throbber
Trials@uspto.gov
`571-272-7822
`
`Paper 47
`Date: August 18, 2020
`
`UNITED STATES PATENT AND TRADEMARK OFFICE
`
`BEFORE THE PATENT TRIAL AND APPEAL BOARD
`
`FOUNDATION MEDICINE, INC.,
`Petitioner,
`v.
`GUARDANT HEALTH, INC.,
`Patent Owner.
`
`IPR2019-00652
`Patent 9,834,822 B2
`
`
`
`
`
`
`
`
`
`Before SUSAN L. C. MITCHELL, TINA E. HULSE, and KRISTI L. R.
`SAWERT, Administrative Patent Judges.
`SAWERT, Administrative Patent Judge.
`
`
`
`
`JUDGMENT
`Final Written Decision
`Determining Some Claims Unpatentable
`Dismissing in Part and Denying in Part Petitioner’s Motion to Exclude
`Dismissing in Part and Denying in Part Patent Owner’s Motion to Exclude
`35 U.S.C. § 318(a)
`
`
`
`
`
`
`
`
`00001
`
`EX1074
`
`

`

`IPR2019-00652
`Patent 9,834,822 B2
`
`INTRODUCTION
`I.
`This is a Final Written Decision in an inter partes review challenging
`the patentability of claims 1–13 and 17–20 (“the challenged claims”) of
`U.S. Patent No. 9,834,822 B2 (Ex. 1001, “the ’822 patent”). We have
`jurisdiction under 35 U.S.C. § 6 and enter this Decision pursuant to
`35 U.S.C. § 318(a) and 37 C.F.R. § 42.73. For the reasons set forth below,
`we determine that Petitioner has shown, by a preponderance of the evidence,
`that claims 1–11, 13, and 17–20 are unpatentable. We determine that
`Petitioner has not shown, by a preponderance of the evidence, that claim 12
`is unpatentable. See 35 U.S.C. § 316(e) (2012).
`A. Procedural History
`Foundation Medicine, Inc. (“Petitioner”) filed a Petition for an inter
`partes review under 35 U.S.C. § 311. Paper 2 (“Pet.”). Petitioner supported
`its Petition with the Declaration of Stacey Gabriel, Ph.D. Ex. 1002.
`Guardant Health, Inc. (“Patent Owner”) filed a Preliminary Response.
`Paper 6. On our authorization (Paper 9), Petitioner filed a Reply to Patent
`Owner’s Preliminary Response (Paper 11).
`On August 19, 2019, pursuant to 35 U.S.C. § 314(a), we instituted
`trial to determine whether any challenged claim of the ’822 patent is
`unpatentable based on the grounds raised in the Petition:
`
`2
`
`00002
`
`

`

`IPR2019-00652
`Patent 9,834,822 B2
`Claims Challenged 35 U.S.C. § Reference(s)/Basis
`1–13, 17–20
`103(a)1
`Schmitt,2 Schmitt 2012,3 and Fan4 or
`Forshew5
`
`Paper 12, 7, 36 (“Institution Decision” or “Inst. Dec.”).
`Patent Owner filed a Response. Paper 26 (“PO Resp.”). Patent
`Owner supported its Response with the Declaration of Jay Shendure, M.D.,
`Ph.D., Ex. 2023, and the Declaration of John Quackenbush, Ph.D., Ex. 2025.
`Petitioner filed a Reply to Patent Owner’s Response. Paper 32 (“Pet.
`Reply”). Petitioner supported its Reply with a Reply Declaration of
`Dr. Gabriel. Ex. 1104. Patent Owner filed a Sur-Reply. Paper 34 (“PO Sur-
`Reply”). Patent Owner supported its Sur-Reply with a Supplemental
`Declaration of Dr. Quackenbush. Ex. 2042.
`
`
`1 The Leahy-Smith America Invents Act (“AIA”), Pub. L. No. 112-29,
`125 Stat. 284, 287–88 (2011), amended 35 U.S.C. § 103, effective March 16,
`2013. Because the challenged claims have an effective filing date before
`this date, the pre-AIA version of § 103 applies.
`2 Michael Schmitt et al., U.S. Patent No. 9,752,188 B2, issued Sept. 5,
`2017 (Ex. 1011, “Schmitt”).
`3 Michael W. Schmitt et al., Detection of Ultra-rare Mutations by
`Next-generation Sequencing, 109(36) PROC. NATL. ACAD. SCI. 14508–513
`(2012) (Ex. 1047, “Schmitt 2012”).
`4 Christina Fan et al., Noninvasive diagnosis of fetal aneuploidy by
`shotgun sequencing DNA from maternal blood, 105(42) PROC. NATL. ACAD.
`SCI. 16266–271 (2008) (Ex. 1048, “Fan”)
`5 Tim Forshew et al., Noninvasive Identification and Monitoring of
`Cancer Mutations by Targeted Deep Sequencing of Plasma DNA, 4(136)
`SCI. TRANSL. MED. 1–34 (2012) (Ex. 1004, “Forshew”).
`
`
`3
`
`00003
`
`

