IN THE UNITED STATES PATENT AND TRADEMARK OFFICE
`
`Patent of Jingyue Ju. et al.
`In Re:
`Patent No.: 7,790,869
`Appl. No.: 11/810,509
`Issue Date: September 7, 2010
`For:
`MASSIVE PARALLEL METHOD FOR DECODING DNA
`AND RNA
`
`Mail Stop PATENT BOARD
`Patent Trial and Appeal Board
`United States Patent and Trademark Office
`P.O. Box 1450
`Alexandria, VA 22313-1450
`
`DECLARATION OF GEORGE WEINSTOCK UNDER RULE 37 C.F.R. §
`1.132
`
`I, George Weinstock, declare as follows:
`
`1.
`
`I have been retained by the firm of Reinhart Boerner Van
`
`Deuren s.c., who represent Illumina Incorporated (“Illumina”) in this proceeding,
`
`as an expert regarding technical issues in this proceeding. My curriculum vitae is
`
`attached as Exhibit A, which includes all publications I have authored in the
`
`previous 10 years.
`
`2.
`
`Illumina has requested I provide my opinion of the validity of
`
`claims 12-13, 15-17, 20-26, 28, 31, and 33 of U.S. Patent No. 7,790,869 to Jingyue
`
`Ju. et al. ("the '869 patent") in light of prior art in the field. In forming my opinion,
`
`Columbia Ex. 2040
`Illumina, Inc. v. The Trustees
`Illumina, Inc.
`of Columbia University
`Exhibit No. 1021
`in the City of New York
`IPR2020-01177
`Page 1
`
`
`
`Patent of Jingyue Ju. et al.
`In Re:
`Patent No.: 7,790,869
`Appl. No.: 11/810,509
`Issue Date: September 7, 2010
`For:
`MASSIVE PARALLEL METHOD FOR DECODING DNA
`AND RNA
`
`Mail Stop PATENT BOARD
`Patent Trial and Appeal Board
`United States Patent and Trademark Office
`P.O. Box 1450
`Alexandria, VA 22313-1450
`
`DECLARATION OF GEORGE WEINSTOCK UNDER RULE 37 C.F.R. §
`1.132
`
`I, George Weinstock, declare as follows:
`
`1.
`
`I have been retained by the firm of Reinhart Boerner Van
`
`Deuren s.c., who represent Illumina Incorporated (“Illumina”) in this proceeding,
`
`as an expert regarding technical issues in this proceeding. My curriculum vitae is
`
`attached as Exhibit A, which includes all publications I have authored in the
`
`previous 10 years.
`
`2.
`
`Illumina has requested I provide my opinion of the validity of
`
`claims 12-13, 15-17, 20-26, 28, 31, and 33 of U.S. Patent No. 7,790,869 to Jingyue
`
`Ju. et al. ("the '869 patent") in light of prior art in the field. In forming my opinion,
`
`Columbia Ex. 2040
`Illumina, Inc. v. The Trustees
`Illumina, Inc.
`of Columbia University
`Exhibit No. 1021
`in the City of New York
`IPR2020-01177
`Page 1
`
`
`
`I have relied on my own experience and have studied the '869 patent and the
`
`patents and references identified in this declaration.
`
`QUALIFICATIONS
`
`3.
`
`I am Associate Director of The Genome Institute at Washington
`
`University School of Medicine in St. Louis Missouri, where I am also a Professor
`
`of Genetics and a Professor of Molecular Microbiology.
`
`4.
`
`I received a Bachelor‘s degree in Biophysics in 1970 from the
`
`University of Michigan. I was a PHS predoctoral Trainee in the Department of
`
`Biology at the Massachusetts Institute of Technology in Cambridge, Massachusetts
`
`from 1970 until 1977. I received my Ph.D. in Microbiology from the
`
`Massachusetts Institute of Technology in 1977. My doctoral research was on the
`
`subject of bacteriophage P22 and translocatable elements. From 1977 until 1980 I
`
`was a postdoctoral fellow in the Department of Biochemistry at Stanford
`
`University Medical School in Stanford, California. While I was a postdoctoral
`
`fellow, I studied the RecA protein of Escherichia coli.
`
`5.
`
`Since 1980, I have held a number of academic appointments
`
`and employment positions, including academic positions at the University of
`
`Maryland Baltimore County, The University of Texas-Houston, Baylor College of
`
`Medicine, and Washington University at St. Louis, and a research staff position at
`
`
`
`2
`
`Exhibit No. 1021
`Page 2
`
`
`
`NCI-Frederick Cancer Research Facility in Frederick, Maryland. Since 1977, I
`
`have received a number of awards for my work in the areas of biomedical sciences,
`
`genetics and microbiology including the University of Texas Chancellor‘s
`
`Entrepreneurship and Innovation Award, the John P. McGovern Outstanding
`
`Teacher Award, and election to fellowship in the American Academy of
`
`Microbiology and the American Association for the Advancement of Science.
