the vast majority of noise described above.
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`46.
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`As the Asserted Patents explain, Guardant’s approach processes amplified
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`copies of an original cfDNA molecule so as to be analyzed as a group, or family of related
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`7 Ex. 5 [R.B. Lanman, et al., Analytical and clinical validation of a digital sequencing panel], p. 6, Fig. 2.
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`16
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`Case 1:20-cv-01580-LPS Document 14 Filed 12/18/20 Page 17 of 94 PageID #: 2717
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`sequences. By analyzing families of sequences, a consensus sequence can be generated that
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`substantially eliminates errors that may have arisen in any single sequence analysis.
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`47.
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`Guardant’s methods involve tagging cfDNA molecules prior to amplification.
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`This allows treatment of all similarly tagged molecules as members of the same family,
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`containing the same information. In this way, any noise that may be introduced to one
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`particular observation will not affect the total output of the whole family.
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`48.
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`Applying these innovative techniques reduces errors to lower than one in a
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`million base pairs, allowing true mutations, even ones that are extremely rare, to be
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`distinguished. This is shown in the figure below, again from Guardant’s publication. Using
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`Guardant’s digital sequencing technology, the noise, which is shown as the black dots, largely
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`vanishes. The true mutations, which are shown in red, are easily identified.
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`Fig. 88
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`49.
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`The process begins by keeping track of cfDNA molecules obtained from a
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`patient. Guardant does this by attaching molecular identifiers, also known as barcodes, to both
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`ends of the cfDNA molecule. The figure below is from another of Guardant’s publications.
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`8 Ex. 5 [R.B. Lanman, et al., Analytical and clinical validation of a digital sequencing
`panel], p. 6, Fig. 2A.
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`17
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`Case 1:20-cv-01580-LPS Document 14 Filed 12/18/20 Page 18 of 94 PageID #: 2718
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`On the left, there is cell free DNA. The red and green colored fragments are the tumor DNA.
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`Barcodes are represented as colored segments at the ends of each piece of DNA. The cfDNA
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`fragments with their barcodes are copied (amplified) to increase the overall signal. Because
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`each copy of a tagged molecule will have the same barcodes, the barcodes can be used to help
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`identify the DNA sequence information that originated from a particular tagged cell free DNA
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`molecule.
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`Fig. 99
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`50.
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`A challenge arises from the fact that there are often billions of fragments of
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`cfDNA fragments in each sample that must be identified. Tagging each fragment with a
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`different barcode typically involves the generating random sequence barcodes that may, for
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`example, vary considerably from batch-to-batch, leading to sequences that interfere with one
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`another or with cfDNA fragments, pose difficulties to the sequencers, and otherwise reduce
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`consistency, efficiency, and/or accuracy of cfDNA testing.
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`51.
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`Guardant’s inventors recognized that uniquely tagging each cfDNA fragment
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`is not necessary. Rather, the number of tags need only meet a sufficient threshold, depending
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`9 From J.I. Odegaard, et al., Validation of a plasma-based comprehensive cancer genotyping assay utilizing orthogonal
`tissue- and plasma-based methodologies at 3542.
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`18
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`Case 1:20-cv-01580-LPS Document 14 Filed 12/18/20 Page 19 of 94 PageID #: 2719
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`on the amount of DNA that is being analyzed.
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`52.
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`Once cfDNA is tagged, it is amplified, or copied using known techniques. The
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`copied DNA is sequenced, generating sequence reads.
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`53.
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`Guardant’s proprietary algorithms compare each single sequence read to a
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`reference genome, which is simply a digital representation of a previously determined
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`sequence for a representative haploid human genome. This process is commonly referred to
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`as mapping or aligning, and allows one to determine where a sequence is from in the genome.
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`54.
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`The mapping process provides additional context to determine whether
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`sequence reads are copies of the same parent. This is especially important when not every
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`cfDNA is uniquely tagged.
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`19
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`Case 1:20-cv-01580-LPS Document 14 Filed 12/18/20 Page 20 of 94 PageID #: 2720
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`10 From Guardant Health, Inc.’s Technology Tutorial from Case Nos. 1:17-cv-01616 (D.I. 52) and 1:17-cv-01623 (D.I.
`58).
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`20
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`Case 1:20-cv-01580-LPS Document 14 Filed 12/18/20 Page 21 of 94 PageID #: 2721
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`11 Based on Guardant Health, Inc.’s Technology Tutorial from Case Nos. 1:17-cv-01616 (D.I. 52) and 1:17-cv-01623
`(D.I. 58).
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`12 From Guardant Health, Inc.’s Technology Tutorial from Case Nos. 1:17-cv-01616 (D.I. 52) and 1:17-cv-01623 (D.I.
`58).
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`21
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`Case 1:20-cv-01580-LPS Document 14 Filed 12/18/20 Page 22 of 94 PageID #: 2722
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`V.
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`THE ’086 PATENT
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`62.
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`63.
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`The ’086 patent claims an exemplary embodiment of Guardant’s processes.
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`Claim 1 of the ’086 Patent recites:
`
`1. A method for detecting a presence or absence of one or more somatic genetic
`variants in cell-free deoxyribonucleic acid (cfDNA) molecules from a bodily fluid sample
`of a subject, comprising:
`
`(a) non-uniquely tagging a plurality of cfDNA molecules from a population of
`cfDNA molecules obtained from the bodily fluid sample with molecular barcodes from a
`set of molecular barcodes to produce non-uniquely tagged parent polynucleotides,
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`wherein the non-uniquely tagging comprises ligating molecular barcodes from the
`set of molecular barcodes to both ends of a cfDNA molecule from the plurality of cfDNA
`molecules using more than a 10x molar excess of molecular barcodes relative to the
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`
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`22
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`Case 1:20-cv-01580-LPS Document 14 Filed 12/18/20 Page 23 of 94 PageID #: 2723
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`population of cfDNA molecules,
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`wherein the cfDNA molecules that map to a mappable base position of a reference
`sequence are tagged with a number of diffrent molecular barcodes ranging from at least 2
`and fewer than a number of cfDNA molecules that map to the mappable base position, and
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`wherein at least 20% of the cfDNA molecules from the population of cfDNA
`molecules are attached to molecular barcodes;
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`(b) amplifying a plurality of the non-uniquely tagged parent polynucleotides to
`produce progeny polynucleotides with associated molecular barcodes;
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`(c) sequencing a plurality of the progeny polynucleotides to produce sequencing
`reads of the progeny polynucleotides with associated molecular barcodes;
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`(d) mapping a plurality of the sequencing reads to the reference sequence to
`generate mapped sequencing reads;
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`(e) grouping a plurality of the mapped sequencing reads into a plurality of families
`based on sequence information from the molecular barcodes and at least (1) a start base
`position of a given mapped sequencing read from among the mapped sequencing reads at
`which the given mapped sequencing read is determined to start mapping to the reference
`sequence and/or (2) a stop base position of the given mapped sequencing read at which the
`given mapped sequencing read is determined to stop
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