`
`
`
`
`
`
`
`
`
`
`
`UNITED STATES PATENT AND TRADEMARK OFFICE
`_____________________
`
`BEFORE THE PATENT TRIAL AND APPEAL BOARD
`_____________________
`
`
`GENEDX, INC.
`Petitioner
`
`v.
`
`MYRIAD GENETICS, INC.
`Patent Owner
`
`U.S. Patent No. 6,051,379
`_____________________
`
`Inter Partes Review Case No. Unassigned
`_____________________
`
`DECLARATION OF MADHURI HEGDE, PH.D, FACMG
`
`
`
`GeneDX 1002, pg. 1
`
`

`

`
`
`
`
`TABLE OF CONTENTS
`
`
`
`I.
`
`Introduction ..................................................................................................... 1
`
`II. My Background and Qualifications ................................................................ 2
`
`III. List of Documents I Considered in Formulating My Opinions ..................... 4
`
`IV. Person of Ordinary Skill in the Art ................................................................. 6
`
`V.
`
`The ‘379 Patent Specification ......................................................................... 8
`
`VI. Overview of the Challenged Claims of the ‘379 patent ................................. 9
`
`VII. Claim Construction ....................................................................................... 11
`
`VIII. State of the Art as of September 23, 1997 .................................................... 13
`
`IX. Summary Chart of Analysis Over the Art .................................................... 26
`
`X.
`
`The Basis of my Analysis with Respect to Obviousness ............................. 27
`
`XI. Ground 1: Tavtigian in view of Shattuck-Eidens provide a reason to arrive at
`
`the invention of Claims 7, 8, 13, 14, 16, 17, 19, 20, 32, and 33 with a
`
`reasonable expectation of success ................................................................ 28
`
`XII. Ground 2: Wooster in view of Shattuck-Eidens provide a reason to arrive at
`
`the invention of claims 7, 8, 13, 14, 16, 17, 19, 20, 32, and 33 with a
`
`reasonable expectation of success ................................................................ 65
`
`
`
`
`
`GeneDX 1002, pg. 2
`
`

`

`
`XIII. Objective Indicia of Nonobviousness ........................................................... 99
`
`
`
`XIV. Conclusion .................................................................................................. 105
`
`
`
`
`
`
`
`
`
`GeneDX 1002, pg. 3
`
`

`

`Inter Partes Review of USPN 6,051,379
`Declaration of Madhuri Hegde, Ph.D, FACMG (Exhibit GDX1002)
`
`
`
`
`I, Madhuri Hegde, Ph.D, FACMG, hereby declare as follows.
`I.
`
`Introduction
`I am over the age of eighteen (18) and otherwise competent to make
`
`1.
`
`this declaration.
`
`2.
`
`I have been retained as an expert witness on behalf of GENEDX, INC.,
`
`(“GENEDX”) for the above-captioned inter partes review (IPR). I am being
`
`compensated for my time in connection with this IPR at my standard legal
`
`consulting rate, which is $350 per hour. I understand that the petition for inter
`
`partes review involves U.S. Patent No. 6,051,379 (“the ‘379 patent”), GDX1001,
`
`which resulted from U.S. Application No. 08/984,034 (“the ‘034 application”). I
`
`understand that the '379 patent claims priority to U.S. Patent Application No.
`
`60/059,595, filed September 23, 1997. The ‘379 patent names Jennifer Lee
`
`Lescallett, Tammy Lawrence, Antonette Preisinger Allen, Sheri Jon Olson, Denise
`
`Bernadette Thurber, and Marga Belle White as inventors. The ‘379 patent issued
`
`on April 18, 2000 from the ‘034 application. I understand that, according to the
`
`USPTO records, the ‘379 patent is currently assigned to Myriad Genetics, Inc.
`
`(“the patentee”).
`
`3.
`
`In preparing this Declaration, I have reviewed the ‘379 patent and
`
`each of the documents cited herein, in light of general knowledge in the art. In
`
`formulating my opinions, I have relied upon my experience, education and
`
`
`
`- 1 -
`
`GeneDX 1002, pg. 4
`
`