`
`6.
`
`Since 1985, I have held a number of consulting positions and
`
`board memberships including scientific advisory positions to genome centers and
`
`large-scale research projects performing high throughput DNA sequencing. I have
`
`been an invited professor and guest lecturer at numerous universities, companies,
`
`and other organizations on various subjects, including genetics, genomics,
`
`biochemistry, molecular biology, and biochemistry. I am a member of the
`
`following societies and organizations: American Academy of Microbiology,
`
`American Association for the Advancement of Science, American Society for
`
`Biochemistry and Molecular Biology, American Society of Human Genetics,
`
`American Society of Microbiology, Association for Computer Machinery,
`
`Federation of American Scientists, Genetics Society of America, Human Genome
`
`Organization International, Institute of Electrical and Electronics Engineers, and
`
`Sigma Xi.
`
`
`
`3
`
`Exhibit No. 1021
`Page 3
`
`
`
`7.
`
`I have held various editorial positions for a number of scientific
`
`journals and participated in and organized a number of symposia and conferences.
`
`I have received funding for my research laboratory continuously for over 30 years
`
`and currently have 10 contracts and grants that are active, including projects
`
`funded by the National Institutes of Health, the United States Department of
`
`Agriculture, the Foundation Fighting Blindness, and the Bill and Melinda Gates
`
`Foundation. I have received other funding and support for a number of other
`
`research projects. I have also authored and contributed to more than 280
`
`publications. My major research interests involve genetics and genomics and their
`
`application to understanding infectious diseases and other human medical
`
`conditions.
`
`8.
`
`I have extensive, hands-on experience with many sequencing
`
`technology platforms, including the accused Illumina products in this case. I have
`
`over 40 years of experience working in the field of genomics, including over 15
`
`years managing DNA sequencing projects, and first-hand experience in the use of
`
`DNA sequencing platforms such as the Illumina Genome Analyzer, HiSeq, and
`
`MiSeq, Roche 454 GS20 and FLX Titanium models, Life Technologies/Applied
`
`Biosystems SOLiD and capillary sequencing instruments, Pacific BioSciences RS,
`
`and Life Technologies/Ion Torrent Personal Genome Machine.
`
`
`
`4
`
`Exhibit No. 1021
`Page 4
`
`
`
`9.
`
`Since 1999 I have been a director of two of the three large scale
`
`genome centers in the United States funded by and comprising the National
`
`Institutes of Health DNA sequencing network. I am currently an associate director
`
`at one of these centers, The Genome Institute at Washington University. I was co-
`
`director of another of these centers, the Human Genome Sequencing Center at
`
`Baylor College of Medicine prior to joining the faculty at Washington University.
`
`The third genome center in the NIH network is at the Broad Institute. There are
`
`only two other genome centers of this scale, both outside the United States:
`
`Wellcome Trust Sanger Institute in the United Kingdom and the Beijing Genome
`
`Institute (BGI) in Shenzhen, China.
`
`10.
`
`Part of the mission of the NIH genome centers is to acquire and
`
`investigate DNA sequencing technologies including interacting with companies to
`
`beta-test and provide feedback on their instruments. I regularly evaluate new
`
`sequencing technology as part of my position overseeing a large-scale sequencing
`
`center.
`
`11.
`
`For my work related to this inter partes review, I am being
`
`compensated at a rate of $600 per hour. I have no financial interest in this
`
`proceeding, and my compensation is unaffected by the content of my testimony or
`
`the outcome of this proceeding.
`
`
`
`5
`
`Exhibit No. 1021
`Page 5
`
`
`
`CLAIM INTERPRETATION AND LEVEL OF ORDINARY SKILL
`IN THE ART
`
`12.
`
`I obtained all knowledge of relevant legal principles relating to
`
`patent law from both my experience as an expert witness in prior cases and from
`
`counsel for Illumina. If asked, I may testify as to my understanding of the legal
`
`principles set forth below.
`
`13.
`
`I am informed that there are basic rules for claim interpretation.
