`
`
`
`UNITED STATES PATENT AND TRADEMARK OFFICE
`
`_________________________
`
`BEFORE THE PATENT TRIAL AND APPEAL BOARD
`
`_________________________
`
`
`
`MYRIAD GENETICS, INC., MYRIAD GENETIC LABORATORIES, INC.,
`BIO-RAD LABORATORIES, INC., and RAINDANCE TECHNOLOGIES, INC.
`
`Petitioners
`
`v.
`
`THE JOHNS HOPKINS UNIVERSITY
`
`Patent Owner
`
`U.S. Patent No. 7,824,889
`
`_________________________
`
`Case No. To be assigned
`
`_________________________
`
`
`
`DECLARATION OF MICHAEL L. METZKER, PH.D.
`
`
`
`
`
`MYR1002
`Myriad Genetics, Inc. et al. (Petitioners) v. The Johns Hopkins University (Patent Owner)
`IPR For USPN 7,824,889
`
`Page 1 of 184
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`

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`
`
`I.
`
`II.
`
`TABLE OF CONTENTS
`
`Page
`
`OVERVIEW AND SUMMARY OF OPINIONS ........................................... 1
`
`LIST OF DOCUMENTS I CONSIDERED IN FORMULATING MY
`OPINIONS ..................................................................................................... 12
`
`III. PERSON OF ORDINARY SKILL IN THE ART ........................................ 17
`
`IV. STATE OF THE ART BEFORE AUGUST 2, 1999 .................................... 18
`
`V. OVERVIEW OF THE '889 PATENT ........................................................... 22
`
`VI. THE '889 FILE HISTORY AND REEXAMINATION FILE
`HISTORY ...................................................................................................... 29
`
`VII. CLAIM CONSTRUCTION .......................................................................... 33
`
`VIII. BASIS OF MY ANALYSIS WITH RESPECT TO ANTICIPATION ........ 37
`
`IX. BASIS OF MY ANALYSIS WITH RESPECT TO OBVIOUSNESS
`AND OBJECTIVE INDICIA OF NONOBVIOUSNESS ............................ 37
`
`X.
`
`SUMMARY OF GROUNDS ........................................................................ 39
`
`XI. GROUND 1: CLAIMS 1, 5, 8-9, 12-15, AND 18-22 OF THE '889
`PATENT ARE ANTICIPATED BY SIMMONDS ...................................... 40
`
`XII. GROUND 2: CLAIMS 16-17 OF THE '889 PATENT WOULD
`HAVE BEEN OBVIOUS IN VIEW OF SIMMONDS COMBINED
`WITH BROWN ............................................................................................. 91
`
`XIII. GROUND 3: CLAIMS 4, 6 AND 7 OF THE '889 PATENT WOULD
`HAVE BEEN OBVIOUS IN VIEW OF SIMMONDS COMBINED
`WITH HEID ................................................................................................ 103
`
`XIV. GROUND 4: CLAIMS 1, 5, 8-9, 12-15, AND 18-22 OF THE '889
`PATENT ARE ANTICIPATED BY SYKES ............................................. 114
`
`XV. GROUND 5: CLAIMS 16-17 OF THE '889 PATENT WOULD
`HAVE BEEN OBVIOUS IN VIEW OF SYKES COMBINED WITH
`BROWN....................................................................................................... 157
`
`
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`Page 2 of 184
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`XVI. GROUND 6: CLAIMS 4, 6, AND 7 OF THE '889 PATENT
`WOULD HAVE BEEN OBVIOUS IN VIEW OF SYKES
`COMBINED WITH HEID .......................................................................... 167
`
`XVII. OBJECTIVE INDICIA OF NON-OBVIOUSNESS ................................... 174
`
`XVIII.CONCLUSION ........................................................................................... 179
`
`
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`Page 3 of 184
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`Inter Partes Review of USPN 7,824,889
`Declaration of Michael L. Metzker, Ph.D.
`
`I, Michael Metzker, hereby declare as follows.
`
`1.
`
`I am over the age of eighteen (18) and otherwise competent to make
`
`this declaration.
`
`2.
`
`I have been retained as an expert witness on behalf of Myriad
`
`Genetics, Inc., Myriad Genetic Laboratories, Inc. (together, "Myriad"), Bio-Rad
`
`Laboratories, Inc., and RainDance Technologies, Inc. in connection with the
`
`above-captioned requested inter partes review ("IPR"). I am being compensated
`
`for my time in connection with this IPR at my standard consulting rate, which is
`
`$750 per hour.
