`
`
`
`
`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 No. IPR2017-02086 (U.S. Patent No. 6,440,706)
`Case No. IPR2017-02093 (U.S. Patent No. 7,824,889)
`Case No. IPR2017-02095 (U.S. Patent No. 7,915,015)
`
`
`
`DECLARATION OF FRED RUSSELL KRAMER, PH.D.
`
`
`
`
`
`
`The Johns Hopkins University Exhibit JHU2001 - Page 1 of 72
`
`
`
`IPR2017-02086, -02093, -02095
`
`
`
`
`
`
`Patent Nos. 6,440,706; 7,824,889; 7,915,015
`Declaration of Fred Russell Kramer, Ph.D.
`
`
`I, Fred Russell Kramer, Ph.D., declare as follows:
`
`I.
`
`1.
`
`Introduction
`
`I am over the age of eighteen (18) and am otherwise competent to make this
`
`declaration.
`
`2.
`
`I have been engaged by the law firm of Kilpatrick, Townsend & Stockton
`
`LLP, counsel for Laboratory Corporation of America Holdings (LabCorp), to
`
`consult with legal counsel, to prepare this and potentially other declarations, and to
`
`be available for deposition in connection with responding to the Petitions for Inter
`
`Partes Review of U.S. Patent No. 6,440,706 (“the ’706 patent”); U.S. Patent No.
`
`8,859,206 (“the ’206 patent”); U.S. Patent No. 7,824,889 (“the ’889 patent”); and
`
`U.S. Patent No. 7,915,015 (“the ’015 patent”) (collectively, “the Petitions”) filed
`
`by Ambry Genetics Corporation (“the Petitioner”).1 I am being compensated for
`
`my time in connection with the Petitions at my standard consulting rate. My
`
`
`1 In each Petition, the respective patent is identified as Exhibit AMB1001. When I
`
`refer to specific portions of the patents in my comments below, I identify the patent
`
`by this exhibit number and also identify which of the four patents to which I am
`
`referring.
`
`
`
`2
`
`The Johns Hopkins University Exhibit JHU2001 - Page 2 of 72
`
`
`
`
`
`IPR2017-02086, -02093, -02095
`
`
`
`
`Patent Nos. 6,440,706; 7,824,889; 7,915,015
`Declaration of Fred Russell Kramer, Ph.D.
`
`
`compensation is hourly and is unaffected by the substance of my opinion or the
`
`outcome of the proceedings.
`
`II. Expertise
`
`3.
`
`I am qualified based on my education and experience to testify as an expert
`
`in the field of molecular biology. My education and experience qualified me as a
`
`person of at least ordinary skill in the art at the time of the invention in 1999. A
`
`true and correct copy of my curriculum vitae is attached as Exhibit No. JHU2002.
`
`Additionally, I provide the following overview of my background as it pertains to
`
`my qualifications for providing expert testimony in this matter.
`
`4.
`
`I am currently a Professor of Microbiology, Biochemistry and Molecular
`
`Genetics at the Public Health Research Institute (PHRI), New Jersey Medical
`
`School, at Rutgers University, The State University of New Jersey. I am currently
`
`the Co-Director of the Laboratory of Molecular Genetics at PHRI. I am also an
`
`Associate Member of the Cancer Institute of New Jersey.
`
`5.
`
`For 27 years, I served as a Research Professor or Adjunct Professor at the
`
`New York University School of Medicine in the Department of Microbiology, and
`
`I was a professor and conducted research prior to that for 17 years at Columbia
`
`
`
`3
`
`The Johns Hopkins University Exhibit JHU2001 - Page 3 of 72
`
`
`
`
`
`IPR2017-02086, -02093, -02095
`
`
`
`
`Patent Nos. 6,440,706; 7,824,889; 7,915,015
`Declaration of Fred Russell Kramer, Ph.D.
`
`
`University in the Department of Genetics and Development and the Institute of
`
`Cancer Research at the College of Physicians and Surgeons.
`
`6.
`
`I earned my Bachelor of Science Degree from the University of Michigan in
`
`1964 and my Ph.D. from the Rockefeller University in 1969. I conducted
`
`postdoctoral research with Dr. Sol Spiegelman at Columbia University from
`
`1969-1972.
