Trials@uspto.gov
`Tel: 571-272-7822
`
`
`
`
`Paper No. 7
`Entered: March 19, 2018
`
`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 IPR2017-02096
`Patent 8,859,206 B2
`_______________
`
`
`Before LORA M. GREEN, TINA E. HULSE, and RICHARD J. SMITH,
`Administrative Patent Judges.
`
`GREEN, Administrative Patent Judge.
`
`
`
`DECISION
`Denying Institution of Inter Partes Review
`37 C.F.R. § 42.108
`
`
`
`
`
`
`
`
`
`
`Tel: 571-272-7822
`
`
`
`
`Paper No. 7
`Entered: March 19, 2018
`
`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 IPR2017-02096
`Patent 8,859,206 B2
`_______________
`
`
`Before LORA M. GREEN, TINA E. HULSE, and RICHARD J. SMITH,
`Administrative Patent Judges.
`
`GREEN, Administrative Patent Judge.
`
`
`
`DECISION
`Denying Institution of Inter Partes Review
`37 C.F.R. § 42.108
`
`
`
`
`
`
`
`
`
`
`
`Case IPR2017-02096
`Patent 8,859,206 B2
`
`
`INTRODUCTION
`I.
`Ambry Genetics Corporation (“Petitioner”) filed a Petition to institute
`an inter partes review of claims 1, 3, 15, 20, and 21 of U.S. Patent 8,859,206
`B2 (the “’206 patent”). Paper 1 (“Pet.”) The Johns Hopkins University
`(“Patent Owner”) filed a Preliminary Response to the Petition. Paper 6
`(“Prelim. Resp.”).
`Institution of an inter partes review is authorized by statute when “the
`information presented in the petition . . . and any response . . . shows that
`there is 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; see
`37 C.F.R. §§ 42.4, 42.108. Upon considering the Petition and Preliminary
`Response, we determine that Petitioner has not shown a reasonable
`likelihood that it would prevail in showing the unpatentability of challenged
`claims 1, 3, 15, 20, and 21. Accordingly, we decline to institute an inter
`partes review of those claims.
`Related Proceedings
`A.
`The ’206 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.
`Pet. 1–2; Paper 3, 2. The ’206 patent was also asserted in 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.
`Petitioner also filed petitions for inter partes review of certain claims
`
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`of related U.S. Patent No. 6,440,706 (IPR2017-02086); U.S. Patent No.
`7,915,015 (IPR2017-02095); and U.S. Patent No. 7,824,889 (IPR2017-
`02093). Pet. 2; Paper 3, 2.
`
`The ’206 Patent
`B.
`The ’206 patent issued on October 14, 2014, with Bert Vogelstein and
`Kenneth W. Kinzler as the listed co-inventors. Ex. 1001. The ’206 patent
`relates to diagnostic genetic analyses. Id. at 1:12. 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 1:19–
`22. 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 1:27–33. Thus, it is important to
`be able to detect small populations of mutant cells among a large excess of
`normal cells. Id. at 1:25–27. 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 1:65–67.
`The claimed 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 4:12–16. 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 3:66–4:2.
`With this method, single template molecules can be amplified so that the
`products are completely mutant or completely wild-type. Id. at 4:3–5.
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`The specification refers to this method as “[d]igital amplification.” Id.
`at 4:34–35. 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 5:51–53. The specification states further 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 5:53–55.
`Illustrative Claim
`C.