`
`I.
`
`OVERVIEW AND SUMMARY OF OPINIONS
`
`3.
`
`I understand that a petition for inter partes review has been filed
`
`regarding U.S. Patent No. 7,824,889 ("the '889 Patent") (MYR1001), which
`
`resulted from U.S. Application No. 11/709,742 ("the '742 Application"), filed on
`
`February 23, 2007, naming Bert Vogelstein and Kenneth W. Kinzler as inventors.
`
`I understand that the petition for inter partes review challenges claims 1, 4-9, and
`
`12-22 of the '889 Patent as anticipated and/or obvious.
`
`4.
`
` The '889 Patent originally issued on November 2, 2010, from the '742
`
`application.
`
` The USPTO subsequently granted a petition for ex parte
`
`reexamination of the '889 Patent, finding substantial new questions of patentability
`
`for 22 claims. To overcome rejections over multiple prior art references during ex
`
`
`
`1
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`
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`parte reexamination, a number of claims of the '889 Patent were amended. The
`
`Inter Partes Review of USPN 7,824,889
`Declaration of Michael L. Metzker, Ph.D.
`
`reexamination certificate issued October 31, 2014.
`
`5.
`
`I note that although certain of the prior art that I discuss in this
`
`declaration as invalidating the '889 Patent (e.g., Simmonds, Sykes, as defined
`
`below) was technically before the USPTO during the ex parte reexamination
`
`proceedings, the proceedings focused on different art and on different arguments
`
`from those that I advance below. See Simmonds, 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 (1990)
`
`("Simmonds") (MYR1012); Sykes et al., Quantitation of targets for PCR by use of
`
`limiting dilution. BIOTECHNIQUES 13:444-449 (1992) ("Sykes") (MYR1013).
`
`6.
`
`In particular, the ex parte reexamination proceedings focused on prior
`
`art involving distribution of single cells into compartments, rather than on
`
`distribution of isolated nucleic acids, and was overcome on that basis. The claims
`
`were amended to specify that the method involves "isolated" or "cell-free" nucleic
`
`acids rather than whole cells, in light of this art. MYR1008. While these
`
`amendments addressed the prior art discussed during the ex parte reexamination,
`
`they did nothing to address the Mullis chapter or other prior art references
`
`discussed in this petition for inter partes review. The prior art that I rely on here
`
`was never discussed by the USPTO during the ex parte reexamination proceedings
`
`
`
`2
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`and cannot be distinguished by any single cell versus isolated nucleic acid
`
`Inter Partes Review of USPN 7,824,889
`Declaration of Michael L. Metzker, Ph.D.
`
`argument.
`
`7.
`
`I further understand that the '889 Patent is currently assigned to The
`
`Johns Hopkins University ("the Patentee"). MYR1031, ¶14.
`
`8.
`
`I understand that the earliest possible priority date for the '889 Patent
`
`is August 2, 1999, the filing date of provisional application no. 60/146,792 ("the
`
`'792 Provisional") (MYR1011). I have seen no evidence to suggest that any claim
`
`of the '889 Patent should get the benefit of an earlier priority date. I am also not
`
`aware of any claim by Patent Owner to an earlier priority date that would change
`
`any of my opinions set forth in this declaration. I reserve the right to respond with
`
`specificity if the Patentee alleges an earlier priority date.
`
`9.
`
`In preparing this Declaration, I have reviewed the '889 Patent, its file
`
`history (MYR1005), its reexamination file history (MYR1009), and the '792
`
`Provisional and considered each of the documents cited herein, in light of general
`
`knowledge in the art (i.e., field) before August 2, 1999. In formulating my
`
`opinions, I have relied upon my more than 30 years' experience, education, and
`
`knowledge in the relevant art. In formulating my opinions, I have also considered
`
`the viewpoint of one of ordinary skill in the art before August 2, 1999. A summary
`
`of my opinions follows.
`
`
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`3
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`10. The technology disclosed in the '889 Patent is a method that the Patent
`
`Inter Partes Review of USPN 7,824,889
`Declaration of Michael L. Metzker, Ph.D.