`
`I understand that terms used in the claims are generally given the meaning that is
`
`ordinary and customary to a person of ordinary skill in the art at the time of
`
`invention. I further understand that when the ordinary meaning is not readily
`
`apparent, the Patent Office will look to public sources that show what a person of
`
`ordinary skill in the art would have understood the claim language to mean, and
`
`that those sources include the intrinsic evidence – the words of the claims
`
`themselves, the specification of the patent, and the patent file history – as well as
`
`extrinsic evidence concerning relevant scientific principles, the meaning of
`
`technical terms, and the state of the art. I understand that claims do not stand alone
`
`and that claims must be read in view of the patent's specification.
`
`14.
`
`I am informed that claims are to be understood from the
`
`perspective of a person of ordinary skill in the relevant art and their understanding
`
`at the time the application was filed.
`
`
`
`6
`
`Exhibit No. 1021
`Page 6
`
`
`
`15.
`
`In defining “one of ordinary skill in the art,” I have been
`
`advised to consider factors such as the educational level and years of experience
`
`not only of the person or persons who have developed the invention that is the
`
`subject of the case, but also others working in the pertinent art at the time of the
`
`invention; the types of problems encountered in the art; the teachings of the prior
`
`art; patents and publications of other persons or companies; and the sophistication
`
`of the technology. I understand the person of ordinary skill in the art is not a
`
`specific real individual, but rather a hypothetical individual having the qualities
`
`reflected by the factors discussed above.
`
`16.
`
`I have assessed the level of ordinary skill in the art based upon
`
`my review of the art, my 40 years of working in the field of genomics, including
`
`over 15 years managing DNA sequencing projects, and first-hand experience in the
`
`use of DNA sequencing platforms such as the Illumina Genome Analyzer, HiSeq,
`
`and MiSeq, Roche 454 FLX, Life Technologies Applied Biosystems SOLiD and
`
`capillary sequencing instruments, Pacific BioSciences RS and Life Technologies
`
`Ion Torrent Personal Genome Machine.
`
`17.
`
`I am knowledgeable about the level of ordinary skill in the art at
`
`the time of the '869 patent's earliest claimed priority date of October 6, 2000. In my
`
`opinion, the field of invention is DNA sequencing. One of skill in the art as of that
`
`
`
`7
`
`Exhibit No. 1021
`Page 7
`
`
`
`date would have been a Ph.D. or equivalent in molecular biology or associated
`
`sciences. In addition, a person of ordinary skill in the art would have had over 5
`
`years of laboratory experience.
`
`18.
`
` As of October 6, 2000, I had earned a Ph.D. in Microbiology
`
`and had three years of post-doctoral laboratory experience and over twenty years'
`
`experience as a faculty member, running my own research laboratory, with the
`
`current status of tenured full Professor, and had supervised technicians, graduate
`
`students, postdoctoral fellows, and visiting scientists as well as collaborated with a
`
`number of research groups, and had taught genetics courses at the Cold Spring
`
`Harbor Laboratory in New York (for five years) and the International Centre for
`
`Genetic Engineering and Biotechnology in Trieste, Italy (for four years), and
`
`served as Co-Director of the Human Genome Sequencing Center at Baylor College
`
`of Medicine, and so was familiar with the level of ordinary skill in the art.
`
`BACKGROUND OF THE '869 PATENT
`
`19.
`
`I have read and understand U.S. Patent No. 7,790,869 to
`
`Jingyue Ju. et al., entitled Massive Parallel Method For Decoding DNA And RNA
`
`("the '869 patent").
`
`20.
`
`I understand and believe that the earliest filing date to which the
`
`'869 patent may be entitled is October 6, 2000. I understand this because my
`
`
`
`8
`
`Exhibit No. 1021
`Page 8
`
`
`
`review of the '869 patent shows that: the '869 patent issued on September 7, 2010
`
`from U.S. Application No. 11/810,509 filed June 5, 2007; the '869 patent was filed
`
`as a continuation of application No. 10/702,203, filed on Nov. 4, 2003, now Pat.
`
`No. 7,345,159, which is a division of application No. 09/972,364, filed on Oct. 5,
`
`2001, now Pat. No. 6,664,079, claiming the benefit of provisional application No.
`
`60/300,894, filed June 26, 2001 and is a continuation-in-part of application No.
`
`09/684,670, filed on Oct. 6, 2000, now abandoned.
`
`21.
`
`The '869 patent is generally directed to a "sequencing by
`
`synthesis" method of determining the sequence of a polynucleic acid, such as DNA
`
`or RNA. See '869 Abstract.
`
`22.