`

`IPR2019-00652
`Patent 9,834,822 B2
`Petitioner and Patent Owner each filed respective Motions to Exclude
`Evidence. See Paper 38 (“Pet. Mot.”); Paper 39 (“PO Mot.”). Petitioner
`filed an Opposition to Patent Owner’s Motion, Paper 40 (“Pet. Opp.”), to
`which Patent Owner filed a Reply, Paper 42 (“PO Reply”). Patent Owner
`filed an Opposition to Petitioner’s Motion, Paper 41 (“PO Opp.”), to which
`Petitioner filed a Reply, Paper 43 (“Pet. Reply Opp.”).
`An oral hearing was held on May 13, 2020. A transcript of the
`hearing is included in the record. Paper 46 (“Tr.”).
`B. Real Parties in Interest
`Petitioner identifies Foundation Medicine, Inc., Roche Holdings, Inc.,
`Roche Finance Ltd., and Roche Holding Ltd. as the real parties-in-interest.
`Pet. 73. Patent Owner identifies Guardant Health, Inc., as the real party-in-
`interest. Paper 4, 2.
`C. Related Matters
`Patent Owner has asserted the ’822 patent against Petitioner in
`Guardant Health, Inc. v. Foundation Medicine, Inc., Case No. 17-cv-1616
`(D. Del.) (“the co-pending litigation”). Pet. 74; Paper 4, 2. Patent Owner
`has also asserted the ’822 patent against Personal Genome Diagnostics, Inc.
`(“PGDx”) in Guardant Health, Inc. v. Personal Genome Diagnostics, Inc.,
`Case No. 17-cv-1623 (D. Del.). Pet. 74; Paper 4, 2.
`Petitioner filed a second petition seeking inter partes review of the
`’822 patent, designated IPR2019-00653. Paper 4, 2. A Decision denying
`institution in that case was issued on August 19, 2019 (Paper 12), and a
`Decision denying Petitioner’s request for rehearing issued on January 22,
`2020 (Paper 14).
`Petitioner also filed several petitions seeking inter partes review of
`patents related to the ’822 patent, including: IPR2017-01170, IPR2017-
`
`4
`
`00004
`
`

`

`IPR2019-00652
`Patent 9,834,822 B2
`01447, and IPR2017-01448 (challenging U.S. Patent No. 9,340,830);
`IPR2019-00130 (challenging U.S. Patent No. 9,598,731); IPR2019-00634
`(challenging U.S. Patent No. 9,840,743); and IPR2019-00636 and IPR2019-
`00637 (challenging U.S. Patent No. 9,902,992). Of these cases, only
`IPR2019-00634 is pending.
`PGDx also filed petitions seeking post-grant review of the ’822
`patent, designated PGR2018-00058, and of U.S. Patent No. 9,840,743,
`designated PGR2018-00057. Id. at 2. Both petitions were dismissed before
`a decision on institution.
`D. Summary of the ’822 Patent
`The ’822 patent relates to methods for detecting rare mutations and
`copy number variations in cell free polynucleotides. Ex. 1001, code (57).
`The ’822 patent states that cell-free DNA (“cfDNA”), found in different
`types of bodily fluids, may be used to detect and monitor disease. Id. at
`1:29–45. For instance, cfDNA may contain genetic aberrations—like a
`change in copy number variations and/or single or multiple sequence
`variations associated with a particular disease—that can be used to detect or
`monitor such disease. Id. at 1:29–41, 30:8–14. The ’822 patent states that
`“there is a need in the art for improved methods and systems for using cell
`free DNA to detect and monitor disease.” Id. at 1:41–45.
`The ’822 patent states that the disclosed methods generally “comprise
`sample preparation, or the extraction and isolation of cell free polynucleotide
`sequence[s] from a bodily fluid; subsequent sequencing of cell free
`polynucleotides by techniques known in the art; and application of
`bioinformatics tools to detect rare mutations and copy number variations as
`compared to a reference.” Id. at 30:4–14. The ’822 patent states that
`“[s]ample preparation typically involves converting polynucleotides in a
`
`5
`
`00005
`
`