`
`7.
`
`I have worked in the areas of microbiology, biochemistry, and molecular
`
`genetics for 48 years, and I have worked in research related to nucleic acid
`
`detection using a variety of techniques, including polymerase chain reaction (PCR)
`
`assays, for over 33 years. For example, I have designed extremely sensitive,
`
`multiplex, clinical PCR assays that simultaneously detect four different pathogenic
`
`retroviruses in blood, and I have demonstrated the use of Molecular Beacons in
`
`PCR assays, including their use in the detection of rare mutations. I also developed
`
`a single-tube version of a PCR assay that rapidly identifies multidrug-resistant
`
`Mycobacterium tuberculosis in sputum samples, which is now the principal assay
`
`for the direct detection of tuberculosis utilized throughout the world. The ongoing
`
`focus of my research is the development of highly selective PCR assays for the
`
`
`
`4
`
`The Johns Hopkins University Exhibit JHU2001 - Page 4 of 72
`
`
`
`
`
`IPR2017-02086, -02093, -02095
`
`
`
`
`Patent Nos. 6,440,706; 7,824,889; 7,915,015
`Declaration of Fred Russell Kramer, Ph.D.
`
`
`detection of rare somatic mutations related to cancer diagnosis, prognosis, and
`
`therapy.
`
`8.
`
`In forming my opinions, I relied on my knowledge and experience in the
`
`field, as well as on documents and information referenced in this Declaration.
`
`All statements in my Declaration, unless indicated otherwise, are based on my
`
`knowledge and experience in the field.
`
`III. Materials Considered
`
`9.
`
`In forming my opinions, in addition to my knowledge and experience, I have
`
`considered the following documents and things that I have obtained or that have
`
`been provided to me:
`
`
`
`
`
`
`
`
`
`
`U.S. Patents Nos. 6,440,706; 8,859,206; 7,824,889; and 7,915,015;
`Levran et al., 1997, Sequence Variation in the Fanconi Anemia Gene
`FAA, PNAS 94:13051-13056 (“Levran”);
`Simmonds et al., 1990, Human Immunodeficiency Virus-Infected
`Individuals Contain Provirus in Small Numbers of Peripheral
`Mononuclear Cells and at Low Copy Numbers, Journal of Virology
`64:864-872 (“Simmonds”);
`Sykes et al., 1992, Quantitation of Targets for PCR by Use
`of Limiting Dilution, BioTechniques 13:444-449 (“Sykes”);
`U.S. Patent No. 6,143,496 (Brown et al.) (“Brown”);
`
`
`
`5
`
`The Johns Hopkins University Exhibit JHU2001 - Page 5 of 72
`
`
`
`
`
`IPR2017-02086, -02093, -02095
`
`
`
`
`Patent Nos. 6,440,706; 7,824,889; 7,915,015
`Declaration of Fred Russell Kramer, Ph.D.
`
`
`
`
`
`Chiang et al., 1996, Use of a Fluorescent-PCR Reaction to Detect
`Genomic Sequence Copy Number and Transcriptional Abundance,
`Genome Research 6: 1013-1026 (“Chiang”);
`Inter partes petitions of Ambry Genetics Corporation for IPR2017-
`02086; IPR2017-02093; IPR2017-02095;
`Buck declarations in support of the Ambry Genetics Corporation
`petitions for IPR2017-02086; IPR2017-02093; IPR2017-02095; and
`
`All additional references cited herein.
`I further performed internet research and document review to confirm
`
`
`
`
`
`10.
`
`my recollection of technology that was available prior to August 1999.
`
`IV. Level of Ordinary Skill and the Relevant Art
`
`11. Dr. Buck appears to contend that one of ordinary skill in the art would be
`
`familiar with the relevant scientific field and its literature at the time when the
`
`patent application was filed on August 2, 1999. AMB1007, ¶ 10. In particular,
`
`Dr. Buck contends that a person of ordinary skill in the art would typically have
`
`either a Master’s degree in the biological sciences or a related field, plus at least
`
`four years of laboratory experience, or a Ph.D. degree in the biological sciences or
`
`a related field, plus at least two years of molecular biology laboratory experience.