`
`Owner calls "digital PCR." This method involves distributing a DNA sample into
`
`assay samples (i.e., compartments) such that each compartment contains, ideally,
`
`one or zero molecules of DNA from the sample, carrying out PCR in each
`
`compartment, and then analyzing the resulting amplified DNA molecules to
`
`determine how many compartments contain each different template DNA
`
`molecule. The figure below shows the basic steps of the method, which involve
`
`distributing a DNA sample into compartments such that each compartment
`
`contains, ideally, one or zero molecules of DNA from the sample, carrying out
`
`PCR in each compartment, and then analyzing the resulting amplified DNA
`
`molecules, to determine how many compartments contain each different template
`
`DNA molecule:
`
`Baker, Digital PCR hits its stride. NATURE METHODS 9:541-544 (2012) ("Baker
`
`
`
`2012") (MYR1018)
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`4
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`Inter Partes Review of USPN 7,824,889
`Declaration of Michael L. Metzker, Ph.D.
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`11. The steps comprising what the patent Owner calls "digital PCR" were
`
`well known in the art before the earliest possible priority date for the '889 patent.1
`
`In the prior art, this method was often called "limiting dilution analysis" or
`
`"limiting dilution PCR" ("LDPCR") because the sample is diluted down to the
`
`point at which some compartments will be "positive," i.e., contain a PCR-amplified
`
`product, and some will be "negative," i.e., contain no PCR-amplified product. For
`
`LDPCR, terms such as "assay samples," "replicates," "compartments," "sample
`
`chambers," "wells," or "microreactors" all represent the same functional element –
`
`a separate space where a diluted single template molecule can undergo PCR
`
`without cross-contamination, and produce pure or homogeneous amplified product.
`
`Id. MYR1002, ¶11.
`
`12. The prior art discloses performing "multiple replicates at serial
`
`dilutions" of the original sample. As I explain below, the phrase "multiple
`
`replicates at serial dilutions" is just another way of saying dilute and distribute
`
`
`1 The earliest application to which the '889 patent claims priority is provisional
`
`application 60/146,792, filed 8/2/1999. MYR1011. Given that, I rely almost
`
`exclusively on prior art under 35 U.SC. §102(b), and I am not aware of any claim
`
`to an earlier priority date that would affect any of the arguments set forth herein. I
`
`reserve the right to respond should Patent Owner allege an earlier priority date.
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`samples into compartments such that each compartment contains very few
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`Inter Partes Review of USPN 7,824,889
`Declaration of Michael L. Metzker, Ph.D.
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`template molecules, preferably, one or zero.
`
`13. First, a particular sample is serially diluted, for example, 1:10, 1:100,
`
`1:1000, and so on. Then, replicates of each dilution are made – meaning that each
`
`dilution is distributed into a number of compartments or reaction wells (each
`
`compartment or well is a "replicate" of the original dilution). PCR is then
`
`performed on each replicate to amplify the template sequence(s) in the original
`
`sample, if present. When the sample is so dilute that it is at the "limit of dilution,"
`
`most of the replicates will contain either one or zero template molecules. As a
`
`result, some of the replicates will give rise to a PCR product and some will not –
`
`some of the replicates will be "positive" and some will be "negative."
`
`14. At this point, the replicates can be analyzed in different ways. The
`
`number of positive replicates containing amplified copies of the first template can
`
`be counted and compared to the number of positive replicates containing amplified
`
`copies of the second template, to determine a ratio of the two, for example. Also,
`
`Poisson statistics can be used to analyze the replicates – these statistics allow the
`
`number of template molecules in the original sample to be derived from the
`
`numbers of "positive" and "negative" replicates.
`
`15. By 1994, Kary Mullis, the Nobel Prize winning inventor of PCR, had
`
`edited a book on PCR (MYR1014) that included a chapter on quantitative PCR, the
`
`
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`6
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`Inter Partes Review of USPN 7,824,889
`Declaration of Michael L. Metzker, Ph.D.