`

`
`
`
`knowledge in the relevant art. In formulating my opinions, I have also considered
`
`Inter Partes Review of USPN 6,051,379
`Declaration of Madhuri Hegde, Ph.D, FACMG (Exhibit GDX1002)
`
`the viewpoint of a person of ordinary skill in the art (“POSA”) (i.e., a person of
`
`ordinary skill in the field of genetics, defined further below in Section IV) prior to
`
`September 23, 1997.
`
`II. My Background and Qualifications
`I am an expert in the field of recombinant DNA technology, medical
`4.
`
`genetics, and genetic diagnostics.
`
`I
`
`received my B.S. and M.Sc.
`
`in
`
`Microbiology/Genetics from the University of Bombay, Bombay, India in 1987
`
`and 1992, respectively. I was a Senior Research Fellow at University Hospital,
`
`University of Bombay, Bombay, India in 1992-1995 and Scientific Officer at DNA
`
`Diagnostic Laboratory, Auckland Hospital, Auckland, New Zealand in 1995-1996.
`
`I received my Ph.D. in Applied Science, with thesis titled "Molecular – Based
`
`Diagnostics of Inherited Disorders: Multiple Exon and Trinucleotide Repeat
`
`Expansion Analysis," from the University of Auckland, Auckland, New Zealand in
`
`2000, and I was a Postdoctoral Fellow in Clinical Molecular Genetics at the
`
`Department of Human Genetics at Baylor College of Medicine, Houston, Texas in
`
`2000-2003.
`
`5.
`
`I became an Assistant Professor in the Department of Human Genetics
`
`at Baylor College of Medicine, Houston, Texas in 2003, and then an Assistant
`
`Professor in the Department of Human Genetics, Emory University School of
`
`
`
`- 2 -
`
`GeneDX 1002, pg. 5
`
`

`

`
`
`
`Medicine, Atlanta, Georgia in 2006. I was an Associate Professor in the
`
`Inter Partes Review of USPN 6,051,379
`Declaration of Madhuri Hegde, Ph.D, FACMG (Exhibit GDX1002)
`
`Department of Human Genetics, Emory University School of Medicine, Atlanta,
`
`Georgia in 2009-2013, and I became a Professor in the Department of Human
`
`Genetics, Emory University School of Medicine, Atlanta, Georgia in 2013. I am
`
`currently an Adjunct Associate Professor since 2004, at the School of Health
`
`Sciences, University of Texas M.D. Anderson Cancer Center, Houston, Texas.
`
`6.
`
`I have also been a Scientific Director at DNA Diagnostic Laboratory,
`
`Auckland Hospital, Auckland, New Zealand
`
`in 1996-2000; an Assistant
`
`Laboratory Director in 2001-2006 and a Co-Director in 2006 at DNA Diagnostic
`
`Laboratory, Department of Human Genetics, Baylor College of Medicine,
`
`Houston, Texas; and, a Senior Laboratory Director in 2006-2010 and Scientific
`
`Director in 2010-2012 at Emory Genetics Laboratory, Atlanta, Georgia. Since
`
`2012, I am an Executive Director at Emory Genetics Laboratory, Atlanta, Georgia.
`
`7.
`
`I am American Board of Medical Genetics certified Clinical
`
`Molecular Geneticist. I have received numerous grants and awards related to my
`
`research in recombinant DNA technology, medical genetics, and genetic
`
`diagnostics. I have published more than 74 research articles and several book
`
`chapters related to recombinant DNA technology, medical genetics, and genetic
`
`diagnostics, with a focus on novel gene discovery and functional analysis of
`
`sequence variants in disease associated genes. I also have an extensive research
`
`
`
`- 3 -
`
`GeneDX 1002, pg. 6
`
`