`
`AMB1007, ¶ 11.
`
`
`
`6
`
`The Johns Hopkins University Exhibit JHU2001 - Page 6 of 72
`
`
`
`IPR2017-02086, -02093, -02095
`
`
`
`
`
`
`Patent Nos. 6,440,706; 7,824,889; 7,915,015
`Declaration of Fred Russell Kramer, Ph.D.
`
`
`12.
`
`I disagree with Dr. Buck’s interpretation as to the level of one of ordinary
`
`skill in the art. In my opinion, this person is someone with training and education
`
`in molecular biology techniques such as PCR and related laboratory procedures.
`
`This could include a person with a Bachelor’s degree in biological or chemical
`
`sciences and at least three years of experience in a laboratory, or a person with
`
`a Master’s degree in biochemical sciences and at least one year of laboratory
`
`experience. I base this opinion on my experience with trained laboratory
`
`technicians and graduate students with Bachelor’s and/or Master’s degrees, who
`
`are aware of the literature and aware of the various available laboratory techniques.
`
`V. Legal Standards
`
`13. The section below sets forth certain legal standards that have been provided
`
`to me by attorneys for LabCorp. I understand that the issues presented in these
`
`inter partes reviews must be considered in view of particular legal standards. I am
`
`not an attorney, however, and I am relying on these legal standards only to guide
`
`my analysis.
`
`14.
`
`I understand that the proposed grounds for institution of IPR2017-02086,
`
`IPR2017-02093, and IPR2017-02095 rely upon allegations that the challenged
`
`claims are anticipated and/or obvious. I further understand that the scope of issues
`
`
`
`7
`
`The Johns Hopkins University Exhibit JHU2001 - Page 7 of 72
`
`
`
`
`
`IPR2017-02086, -02093, -02095
`
`
`
`
`Patent Nos. 6,440,706; 7,824,889; 7,915,015
`Declaration of Fred Russell Kramer, Ph.D.
`
`
`to be considered in an inter partes review are limited to those grounds disclosed
`
`in the Petition, and so I limit my analysis to those grounds.
`
`15.
`
`I understand that, in an inter partes review, claim terms in an unexpired
`
`patent are interpreted according to their broadest reasonable interpretation
`
`consistent with the specification of the patent in which they appear.
`
`16.
`
`I have been informed that a claimed invention is not patentable if it is
`
`anticipated. I understand that a claimed invention is anticipated if each and every
`
`element as set forth in the claimed invention is found, either expressly or
`
`inherently described, in a single prior art reference. I understand that “inherent”
`
`disclosure means that the claim element, although not expressly described by the
`
`prior art reference, must necessarily be present based on the disclosure.
`
`I understand that a mere possibility or even probability that the element is present
`
`is not sufficient to qualify as “inherent disclosure.” Therefore, I understand that
`
`a claim is not anticipated if the single prior art reference does not expressly or
`
`inherently teach each element of the claimed invention. It is my understanding that
`
`to anticipate a claimed invention when the reference is silent as to an alleged
`
`inherent characteristic, the gap in the reference may be filled in by extrinsic
`
`evidence, i.e., evidence outside the disclosure of the reference. Such extrinsic
`
`
`
`8
`
`The Johns Hopkins University Exhibit JHU2001 - Page 8 of 72
`
`
`
`
`
`IPR2017-02086, -02093, -02095
`
`
`
`
`Patent Nos. 6,440,706; 7,824,889; 7,915,015
`Declaration of Fred Russell Kramer, Ph.D.
`
`
`evidence must make clear that the missing descriptive matter is necessarily present
`
`in the described reference.
`
`17.
`
`I also have been informed that a claimed invention is not patentable if it is
`
`obvious. I understand that a claimed invention is obvious if the differences
`
`between the claimed subject matter and the prior art reference or references are
`
`such that the subject matter as a whole would have been obvious to one of ordinary
`
`skill in the art at the time of the invention. I understand that several factual
`
`inquiries underlie a determination of obviousness. These inquiries include (1) the
`
`scope and content of the prior art, (2) the level of ordinary skill in the field of the
`
`invention, (3) the differences between the claimed invention and the prior art, and
`
`(4) any objective evidence of non-obviousness. Such objective evidence of
`
`non-obviousness
`
`include
`
`the
`
`invention’s commercial success, commercial
`
`acquiescence (i.e., licensing), a long felt but unresolved need, the failure of others,
`
`skepticism by experts, praise by others, teaching away by others, recognition of a
`
`problem, laudatory statements by the infringer, and copying of the invention by
`
`competitors.