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`use of PCR to quantitate amounts of nucleic acids in a sample. Chapter 6 of PCR:
`
`The Polymerase Chain Reaction 67-88, Kary B. Mullis, Francois Ferre, and
`
`Richard A. Gibbs Eds. (1994) ("the Mullis chapter") (MYR1014). The Mullis
`
`chapter discloses and discusses the work of multiple groups of scientists at the time
`
`who were carrying out and publishing work involving LDPCR. A common feature
`
`of this work is that it involved diluting and distributing nucleic acids down to the
`
`single molecule level in assay samples or compartments, amplifying the single
`
`molecule templates using PCR, and counting or otherwise analyzing the amplified
`
`templates in the assay samples or compartments. As the Mullis chapter disclosed
`
`in 1994:
`
`The principle of limiting dilution can also be called on to achieve
`
`absolute DNA quantitation. It is based on the use of a qualitative all-
`
`or-none endpoint and on the premise that one or more targets in the
`
`reaction mixture give rise to a positive endpoint. . . . Accurate
`
`quantitation can be achieved by performing multiple replicates at
`
`serial dilutions of the material to be assayed (Simmonds, 1990; Lee
`
`et al. 1990; Sykes et al. 1992). At the limit of dilution, where some
`
`end points are positive and some are negative, the number of targets
`
`present can be calculated from the proportion of negative endpoints by
`
`using Poisson statistics. . . . This method quantitates the total number
`
`of initial DNA targets present in a sample. In this type of quantitative
`
`format, it is mandatory that PCR be optimized so that reliable
`
`detection of one or a few DNA targets occurs. Therefore, as long as
`
`
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`Inter Partes Review of USPN 7,824,889
`Declaration of Michael L. Metzker, Ph.D.
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`the one copy level still gives a positive signal, the quantitation is not
`
`dependent on the amplification efficiency. This represents a major
`
`advantage of this PCR format.
`
`MYR1014, 78.
`
`16. As the Mullis chapter discloses, multiple groups of scientists,
`
`including Simmonds et al., "Human Immunodeficiency Virus-Infected Individuals
`
`Contain Provirus in Small Numbers of Peripheral Mononuclear Cells and at Low
`
`Copy Numbers," J. Virol. Vol. 64 (2): 864-872 (1990) ("Simmonds") (MYR1012)
`
`and Sykes et al., "Quantitation of Targets for PCR by Use of Limiting Dilution,"
`
`BioTechniques Vol. 13(3): 444-449 (1992) ("Sykes")(MYR1013) – authors of two
`
`prior art references discussed in detail below – were carrying out LDPCR and
`
`publishing the results of their work prior to the earliest possible priority date for
`
`the '889 patent.
`
`17. Some five years after publication of the Mullis chapter, two professors
`
`and named co-inventors working Patent Owner, Vogelstein and Kinzler, published
`
`a paper in PNAS (MYR1017) in which they disclosed the steps of what they called
`
`"digital PCR." Vogelstein et al., "Digital PCR," Proc. Natl. Acad. Sci. USA Vol.
`
`96:9236-9241 (August 1999). Notably, while much of this paper is reproduced in
`
`the specification of the USPN 6,440,706 patent ("the '706 Patent"), which the '889
`
`patent incorporates by reference, there is one important difference. The PNAS
`
`paper stated that "there are several precedents for the approach described here."
`
`
`
`8
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`Inter Partes Review of USPN 7,824,889
`Declaration of Michael L. Metzker, Ph.D.
`
`MYR1017, 9239 (emphasis added). In the applications filed with the USPTO to
`
`which the '889 patent claims priority, however, Patent Owner abandoned the
`
`candor of the PNAS paper and did not include the statement regarding the
`
`existence of "several precedents."
`
`18. As the PNAS paper admits, there were "several precedents" to Patent
`
`Owner's claimed "digital PCR." The Mullis chapter and cited reference s confirm
`
`the existence of such precedents beyond any reasonable dispute. Every claim of
`
`the '889 patent for which inter partes review is sought is invalid as anticipated
`
`and/or obvious over these precedents.
`
`19. Although the inventors of the '889 Patent did not invent LDPCR, they
`
`appear to have coined the term "digital PCR" to disclose LDPCR. They appear to
`
`have derived the name digital PCR from the particular flavor of LDPCR they
`
`disclose in the '889 Patent, and the '706 Patent which the '889 Patent incorporates
`
`by reference– which involves using a particular type of fluorescent probes
`
`("molecular beacon" probes) to analyze the replicates made at limiting dilution,
`
`after PCR has been performed on each replicate. Using these molecular beacon
`
`probes, the '706 Patent states that replicates containing a wild-type sequence will
`
`fluoresce green, while those containing a mutant or wild-type sequence will
`
`fluoresce red. MYR1001, 3:1-4. The '706 Patent suggests that this green and red
`
`fluorescence technique, when used with 96 well plates, for example, could provide
`
`
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`Inter Partes Review of USPN 7,824,889
`Declaration of Michael L. Metzker, Ph.D.