`

`
`
`
`experience related to recombinant DNA technology, medical genetics, and genetic
`
`Inter Partes Review of USPN 6,051,379
`Declaration of Madhuri Hegde, Ph.D, FACMG (Exhibit GDX1002)
`
`diagnostics.
`
`8.
`
`Accordingly, I am an expert in the field of recombinant DNA
`
`technology, medical genetics, and genetic diagnostics. My full background is
`
`detailed in my curriculum vitae. GDX1003.
`
`III. List of Documents I Considered in Formulating My Opinions
`In formulating my opinions, I have considered all of the references
`9.
`
`cited herein, including those listed below. I have reviewed the Declarations of
`
`Mark Allan Kay, M.D., Ph.D. (GDX1015) and Gregory C. Critchfield, M.D.
`
`(GDX1014), and I disagree with their conclusions. For the reasons set forth in
`
`detail below, I reach the conclusions offered herein.
`
`GDX
`
`Exhibit #
`
`Description
`
`1001 U.S. Patent No. 6,051,379, issued April 18, 2000
`1004
`File History of U.S. Patent No. 6,051,379
`1005 Miki, Y., et al., "Mutation analysis in the BRCA2 gene in primary breast
`cancers," Nature Genetics 13: 245-247 (June 13, 1996)
`1006 Bowcock, A.M., "Molecular cloning BRCA1: a gene for early onset
`familial breast and ovarian cancer," Breast Cancer Research and
`Treatment 28: 121-135 (1993)
`1007 Hacia, J.G., et al., "Detection of heterozygous mutations in BRCA1
`using high density oligonucleotide arrays and two-colour fluorescence
`analysis," Nature Genetics 14: 441-447 (December 14, 1996)
`1008 Grompe, M., "The rapid detection of unknown mutations in nucleic
`acids," Nature Genetics 5: 111-117 (1993)
`
`
`
`- 4 -
`
`GeneDX 1002, pg. 7
`
`

`

`
`
`
`
`
`
`Inter Partes Review of USPN 6,051,379
`Declaration of Madhuri Hegde, Ph.D, FACMG (Exhibit GDX1002)
`
`1010
`
`1012
`
`1009 Orita, M., et al., "Detection of polymorphisms of human DNA by gel
`electrophoresis as single-strand conformation polymorphisms," PNAS
`USA 86: 2766-2770 (1989)
`Scharf, S. J., et al., "Direct Cloning and Sequence Analysis of
`Enzymatically Amplified Genomic Sequences," Science 233: 1076-1078
`(1986)
`1011 Weber, B.H.F., et al., "A Somatic Truncating Mutation in BRCA2 in a
`Sporadic Breast Tumor," Am. J. Hum. Genet. 59: 962-964 (October
`1996)
`Lancaster, J.M., et al., "BRCA2 mutations in primary breast and ovarian
`cancers," Nature Genetics 13: 238-240 (June 13, 1996)
`from
`downloaded
`1013 Myriad Genetics
`2013 Annual Report
`http://files.shareholder.com/downloads/MYGN/3399011197x0x699241/
`42B88246-0E90-4F5C-9697-3DF98027C46D/2013_Annual_Report.pdf
`(last accessed 8/16/2014)
`1014 Declaration of Dr. Gregory C. Critchfield, filed December 23, 2009, in
`Assoc. for Molecular Pathology v. U.S. Patent & Trademark Office, No.
`09-cv-04515-RWS (S.D.N.Y.)
`1015 Declaration of Mark Allan Kay, M.D., Ph.D, filed August 31, 2013, in
`Univ. of Utah Research Foundation et al. v. Ambry Genetics Corp. Case
`No. 2:13-cv-00640-RJS
`Eng, C., et al., "Interpreting epidemiological research: blinded
`comparison of methods used to estimate the prevalence of inherited
`mutations in BRCA1," J. Med. Genet. 38: 824-833 (2001)
`Sambrook, J., et al., Molecular Cloning, A Laboratory Manual, 2nd Ed.,
`Cold Spring Harbor Laboratory Press, §§ 5.28-5.32, 6.36-6.48, 13.6-
`13.77, and 14.5-14.21 (1989)
`1018 Conner, B.J., et al., "Detection of sickle cell βS-globin allele by
`hybridization with synthetic oligonucleotides," PNAS USA 80: 278-282
`(1983)
`Teng, D.H.F., et al., "Low incidence of BRCA2 mutations in breast
`carcinoma and other cancers," Nature Genetics 13: 241-244 (June 13,
`1996)
`1020 Cotton, R.G.H., "Current methods of mutation detection," Mutation
`Research 285: 125-144 (1993)
`1021 Handelin, B., et al., "Simultaneous Detection of Multiple Point
`Mutations Using Allele-Specific Oligonucleotides," Current Protocols
`in Human Genetics Suppl. 6: 9.4.1-9.4.8, online publication of May 1,
`2001 corresponding to August 1995 print publication
`
`1016
`
`1017
`
`1019
`
`- 5 -
`
`GeneDX 1002, pg. 8
`
`