`
`18.
`
`I have been informed that obviousness is determined by looking at the
`
`claimed subject matter as a whole through the eyes of one of ordinary skill in the
`
`
`
`9
`
`The Johns Hopkins University Exhibit JHU2001 - Page 9 of 72
`
`
`
`
`
`IPR2017-02086, -02093, -02095
`
`
`
`
`Patent Nos. 6,440,706; 7,824,889; 7,915,015
`Declaration of Fred Russell Kramer, Ph.D.
`
`
`art at the time the claimed invention was made. Therefore, it is my understanding
`
`that a claim is not obvious if the combined references fail to disclose or suggest at
`
`least one element of the claim. Further, I understand that a claim is not obvious if
`
`there is no teaching, suggestion, or motivation to combine the references, or some
`
`articulated reasoning with a rational underpinning to support the combination of
`
`the references.
`
`19.
`
`I have further been informed that a claim is not proven obvious by merely
`
`demonstrating that each of the elements was independently known in the prior art.
`
`Most, if not all, inventions rely on building blocks long since uncovered, and
`
`claimed discoveries, almost of necessity will likely be combinations of what is
`
`already known. Thus, I understand that it is important to identify whether a reason
`
`existed at the time of invention that would have prompted a person of ordinary
`
`skill in the art in the relevant field to combine the known elements in the same way
`
`the claimed invention does.
`
`20.
`
`I understand that, in assessing obviousness, one should consider whether the
`
`invention was obvious as of the filing date of the earliest application to which the
`
`patent claims priority without resorting to hindsight. In other words, the patent
`
`claims cannot be used as a roadmap to combine the prior art.
`
`
`
`10
`
`The Johns Hopkins University Exhibit JHU2001 - Page 10 of 72
`
`
`
`IPR2017-02086, -02093, -02095
`
`
`
`
`
`
`Patent Nos. 6,440,706; 7,824,889; 7,915,015
`Declaration of Fred Russell Kramer, Ph.D.
`
`
`21.
`
`I have been informed that dependent claims include all of the limitations of
`
`the independent claim from which they depend. Therefore, it is my understanding
`
`that, if a reference or combination of references fails to properly disclose or
`
`suggest a limitation of an independent claim, they also fail to do so when that
`
`limitation is deemed incorporated into all the dependent claims. Thus, I have been
`
`informed and understand that, if an independent claim is found to be novel and
`
`non-obvious, every claim which depends from the independent claim is also novel
`
`and non-obvious.
`
`VI. Overview of the Claimed Invention
`
`22.
`
`I understand that this declaration is being submitted together with the Patent
`
`Owner’s Preliminary Responses to the petitions for inter partes review regarding
`
`the ’706 patent (IPR2017-02086); the ’889 patent (IPR2017-02093), and the ’015
`
`patent (IPR2017-02095).
`
`23. The technology claimed in the ’706 patent includes methods for determining
`
`the relative abundance of two sequences in a sample. The methods include
`
` (1) diluting the sequences into assay samples, (2) amplifying the sequences,
`
` (3) analyzing the amplified molecules by determining the number of assay
`
`samples of the set that contain one sequence and the number of assay samples of
`
`
`
`11
`
`The Johns Hopkins University Exhibit JHU2001 - Page 11 of 72
`
`
`
`
`
`IPR2017-02086, -02093, -02095
`
`
`
`
`Patent Nos. 6,440,706; 7,824,889; 7,915,015
`Declaration of Fred Russell Kramer, Ph.D.
`
`
`the set that contain the second sequence, and (4) comparing the numbers to
`
`ascertain a ratio that reflects the composition of the sample. See, e.g., ’706 patent
`
`(AMB1001), 2:7-17; AMB1003, 1:24-2:3, 2:12-33.