`

`IPR2019-00652
`Patent 9,834,822 B2
`sample into a form compatible with the sequencing platform used.” Id. at
`32:58–61. “This conversion [c]an involve tagging polynucleotides” with
`“polynucleotide sequence[s].” Id. at 32:61–63. The ’822 patent refers to
`these polynucleotide sequences as “identifiers.” Id. at 38:3–6. The
`identifier may be a molecular barcode. Id. at 38:6–7.
`The ’822 patent explains that “the efficient conversion of individual
`polynucleotides in a sample of initial genetic material into sequence-ready
`tagged parent polynucleotides” is an important tool “for detecting with high
`sensitivity genetic variation in a sample of initial genetic material.” Id. at
`32:33–39. According to the ’822 patent, efficient conversion “increase[s]
`the probability that individual polynucleotides in a sample of initial genetic
`material will be represented in a sequence-ready sample” and “can produce
`sequence information about more polynucleotides in the initial sample.” Id.
`at 32:39–42.
`
`The ’822 patent states that the parent polynucleotides may be tagged
`with either unique or non-unique identifiers. Id. at 37:44–49; see also id. at
`3:10–15 (stating that, in some embodiments, the barcodes are unique, but in
`other embodiments, the barcodes are not unique); see also id. at 6:26–28
`(stating that, in some embodiments, “each tagged parent polynucleotide in
`the set is uniquely tagged,” whereas in other embodiments, “the tags are
`non-unique”). In the case of non-uniquely tagged parent polynucleotides,
`the ’822 patent explains that “the use of non[-]unique barcodes, in
`combination with sequence data at the beginning (start) and end (stop)
`portions of individual sequencing reads and sequencing read length may
`allow for the assignment of a unique identity to individual sequences.” Id. at
`37:43–48.
`
`6
`
`00006
`
`

`

`IPR2019-00652
`Patent 9,834,822 B2
`E. Illustrative Claim
`Claim 1 is the only independent claim. Claims 2–13 and 17–20
`depend directly from claim 1. See Ex. 1001, 62:51–64:22. Claim 1 is
`illustrative and reproduced 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;
`
`
`amplified progeny
`the population of
`d) sequencing
`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;
`
`7
`
`00007
`
`

`

`IPR2019-00652
`Patent 9,834,822 B2
`
`h) determining a frequency of one or more bases called at the
`locus from among the families.
`
`
`Ex. 1001, 62:18–48.
`II. PETITIONER’S MOTION TO EXCLUDE
`Petitioner moves to exclude Exhibits 2002, 2032, 2036, 2037, 2038,
`2039, 2040, and 2041 in their entirety and Exhibits 2023 and 2025 in whole
`or in part. Pet. Mot. 1.
`We dismiss as moot Petitioner’ Motion to Exclude as it relates to
`Exhibits 2002, 2032, 2036, 2037, 2038, 2039, 2040, and 2041, for the
`following reasons. First, we do not rely on or cite to Exhibits 2032, 2036,
`2037, or 2038 in this Decision. Second, Patent Owner cites to Exhibits
`2002, 2039, 2040, and 2041 as support for its arguments about reasonable
`expectation of success. To the extent we refer to these exhibits herein, we
`determine that the record as a whole supports Petitioner’s position as to
`reasonable expectation of success. Infra § IV.E.2.b. Third, Exhibit 2023 is
`the Declaration of Dr. Shendure that is limited in scope to the applicability
`of Schmitt to cfDNA. Ex. 2023 ¶¶ 16–37. Again, to the extent we refer to
`Exhibit 2023, we determine that the record as a whole supports Petitioner’s
`position as to motivation to combine the Schmitt references with Fan or
`Forshew and as to reasonable expectation of success. Infra § IV.E.2.a–b.
`Thus, as to Exhibits 2002, 2023, 2032, 2036, 2037, 2038, 2039, 2040, and
`2041, on which we do not rely to support our decision, Petitioner’s Motion
`to Exclude is dismissed as moot.
`Exhibit 2025 is the Declaration of Dr. Quackenbush. Petitioner
`contends that Dr. Quackenbush’s Declaration should be excluded under
`Federal Rules of Evidence 702, 703, 705, and 401–403. Pet. Mot. 5–7.
`
`8
`
`00008
`
`