`

`
`
`
`
`Inter Partes Review of USPN 6,051,379
`Declaration of Madhuri Hegde, Ph.D, FACMG (Exhibit GDX1002)
`
`1024
`
`1026
`
`1022 Wooster, R., et al., "Localization of a Breast Cancer Susceptibility
`Gene, BRCA2, to Chromosome 13q12-13," Science 265: 2088-2090
`(1994)
`1023 Wooster, R., et al., "Identification of the breast cancer susceptibility
`gene BRCA2," Nature 378:789-792 (1995)
`Schutte, M., et al., "Identification by representational difference analysis
`of a homozygous deletion in pancreatic carcinoma that lies within the
`BRCA2 region," Proc. Natl. Acad. Sci. USA 92: 5950-5954 (1995)
`1025 Alberts, et al. "Molecular Biology of the Cell," 3rd Ed., pp. 98-99, 104-
`106, 242-243, 292-293, 314-317, 337, 339, 1072-1073, G-5-G-6, G-10,
`G-17 (1994)
`Tavtigian, S.V., et al., "The complete BRCA2 gene and mutations in
`chromosome 13q-linked kindreds," Nature Genetics 12: 333-337 (March
`12, 1996)
`1027 GenBank Accession No. U43746, "Human breast cancer susceptibility
`(BRCA2) mRNA, complete cds," modification date of September 3,
`1996, available at
`http://www.ncbi.nlm.nih.gov/nuccore/1161383?sat=13&satkey=655953
`2
`(last accessed August 6, 2014)
`1028 GenBank Accession No. AAB07223, "BRCA2 [Homo sapiens],"
`modification date of September 3, 1996, available at
`http://www.ncbi.nlm.nih.gov/protein/1161384?sat=13&satkey=6559532
`(last accessed August 6, 2014)
`Shattuck-Eidens et al., "In Vivo Mutations and Polymorphisms in the
`17q-linked Breast and Ovarian Cancer Susceptibility Gene," WO
`96/05306 (filed August 11, 1995; published on February 22, 1996)
`
`1029
`
`
`
`IV. Person of Ordinary Skill in the Art
`I understand that a person of ordinary skill in the art (“POSA”) is a
`10.
`
`hypothetical person who is presumed to be aware of all the pertinent art, thinks
`
`along conventional wisdom in the art, and is a person of ordinary creativity. With
`
`respect to the subject matter of the ‘379 patent, a POSA would typically have had
`
`
`
`- 6 -
`
`GeneDX 1002, pg. 9
`
`