`Petitioner challenges claims 1, 3, 15, 20, and 21 of the ’206 patent, of
`which claim 1 is an independent claim. Claim 1 is reproduced below:
`1. A method for detecting quantity of a genetic sequence in
`a mixed population of human genomic nucleic acid sequences
`comprising at least a first and a second human genomic
`sequence, wherein the first sequence is a sequence of a wild-
`type allele of a locus and a second sequence is a sequence of a
`mutant allele of the locus, comprising:
`[(a)] distributing or diluting a mixed population of cell-free,
`human genomic nucleic acid template molecules from a
`sample in which the fraction of mutant alleles is less than
`20%, into a set comprising at least fifteen assay samples
`such that said at least fifteen assay samples each
`comprises less than ten template molecules;
`[(b)] amplifying the template molecules in the assay
`samples, wherein an assay sample with a single template
`molecule forms homogeneous amplification products in
`the assay sample;
`[(c)] analyzing by determining nucleic acid sequence of
`amplification products in the assay samples of the set
`with homogeneous amplification products to determine a
`first number of assay samples in the set which contain the
`
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`Case IPR2017-02096
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`first sequence and a second number of assay samples in
`the set which contain the second sequence;
`[(d)] comparing the first number to the second number to
`ascertain a ratio which reflects the composition of the
`mixed population;
`[(e)] identifying a mutation in the mixed population if a
`statistically significant fraction of assay samples
`comprises the second sequence.
`Ex. 1001, 15:43‒67; 16:41‒43 (with step designations used by Petitioner
`added in brackets).
`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]
`Sykes1
`
`Claims challenged
`1, 3, 20, 21
`
`Basis
`§ 102(b)
`
`Sykes and Brown2
`
`§103
`
`15
`
`
`Petitioner also relies on the Declaration of Gregory A. Buck, Ph.D.
`Ex. 1007.
`Patent Owner submitted the Declaration of its expert, Fred Russell
`Kramer, Ph.D. (Ex. 2001), with its Preliminary Response.
`
`
`1 P.J. Sykes et al., Quantitation of Targets for PCR by Use of Limiting
`Dilution, 13 BIOTECHNIQUES 444–49 (1992) (“Sykes”) (Ex. 1011).
`2 Brown et al., US Patent No. 6,143,496, issued Nov. 7, 2000 (“Brown”)
`(Ex. 1010).
`
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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 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 (citing Ex. 1007 ¶ 12).
`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. 3 (citing Ex. 2001 ¶ 12).
`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
`
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`Indus. Prods., Inc. v. Solid State Sys. Corp., 755 F.2d 158, 163 (Fed. Cir.
`1985)).
`
`Claim Construction
`B.
`We interpret claims using the “broadest reasonable construction in
`light of the specification of the patent in which [they] appear[].” 37 C.F.R.
`§ 42.100(b); see also Cuozzo Speed Techs., LLC v. Lee, 136 S. Ct. 2131,
`2144–46 (2016). Under the broadest reasonable construction standard, claim
`terms are generally given their ordinary and customary meaning, as would
`be understood by one of ordinary skill in the art at the time of the invention.
`In re Translogic Tech., Inc., 504 F.3d 1249, 1257 (Fed. Cir. 2007). “Absent
`claim language carrying a narrow meaning, the PTO should only limit the
`claim based on the specification . . . when [it] expressly disclaim[s] the
`broader definition.” In re Bigio, 381 F.3d 1320, 1325 (Fed. Cir. 2004).
`“Although an inventor is indeed free to define the specific terms used to
`describe his or her invention, this must be done with reasonable clarity,
`deliberateness, and precision.” In re Paulsen, 30 F.3d 1475, 1480 (Fed. Cir.
`1994).
`We determine that at this stage of the proceeding, we need only
`determine whether the preamble should be read as limiting the claimed
`method steps. 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))).
`
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`“A method for detecting quantity of a genetic sequence in a mixed
`population of human genomic nucleic acid sequences comprising at least a
`first and a second human genomic sequence, wherein the first sequence is a
`sequence of a wild-type allele of a locus and a second sequence is a
`sequence of a mutant allele of the locus”
`Petitioner asserts that under the broadest reasonable construction of
`
`the method of independent claim 1, the preamble should not be read as
`limiting. Pet. 9. Patent Owner responds that “the preamble of claim 1 is
`limiting because it provides definitions and antecedent basis for the first and
`second sequences, which are referenced in the analyzing step and the
`identifying step.” Prelim. Resp. 12.