`
`In the sequencing by synthesis method of the '869 patent, 1) a
`
`nucleic acid template is attached to a solid support, 2) a primer hybridizes to the
`
`template, 3) a polymerase adds a 3'-OH blocked and labeled nucleotide (i.e., a
`
`nucleotide including a capping group at the 3 position on the ribose of the
`
`nucleotide and a label that identifies the nucleotide base) to form a primer
`
`extension strand, 4) the unique label on the nucleotide is detected to determine the
`
`type of nucleotide that was added by the polymerase, 5) removing the group
`
`capping the 3'-OH of the nucleotide that was incorporated into the primer
`
`extension strand, thereby permitting addition of further nucleotides, and 6)
`
`
`
`9
`
`Exhibit No. 1021
`Page 9
`
`
`
`repeating the process to add and detect additional nucleotides added to the primer
`
`extension strand to determine the sequence of the nucleic acid template. See '869
`
`patent, col. 8, lines 8-52.
`
`23.
`
`The 3'-OH capping group acts to ensure that only one base is
`
`incorporated into the growing primer extension strand at a time, and removal of the
`
`3'-OH capping group then allows the next the nucleotide to be added by the
`
`polymerase. See '869 patent, col. 19, lines 52-65.
`
`24.
`
`Independent claim 12 of the '869 patent relates to nucleotide
`
`analogs usable in sequencing by synthesis methods. Claim 12 is directed to a
`
`nucleotide analog with 1) a "cleavable linker" which links a detectable label to the
`
`base of the nucleotide, and 2) a "cleavable chemical group" capping the 3' OH
`
`group of the ribose of the nucleotide. Both the linker and the capping group are
`
`cleavable by "a means selected from the group consisting of one or more of a
`
`physical means, a chemical means, a physical chemical means, heat, and light."
`
`'869 patent, claim 12.
`
`25.
`
`An "analogue of a nucleotide base" is defined in the '869
`
`specification as "…a structural and functional derivative of the base of a nucleotide
`
`which can be recognized by polymerase as a substrate." '869 patent, col. 7, ll. 37-
`
`39.
`
`
`
`10
`
`Exhibit No. 1021
`Page 10
`
`
`
`26.
`
`A "nucleotide analogue" is defined in the '869 specification as
`
`"…a chemical compound that is structurally and functionally similar to the
`
`nucleotide, i.e. the nucleotide analogue can be recognized by polymerase as a
`
`substrate." '869 patent, col. 7, ll. 48-51. Thus, a nucleotide having as its base an
`
`analogue of a nucleotide base is a "nucleotide analogue.
`
`27.
`
`Specific examples provided in the '869 patent of "nucleotide
`
`analogues" are nucleotides having 7-deaza-adenine and 7-deaza-guanine as the
`
`nucleobase. '869 patent, col. 7, ll. 58-63.
`
`28.
`
`The only examples of 3'-OH cleavable groups presented in the
`
`'869 patent are --CH2OCH3 and --CH2CH=CH2. '869 patent, col. 9, ll. 52-58.
`
`29.
`
`The only specific example of a cleavable linker in the ‘869
`
`patent is a 2-nitrobenzyl linker, which is a cleavable by light, i.e. photocleavable.
`
`'869 patent, col. 23, ll. 29-35.
`
`30.
`
`The specific example of the linker attaching the label to the
`
`nucleotide base given in the '869 patent specification is "…a label is attached
`
`through a cleavable linker to the 5-position of cytosine or thymine or to the 7-
`
`position of deaza-adenine or deaza-guanine." '869 patent, col. 7, ll. 63-66.
`
`
`
`11
`
`Exhibit No. 1021
`Page 11
`
`
`
`PRIOR ART REFERENCES CONSIDERED IN THIS DECLARATION
`
`31.
`
`I have read and understand at least the following:
`
`(a)
`
` International Application Publication WO 91/06678 to Tsien et
`al. entitled DNA Sequencing ("Tsien") which was published
`May 16, 1991.
`
`(b) U.S. Patent No. 5,547,839 to Dower et al. entitled Sequencing
`of Surface Immobilized Polymers Utilizing Microfluorescence
`Detection ("Dower") which issued August 20, 1996.
`
`(c)
`
`(d)
`
`(e)
`
`(f)
`
`International Application Publication WO 96/27025 to Rabani
`entitled Device, Compounds, Algorithms, and Methods of
`Molecular Characterization and Manipulation with Molecular
`Parallelism ("Rabani") which was published September 6,
`1996.
`
`International Application Publication WO 00/53805 to Stemple
`et al. entitled A Method for Direct Nucleic Acid Sequencing
`("Stemple II") which was published September 14, 2000.
`
`U.S. Patent No. 7,270,951 to Stemple et al. entitled Method for
`Direct Nucleic Acid Sequencing, ("Stemple III") issued
`September 18, 2007.