`

`
`
`
`(i) a Ph.D. in genetics, molecular genetics, or molecular biology, or in a related
`
`Inter Partes Review of USPN 6,051,379
`Declaration of Madhuri Hegde, Ph.D, FACMG (Exhibit GDX1002)
`
`field in the biological sciences, and have experience in recombinant DNA
`
`technology, medical genetics, or genetic diagnostics, or (ii) a Master's degree in
`
`genetics, molecular genetics, or molecular biology, or in a related field in the
`
`biological sciences, and have at least 2 years of experience in recombinant DNA
`
`technology, medical genetics, or genetic diagnostics.
`
`11. A POSA would have known how to research the scientific literature
`
`regarding recombinant DNA technology, medical genetics, or genetic diagnostics.
`
`Also, a POSA may be comprised of a multidisciplinary team with each member
`
`drawing upon not only his or her own skills, but also taking advantage of certain
`
`specialized skills of others in the team, e.g., to solve a given problem. For
`
`example, a molecular biologist and a physician may have been part of the team.
`
`12. As of September 23, 1997, a POSA of recombinant DNA technology,
`
`medical genetics, or genetic diagnostics would have had knowledge of scientific
`
`literature concerning methods for identifying and cloning genes or gene sequences
`
`and methods for screening or detecting alterations in the genes. Such a POSA
`
`would have had knowledge of strategies for identifying and cloning genes or gene
`
`sequences and for screening or detecting alterations in the genes.
`
`
`
`- 7 -
`
`GeneDX 1002, pg. 10
`
`

`

`
`
`
`
`Inter Partes Review of USPN 6,051,379
`Declaration of Madhuri Hegde, Ph.D, FACMG (Exhibit GDX1002)
`
`V.
`
`The ‘379 Patent Specification
`13. This declaration is being submitted together with a petition for inter
`
`partes review of claims 7, 8, 13, 14, 16, 17, 19, 20, 32, and 33 of the ‘379 patent.
`
`14.
`
`I have reviewed the ‘379 patent (GDX1001) and its file history
`
`(GDX1004). And, in assessing the ‘379 patent, I have considered the teachings of
`
`the scientific literature as of September 23, 1997, in light of general knowledge in
`
`the art as of that date. I understand that September 23, 1997 is the earliest possible
`
`priority date of the ‘379 patent.
`
`15. The ‘379 patent is directed to mutations identified in the BRCA2 gene
`
`“at nucleotide numbers 2192, 3772, 5193, 5374, 6495 or 6909 of the published
`
`nucleotide sequence of BRCA2 gene.” GDX1001, 1:Abstract1. The ‘379 patent is
`
`further directed to “[a] process for identifying a sequence variation in a BRCA2
`
`polynucleotide sequence” and “[t]he identification process includes allele specific
`
`sequence-based assays of known sequence variations.” Id.
`
`
`1 Citations to GDX1001 use the format x:y:z, where x is the exhibit page
`
`number, y is the column number, and z is the line number(s). For GDX1029, x is
`
`the exhibit page number and y is the line number(s). For citations to all other non-
`
`patent publications, x is the exhibit page number and y is the column number.
`
`
`
`- 8 -
`
`GeneDX 1002, pg. 11
`
`

`

`
`
`
`
`Inter Partes Review of USPN 6,051,379
`Declaration of Madhuri Hegde, Ph.D, FACMG (Exhibit GDX1002)
`
`16. The ‘379 patent acknowledges that the BRCA2 gene was known and
`
`that a sequence was publically available as GenBank accession number U43746.
`
`GDX1001, 1:Abstract, 2:1:25-28.
`
`VI. Overview of the Challenged Claims of the ‘379 patent
`Independent claims 7, 13, and 16 of the ‘379 patent are generally
`17.
`
`directed to isolated oligonucleotides that are capable of detecting a particular
`
`mutation at nucleotide number 5193, 6495, or 6909, respectively, of a BRCA2 gene
`
`by specifically hybridizing to a region of the gene that contains the nucleotide
`
`number.
`
` Dependent claims 19-20 are generally directed
`
`to
`
`isolated
`
`oligonucleotides bound to labels, including the oligonucleotides of claims 7, 13,
`
`and 16. Claims 8, 14, and 17 are generally directed to isolated oligonucleotides
`
`having the sequences of SEQ ID NOs:11, 19, and 23, respectively, or their
`
`complementary sequences. Claims 32-33 are generally directed to methods of
`
`detecting a predisposition or higher susceptibility to cancer in an individual,
`
`wherein the presence of a sequence variation at nucleotide number 2192, 3772,
`
`5193, 5374, 6495, or 6909 indicates a predisposition or higher susceptibility to
`
`cancer.
`
`18. Claim 7, for example, recites:
`
`7. An isolated oligonucleotide
`
`
`
`- 9 -
`
`GeneDX 1002, pg. 12
`
`