`If the claim preamble, when read in the context of the
`entire claim, recites limitations of the claim, or, if the claim
`preamble is “necessary to give life, meaning, and vitality” to the
`claim, then the claim preamble should be construed as if in the
`balance of the claim. . . . If, however, the body of the claim
`fully and intrinsically sets forth the complete invention,
`including all of its limitations, and the preamble offers no
`distinct definition of any of the claimed invention’s limitations,
`but rather merely states, for example, the purpose or intended
`use of the invention, then the preamble is of no significance to
`claim construction because it cannot be said to constitute or
`explain a claim limitation.
`Pitney Bowes, Inc. v. Hewlett Packard Co., 182 F.3d 1298, 1305 (Fed. Cir.
`1999).
`Here, we agree with Patent Owner that the preamble should be read as
`limiting the claimed method. In particular, the claimed analyzing step
`recites “analyzing by determining nucleic acid sequence of amplification
`products in the assay samples of the set with homogeneous amplification
`products to determine a first number of assay samples in the set which
`contain the first sequence and a second number of assay samples in the set
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`Case IPR2017-02096
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`which contain the second sequence.” Ex. 1001, 15:59‒64 (emphasis added).
`The only portion of the claim that defines the relationship of the first
`sequence to the second sequence, and, thus, defines the scope of the claim, is
`the preamble. Specifically, the preamble requires that “the first sequence is
`a sequence of a wild-type allele of a locus and a second sequence is a
`sequence of a mutant allele of the locus.” Id. at 15:46‒48. The preamble,
`therefore, limits the scope of the first and second sequences as being a wild-
`type allele of a locus and a mutant allele of a locus. See Seachange
`International, Inc. v. C-Cor Inc., 413 F.3d 1361, 1376 (Fed. Cir. 2005)
`(construing the preamble as limiting where it “provide[d] the only
`antecedent basis and thus the context essential to understand the meaning”
`and scope of a term that derived antecedent basis from the preamble).
`Anticipation by Sykes3
`C.
`Petitioner asserts that claims 1, 3, 20, and 21 are anticipated by Sykes.
`Pet. 10‒17. Patent Owner contends that Petitioner has not established a
`reasonable likelihood that Sykes anticipates those claims. Prelim. Resp. 19‒
`29.
`
`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.” Ex. 1011, Abstract. Sykes uses the rearranged immunoglobulin
`
`
`3 Patent Owner argues also that we should exercise our discretion under 35
`U.S.C. § 325(d) and decline to institute trial as Sykes and Brown have
`already been considered by the office. Prelim. Resp. 7‒9. As we determine
`that Petitioner has not established a reasonable likelihood that the challenged
`claims are unpatentable, we need not address this argument.
`
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`heavy chain (IgH) gene from a leukemic clone as an example. Id. at 444. In
`a particular patient with acute lymphoblastic leukemia, 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. at Abstract.
`Sykes identified 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 PCR. Id. at 444. 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.
`Analysis
`2.
`Petitioner relies on Sykes for its teaching of quantifying the number of
`initial target nucleic acids in a sample using limiting dilution PCR and
`Poisson statistics. Pet. 10 (citing Ex. 1011, Abstract). According to
`Petitioner, the method taught by Sykes allowed for the detection of two
`potentially amplifiable leukemic IgH target nucleic acids in the presence of
`160,000 competing non-leukemic genomes. Id. at 10‒11 (citing Ex. 1011,
`Abstract; Ex. 1007 ¶ 38).
`
`Specifically, Petitioner asserts that the target nucleic acid of Sykes
`was a rearranged immunoglobulin heavy chain from a leukemic Ho clone.