`
`U.S. application serial no. 09/266,187 ("Stemple I"), filed
`March 10, 1999, to which Stemple III claims priority.
`
`(g) A System for Rapid DNA Sequencing with Fluorescent Chain-
`Terminating Dideoxynucleotides by Prober et al., Science 238,
`336-341 (1987) ("Prober I") which was published in 1987.
`
`(h) U.S. Patent No. 5,242,796 issued September 7, 1993 to Prober
`entitled Method, System and Reagents for DNA Sequencing
`("Prober II") issued September 7, 1993.
`
`(i)
`
`PCT Application WO98/33939 Anazawa et al. entitled Method
`for Determining Nucleic Acids Base Sequence and Apparatus
`Therefor ("Anazawa") published August 6, 1999, as translated
`from Japanese.
`
`
`
`12
`
`Exhibit No. 1021
`Page 12
`
`
`
`(j)
`
`U.S. Patent No. 5,047,519 to Hobbs et al. entitled
`Alkynylamino-Nucleotides ("Hobbs") issued September 10,
`1991.
`
`(k) U.S. Patent No. 4,804,748 to Seela entitled 7-Deaza-
`2'deoxyguanosine Nucleotides ("Seela I") issued February 14,
`1989.
`
`(l)
`
`U.S. Patent No. 5,844,106 to Seela et al. entitled Modified
`Oligonucleotides, Their Preparation And Their Use ("Seela II")
`issued December 1, 1998.
`
`(m)
`
`PCT Publication WO 89/11548 to Saiki ("Saiki"), published
`November 30, 1989.
`
`32.
`
`I understand the following about the timing of these references:
`
`(a)
`
`Tsien qualifies as prior art against the '869 patent under 35
`U.S.C. § 102(b) because it was published on May 16, 1991,
`more than one year before the earliest filing date to which the
`'869 patent could possibly be entitled ("Earliest Filing Date").
`
`(b) Dower qualifies as prior art against the '869 patent under 35
`U.S.C. § 102(b) because it issued on August 20, 1996, more
`than one year before the Earliest Filing Date.
`
`(c)
`
`(d)
`
`(e)
`
`Rabani qualifies as prior art against the '869 patent under 35
`U.S.C. § 102(b) because it was published on September 6,
`1996, more than one year before the Earliest Filing Date.
`
`Stemple II qualifies as prior art against the '869 patent under 35
`U.S.C. § 102(a) because it was published on September 16,
`2000, before the Earliest Filing Date.
`
`Stemple III qualifies as prior art against the '869 patent under
`35 U.S.C. § 102(e) because it claims priority as a continuation-
`in-part to an application (Stemple I) for patent filed on March
`10, 1999, before the Earliest Filing Date, and because of the
`identity of relevant disclosures between Stemple I and Stemple
`III. Stemple I includes every relevant technical disclosure of
`Stemple III as set out in claim chart no. 6.
`
`
`
`13
`
`Exhibit No. 1021
`Page 13
`
`
`
`(g)
`
`(f)
`
`Prober I qualifies as prior art against the '869 patent under 35
`U.S.C. § 102(b) because it was published in 1987, more than
`one year before the Earliest Filing Date.
`
`Prober II qualifies as prior art against the '869 patent under 35
`U.S.C. § 102(b) because it issued on September 7, 1993, more
`than one year before the Earliest Filing Date.
`
`(g) Anazawa qualifies as prior art against the '869 patent under 35
`U.S.C. § 102(b) because it was published August 6, 1998.
`
`(h) Hobbs qualifies as prior art against the '869 patent under 35
`U.S.C. § 102(b) because it issued on September 10, 1991, more
`than one year before the Earliest Filing Date.
`
`(i)
`
`(j)
`
`Seela I qualifies as prior art against the '869 patent under 35
`U.S.C. § 102(b) because it issued on February 14, 1989, more
`than one year before the Earliest Filing Date.
`
`Seela II qualifies as prior art against the '869 patent under 35
`U.S.C. § 102(b) because it issued on December 1, 1998, more
`than one year before the Earliest Filing Date.
`
`TECHNICAL DISCLOSURES OF THE PRIOR ART IN REFERENCE TO
`THE '869 PATENT
`
`33.