`

`
`
`
`
`
`
`Inter Partes Review of USPN 6,051,379
`Declaration of Madhuri Hegde, Ph.D, FACMG (Exhibit GDX1002)
`
`wherein the oligonucleotide is capable of detecting a substitution of G
`for C at nucleotide number 5193 of a BRCA2 gene by specifically
`hybridizing to the region containing nucleotide number 5193 of the
`BRCA2 gene.
`
`19. Claim 8, for example, recites:
`
`8. An isolated oligonucleotide
`
`having the sequence 5'ACT TGT TAC ACA AAT CA3', SEQ ID
`NO:11, or the complementary oligonucleotide thereto.
`
`
`
`20. Claim 32, for example, recites:
`
`32. A method of detecting a predisposition or higher susceptibility to
`cancer in an individual, comprising:
`
`(a) digesting DNA from an individual to obtain DNA fragments;
`
`(b) separating said DNA fragments;
`
`(c) detecting a DNA fragment containing nucleotide number 2192,
`3772, 5193, 5374, 6495 or 6909 of the BRCA2 gene sequence or a
`sequence variation at nucleotide number 2192, 3772, 5193, 5374,
`6495 or 6909 of the BRCA2 gene sequence by sequencing;
`
`(d) comparing the sequence of said fragment with the BRCA2 gene
`sequence to determine the presence or absence of a sequence variation
`at nucleotide number 2192, 3772, 5193, 5374, 6495 or 6909, wherein
`the presence of a sequence variation indicates a predisposition or
`higher susceptibility to cancer.
`
`- 10 -
`
`GeneDX 1002, pg. 13
`
`

`

`
`
`
`
`Inter Partes Review of USPN 6,051,379
`Declaration of Madhuri Hegde, Ph.D, FACMG (Exhibit GDX1002)
`
`
`VII. Claim Construction
`I understand that terms of the claims are to be given their broadest
`21.
`
`reasonable interpretations in light of the specification of the ‘379 patent.
`
`22.
`
`Isolated. Claims 7-8, 13-14, 16-17, and 19-20 recite “isolated
`
`oligonucleotides.” The ‘379 patent states that “[t]he term ‘isolated’ as used herein
`
`refers to being substantially free of other polynucleic acids, proteins, lipids,
`
`carbohydrates or other materials with which they may be associated. Such
`
`association being either in cellular material or in a synthesis medium.” GDX1001,
`
`7:11:27-31. Accordingly, a POSA would construe the term “isolated” consistent
`
`with the definition in the ‘379 patent.
`
`23. Region. Claims 7, 13, and 16 recite “region containing nucleotide
`
`number [5193, 6495, or 6909, respectively] of the BRCA2 gene.” The ‘379 patent
`
`states that “‘[r]egion’ as used herein generally refers to an area from several
`
`nucleotides upstream to several nucleotides downstream from the specific
`
`nucleotide mentioned. ‘Region’ also includes the complementary nucleotides on
`
`the antisense strand of sample DNA.” GDX1001, 7:12:36-40. Accordingly, a
`
`POSA would construe the term “region” consistent with its definition in the ‘379
`
`patent.
`
`24. BRCA2 gene. Claims 7, 13, 16, and 32 recite “BRCA2 gene.” The
`
`‘379 patent states that:
`
`
`
`- 11 -
`
`GeneDX 1002, pg. 14
`
`