`
`24. The technology claimed in the ’889 patent includes methods for determining
`
`an allelic imbalance in a biological sample by distributing nucleic acid molecules
`
`to form a set of assay samples, amplifying the template molecules, and analyzing
`
`the amplified molecules to determine a first number of assay samples of the set that
`
`contain a selected genetic sequence on a first chromosome and a second number of
`
`assay samples of the set that contain a reference genetic sequence on a second
`
`chromosome, and comparing the first number to the second number to ascertain an
`
`allelic imbalance. See, e.g., ’889 patent (AMB1001), 2:11-22; AMB1003, 1:22-43.
`
`25. The technology claimed in the ’015 patent includes methods for determining
`
`an allelic imbalance in a biological sample by distributing nucleic acid molecules
`
`to form a set of assay samples, amplifying the template molecules, and analyzing
`
`the amplified molecules to determine a first number of assay samples of the set that
`
`contain a first allelic form of a marker and a second number of assay samples of
`
`the set that contain a second allelic form of the marker, and comparing the first
`
`
`
`12
`
`The Johns Hopkins University Exhibit JHU2001 - Page 12 of 72
`
`
`
`
`
`IPR2017-02086, -02093, -02095
`
`
`
`
`Patent Nos. 6,440,706; 7,824,889; 7,915,015
`Declaration of Fred Russell Kramer, Ph.D.
`
`
`number to the second number to ascertain an allelic imbalance. See, e.g., ’015
`
`patent (AMB1001), 2:11-22; 1:22-2:6, 2:12-28.
`
`VII. General View of the Field
`
`26.
`
`I understand that August 2, 1999 is the earliest U.S. priority date to which
`
`the Patent Owner may claim the ’706,’889, and ’015 patents are entitled.
`
`27. Prior to August 1999, a need existed for molecular diagnostic methods
`
`sensitive enough to detect a mutant nucleic acid sequence among a background of
`
`normal nucleic acid sequences or a subtle allelic imbalance. Such methods were
`
`needed, for example, to detect mutations present during the early stages of cancer
`
`in patient samples. See, for example, references characterizing the art at the time
`
`that digital PCR was invented (Pohl and Shih, Expert Rev. Mol. Diagnostics
`
`(2004), 4:41-47 (JHU2003); and Diehl and Diaz (2007), Curr. Opin. Oncol. 19:36-
`
`42 (JHU2004)). At the time Drs. Vogelstein and Kinzler filed their first patent
`
`application related to digital PCR, DNA sequencing was the preferred technique
`
`for the detection of mutations, but DNA sequencing had substantial shortcomings.
`
`They note, for example, in the Background section of the application, that DNA
`
`sequencing was useful only if the fraction of mutated molecules was greater than
`
`approximately twenty percent of the total. See, e.g., ’706 patent (AMB1001),
`
`
`
`13
`
`The Johns Hopkins University Exhibit JHU2001 - Page 13 of 72
`
`
`
`
`
`IPR2017-02086, -02093, -02095
`
`
`
`
`Patent Nos. 6,440,706; 7,824,889; 7,915,015
`Declaration of Fred Russell Kramer, Ph.D.
`
`
`1:42-45. Other techniques known at the time, e.g., the use of mutant-specific
`
`oligonucleotides or the digestion of polymerase chain reaction (PCR) products
`
`with specific restriction endonucleases, were also problematic. See, e.g., ’706
`
`patent (AMB1001), 1:45-54. The existing methods had widely variable signal-to-
`
`noise ratios that made it difficult to distinguish two different templates. See, e.g.,
`
`’706 patent (AMB1001), 1:42-58. Additionally, the existing methods, although
`
`sensitive, presented problems with quantification of the fraction of mutant
`
`molecules in the starting population. ’706 patent (AMB1001), 1:54-58. I agree
`
`with these observations.
`
`28.
