`Tel: 571-272-7822
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`Paper No. 7
`Entered: March 19, 2018
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`UNITED STATES PATENT AND TRADEMARK OFFICE
`_______________
`BEFORE THE PATENT TRIAL AND APPEAL BOARD
`_______________
`AMBRY GENETICS CORPORATION,
`Petitioner
`v.
`THE JOHNS HOPKINS UNIVERSITY
`Patent Owner
`_______________
`
`Case IPR2017-02095
`Patent 7,915,015 B2
`_______________
`
`
`Before LORA M. GREEN, TINA E. HULSE, and RICHARD J. SMITH,
`Administrative Patent Judges.
`
`SMITH, Administrative Patent Judge.
`
`
`
`DECISION
`Denying Institution of Inter Partes Review
`37 C.F.R. § 42.108
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`INTRODUCTION
`I.
`Ambry Genetics Corporation (“Petitioner”) filed a Petition (“Pet.”) to
`institute an inter partes review of claims 1, 5, and 10 of U.S. Patent 7,915,015 B2
`(the “’015 patent”). 35 U.S.C. § 311. The Johns Hopkins University (“Patent
`Owner”) filed a Preliminary Response to the Petition. Paper 6 (“Prelim. Resp.”).
`We have authority to determine whether to institute an inter partes review
`under 35 U.S.C. § 314. To institute an inter partes review, we must determine that
`the information presented in the Petition shows “a reasonable likelihood that the
`petitioner would prevail with respect to at least 1 of the claims challenged in the
`petition.” 35 U.S.C. § 314(a). For the reasons set forth below, we conclude that
`Petitioner has not established a reasonable likelihood that it would prevail in
`showing the unpatentability of any challenged claim of the ’015 patent. Therefore,
`we do not institute an inter partes review for any challenged claim of the ’015
`patent.
`
`Related Proceedings
`A.
`The ’015 patent has been asserted in pending district court proceedings:
`Esoterix Genetic Laboratories, LLC and The Johns Hopkins University v. Ambry
`Genetics Corporation, United States District Court for the Middle District of North
`Carolina, Case No. 1:16-cv-1111-WO-JEP (the “Ambry Litigation”). Pet. 1–2;
`Paper 3, 2. The ’015 patent was also asserted in litigation styled Esoterix Genetic
`Laboratories, LLC and The Johns Hopkins University v. Myriad Genetics, Inc. and
`Myriad Genetics Laboratories, Inc., United States District Court for the Middle
`District of North Carolina, Case No. 1:16-cv-1112-WE-JEP, but that case has been
`dismissed. Pet. 2; Paper 3, 2. The ’015 patent was also asserted in litigation styled
`Esoterix Genetic Laboratories, LLC and The Johns Hopkins University v. Life
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`Technologies Corp, et al., Civil Action No. 1:12-cv-01173-CCE-JEP (MDNC).
`Paper 3, 2–3.
`Petitioner also filed petitions for inter partes review of certain claims of
`related U.S. Patent No. 6,440,706 (IPR2017-02086); U.S. Patent No. 7,824,889
`(IPR2017-02093); and U.S. Patent No. 8,859,206 (IPR2017-02096). Pet. 2; Paper
`3, 2.
`
`The ’015 Patent
`B.
`The ’015 patent relates to diagnostic genetic analyses. Ex. 1001, 1:20. With
`the understanding that somatic mutations are the primary cause of cancer, new
`opportunities for basic research into the pathogenesis of cancer have arisen. Id. at
`1:27–32. For example, in some cases, detecting neoplastic cells in urine, stool, and
`sputum is possible at a stage when the primary tumors are still curable and the
`patients are asymptomatic. Id. at 1:35–40. Thus, it is important to be able to
`detect small populations of mutant cells among a large excess of normal cells. Id.
`at 1:33–35, 44–46. Accordingly, the specification states that “[i]t is an object of
`the present invention to provide methods for determining the presence of a selected
`genetic sequence in a population of genetic sequences.” Id. at 2:3–5.
`The disclosed method involves diluting a biological sample to a point where
`a practically usable number of the diluted samples contain a proportion of the
`selected genetic sequence (analyte) relative to total template molecules. Id. at
`4:20–23. The diluted samples are separately amplified so that the amplified
`products have a proportion of the analyte sequence that is detectable by the
`detection means chosen. Id. at 4:7–10. With this method, single template
`molecules can be amplified so that the products are completely mutant or
`completely wild-type. Id. at 4:11–13.