`
`a "digital readout" to evaluate the results of the LDPCR. MYR1001, 4:9-12. I
`
`note that the claims relating to this particular molecular beacon technique are not at
`
`issue in this IPR, and I have not formulated an opinion as to whether or not the use
`
`of molecular beacon probes as an analytical tool to be combined with LDPCR was
`
`novel or nonobvious as of August 2, 1999. Every claim at issue in this IPR relates
`
`to the general LDPCR technique and does not disclose or claim the use of
`
`molecular beacon probes
`
`20. Claims 1, 5, 8-9, 12-15, and 18-22 of the '889 Patent are anticipated
`
`by the disclosures of Simmonds, which discloses every limitation of these claims.
`
`Simmonds describes using LDPCR to quantitate and analyze different HIV isolates
`
`from patients' blood samples. Simmonds discloses a "dilution and distribution
`
`method," which permits "separate amplification of individual molecules from a
`
`mixture after dilution and distribution." MYR1012 at 871 and 867, respectively.
`
`Simmonds discloses starting with a mixture of two isolated nucleic acid sequences
`
`(selected and reference), diluting these sequences down to the single molecule
`
`level, and distributing them to form a set of assay samples, most of which contain
`
`either a single molecule of template or no template molecule. MYR1012, 867.
`
`Simmonds further discloses amplifying the template molecules in these assay
`
`samples using PCR, and then analyzing the amplified molecules in these assay
`
`samples to determine a first number of assay samples that contains one sequence,
`
`
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`10
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`Inter Partes Review of USPN 7,824,889
`Declaration of Michael L. Metzker, Ph.D.
`
`and a second number of assay samples that contains a second sequence.
`
`Simmonds further discloses comparing the first number to the second number to
`
`ascertain a ratio that reflects the composition of the biological sample. Simmonds
`
`also discloses analyzing the PCR-amplified products by sequencing.
`
`21. To the extent any claim of the '889 Patent is not anticipated by the
`
`disclosures of Simmonds, it is rendered obvious by the combination of Simmonds
`
`with U.S. Patent No. 6,143,496 ("Brown") (MYR1015), or Heid et al., Real time
`
`quantitative PCR. GENOME RESEARCH 6:986-994 (1996) ("Heid") (MYR1024). In
`
`particular, Claims 16-17 of the '889 Patent are rendered obvious by the
`
`combination of Simmonds with Brown, and Claims 4 and 6-7 of the '889 Patent are
`
`rendered obvious by the combination of Simmonds with Heid.
`
`22. Claims 1, 5, 8-9, 12-15, and 18-22 of the '889 Patent are also
`
`anticipated by the disclosures of Sykes, which discloses every limitation of these
`
`claims. Sykes discloses using LDPCR to quantitate and analyze subpopulations of
`
`leukemic cells in a background of non-leukemic cells. Sykes discloses a "general
`
`method to quantitate the total number of initial targets present in a sample using
`
`limiting dilution, PCR, and Poisson statistics." MYR1013, 444. Sykes discloses
`
`"using the rearranged immunoglobulin heavy chain (IgH) gene as target DNA in
`
`the PCR to study patients with acute lymphoblastic leukemia (ALL) in order to
`
`detect and quantitate a minor population of leukemic cells within a larger
`
`
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`11
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`Inter Partes Review of USPN 7,824,889
`Declaration of Michael L. Metzker, Ph.D.
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`population of normal lymphoid and non-lymphoid cells." Id . Sykes further
`
`discloses creating replicate samples at limiting dilutions, amplifying the template
`
`molecules in these assay samples using PCR, and then analyzing the amplified
`
`molecules in these assay samples to determine a first number of assay samples that
`
`contains one sequence, and a second number of assay samples that contains a
`
`second sequence. MYR1013, abstract, 444, 446-7, 448. Sykes further discloses
`
`comparing the first number to the second number to ascertain a ratio that reflects
`
`the composition of the biological sample. Id.
`
`a. My Background And Qualifications
`
`23.
`
`I am an expert in the fields of molecular biology and genome
`
`research. I have been an expert in these fields since well before 1999.
`
`24. A list of my publications and presentations is found in my curriculum
`
`vitae. MYR1003.
`
`25.
`
`In view of my education, experience, and expertise described above, I
`
`am an expert in these fields of molecular biology and genome research.
`
`II.
`
`LIST OF DOCUMENTS I CONSIDERED IN FORMULATING MY
`OPINIONS
`
`26.