`Id. at 11 (citing Ex. 1011, 444‒445). “Serial dilutions of 10 replicates of Ho
`
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`DNA were made and amplified by PCR,” and “10 replicates were tested for
`IgH and 10 replicates were tested for N-ras.” Id. (citing Ex. 1011, 446
`(Table 1)). Amplification of N-ras was used by Sykes as “an internal
`control to quantitate the number of potentially amplifiable genomes present
`in a sample.” Id. (quoting Ex. 1011, Abstract). Sykes also “discloses
`diluting the Ho DNA to form a set of at least 20 assay samples.” Id. Sykes
`teaches further, Petitioner asserts, that “[a]s seen in Table 1, the positive
`number of IgH (mutant allele) was only 1 per 10 tubes for the 0.375 copies
`added and the 0.113 copies added reactions,” thus, Petitioner asserts, “Sykes
`discloses that the fraction of mutant alleles is less than 20%.” Id. Petitioner
`contends, therefore, that Sykes teaches step (a) of claim 1, as Sykes teaches
`that “less than ten template molecules (IgH and N-ras) were added to thirty
`of the PCR reaction tubes (Table 1, “Number of Copies Added” columns).”
`Id. (citing Ex. 1007 ¶ 39).
`
`Petitioner argues further that Sykes amplified the IgH genes and the
`N-ras genes in the Ho DNA sample. Id. As “an amplification reaction with
`a single template molecule inherently forms a homogeneous amplification
`product as the sole amplification product,” Petitioner asserts that Sykes also
`teaches step (b) of claim 1. Id. (citing Ex. 1007 ¶ 40). Moreover, Petitioner
`avers, Sykes counted the number of assay samples with IgH and the number
`of assay samples with N-ras, and used Poisson statistics to quantitate the
`number of initial leukemic and non-leukemic templates present. Id. at 12
`(citing Ex. 1011, Abstract, 444, 446‒447). Thus, Petitioner contends, Sykes
`teaches step (c) of challenged claim 1. Id. (citing Ex. 1007 ¶¶ 42‒44).
`
`Regarding step (d), the comparing step, Petitioner asserts that Sykes
`teaches comparing the number of assay samples that contain IgH to the
`
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`assay samples containing the total templates, “to ascertain a ratio (‘Ratio N-
`ras/IgH,’ Table 2) which reflects the composition of the mixed population
`(i.e., Ho DNA).” Id. (citing Ex. 1007 ¶ 45).
`
`With respect to step (e), Petitioner asserts “Sykes discloses that in two
`experiments, 1.7 and 2.6 copies of N-ras could be detected, and in three
`experiments, 3.5, 6.1 and 10 copies of Ho IgH could be detected in the
`presence of 1 μg of PBL1 DNA,” and that the data was consistent with a
`Poisson distribution. Id. (citing Ex. 1011, 446 (Table 1), 447). Thus,
`according to Petitioner, “Sykes teaches identifying a mutation (IgH) in the
`mixed population.” Id. (citing Ex. 1007 ¶ 46).
`
`Patent Owner responds that Sykes fails to teach the “analyzing,”
`“comparing,” and “identifying” steps, that is, steps (c), (d), and (e) as
`identified by Petitioner. Prelim. Resp. 20.
`
`Specifically, as to the “analyzing step” (step (c)), Patent Owner
`contends that the “claims require that the first and second sequences in the
`mixed population be sequences of a wild-type allele of a locus and a mutant
`allele of the locus, respectively.” Id. at 21 (citing Ex. 1001, 15:42‒47).
`Patent Owner asserts, however, that “Sykes discloses analyzing mutant IgH
`(a first gene at a first locus) and wild-type N-ras (a second gene at a second
`locus) in a patient sample, but IgH and N-ras are alleles of two different
`loci.” Id. at 22 (citing Ex. 2001 ¶¶ 41, 44).
`
`We agree with Patent Owner that Petitioner has not established a
`reasonable likelihood that Sykes anticipates challenged claim 1.