`
`Prior to the Earliest Filing Date, and in many cases more than a
`
`year prior, it was known to use nucleotides in sequencing by synthesis methods in
`
`which 3'-OH capped (e.g., chain terminating) and labeled nucleotide analogous are
`
`mixed with a primed, nucleic acid template attached to a solid surface; a single
`
`nucleotide analogue is added to the primer or primer extension strand
`
`complementary to the opposite nucleotide of the DNA template; the label (e.g., a
`
`fluorescent label attached to the base) is then detected to identify the type of
`
`nucleotide (e.g., A, G, C or T) that was added to the strand; and following removal
`
`
`
`14
`
`Exhibit No. 1021
`Page 14
`
`
`
`of the 3'-OH capping group, the process is repeated to identify the sequence of the
`
`DNA template. Specific examples of sequencing as set out immediately above are
`
`disclosed in at least Dower, Tsien, Rabani and Stemple I, II and III.
`
`34.
`
`For reference, and to illustrate the numerical nomenclature of
`
`purine nucleobases, the purine nucleobase adenine is show below with standard
`
`position numbers shown in red:
`
`35.
`
`In organic molecule nomenclature, the prefix "deaza" refers to
`
`the substitution of a carbon atom for a naturally-present nitrogen atom. Thus, for
`
`example, in a molecule called a "deazapurine," a nitrogen atom normally present in
`
`a purine nucleobase (i.e., adenine or guanine) has been replaced with a carbon
`
`atom.
`
`36.
`
`In a "7-deazapurine," the natural 7-position nitrogen atom is
`
`replaced with a carbon atom.
`
`
`
`15
`
`Exhibit No. 1021
`Page 15
`
`
`
`37.
`
`The use of nucleotide analogs including deazapurine, and a
`
`label attached at the 7-position thereof, was known in the nucleic acid sequencing
`
`field at least as early as the late 1980s.
`
`38.
`
`Seela I states that deaza bases can advantageously be used in
`
`place of regular bases in polymerase-based sequencing methods. See, e.g., Seela I
`
`at col. 2, lines 23-29.
`
`39.
`
`While much of Seela I is directed to Sanger sequencing, Seela I
`
`states that this teaching about using deaza bases is not limited to Sanger
`
`sequencing. See, e.g., Seela I at col. 4, lines 4-10.
`
`40.
`
`Seela I states that deaza bases can be used in place of regular
`
`bases in any DNA sequencing method that uses a DNA polymerase. Seela I, col.
`
`4, lines 4-10.
`
`41.
`
`Seela I observes that the deaza bases can be used without
`
`changing the other conditions of the sequencing reaction. See Seela I, col. 4, lines
`
`11-13.
`
`42.
`
`It was widely known to use deazapurine-based nucleotides in
`
`the sequencing by synthesis methods at least 10 years prior to the filing date of the
`
`
`
`16
`
`Exhibit No. 1021
`Page 16
`
`
`
`'869 patent. See e.g., Dower, Tsien, Stemple II and the references cited therein,
`
`including Prober I and Anazawa.
`
`43.
`
`Multiple prior art references recognized a number of advantages
`
`for using deazapurines as the base in nucleotide analogs for sequencing.
`
`44.
`
`For example, the prior art taught that deazaguanine-based
`
`nucleotides allow for effective sequencing of cytosine-guanine rich areas. See e.g.,
`
`Seela I, col. 2, lines 31-33.
`
`45.
`
`Prober I demonstrated that labels attached to the 7-position of
`
`deaza purines could be successfully incorporated by polymerase. Prober I, page
`
`340, col. 1.
`
`46.
`
`Hobbs reflects a synthesis scheme used to make the nucleotides
`
`of Prober I.
`
`47.
`
`Hobbs teaches that the 7 position of a purine base is a
`
`particularly advantageous location to place a label, as that location least interferes
`
`with the incorporation of the nucleotide into a DNA strand by a polymerase.
`
`Hobbs, col. 8, lines 54-60.
`
`48.
`
`Hobbs also teaches that when a label is placed at the
`
`advantageous 7 position of a purine base, the 7 position needs to be converted from
`
`
`
`17
`
`Exhibit No. 1021
`Page 17
`
`
`
`an N to a C (i.e. needs to be “deaza”) in order to form a stable glycosidic linkage
`
`between the base and ribose portions of the nucleotide. See, e.g., Hobbs, col. 10,
`
`lines 67 - col. 11, line 4.
`
`49.
`
`In light of this express motivation in Hobbs, it is my opinion
`
`that a person of ordinary skill in the art prior to October 6, 2000 would have been
`
`motivated to make the nitrogen to carbon substitution (i.e. make the base a “deaza”
`
`base) when attaching a label to the 7 position of a purine base of a nucleotide, as
`
`disclosed in the prior art discussed in the '869 patent Background section. See '869
`
`patent, col. 2, lines 45-51.
`
`50.