`
`In formulating my opinions, I considered all of the references cited in
`
`this Declaration, including the documents listed below.
`
`Myriad Exhibit
`Number
`
`Description
`
`
`
`12
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`
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`Myriad Exhibit
`Number
`
`Description
`
`Inter Partes Review of USPN 7,824,889
`Declaration of Michael L. Metzker, Ph.D.
`
`1001
`
`1002
`
`1003
`
`1004
`
`1005
`
`1006
`
`1007
`
`1008
`
`1009
`
`1010
`
`1011
`
`1012
`
`1013
`
`1014
`
`
`
`Vogelstein et al., "Digital Amplification," U.S. Patent
`No.7,824,889 (filed on Feb. 23, 2007, issued on Nov. 2,
`2010, Ex Parte Reexamination Certificate Issued: October
`31, 2014)
`
`Declaration of Michael L. Metzker, Ph.D.
`
`Curriculum Vitae of Michael L. Metzker, Ph.D.
`
`File History for U.S. Patent No. 6,440,706
`
`File History for U.S. Patent No. 7,824,889
`
`File History for U.S. Patent No. 7,915,015
`
`File History for U.S. Patent No. 8,859,206
`
`Ex Parte Reexamination File History for U.S. Patent No.
`6,440,706
`
`Ex Parte Reexamination File History for U.S. Patent No.
`7,824,889
`
`Ex Parte Reexamination File History for U.S. Patent No.
`7,915,015
`
`U.S. Provisional Patent Application No 60/146,792 (Filed:
`August 2, 1999)
`
`Simmonds et al., Human Immunodeficiency Virus-Infected
`Individuals Contain Provirus in Small Numbers of
`Peripheral Mononuclear Cells and at Low Copy Numbers,
`JOURNAL OF VIROLOGY 64 (2): 864-872 (1990)
`
`Sykes et al., Quantitation of Targets for PCR by Use of
`Limiting Dilution, BIOTECHNIQUES 13(3): 444-449 (1992)
`
`Chapter 6 of PCR: The Polymerase Chain Reaction 67-88,
`Kary B. Mullis, Francois Ferre, and Richard A. Gibbs Eds.
`(1994)
`
`13
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`
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`Myriad Exhibit
`Number
`
`1015
`
`1016
`
`1017
`
`1018
`
`1019
`
`1020
`
`1021
`
`1022
`
`1023
`
`Inter Partes Review of USPN 7,824,889
`Declaration of Michael L. Metzker, Ph.D.
`
`Description
`
`Brown et al., "Method Of Sampling, Amplifying And
`Quantifying Segment Of Nucleic Acid, Polymerase Chain
`Reaction Assembly Having Nanoliter-Sized Sample
`Chambers, And Method Of Filling Assembly," U.S. Patent
`No. 6,143,496 (filed on April 17, 1997, issued on November
`7, 2000)
`
`Kellogg et al., TaqStart Antibody: 'Hot Start' PCR
`Facilitated by a Neutralizing Monoclonal Antibody Directed
`Against Taq DNA Polymerase, BIOTECHNIQUES 16 (6):1134-
`1136 (1994)
`
`Vogelstein et al., Digital PCR, PROCEEDINGS OF THE
`NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES
`96:9236-9241 (1999)
`
`Monya Baker, Digital PCR hits its stride, NATURE METHODS
`9 (6):541-544 (2012)
`
`Wei et al., Viral dynamics in human immunodeficiency virus
`type 1 infection, NATURE 373:117-122 (1995)
`
`Ho et al., Rapid turnover of plasma virions and CD4
`lymphocyte in HIV-1 infection, NATURE 373:123-126 (1995)
`
`Coffin, HIV population dynamics in vivo: Implications for
`genetic variation, pathogenesis and therapy, SCIENCE
`267:483-489 (1995)
`
`Perelson et al., HIV-1 dynamics in vivo: virion clearance
`rate, infected cell life-span, and viral generation time,
`SCIENCE, 271:1582-1586 (1996)
`
`Amneal Pharmaceuticals, LLC v. Supernus Pharmaceuticals,
`Inc., IPR2013-00368, Paper No. 8 at 13 (December 17,
`2013)
`
`
`
`14
`
`
`
`Page 17 of 184
`
`

`

`Myriad Exhibit
`Number
`
`Description
`
`Inter Partes Review of USPN 7,824,889
`Declaration of Michael L. Metzker, Ph.D.