`

`IPR2019-00652
`Patent 9,834,822 B2
`Specifically, Petitioner contends that we should exclude at least certain
`paragraphs of Dr. Quackenbush’s Declaration because “they lack a disclosed
`basis of sufficient facts or data,” “are not based on sufficient facts or data,
`the product of reliable principles and methods, and/or a reliable application
`of the principles and methods to the facts,” and “are misleading, confusing,
`and/or needlessly cumulative.” Id. at 5.
`We have considered Petitioner’s arguments but are not persuaded that
`Exhibit 2025 should be excluded in whole or in part. Patent Owner has
`shown, and Petitioner does not dispute, that Dr. Quackenbush is qualified to
`opine as to the perspective of an ordinarily skilled artisan at the time of the
`invention. PO. Opp. 5–93; see also infra § IV.B. As such,
`Dr. Quackenbush’s testimony is highly relevant about how an ordinarily
`skilled artisan would have interpreted the prior-art references, as well as to
`the general knowledge in the field at the time the invention was made. Any
`deficiencies in Dr. Quackenbush’s Declaration go to the weight that we
`should afford his testimony and do not support a motion to exclude. See,
`e.g., Yorkey v. Diab, 601 F.3d 1279, 1284 (Fed. Cir. 2010) (holding that the
`Board has discretion to give more weight to one item of evidence over
`another “unless no reasonable trier of fact could have done so”); In re Am.
`Acad. of Sci. Tech Ctr., 367 F.3d 1359, 1368 (Fed. Cir. 2004) (“[T]he Board
`is entitled to weigh the declarations and conclude that the lack of factual
`corroboration warrants discounting the opinions expressed in the
`declarations.”). Thus, as to Exhibit 2025, Petitioner’s Motion is Exclude is
`denied.
`
`III. PATENT OWNER’S MOTION TO EXCLUDE
`Patent Owner moves to exclude Exhibits 1002, 1007, 1013, 1016–
`1020, 1022, 1036, 1037, 1055, 1080, 1082, 1084–1093, 1100, 1101, 1104,
`
`9
`
`00009
`
`

`

`IPR2019-00652
`Patent 9,834,822 B2
`1110, and 1111. PO Mot. 1. We do not rely on Exhibits 1007, 1013, 1016–
`1020, 1022, 1036, 1037, 1055, 1080, 1082, 1084–1093, 1100, 1110, or 1111
`in this Decision. Thus, we dismiss as moot Patent Owner’s Motion to
`Exclude as it relates to Exhibits 1007, 1013, 1016–1020, 1022, 1036, 1037,
`1055, 1080, 1082, 1084–1093, 1100, 1110, and 1111.
`Exhibits 1002 and 1104 are the first and second Declarations of
`Dr. Gabriel, respectively. PO Mot. 1–8. Patent Owner argues that Exhibit
`1002 should be excluded in its entirety because the “entire declaration is
`premised on an impossible standard to be met by a person of ordinary skill
`in the art” and “Dr. Gabriel uses this impossible perspective to support a
`hindsight-based obviousness analysis.” Id. at 1–3. We agree with
`Petitioner, however, that Patent Owner’s arguments constitute a
`disagreement about a question of fact (i.e., the proper definition of an
`ordinarily skilled artisan), and “[a] motion to exclude is not the proper
`mechanism to direct [its] attention to differences in the evidence.” Pet. Opp.
`2 (quoting Google Inc. v. Visual Real Estate, Inc., IPR2014-01339, Paper 39
`at 37 (PTAB Jan. 25, 2016)). Moreover, we note that Dr. Gabriel applies in
`her Declarations the same definition of an ordinarily skilled artisan as that
`we adopted in our Institution Decision and reaffirm here. Inst. Dec. 7–8;
`infra § IV.B. Thus, we are not persuaded that we should exclude
`Dr. Gabriel’s Declarations Exhibits 1002 and 1104 for this reason.
`Patent Owner also argues that Dr. Gabriel’s second Declaration
`(Exhibit 1104) should be excluded because it attempts to “fill[] a gap in
`[Petitioner’s] prima facie case,” relies on “new theories regarding the
`teachings of Schmitt,” and “presents an entirely different theory of
`obviousness with respect to the ‘non-uniquely tagged’ limitation.” PO
`Mot. 3–8. We are not persuaded, however, that Exhibits 1002 and 1104
`
`10
`
`00010
`
`