`
`Other references similarly demonstrate that the use of 7-deaza-
`
`substituted nucleotide analogs was known in the field of DNA sequencing.
`
`51.
`
`Prober II states that the 7-deaza modification is necessary for
`
`the stability of the nucleotide. See, e.g., col. 18, line 58 to col. 19, line 11.
`
`52.
`
`Prober II also teaches that the 7-position is an ideal location to
`
`attach a fluorescent label. Id.
`
`53.
`
`Nucleotides having deaza bases were also known to include
`
`benefits for sequencing DNA using a DNA polymerase, as taught in the
`
`
`
`18
`
`Exhibit No. 1021
`Page 18
`
`
`
`sequencing by synthesis references. See e.g., Dower, Tsien, Stemple II and the
`
`references cited therein, including Prober I and Anazawa.
`
`54.
`
`For example, deaza bases were known to simplify polymerase
`
`extension with a DNA polymerase when the target DNA was susceptible to
`
`forming secondary structure. See, e.g., Saiki at p. 5, lines 1-5.
`
`55.
`
`Fourth, the obvious interchangeability of regular and deaza
`
`bases was also known in the art prior to October 6, 2000.
`
`56.
`
`For example, Dower teaches that sequencing by synthesis
`
`methods employing modified nucleotides having a 3'-OH "blocking agent" are
`
`"analogous to the dideoxy nucleotides used in the Sanger and Coulson sequencing
`
`procedure, but in certain embodiments here, the blockage is reversible." Dower,
`
`col. 14, ll. 53-56.
`
`57.
`
`Tsien teaches that the synthesis scheme for ddNTPs used in
`
`Prober I should be used in Tsien to produce "fluorescent dNTPs." Tsien, p. 29, ll.
`
`10-19.
`
`58.
`
`The interchangeability is also reflected in a number of other
`
`prior art, next-generation sequencing patents filed around the same time as the ‘869
`
`patent’s earliest claimed priority date. See, e.g., U.S. Pat. No. 7,037,687 to P.
`
`
`
`19
`
`Exhibit No. 1021
`Page 19
`
`
`
`Williams (col. 4, lines 1-11); U.S. Pat. No. 6,255,083 to J. Williams (col. 5, lines
`
`46-53); and U.S. Pat. No. 6,001,566 to Canard (see col. 3, lines 19-41). Each of
`
`these references are directed to next generation sequencing methods based on
`
`polymerase extension, and each refers to the use of labeled deazapurine bases as a
`
`known alternative to using regular purine bases.
`
`59.
`
`The Background of the Invention section of the '869 patent
`
`admits that the following were each known in the prior art:
`
`
`
`1) that sequencing by synthesis was known at least by 1988 stating:
`
`"The concept of sequencing DNA by synthesis without using electrophoresis
`
`was first revealed in 1988 (Hyman, 1988)." See '869 patent, col. 2, lines 9-
`
`10 (emphasis added); see also, Dower, Tsien, Rabani, and Stemple I, II and
`
`III.
`
`
`
`2) that it was known to couple the DNA template to a chip and to use
`
`labeled nucleotides stating "Such a scheme coupled with the chip format and
`
`laser-induced fluorescent detection has the potential to markedly increase
`
`the throughput of DNA sequencing projects. Consequently, several groups
`
`have investigated such a system with an aim to construct an ultra high-
`
`throughput DNA sequencing procedure (Cheeseman 1994, Metzker et al.
`
`1994)." See '869 patent, col. 2, lines 13-19 (emphasis added); see also,
`
`Dower, Tsien, Rabani, and Stemple I, II and III.
`
`
`
`20
`
`Exhibit No. 1021
`Page 20
`
`
`
`
`
`3) that it was known to attach label groups to the nucleotide base
`
`stating "it is known that modified DNA polymerases (Thermo Sequenase
`
`and Taq FS polymerase) are able to recognize nucleotides with extensive
`
`modifications with bulky groups such as energy transfer dyes at the 5-
`
`position of the pyrimidines (T and C) and at the 7-position of purines (G and
`
`A) (Rosenblum et al. 1997, Zhu et al. 1994)." See '869 patent, col. 2, lines
`
`45-51 (emphasis added); see also, Dower, Tsien, Rabani, and Stemple I, II
`
`and III.
`
`
`
`4) that it was known to use small chemical groups as 3'-OH blocking
`
`groups on nucleotides during sequencing reactions stating "It is known that
`
`MOM (--CH 2OCH3) and allyl (--CH 2CH=CH 2) groups can be used to cap
`
`an --OH group, and can be cleaved chemically with high yield (Ireland et al.