`The specification refers to this method as “digital amplification.” Id. at
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`4:42–43. According to the specification, “[t]he ultimate utility of Digital
`Amplification lies in its ability to convert the intrinsically exponential nature of
`PCR to a linear one.” Id. at 5:65–67. The specification further states that “[i]t
`should thereby prove useful for experiments requiring the investigation of
`individual alleles, rare variants/mutations, or quantitative analysis of PCR
`products.” Id. at 5:67–6:2. For example, the specification identifies “allelic
`imbalance” as a potential application of digital amplification. Id. at 5:29–30; 43–
`64 (Table 1). According to the specification, “[a]llelic imbalances often result
`from a disease state.” Id. at 7:8–9.
`Illustrative Claim
`C.
`Petitioner challenges claims 1, 5, and 10 of the ’015 patent, of which claim 1
`is an independent claim. Claim 1, as amended during ex parte reexamination, is
`reproduced below:
`1. A method for determining an allelic imbalance in a biological
`sample, comprising the steps of:
`
`distributing isolated nucleic acid template molecules to form a
`set comprising a plurality of assay samples, wherein the nucleic acid
`template molecules are isolated from the biological sample;
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`amplifying the isolated nucleic acid template molecules within
`the set to form a population of amplified molecules in individual assay
`samples of the set;
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`analyzing the amplified molecules in the assay samples of the set
`to determine a first number of assay samples which contain a first allelic
`form of a marker and a second number of assay samples which contain
`a second allelic form of the marker, wherein between 0.1 and 0.9 of the
`assay samples yield an amplification product of at least one of the first
`and second allelic forms of the marker;
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`comparing the first number to the second number to ascertain an
`allelic imbalance in the biological sample; and
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`identifying an allelic imbalance in the biological sample.
`Ex. 1001, 20.
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`Claim 5 depends from claim 1, and claim 10 depends from claims 1 or 8.
`Claim 8 is an independent claim but is not addressed by Petitioner. Accordingly,
`we treat Petitioner’s reference to claim 10 in the Petition as solely based on its
`dependency on claim 1.
`The Asserted Grounds of Unpatentability
`D.
`Petitioner contends that the challenged claims are unpatentable under 35
`U.S.C. §§ 102(b) and/or 103 based on the following specific grounds. Pet. 4.
`Reference[s]
`Basis
`Claims challenged
`Chiang1
`§ 102(b)
`1, 5
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`Sykes2
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`§ 102(b)
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`Chiang and/or Sykes
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`§ 102(b)/§103
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`1, 5, 10
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`1, 5, 10
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`Petitioner also relies on the Declaration of Gregory A. Buck, Ph.D.
`Ex. 1007.
`
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`1 Pie-Wen Chiang et al., Use of a Fluorescent-PCR Reaction to Detect Genomic
`Sequence Copy Number and Transcriptional Abundance, 6 GENOME RESEARCH
`1013–26 (1996) (“Chiang”). Ex. 1031.
`2 P.J. Sykes et al., Quantitation of Targets for PCR by Use of Limiting Dilution, 13
`BIOTECHNIQUES 444–49 (1992) (“Sykes”). Ex. 1011.
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` ANALYSIS
`Person of Ordinary Skill in the Art
`A.
` Petitioner asserts that as of August 2, 1999, a person of ordinary skill in the
`art “would typically have earned a Master’s degree in the biological sciences or a
`related field, and have at least four years of molecular biology laboratory
`experience, or alternatively, have a Ph.D. degree in the biological sciences or a
`related field, and have at least two years of molecular biology laboratory
`experience.” Pet. 8–9.
`Patent Owner disagrees with Petitioner, and contends that one of ordinary
`skill in the art “would have been a person with training and education in molecular
`biology techniques, such as PCR and related laboratory procedures, having either a
`Bachelor’s degree in biological or chemical sciences and at least three years of
`experience in a laboratory, or a Master’s degree in biochemical sciences and at
`least one year of laboratory experience.” Prelim. Resp. 2–3.
`On this record and at this stage of the proceeding, we do not discern an
`appreciable difference in the parties’ respective definitions of a person of ordinary
`skill in the art. Accordingly, we find that a person of ordinary skill in the art (1)
`would have had a Master’s degree in the biological or biochemical sciences, and
`(2) at least two years of molecular biology laboratory experience.
`We further note that the prior art itself demonstrates the level of skill in the
`art at the time of the invention. See Okajima v. Bourdeau, 261 F.3d 1350, 1355
`(Fed. Cir. 2001) (explaining that specific findings regarding ordinary skill level are
`not required “where the prior art itself reflects an appropriate level and a need for
`testimony is not shown”) (quoting Litton Indus. Prods., Inc. v. Solid State Sys.