`

`IPR2019-00652
`Patent 9,834,822 B2
`should be excluded. “A motion to exclude is not a mechanism to argue that
`a reply contains new arguments or relies on evidence necessary to make out
`a prima facie case.” Vibrant Media, Inc. v. General Elec. Co., IPR2013-
`00170, Paper 56 at 31 (PTAB June 26, 2014). Thus, Patent Owner’s
`arguments in this regard are improper.
`In any event, Petitioner has shown, and Patent Owner does not
`dispute, that Dr. Gabriel is qualified to opine as to the perspective of an
`ordinarily skilled artisan at the time of the invention. Pet. Opp. 2–3; see also
`infra § IV.B. As with Dr. Quackenbush’s testimony above, Dr. Gabriel’s
`testimony is highly relevant about how an ordinarily skilled artisan would
`have interpreted the prior-art references, as well as to the general knowledge
`in the field at the time the invention was made. And any deficiencies in
`Dr. Gabriel’s Declaration go to the weight that we should afford her
`testimony and do not support a motion to exclude.
`For these reasons, as to Exhibits 1002 and 1104, Patent Owner’s
`Motion to Exclude is denied.
`
`IV. ANALYSIS
`We have reviewed the parties’ respective briefs as well as the relevant
`evidence discussed in those papers. For the reasons discussed in detail
`below, we determine that Petitioner has shown by a preponderance of the
`evidence that claims 1–11, 13, and 17–20 of the ’822 patent are unpatentable
`under 35 U.S.C. § 103 as having been obvious, but not that claim 12 would
`have been unpatentable as obvious.
`A. Principles of Law
`To prevail in its challenges to the patentability of all claims of the
`’822 patent, Petitioner must demonstrate by a preponderance of the evidence
`that the claims are unpatentable. 35 U.S.C. § 316(e) (2012); 37 C.F.R.
`
`11
`
`00011
`
`

`

`IPR2019-00652
`Patent 9,834,822 B2
`§ 42.1(d) (2018). “In an [inter partes review], the petitioner has the burden
`from the onset to show with particularity why the patent it challenges is
`unpatentable.” Harmonic Inc. v. Avid. Tech., Inc., 815 F.3d 1356, 1363
`(Fed. Cir. 2016); see also 35 U.S.C. § 312(a)(3) (requiring inter partes
`review petitions to identify “with particularity . . . the evidence that supports
`the grounds for the challenge to each claim”). That burden of persuasion
`never shifts to Patent Owner. Dynamic Drinkware, LLC v. Nat’l Graphics,
`Inc., 800 F.3d 1375, 1378 (Fed. Cir. 2015); see also In re Magnum Oil Tools
`Int’l, Ltd., 829 F.3d 1364, 1375–78 (Fed. Cir. 2016) (discussing the burden
`of proof in inter partes review).
`A claim is unpatentable for obviousness if, to one of ordinary skill in
`the pertinent art, “the differences between the subject matter sought to be
`patented and the prior art are such that the subject matter as a whole would
`have been obvious at the time the invention was made.” 35 U.S.C. § 103(a)
`(2006); see also KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 406 (2007).
`The question of obviousness is resolved on the basis of underlying factual
`determinations including the scope and content of the prior art, any
`differences between the claimed subject matter and the prior art, the level of
`ordinary skill in the art, and objective evidence of nonobviousness. Graham
`v. John Deere Co., 383 U.S. 1, 17–18 (1966). A petitioner cannot satisfy its
`burden of proving obviousness by employing “mere conclusory statements.”
`Magnum Oil, 829 F.3d at 1380. Moreover, a decision on the ground of
`obviousness must include “articulated reasoning with some rational
`underpinning to support the legal conclusion of obviousness.” KSR, 550
`U.S. at 418 (citing In re Kahn, 441 F.3d 977, 988 (Fed. Cir. 2006)).
`We analyze Petitioner’s asserted grounds of unpatentability in
`accordance with the above-stated principles.
`
`12
`
`00012
`
`