`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
`
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`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.
`
`Petitioner equates the IgH gene from a leukemic clone Ho as the
`target DNA, i.e., the second sequence, and appears to equate the N-ras gene
`with the first sequence required by claim 1. See Pet. 11‒16. As discussed
`above, however, we have construed the preamble of claim 1 as limiting the
`claimed method as it defines the relationship of first sequence to the second
`sequence, defining the scope of the claim. The preamble of claim 1 specifies
`that “the first sequence is a sequence of a wild-type allele of a locus and a
`second sequence is a sequence of a mutant allele of the locus.” That is,
`claim 1 requires that the first and second sequences correspond to alleles of
`the same locus. Petitioner, however, does not explain why the IgH gene
`would be considered by the ordinary artisan to be a mutant allele of the N-
`ras gene.
`Accordingly, we are not persuaded that Petitioner has shown a
`reasonable likelihood that Sykes anticipates independent claim 1. Claims 3,
`20, and 21 depend from claim 1, and incorporate all of the limitations of that
`claim, and, thus, the challenge as to those claims suffers the same
`deficiencies discussed above with respect to claim 1. We, thus, decline to
`institute inter partes review as to the challenge of claims 1, 3, 20, and 21 as
`being anticipated by Sykes.
`D. Obviousness over Sykes and Brown
`Petitioner asserts that claim 15 is rendered obvious by the
`combination of Sykes and Brown. Pet. 17–18. Patent Owner contends that
`Petitioner has not established a reasonable likelihood that the combination of
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`Sykes and Brown renders that claim obvious. Prelim. Resp. 29‒33.
`Brown (Ex. 1010)
`1.
`Brown describes “[m]ethods of filling miniaturized sample chambers”
`and “methods for determining the number of template molecules in a sample
`by conducting replicate nucleic acid sequence amplification reactions on a
`set of terminally diluted samples and counting the number of positive
`amplification reactions. The methods can be used to detect a single starting
`nucleic acid target molecule.” Ex. 1010, Abstract. Brown further states that
`“[p]referred sample chambers according some embodiments of the
`invention, for nucleic acid amplification methods to detect single target
`nucleic acid molecules, have volumes of from about 1 microliter to about 1
`picoliter or less. . . . Photolithographic methods can provide from about
`10,000 to over 100,000 sample chambers of about 100 picoliters each on a
`1"×3" substrate.” Id. at 16:1–4 and 17–19.
`Analysis
`2.
`Petitioner has not established a reasonable likelihood that it would
`prevail in showing that the combination of Sykes of Brown renders claim 15
`obvious.
`Petitioner relies on Sykes as set forth above with respect to the
`anticipation challenge discussed above. See Pet. 17. As noted by Patent
`Owner (Prelim. Resp. 32), Petitioner does not rely on Brown to remedy the
`deficiency of Sykes as set forth in our analysis of the anticipation challenge.
`
`Accordingly, we conclude that Petitioner has not established a
`reasonable likelihood that claim 15 is rendered obvious by the combination
`of Sykes and Brown.
`
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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, 3, 15, 20, and 21 of the ’206 patent are unpatentable.
` ORDER
`In consideration of the foregoing, it is hereby ORDERED that the
`Petition is denied.
`
`
`
`
`
`PETITIONER:
`
`Bhanu K. Sadasivan
`Jacqueline F. Mahoney
`MCDERMOTT WILL & EMERY LLP
`bsadasivan@mwe.com
`jfmahoney@mew.com
`
`
`
`PATENT OWNER:
`
`Tina McKeon
`John Alemanni
`KILPATRICK TOWNSEND & STOCKTON LLP
`tmckeon@kilpatricktownsend.com
`jalemanni@kilpatricktownsend.com
`
`Benjamin Hsing
`BAKER & HOSTETLER, LLP
`bhsing@bakerlaw.com
`
`
`
`
`
`15
`
`
`
`
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