`
`1024
`
`1025
`
`1026
`
`1027
`
`1028
`
`1029
`
`1030
`
`1031
`
`Heid et al., Real time quantitative PCR, GENOME RESEARCH
`6:986-994 (1996)
`
`Carteau et al., Chromosome structure and human
`immunodeficiency virus type 1 cDNA integration:
`Centromeric alphoid repeats are a disfavored target,
`JOURNAL OF IMMUNOLOGY 72:4005-4014 (1998)
`
`Ruano et al., Haplotype of multiple polymorphisms resolved
`by enzymatic amplification of single DNA molecules,
`PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF
`THE UNITED STATES 87:6296-6300 (1990)
`
`Sykes et al., Limiting dilution polymerase chain reaction,
`chapter 8 of Reverse Transcriptase PCR, Larrick and Siebert,
`Eds. (1995)
`
`Birch et al., "Nucleic Acid Amplification Using A Reersibly
`(sic) Inactivated Thermostable Enzyme," U.S. Patent No.
`5,677,152 (filed on July 19, 1996, issued on October 14,
`1997)
`
`Birch et al., "Nucleic Acid Amplification Using A
`Reversibly Inactivated Thermostable Enzyme," U.S. Patent
`No. 5,773,258 (filed on July 11, 1996, issued on June 30,
`1998)
`
`Andrew Leigh Brown and Peter Simmonds, Sequence
`analysis of virus variability based on the poymerase (sic)
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`Approach, Jonathan Karn, Ed. (1995)
`
`Complaint, Esoterix Genetic Laboratories, LLC and The
`Johns Hopkins University v. Myriad Genetics, Inc. et al., 16-
`cv-1112, D.I. 1 (M.D.N.C. Sept. 7, 2016)
`
`
`
`15
`
`
`
`Page 18 of 184
`
`

`

`Myriad Exhibit
`Number
`
`Description
`
`Inter Partes Review of USPN 7,824,889
`Declaration of Michael L. Metzker, Ph.D.
`
`1032
`
`1033
`
`1034
`
`1035
`
`1036
`
`1037
`
`1038
`
`1039
`
`1040
`
`1041
`
`Supplemental Joint Claim Construction Statement, Esoterix
`Genetic Laboratories, LLC and The Johns Hopkins
`University v. Life Technologies Corporation et al., 12-cv-
`1173-CCE-JEP, D.I. 71 (M.D.N.C. Oct. 29, 2013)
`
`Plaintiffs’ Opening Claim Construction Brief, Esoterix
`Genetic Laboratories, LLC and The Johns Hopkins
`University v. Life Technologies Corporation et al., 12-cv-
`1173-CCE-JEP, D.I. 78 (M.D.N.C. Nov. 5, 2013)
`
`'706 Patent File History Excerpt (response to rejection over
`Ruano) [Response to Office Action, July 12, 2001]
`
`'706 Patent Reexamination File History Excerpt (response to
`rejections adding “isolated”) [Response to Final Office
`Action, 7/9/2014]
`
`'206 File History Excerpt (rejection over Ruano)[Final Office
`Action, 6/27/2013]
`
`'206 File History Excerpt (response to rejection over Ruano)
`[Response to Final Office Action, 9/25/2013]
`
`'206 File History Excerpt (response to rejection over
`Simmonds) [Office Action, 10/10/2012]
`
`'206 File History Excerpt (response to rejection over
`Simmonds) [Response to Office Action, 3/11/2013]
`
`Myriad Answer, Affirmative Defenses, and Counterclaims,
`Esoterix Genetic Laboratories, LLC and The Johns Hopkins
`University v. Myriad Genetics, Inc. et al., 16-cv-1112, D.I.
`22 (M.D.N.C. Nov. 2, 2016)
`
`Zimmermann et al., Digital PCR: a powerful new tool for
`noninvasive prenatal diagnosis? PRENATAL DIAGNOSIS
`28:1087-1093 (2008)
`
`
`
`16
`
`
`
`Page 19 of 184
`
`

`

`Myriad Exhibit
`Number
`
`Description
`
`Inter Partes Review of USPN 7,824,889
`Declaration of Michael L. Metzker, Ph.D.