`
`In my opinion, Drs. Vogelstein and Kinzler overcame many of the
`
`limitations of the existing methods by developing a method that could accurately
`
`and quantitatively detect genetic sequences in mixed populations of sequences, and
`
`I disagree with the characterization in the Petitions that the claimed methods were
`
`taught by references disclosing traditional PCR followed by well-known detection
`
`methods to identify mutations and polymorphisms in a gene. Based on my
`
`experience and knowledge, this characterization clearly ignores certain steps
`
`required by the claimed methods of Vogelstein and Kinzler (e.g., the analyzing and
`
`
`
`14
`
`The Johns Hopkins University Exhibit JHU2001 - Page 14 of 72
`
`
`
`
`
`IPR2017-02086, -02093, -02095
`
`
`
`
`Patent Nos. 6,440,706; 7,824,889; 7,915,015
`Declaration of Fred Russell Kramer, Ph.D.
`
`
`comparing steps) and the valuable additional information that these steps provide
`
`as is discussed in detail below.
`
`29.
`
`I also disagree with the characterization in the Petitions that “digital
`
`amplification” or “digital PCR” as disclosed by Drs. Vogelstein and Kinzler was
`
`well known in the art for about a decade prior to the earliest priority date of the
`
`patents at issue. In my experience, these terms have been used more broadly by
`
`different research groups to include limiting dilution PCR, and this alternative
`
`usage has created confusion in the field. As shown by the patents I am addressing
`
`here, digital PCR is a ratiometric assay. See, e.g., ’706 patent (AMB1001),
`
`2:11-17, 2:23-29, 3:35-45, 11:4-24. More specifically, in my opinion, as based on
`
`my knowledge and experience in this field, the extreme sensitivity of the assay is
`
`achieved by using limiting dilution techniques and then determining the ratios of
`
`the different numbers of assay samples in a single set of assay samples that include
`
`individual genetic sequences.
`
`30. Specifically, based on my knowledge and experience in this field, it is far
`
`more accurate when carrying out experiments to determine the relative abundance
`
`of one sequence in a biological sample compared to the abundance of another
`
`sequence in the same sample, to measure the abundance of each sequence in the
`
`
`
`15
`
`The Johns Hopkins University Exhibit JHU2001 - Page 15 of 72
`
`
`
`
`
`IPR2017-02086, -02093, -02095
`
`
`
`
`Patent Nos. 6,440,706; 7,824,889; 7,915,015
`Declaration of Fred Russell Kramer, Ph.D.
`
`
`same experiment utilizing the same methodology, than it is if one method or set of
`
`assay samples is used to determine the abundance of the first sequence and
`
`a different method or different set of assay samples is used to measure the
`
`abundance of the second sequence. In my opinion, a key characteristic that
`
`distinguishes “digital PCR,” as described and claimed by Drs. Vogelstein and
`
`Kinzler, from earlier “limiting dilution PCR” is that Drs. Vogelstein and Kinzler
`
`realized and demonstrated that the simultaneous measurement of the abundance of
`
`two different sequences in the same limiting dilution PCR assay samples
`
`(accomplished by counting the number of assay samples in a set of assay samples
`
`that contain the first sequence and by counting the number of assay samples in the
`
`same set of assay samples that contain the second sequence), followed by a direct
`
`comparison of the abundance of the two different target sequences in the set,
`
`enables a far more accurate determination of the relative abundance of those
`
`sequences than could be determined by the existing prior art. In my opinion, that is
`
`why digital PCR, as invented by Drs. Vogelstein and Kinzler, has been so widely
`
`adopted in the field of molecular diagnostics.
`
`31. The specification states that digital PCR refers to the method’s ability to
`
`convert the intrinsically exponential nature of PCR to a linear one. ’706 patent
`
`
`
`16
`
`The Johns Hopkins University Exhibit JHU2001 - Page 16 of 72
`
`
`
`
`
`IPR2017-02086, -02093, -02095
`
`
`
`
`Patent Nos. 6,440,706; 7,824,889; 7,915,015
`Declaration of Fred Russell Kramer, Ph.D.
`
`
`(AMB1001), 5:34-36. It is my understanding, based on my familiarity with the
`
`field and the literature, that for each target sequence of interest, the method looks
`
`at the products of each assay sample, and for each assay sample it is determined
`
`whether a particular target sequence is present or absent in the assay sample. See,
`
`e.g., ’706 patent (AMB1001), 4:34-44. 4:54-62, 5:4-15. The answer for each assay
`
`sample is either “yes” (i.e., that particular genetic target sequence is present) or
`
`“no” (i.e., that particular target sequence is not present). See, e.g., ’706 patent
`
`(AMB1001), 2:48-51. In my experience, this type of answer is referred to as
`
`a “binary” response, often represented by the digits “1” if the target is present or
`
`“0” if the target is absent. As such, based on my understanding, the origin of the
`
`term “digital PCR” arises from the ability to easily determine the presence or
`
`absence of each particular single target sequence of interest in the assay samples of
`
`the same set.