`Corp., 755 F.2d 158, 163 (Fed. Cir. 1985)).
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`Claim Construction
`B.
`In an inter partes review, the Board interprets claim terms in an unexpired
`patent according to the broadest reasonable construction in light of the
`specification of the patent in which they appear. 37 C.F.R. § 100(b); Cuozzo Speed
`Techs., LLC v. Lee, 136 S. Ct. 2131, 2142 (2016) (affirming applicability of
`broadest reasonable construction standard to inter partes review proceedings).
`Under that standard, and absent any special definitions, we generally give claim
`terms their ordinary and customary meaning, as would be understood by one of
`ordinary skill in the art at the time of the invention. See In re Translogic Tech.,
`Inc., 504 F.3d 1249, 1257 (Fed. Cir. 2007). Any special definitions for claim terms
`must be set forth with reasonable clarity, deliberateness, and precision. See In re
`Paulsen, 30 F.3d 1475, 1480 (Fed. Cir. 1994).
`Disputed Terms
`Petitioner raises issues with respect to the following phrases in claim 1:
`(1)
`“to form a set comprising a plurality of assay samples;”
`(2)
`“assay samples of the set;” and
`(3)
`“comparing the first number to the second number to ascertain an
`allelic imbalance in the biological sample.”3 Pet. 9–11. As to these phrases,
`Petitioner asserts what it believes to be Patent Owner’s proposed constructions
`based on positions taken in the Ambry Litigation. Id. Patent Owner contends that
`“Petitioner’s proposed constructions are unreasonable” (too broad), and
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`3 Petitioner also argues that “the preamble of claim 1 should not be limiting.” Pet.
`9–10. Patent Owner does not contest that argument. However, we need not reach
`that issue at this stage of the proceeding.
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`“mischaracterize[] Patent Owner’s position in related litigation.” Prelim. Resp. 8–
`9.
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`We determine that at this stage of the proceeding, and solely for purposes of
`this Decision, we need not expressly construe these phrases. Rather, we find that
`the ordinary and customary meaning of these phrases is sufficient for evaluating
`the applicability of the Chiang and Sykes references to the claims at issue in the
`Petition. Moreover, our decision not to institute inter partes review is not
`contingent on a resolution of any of these disputed phases.
`Additional Terms
`Although we need not expressly construe any undisputed terms, we find that
`it would be helpful to explain our understanding of the meaning of certain claim
`terms for purposes of our Decision. See Nidec Motor Corp. v. Zhongshan Broad
`Ocean Motor Co. Ltd., 868 F.3d 1013, 1017 (Fed. Cir. 2017) (“[W]e need only
`construe terms ‘that are in controversy, and only to the extent necessary to resolve
`the controversy’” (quoting Vivid Techs., Inc. v. Am. Sci. & Eng’g, Inc., 200 F.3d
`795, 803 (Fed. Cir. 1999))).
`
`“allelic imbalance”
`The term “allelic imbalance” is not defined in the ’015 patent. However,
`Patent Owner took the position in the reexamination proceeding of the ’015 patent
`that the term “allelic imbalance” means “the difference between the number of a
`first allelic form of a marker and the number of a second allelic form of a marker.”
`Ex. 1004 (Reexamination Control No. 90/012,896, Response to Office Action,
`dated Jan. 27, 2014, at 9). Our understanding of the meaning of “allelic
`imbalance,” solely for the purpose of this Decision, is the same meaning as set
`forth by Patent Owner in the reexamination proceeding.
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`“first allelic form of a marker” and “second allelic form of the marker”
`Claim 1 recites “a first allelic form of a marker” and “a second allelic form
`of the marker.” Ex. 1001, 20. The ’015 patent does not define “first allelic form of
`a marker” or “second allelic form of the marker.” Our understanding of these
`phrases, solely for the purpose of this Decision, is first and second allelic forms of
`the same marker (e.g., gene).
`C. Principles of Law
`Anticipation requires that “each and every element as set forth in the claim is
`found, either expressly or inherently described, in a single prior art reference.” In
`re Robertson, 169 F.3d 743, 745 (Fed. Cir. 1999) (citation omitted). “To establish
`inherency, the extrinsic evidence ‘must make clear that the missing descriptive
`matter is necessarily present in the thing described in the reference.’” Id. In
`considering the disclosure of a reference for anticipation, “it is proper to take into
`account not only specific teachings of the reference but also the inferences which
`one skilled in the art would reasonably be expected to draw therefrom.” In re
`Preda, 401 F.2d 825, 826 (CCPA 1968).