`
`1042
`
`1043
`
`1044
`
`1045
`
`1046
`
`1047
`
`'706 Patent Reexamination File History Excerpt (Lapidus
`Declaration) [Response to Office Action, 9/9/2014]
`
`'706 Patent Reexamination File History Excerpt (Shi
`Declaration) [Response to Office Action, 9/9/2014]
`
`'889 Patent File History Excerpt (response to double
`patenting rejection) (Response to Office Action, 4/22/2009]
`
`'015 Patent File History Excerpt (response to double
`patenting rejection) [Response to Office Action, 10/6/2010]
`
`'015 Patent Reexamination File History Excerpt (response to
`rejections adding “isolated”) [Response to Final Office
`Action, 7/9/2014]
`
`Birch et al., Simplified hot start PCR, NATURE 381:445-446
`(1996)
`
`
`III. PERSON OF ORDINARY SKILL IN THE ART
`
`27. A person of ordinary skill in the art ("POSA" or "one of ordinary skill
`
`in the art") is a hypothetical person who is presumed to be aware of all pertinent
`
`art, thinks along the lines of the conventional wisdom in the art, and is a person of
`
`ordinary creativity. As of August 2, 1999, a POSA in the technical field of the '889
`
`Patent – molecular biology – would have had knowledge of the scientific literature
`
`concerning methods of DNA manipulation and analysis, including amplification
`
`(e.g., PCR), dilution and distribution, including down to the single molecule level
`
`and using techniques such as LDPCR, and methods of nucleic acid analysis (e.g.,
`
`gel electrophoresis, detecting certain sequences using hybridization probes,
`
`
`
`17
`
`
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`Page 20 of 184
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`

`

`quantitating specific sequences in a mixture of different nucleic acids, using
`
`Inter Partes Review of USPN 7,824,889
`Declaration of Michael L. Metzker, Ph.D.
`
`Poisson statistics for DNA quantitation, or sequencing).
`
`28. As of August 2, 1999, a POSA would typically have had (1) a M.D.
`
`degree or a Ph.D. degree in molecular biology, molecular genetics, biology or
`
`equivalent discipline, plus at least two years' experience in a laboratory working in
`
`the field of molecular biology techniques, including in quantitative amplification
`
`techniques, detection, and analysis; (2) a Master's degree in molecular biology,
`
`molecular genetics, biology or equivalent discipline, plus at least five years'
`
`experience in the laboratory working in the field of molecular biology techniques,
`
`including in quantitative amplification techniques, detection, and analysis.
`
`IV. STATE OF THE ART BEFORE AUGUST 2, 1999
`
`29.
`
`I understand that the
`
`'889 Patent claims priority to the
`
`'792
`
`Provisional, which was filed August 2, 1999. MYR1001, 1:3-4. For purposes of
`
`my invalidity analyses below, I have considered the relevant date to be August 2,
`
`1999.
`
`30.
`
`It was recognized long before August 2, 1999 that PCR was a
`
`powerful tool for quantitation of DNA – in particular, absolute quantitation of
`
`DNA, meaning the quantitation of DNA without using an internal standard. The
`
`key development that took place in the late 1980s and early 1990s, was the
`
`realization that some of the potential pitfalls of PCR – biased amplification of
`
`
`
`18
`
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`Page 21 of 184
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`

`

`Inter Partes Review of USPN 7,824,889
`Declaration of Michael L. Metzker, Ph.D.
`
`certain sequences over others and artifacts that arose from using multiple different
`
`pairs of primers in a single reaction – could be avoided through the use of dilution
`
`and distribution, followed by parallel, compartmentalized PCR reactions, each
`
`containing a single molecule of template and a single primer pair. As stated in the
`
`Mullis chapter:
`
`With its impressive sensitivity and specificity set aside, PCR
`
`technology does not seem to be poised to conduct quantitative
`
`analyses. The amplification process, which is exponential and thus
`
`potentially difficult to control, is the natural suspect for anyone
`
`dubious about the quantitative ability of PCR and rightfully so.
`
`Therefore, why is PCR so widely used to quantitate nucleic acids? . . .
`
`we will entertain the concept of absolute quantitation using PCR.
`
`MYR1014, 68.
`
`31. As I discuss above, in the section on absolute quantitation using PCR,
`
`the Mullis chapter discloses the work of the various groups carrying out LDPCR.
`
`32. As the Mullis chapter demonstrates, multiple research groups were
`
`carrying out and publishing LDPCR at least as early as the late 1980s and early
`
`1990s. The Mullis chapter references Simmonds and Sykes i