`

`IPR2019-00652
`Patent 9,834,822 B2
`B. Level of Ordinary Skill in the Art
`We consider the asserted grounds of unpatentability in view of the
`understanding of a person of ordinary skill in the art and, thus, begin with
`the level of ordinary skill in the art. The level of ordinary skill in the art is
`“a prism or lens through which . . . the Board views the prior art and the
`claimed invention” to prevent hindsight bias. Okajima v. Bourdeau, 261
`F.3d 1350, 1355 (Fed. Cir. 2001).
`Relying on the declaration testimony of its declarant, Dr. Gabriel,
`Petitioner contends that a person of ordinary skill in the art for the ’822
`patent “would have had a Ph.D. in genetics, molecular biology,
`bioinformatics or a related field, and at least five years of research in an
`academic or industry setting, including at least two to three years of research
`experience in the field of cancer genomics.” Pet. 20 (citing Ex. 1002 ¶ 72).
`In response, Patent Owner does not appear to dispute the type of experience
`Petitioner proposes for the level of ordinary skill in the art. See generally
`PO Resp. We observe, however, that Patent Owner’s declarants,
`Dr. Shendure and Dr. Quackenbush, contend that Petitioner’s definition of
`an ordinarily skilled artisan relates more to an artisan with “extraordinary,”
`rather than “ordinary,” skill. See Ex. 2023 ¶ 15, Ex. 2025 ¶ 23.
`In our Institution Decision, we preliminarily adopted Petitioner’s
`proposed level of ordinary skill. Inst. Dec. 7–8. We also determined that
`the prior art itself was sufficient to demonstrate the level of ordinary skill in
`the art at the time of the invention. Inst. Dec. 8. For this Decision, we
`maintain that the prior art demonstrates the appropriate level of ordinary
`skill in the art. See Okajima, 261 F.3d at 1355 (the prior art, itself, can
`reflect appropriate level of ordinary skill in art).
`
`13
`
`00013
`
`

`

`IPR2019-00652
`Patent 9,834,822 B2
`Nevertheless, for further clarity, we set forth the definition of an
`ordinarily skilled artisan as follows. As to level of education, because of the
`nature of the subject matter of the ’822 patent, we agree with Petitioner that
`an ordinarily skilled artisan would have had a doctorate degree (Ph.D.) in
`genetics, molecular biology, bioinformatics, or a related field. Ex. 2023
`¶¶ 28–29; Ex. 1002 ¶ 25. We also agree with Petitioner that an ordinarily
`skilled artisan would have had five years’ research experience in industry or
`academia, including at least two to three years of research experience in the
`field of cancer genomics.
`We acknowledge Petitioner’s contention that an ordinarily skilled
`artisan “would have had knowledge of DNA sequencing, including NGS
`[next-generation sequencing] and related sequencing methods, and related
`sample preparation techniques, bioinformatics methods for grouping and
`comparing sequence reads and mapping sequence reads onto genomes, and
`methods for identifying genetic variants in a sample.” Pet. 20. But we
`conclude that these statements more aptly apply to the scope and content of
`the prior art under Graham and, thus, are best addressed in relation to
`Petitioner’s asserted grounds of unpatentability based on obviousness.
`Finally, we have considered the qualifications of Dr. Gabriel,
`Dr. Shendure, and Dr. Quackenbush and find that each is qualified to opine
`as to the perspective of an ordinarily skilled artisan at the time of the
`invention. See Ex. 1003 (Dr. Gabriel’s curriculum vitae); Ex. 2024
`(Dr. Shendure’s curriculum vitae); Ex. 2026 (Dr. Quackenbush’s curriculum
`vitae).
`C. Claim Construction
`The instant Petition was filed on February 2, 2019. Thus, the new
`rules amending the claim construction standard apply here because the
`
`14
`
`00014
`
`

`

`IPR2019-00652
`Patent 9,834,822 B2
`Petition was filed after the November 13, 2018, effective date of the
`amendment. See Changes to the Claim Construction Standard for
`Interpreting Claims in Trial Proceedings Before the Patent Trial and Appeal
`Board, 83 Fed. Reg. 51,340, 51,358 (Oct. 11, 2018) (amending 37 C.F.R.
`§ 42.100(b) effective November 13, 2018) (now codified at 37 C.F.R.
`§ 42.100(b) (2019)). Accordingly, for this inter partes review, the Board
`applies the same claim construction standard as that applied in federal
`courts.
`Under this standard, we construe the claim “in accordance with the
`ordinary and customary meaning of such claim as understood by one of
`ordinary skill in the art and the prosecution history pertaining to the patent.”
`Id.; see also Phillips v. AWH Corp., 415 F.3d 1303, 1312–13 (Fed. Cir.
`2005) (en banc) (stating that claim terms “are generally given their ordinary
`and customary meaning” as understood by a person of ordinary skill in the
`art in question at the time of the invention). Only terms that are in
`controversy need to be construed, and then only to the extent necessary to
`resolve the controversy. Nidec Motor Corp. v. Zhongshan Broad Ocean
`Motor Co., 868 F.3d 1013, 1017 (Fed. Cir. 2017).
`1. Overview
`At the close of trial, the only claim-construction dispute remaining in
`this proceeding concerns the meaning of “non-uniquely tagged” in the
`context of a population of parent polynucleotides, as recited in claim 1. See
`Ex. 1001, 62:22–24 (reciting “converting the population of cfDNA
`molecules into a population of non-uniquely tagged parent
`polynucleotides”). Petitioner contends that “non-uniquely tagged” “means
`that the number of different identifiers attached to the polynucleotides is at
`least 2 and fewer than the number of polynucleotides.” Pet. 21. Patent
`
`15
`
`00015
`
`