`
`1986; Kamal et al. 1999)." See '869 patent, col. 3, lines 26-29 (emphasis
`
`added); see also Dower, Tsien, Rabani, and Stemple I, II and III.
`
`60.
`
`The MOM and allyl groups identified as prior art in the
`
`background section of the '869 patent are 3'-OH capping groups that the '869 patent
`
`identifies as "embodiments of the invention." See '869 patent, col. 12, lines 50-53,
`
`and FIG. 7.
`
`
`
`21
`
`Exhibit No. 1021
`Page 21
`
`
`
`61.
`
`Sequencing by synthesis methods in which a template DNA
`
`strand is coupled to a solid support, and 3' OH blocked and fluorescent labeled
`
`nucleotides are sequentially added to a primer during sequencing were known prior
`
`to October 6, 2000. See, e.g. Tsien. As set forth in Claim Chart 1 of Illumina's
`
`Petition for Inter Partes Review, the nucleotides disclosed by Tsien identically
`
`include every element and limitation of at least claims 12-13, 15-17, 20-26, 28-29,
`
`31, and 33 of the '869 patent.
`
`62.
`
`Tsien discloses removable 3'-OH blocking group having a
`
`molecular weight of less than 300 Daltons. For example, Tsien discloses use of
`
`"formyl, acetyl, [and] isopornaol … esters." Tsien, page 21, ll. 21-30. Tsien also
`
`discloses use of "-F, -NH2 , -OCH3 , -N3 , -OPO3
`
`=" in addition to others as
`
`removable blocking groups. Tsien, page 21, ll. 9-17. Each of these blocking
`
`groups has a molecular weight less than 300 Daltons. Additionally, although the
`
`'869 patent does not provide a reference mass other than 300 Daltons for "small", I
`
`would consider each of these molecules, when used as a blocking group on a
`
`nucleotide, to be a "small chemical moiety." For example, the -F and -NH2
`
`molecules have masses lower than the MOM and allyl blocking groups identified
`
`as "small chemical moieties" by the '869 patent.
`
`
`
`22
`
`Exhibit No. 1021
`Page 22
`
`
`
`63.
`
`In discussing sequencing by synthesis methods utilizing a
`
`dNTP in which the fluorescent label group is coupled to the base of the dNTP,
`
`Tsien references the disclosure of Prober I, Science 238, 336-341 (1987) for its
`
`teaching of preparing nucleotides with fluorescent tags that can be successfully
`
`incorporated by Tsien’s preferred polymerase. See Tsien et al., page 5, lines 22-
`
`23, page 19, lines 4-18; and page 28, lines 5-18. Tsien also states that Prober I,
`
`and the other references discuss in Tsien, are referenced "for their teaching of
`
`synthetic methods, coupling and detection methodologies, and the like." Tsien, p.
`
`3, ll. 11-16 and p. 5, ll. 22-23. I understand Tsien to incorporate the teachings of
`
`Prober I for its teachings regarding of fluorescent label attachment, and in
`
`particular, regarding its teaching regarding attachment of a linker to the 7 position
`
`in the 7-deazapurine.
`
`64.
`
`Additionally, because Tsien directly references Prober I in its
`
`discussion of dNTP label attachment, I understand Tsien to provide an express
`
`teaching to utilize a fluorescent labeled dNTP including the linker and deazapurine
`
`disclosed by Prober I in the sequencing by synthesis method of Tsien.
`
`65.
`
`As I understand Tsien, the reference clearly provides an express
`
`teaching, suggestion, and motivation to combine Tsien with the disclosures of
`
`
`
`23
`
`Exhibit No. 1021
`Page 23
`
`
`
`Prober I with respect to "base moiety derivatized" nucleotide analogues. See Tsien
`
`at page 3, ll. 14-16 and page 28, ll. 16-18, respectively.
`
`66.
`
`As set forth in section V.2 of Illumina's Petition for Inter
`
`Partes Review, Prober I specifically teaches that nucleotide analogues
`
`incorporating 7-deazapurines may be used in sequencing reactions. Thus, the
`
`combination of Tsien and Prober I is the use of the known techniques of Prober I to
`
`improve similar Tsien systems and methods in the same way that the known
`
`features improve the methods and reagents of Prober I. Furthermore, use of the
`
`features taught by Prober I for their intended purpose, as disclosed by Prober I,
`
`would enhance the capability of the Tsien systems and methods in the same way
`
`they enhance the capability of the Prober I methods and reagents. Additionally,
`
`use of the fluorescent labeled deazapurine of Prober I with the sequencing system
`
`and m
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