`
`32. Based on my background and experience, it is my opinion that digital PCR
`
`solved the need for a molecular diagnostic assay that was sufficiently sensitive and
`
`sufficiently specific to identify mutations amongst a large background of normal
`
`cells or nucleic acids. When it was introduced, the power of this new method was
`
`appreciated by those in the field, including myself. For example, Drs. Vogelstein
`
`
`
`17
`
`The Johns Hopkins University Exhibit JHU2001 - Page 17 of 72
`
`
`
`
`
`IPR2017-02086, -02093, -02095
`
`
`
`
`Patent Nos. 6,440,706; 7,824,889; 7,915,015
`Declaration of Fred Russell Kramer, Ph.D.
`
`
`and Kinzler’s scientific publication of digital PCR (1999, PNAS 96:9236-9241)
`
`(JHU2005) has been cited 1,111 times. JHU2006.2 This large number of citations
`
`indicates the significance and transformative nature of digital PCR; it is my
`
`opinion that if the references relied upon by Petitioner had in fact disclosed this
`
`powerful method (in 1992 or 1996), then digital PCR to determine the relative
`
`proportions of two sequences in a biological sample would have been used
`
`throughout the scientific community well before 1999.
`
`33. Digital PCR includes the steps of diluting, amplifying, analyzing, and
`
`comparing, as reflected in the claims of the patents and discussed above. Based on
`
`my knowledge and experience in the field, limiting dilution PCR includes a subset
`
`of those steps but does not include the analyzing and comparing steps. In digital
`
`PCR, amplified molecules in the assay samples of the set (made by limiting
`
`
`2 I determined the number of citations by performing a search for the Vogelstein
`
`and Kinzler PNAS paper using Google Scholar on December 26, 2017 and found
`
`the results at the following website:
`
`https://scholar.google.com/scholar?hl=en&as_sdt=0%2C33&q=vogelstein+kinzler
`
`+digital+pcr&btnG. The search results are shown in JHU2006.
`
`
`
`18
`
`The Johns Hopkins University Exhibit JHU2001 - Page 18 of 72
`
`
`
`
`
`IPR2017-02086, -02093, -02095
`
`
`
`
`Patent Nos. 6,440,706; 7,824,889; 7,915,015
`Declaration of Fred Russell Kramer, Ph.D.
`
`
`dilution) are analyzed to determine a first number of assay samples that contain
`
`the selected genetic sequences (e.g., a mutant sequence) and a second number of
`
`assay samples that contain a reference genetic sequence (e.g., a wild-type genetic
`
`sequence), and the first number is compared to the second number to ascertain
`
`a ratio that reflects the composition of the biological sample or reflects an allelic
`
`imbalance. In my opinion, based on my knowledge and experience in this field,
`
`these aspects are critical to digital PCR, and distinguish digital PCR from limiting
`
`dilution PCR. One of skill in the art would understand that this method requires
`
`that a sufficient number of reliable assay samples be in the set and be analyzed in
`
`order to provide a ratio that accurately reflects the composition of the biological
`
`sample or the allelic imbalance.
`
`VIII. Claim Construction
`
`a. ’706 Patent
`
`34. Claims 1 and 38 of the ’706 patent each recite “to form a set comprising
`
`a plurality of assay samples.” In my opinion, one of skill in the art would interpret
`
`“a plurality of assay samples” to mean two or more assay samples. The term
`
`“plurality” is defined by the Merriam-Webster Dictionary as meaning “the state of
`
`
`
`19
`
`The Johns Hopkins University Exhibit JHU2001 - Page 19 of 72
`
`
`
`
`
`IPR2017-02086, -02093, -02095
`
`
`
`
`Patent Nos. 6,440,706; 7,824,889; 7,915,015
`Declaration of Fred Russell Kramer, Ph.D.