`A conclusion of obviousness “cannot be sustained by mere conclusory
`statements; instead, there must be some articulated reasoning with some rational
`underpinning to support the legal conclusion of obviousness.” KSR Int’l Co. v.
`Teleflex Inc., 550 U.S. 398, 418 (2007) (quoting In re Kahn, 441 F.3d 977, 988
`(Fed. Cir. 2006)).
`We analyze the asserted grounds of unpatentability in accordance with the
`above-stated principles.
`
`Anticipation by Chiang
`D.
`Petitioner asserts that claims 1 and 5 are anticipated by Chiang. Pet. 12–17.
`On this record, we determine that Petitioner has not established a reasonable
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`likelihood that it would prevail in showing that claims 1 or 5 are anticipated by
`Chiang.
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`Chiang (Ex. 1031)
`1.
`Chiang describes the use of a fluorescent-PCR reaction to detect genomic
`sequence copy number and transcriptional abundance. Ex. 1031, 1013 (Abstract).
`Chiang describes an assay in which “[t]wo PCR reactions were performed in
`parallel on both the unknown and the reference samples.” Id. at 1014. Chiang
`used “primers from the experimental S100β marker on chromosome 21” for one of
`the PCR reactions and “primers from the reference (eusomic) IGF-1 marker on
`chromosome 12” for the other PCR reaction. Id. Chiang states that “[b]ecause
`both reactions were monitored in exponential phase, the PCR signal depended
`directly on the initial target concentration.” Id. According to Chiang, “the ratio of
`PCR signal from the two reactions (S100β /IGF-1) in the unknown DNA, divided
`by the ratio of PCR signal from the two reactions (S100β /IGF-1) in the control
`(normal placental) DNA, accurately reflected the relative dosage of S100β to IGF-
`1 in the unknown DNA.” Id. Chiang states that this enabled the calculations that
`one sample had one copy of S100β, two samples had two copies of S100β, and two
`other samples had three copies of S100β. Id. at Table 1.
`Analysis
`2.
`Petitioner has not established a reasonable likelihood that it would prevail in
`showing that Chiang discloses each step of claim 1. For example, claim 1 recites
`an “analyzing” step in which a “first number of assay samples [] contain a first
`allelic form of a marker and a second number of assay samples [] contain a second
`allelic form of the marker.” Ex. 1001, 20. As discussed above, the first and
`second allelic forms of “a marker” and “the marker,” respectively, refer to first and
`second allelic forms of the same marker.
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`In addressing the “analyzing” step, Petitioner refers to Chiang’s use of the
`S100β marker on chromosome 21 and IGF-1 marker on chromosome 12. Pet. 13,
`15–16. However, as noted by Patent Owner, those markers are different and not
`first and second allelic forms of the same marker, as required by claim 1. See
`Prelim. Resp. 19 (“Chiang does not disclose analyzing amplified molecules of a
`first allelic form of a marker and a second allelic form of the same marker.”).
`Claim 1 also recites a “comparing” step; namely, “comparing the first
`number to the second number to ascertain an allelic imbalance in the biological
`sample.” Ex. 1001, 20. In addressing the “comparing” step in its Claim Chart,
`Petitioner says “See Claim 1, step (c)” (the analyzing step). Id. at 16. Petitioner
`thus relies on the analysis of different markers (rather than first and second allelic
`forms of the same marker) for the comparing step. Petitioner does not persuasively
`explain how an analysis or comparison involving the S100β marker on
`chromosome 21 and the IGF-1 marker on chromosome 12 involves comparing first
`and second allelic forms of the same marker.
`Accordingly, we determine that Petitioner has not shown a reasonable
`likelihood that it would prevail on its assertion that claim 1 (and dependent claim
`5, which includes the limitations of claim 1) are anticipated by Chiang.
`Anticipation by Sykes
`E.
`Petitioner asserts that claims 1, 5, and 10 are anticipated by Sykes. Pet. 17–
`26. On this record, we determine that Petitioner has not established a reasonable
`likelihood that it would prevail in showing that claims 1, 5, or 10 are anticipated by
`Sykes.
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`Sykes (Ex. 1011)
`1.
`Sykes “describe[s] a general method to quantitate the total number of initial
`targets present in a sample using limiting dilution, PCR and Poisson statistics.”
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`Ex. 1011, 444. Sykes uses the rearranged immunoglobulin heavy chain (IgH) gene
`from a leukemic clone as an example target. Id. In a particular patient with acute
`lymphoblastic leukemia (ALL), all leukemic cells will have the same rearranged
`IgH gene that can act as a genetic marker to distinguish leukemic cells from
`normal cells. Id. Sykes also used the N-ras gene as an internal control. Id.