`

`IPR2019-00652
`Patent 9,834,822 B2
`Owner argues that “non-uniquely tagged” means “the number of different
`identifiers is at least 2 and fewer than the number of polynucleotides that
`map to the mappable base position.”6 PO Resp. 16.
`As an initial matter, we acknowledge that, in our Institution Decision,
`we referred to “non-uniquely tagged” as both “the number of different
`identifiers attached to the polynucleotides is at least 2 and fewer than the
`number of polynucleotides” and “the number of different identifiers attached
`to the polynucleotides is at least 2 and fewer than the number of
`polynucleotides that map to the mappable base position.” Compare Inst.
`Dec. 9 (“Petitioner contends that ‘[t]he term “non-uniquely tagged” means
`that the number of different identifiers attached to the polynucleotides is at
`least 2 and fewer than the number of polynucleotides.’ We agree.” (quoting
`Pet. 21)), with id. (stating, “In the context of ‘non-unique’ identifiers, the
`’822 patent follows the words ‘non-uniquely tagged’ with ‘that is, the
`number of different identifiers can be at least 2 and fewer than the number of
`polynucleotides that map to the mappable base position.’” (quoting
`Ex. 1001, 41:42–46)). As a result, both parties claim that the Board adopted
`their respective construction of “non-uniquely tagged.” See PO Resp. 15–16
`(stating that “[t]here is no dispute as to the express definition of ‘non-
`uniquely tagged’ in the ’822 patent”); Pet. Reply 3 (stating that “[t]he Board
`should reject Patent Owner’s arguments and reaffirm its construction, which
`is identical to the District Court’s”).
`
`
`6 The Declarants for both parties agree that an ordinarily skilled
`artisan would understand that “mappable base position” means a position in
`the reference sequence to which polynucleotide molecules can be
`confidently mapped. See Ex. 2027 ¶ 67; Ex. 2022, 23:22–24:13, 30:4–18,
`35:5–7; Ex. 2025 ¶ 65. We apply that understanding for this Decision.
`
`16
`
`00016
`
`

`

`IPR2019-00652
`Patent 9,834,822 B2
`To be clear, we have considered the totality of the arguments and
`evidence anew at the close of trial, as well as the reasoning set forth in our
`Institution Decision, and determine, for the reasons discussed below, that
`“non-uniquely tagged” should be construed to mean that “the number of
`different identifiers is at least 2 and fewer than the number of
`polynucleotides” in a sample, without the additional phrase “that map to a
`mappable position.”
`At the heart of the parties’ dispute is the following passage from the
`’822 patent:
`Accordingly, this invention also provides compositions of tagged
`polynucleotides. The polynucleotides can comprise fragmented
`DNA, e.g. cfDNA. A set of polynucleotides in the composition
`that map to a mappable base position in a genome can be non-
`uniquely tagged, that is, the number of different identifiers can
`be [] at least 2 and fewer than the number of polynucleotides that
`map to the mappable base position.
`Ex. 1001, 41:42–47 (emphasis added).
`The parties agree that “non-uniquely tagged” means that “the number
`of different identifiers [i.e., the tag count7] can be at least 2 and fewer than
`the number of polynucleotides,” but disagree whether the phrase “that map
`to the mappable base position” should be included in the construction of
`“non-uniquely tagged.” Put differently, the parties agree that, to be “non-
`uniquely tagged,” the lower limit for the tag count is two, but disagree on the
`upper limit for the tag count.
`
`
`7 As relevant here, the ’822 patent refers to the “number of unique
`identifiers” as the “tag count.” Ex. 1001, 40:63. For clarity, we use these
`terms interchangeably in this Decision.
`
`17
`
`00017
`
`