`
`
`being plural,” with “plural” being defined as “more than one.”3 Based on my
`
`background and experience in the field, in the context of the claim as a whole, and
`
`digital PCR as disclosed in the ’706 patent, one of skill in the art would understand
`
`that the particular number of assay samples required for the method would depend
`
`on the composition of the biological sample. That is, analysis of the plurality of
`
`assay samples enables ascertaining a ratio which reflects the composition of the
`
`biological sample. When a particular sequence is rare, a larger number of samples
`
`would be necessary in order to ascertain a ratio that reflects the composition of the
`
`biological sample with any degree of certainty.
`
`35. Claims 1 and 38 of the ’706 patent each recite “assay samples of the set” in
`
`the amplifying step. Based on my experience and knowledge in the field, one of
`
`skill in the art would understand that the assay samples of the set continue to be
`
`part of the set throughout the assay (i.e., including through the amplifying,
`
`
`3 I performed this internet search on December 26, 2017 and found the results at the
`
`following websites: https://www.merriam-webster.com/dictionary/plurality and
`
`https://www.merriam-webster.com/dictionary/plural. The results are shown in
`
`JHU2012.
`
`
`
`20
`
`The Johns Hopkins University Exhibit JHU2001 - Page 20 of 72
`
`
`
`
`
`IPR2017-02086, -02093, -02095
`
`
`
`
`Patent Nos. 6,440,706; 7,824,889; 7,915,015
`Declaration of Fred Russell Kramer, Ph.D.
`
`
`analyzing, and comparing steps). This inclusion in the set continues, regardless of
`
`the physical location or characteristics of the assay samples at the time of each
`
`step. The fact that the assay samples continue to be part of the set throughout the
`
`assay is necessary in order for the final claim step to be meaningful. That is, in
`
`order to ascertain a ratio which reflects the composition of the biological sample,
`
`the set of assay samples must have originated and be analyzed from the same
`
`biological sample.
`
`36. Claims 1 and 38 of the ’706 patent each recite “comparing the first number
`
`to the second number to ascertain a ratio which reflects the composition of the
`
`biological sample,” which refers to comparing the number of assay samples of the
`
`set that contain the “selected genetic sequence” to the number of assay samples of
`
`the set that contain a “reference genetic sequence.” The Petition does not address
`
`the claim language “to ascertain a ratio that reflects the composition of the
`
`biological sample.” In my opinion, the ratio obtained in the comparing step reflects
`
`and relates to the requirements of the remaining steps of the claimed methods.
`
`Specifically, one of skill in the art would understand that generating a ratio that
`
`reflects the composition of target sequences in a biological sample requires
`
`a sufficient number of reliable assay samples in the set, and requires that
`
`
`
`21
`
`The Johns Hopkins University Exhibit JHU2001 - Page 21 of 72
`
`
`
`
`
`IPR2017-02086, -02093, -02095
`
`
`
`
`Patent Nos. 6,440,706; 7,824,889; 7,915,015
`Declaration of Fred Russell Kramer, Ph.D.
`
`
`a sufficient number of the assay samples be analyzed, in order to provide a ratio
`
`that reflects the composition of the biological sample with any degree of certainty.
`
`37. Based on my knowledge and experience, the number of assay samples that
`
`would be sufficient in any given analysis depends on the frequency of the selected
`
`sequence or mutation or the degree of the allelic imbalance in the biological
`
`sample. See also ’706 patent (AMB1001), 4:8-10, 6:9-10. Once the nucleic acid
`
`template molecules from the original biological sample are diluted to such an
`
`extent that many of the assay samples in the set are negative, then the number of
`
`positive samples that are needed depends on the degree of accuracy desired when
`
`determining the relative abundance of the two different target sequences that are
`
`detected by analyzing the positive samples in the set. Generally, the more assay
`
`samples, the greater is the accuracy of the ratio that is determined. Moreover,
`
`if one of the two target sequences is extremely rare compared to the other target
`
`sequence (for example, when comparing the abundance of a rare somatic mutation
`
`that occurs in canc
Accessing this document will incur an additional charge of $.
After purchase, you can access this document again without charge.
Accept $ Charge
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.
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.
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