`Sykes identifies two problems with quantitating the unique rearrangement of
`the leukemic clones: (1) “only a few copies may be present in a tissue sample
`taken from a patient in remission following treatment” and (2) “germ-line IgH
`genes from cells, other than B lymphocytes, and rearranged IgH genes from
`normal B lymphocytes will be present” and may compete with the target gene in
`the PCR. Id. To address these problems, Sykes uses the principle of limiting
`dilution, which uses a qualitative all-or-none end point. Id. By having some end
`points that are positive and some that are negative, “the number of targets present
`can be calculated from the proportion of negative end points by using Poisson
`statistics.” Id.
`Sykes states that the “problem in our study was the detection of rare
`leukemic cells in a large population of normal cells, which in molecular terms
`became the problem of detection of a rare unique IgH sequence against a
`background of numerous other IgH sequences.” Id. at 448. The described study
`determined ratios of the number of N-ras targets detected to the number of IgH
`targets detected. Id. at 446–447, Table 2. Those ratios were determined based on
`samples in which DNA from patients with ALL (a source of leukemic IgH targets
`and normal N-ras targets) included or excluded PBL1 DNA (a source of normal
`IgH and N-ras targets). Id. at Table 2; 445. Based on those ratios, Sykes states
`that “in the presence of competing targets, it proved possible to amplify a mean of
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`52%, i.e., to detect approximately two (1/0.52) potentially amplifiable leukemic
`targets.” Id. at 447, Table 2.
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`Analysis
`2.
`Petitioner has not established a reasonable likelihood that it would prevail in
`showing that Sykes discloses each step of claim 1. Claim 1 recites an “analyzing”
`step in which a “first number of assay samples [] contain a first allelic form of a
`marker and a second number of assay samples [] contain a second allelic form of
`the marker.” Ex. 1001, 20. As discussed above, the first and second allelic forms
`of “a marker” and “the marker,” respectively, refer to first and second allelic forms
`of the same marker.
`In addressing the analyzing step of claim 1, Petitioner points to “counting
`the number of assay samples with IgH and the number of assay samples with N-
`ras.” Pet. 19; see also id. at 22–23. However, those markers (IgH and N-ras) are
`different and not first and second allelic forms of the same marker as required by
`claim 1. Petitioner also relies on the comparison of N-ras to IgH to address the
`“comparing” step. Id. at 19, 23–24. Petitioner thus relies on the analysis of
`different markers (rather than first and second allelic forms of the same marker) for
`the comparing step. Petitioner does not persuasively explain how an analysis or
`comparison involving N-ras targets and IgH targets involves comparing first and
`second allelic forms of the same marker.
`Accordingly, we determine that Petitioner has not shown a reasonable
`likelihood that it would prevail on its assertion that claim 1 (and dependent claims
`5 and 10 which include the limitations of claim 1) are anticipated by Sykes.
`F. Obviousness over Chiang and/or Sykes
`In a single paragraph, Petitioner asserts that claims 1, 5, and 10 of the
`’015 patent are unpatentable as obvious in view of Chiang and/or Sykes. Pet. 26.
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`Petitioner supports this argument with three conclusory sentences and a citation to
`essentially the same three sentences in the Buck Declaration. Id. (citing Ex. 1007
`¶ 67). Such conclusory statements with no analysis by Petitioner are insufficient to
`establish obviousness. See KSR, 550 U.S. at 418.
`Accordingly, we determine that Petitioner has not shown a reasonable
`likelihood that it would prevail on its assertion that any of claims 1, 5, and 10 are
`unpatentable as obvious in view of Chiang and/or Sykes.
`
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` CONCLUSION
`For the foregoing reasons, we conclude that Petitioner has not established a
`reasonable likelihood of prevailing on its assertion that any of claims 1, 5, and 10
`of the ’015 patent are unpatentable.
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` ORDER
`In consideration of the foregoing, it is hereby ORDERED that the Petition is
`denied.
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`PETITIONER:
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`Bhanu K. Sadasivan
`Jacqueline F. Mahoney
`MCDERMOTT WILL & EMERY LLP
`bsadasivan@mwe.com
`jfmahoney@mew.com
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`PATENT OWNER:
`
`Tina McKeon
`John Alemanni
`KILPATRICK TOWNSEND & STOCKTON LLP
`tmckeon@kilpatricktownsend.com
`jalemanni@kilpatricktownsend.com
`
`Benjamin Hsing
`BAKER & HOSTETLER, LLP
`bhsing@bakerlaw.com
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