`

`IPR2019-00652
`Patent 9,834,822 B2
`2. Patent Owner’s Arguments
`Patent Owner argues that the upper limit on the tag count is “fewer
`than the number of polynucleotides that map to the mappable base position.”
`PO Resp. 15; see also PO Sur-Reply 6 (arguing that “the ’822 patent
`expressly defines ‘non-uniquely tagged’ as limited by the number of
`polynucleotides that map to the mappable base position”). Relying on
`Dr. Quackenbush’s Declaration, Patent Owner offers the following
`schematic distinguishing between (a) the total polynucleotide fragments in a
`sample, (b) the number of polynucleotides that map to a given mappable
`base position, and (c) cognates.8 PO Resp. 13.
`
`
`Schematic submitted by Patent Owner distinguishing between
`the polynucleotides in a sample. PO Resp. 13.
`According to Patent Owner, the upper limit on the number of different
`identifiers does not depend on the total polynucleotide fragments in a sample
`(shown by the light blue circle). Id. at 14. Instead, the tag count “depends
`
`
`8 The ’822 patent defines “cognates” (or “duplicates”) as “more than
`one polynucleotide from different genomes [that] have the same start and
`stop positions.” Ex. 1001, 40:4–8.
`
`18
`
`00018
`
`

`

`IPR2019-00652
`Patent 9,834,822 B2
`. . . on a subpopulation of fragments that map to a given position in the
`reference genome” (shown by the medium blue circle) “and the expected
`number of cognates” (shown by the dark blue circle). Id. (citing Ex. 1001,
`41:6–13). Patent Owner argues that the ’822 patent expressly defines “non-
`uniquely tagged” as limited by the number of polynucleotides that map to
`the mappable base position, and that any argument otherwise “strains
`credulity.” PO Sur-Reply 5–6; see also PO Reply 15.
`3. Petitioner’s Arguments
`Petitioner contends that the upper limit on the number of different
`identifiers is “fewer than the number of polynucleotides” in a sample.
`Pet. 21. Specifically, Petitioner contends that, when “fewer barcodes than
`original DNA fragments” are used, “not every fragment has a unique
`barcode,” and thus the population of polynucleotides are “non-uniquely
`tagged.” Id. at 11–12. As an example, Petitioner contends that “if there are
`1000 DNA fragments and only 500 different barcodes, [then] each fragment
`does not have its own unique barcode,” and thus the population of
`polynucleotides is “non-uniquely tagged” in the context of claim 1. Id. at 12
`(citing Ex. 1002 ¶ 51). Conversely, “if there are 1000 original DNA
`fragments and at least 1000 different barcodes, [then] each fragment will
`have its own unique barcode.” Id. at 11 (citing Ex. 1002 ¶ 50). Petitioner
`contends that we should not include “that map to the mappable base
`position” in the constructio

This document is available on Docket Alarm but you must sign up to view it.


Or .

Accessing this document will incur an additional charge of $.

After purchase, you can access this document again without charge.

Accept $ Charge
throbber

Still Working On It

This document is taking longer than usual to download. This can happen if we need to contact the court directly to obtain the document and their servers are running slowly.

Give it another minute or two to complete, and then try the refresh button.

throbber

A few More Minutes ... Still Working

It can take up to 5 minutes for us to download a document if the court servers are running slowly.

Thank you for your continued patience.

This document could not be displayed.

We could not find this document within its docket. Please go back to the docket page and check the link. If that does not work, go back to the docket and refresh it to pull the newest information.

Your account does not support viewing this document.

You need a Paid Account to view this document. Click here to change your account type.

Your account does not support viewing this document.

Set your membership status to view this document.

With a Docket Alarm membership, you'll get a whole lot more, including:

  • Up-to-date information for this case.
  • Email alerts whenever there is an update.
  • Full text search for other cases.
  • Get email alerts whenever a new case matches your search.

Become a Member

One Moment Please

The filing “” is large (MB) and is being downloaded.

Please refresh this page in a few minutes to see if the filing has been downloaded. The filing will also be emailed to you when the download completes.

Your document is on its way!

If you do not receive the document in five minutes, contact support at support@docketalarm.com.

Sealed Document

We are unable to display this document, it may be under a court ordered seal.

If you have proper credentials to access the file, you may proceed directly to the court's system using your government issued username and password.


Access Government Site

We are redirecting you
to a mobile optimized page.





Document Unreadable or Corrupt

Refresh this Document
Go to the Docket

We are unable to display this document.

Refresh this Document
Go to the Docket