`

`
`
`
`
`Inter Partes Review of USPN 6,051,379
`Declaration of Madhuri Hegde, Ph.D, FACMG (Exhibit GDX1002)
`
`“BRCA2 gene” is a group of compounds and refers to the published
`gene sequences, those appearing in the GENBANK database and the
`BIC database. Other different sequences include polymorphisms and
`genetic alterations, especially those which define other haplotypes for
`the BRCA2 gene. Generally polymorphisms which don't cause an
`amino acid change or which are naturally occurring (wild types),
`which are not associated with pathology are also considered the
`BRCA2 gene. The corresponding nucleotides would then be used
`even if the nucleotide number differs. While the BRCA2 gene
`discussed herein is the human BRCA2 gene, the corresponding assays
`and reagents for the gene in other animals may also be used. The
`BRCA2 gene includes the coding sequences, non-coding sequences
`(e.g. introns) and regulatory regions affecting gene expression.
`GDX1001, 7:12:9-22. Accordingly, a POSA would construe the term “BRCA2
`
`gene” consistent with its definition in the ‘379 patent.
`
`25. Higher susceptibility to. Claim 32 recites “[a] method of detecting a
`
`predisposition or higher susceptibility to cancer in an individual ….” The ‘379
`
`patent states that “[i]n another embodiment of the invention, a method is provided
`
`for diagnosing a subject having a predisposition or higher susceptibility to (at risk
`
`of) breast or ovarian cancer ….” GDX1001, 6:9:27-29. Thus, the ‘379 patent
`
`states that “higher susceptibility to” means “at risk of.” Accordingly, a POSA
`
`would construe the term “higher susceptibility to” consistent with its definition in
`
`the ‘379 patent.
`
`
`
`- 12 -
`
`GeneDX 1002, pg. 15
`
`

`

`
`
`
`
`Inter Partes Review of USPN 6,051,379
`Declaration of Madhuri Hegde, Ph.D, FACMG (Exhibit GDX1002)
`
`26. Any term that I have not expressly interpreted above, I have given its
`
`plain and ordinary meaning to a POSA as of September 23, 1997.
`
`VIII. State of the Art as of September 23, 1997
`27. The ‘379 patent relates to methods for screening individuals for
`
`sequence variations in disease-associated genes, in particular breast and ovarian
`
`cancer genes. Breast and ovarian cancers are common cancers in women and, like
`
`many cancers, are influenced by an individual's genetic makeup, including
`
`inherited mutations.
`
`28. The hereditary information in an individual exists as a genome in
`
`almost every cell of the body and consists of approximately 22,000 genes that are
`
`packed into 23 pairs of chromosomes. Alberts, et al., "Molecular Biology of the
`
`Cell," 3rd Ed., 1994; (GDX1025), 16. The genes form the basis of human
`
`hereditary traits. Genes are composed of two complementary strands of DNA (or
`
`deoxyribonucleic acid) molecules that contain four different chemical units called
`
`nucleotide bases or nucleotides, adenosine (A), thymine (T), cytosine (C), and
`
`guanine (G), that are arranged in a predetermined linear order (called a DNA
`
`sequence or gene sequence). GDX1025, 3-5. The complementarity of the two
`
`strands is determined by specific base pairs that form between the nucleotide bases
`
`in each strand. In general, only two types of base pairs can form between the two
`
`strands of a DNA sequence: an A in one strand can form a base pair with a T in the
`
`
`
`- 13 -
`
`GeneDX 1002, pg. 16
`
`

`

`
`
`
`other strand, or a G in one strand can form a base pair with a C in the other strand.
`
`Inter Partes Review of USPN 6,051,379
`Declaration of Madhuri Hegde, Ph.D, FACMG (Exhibit GDX1002)
`
`GDX1025, 4. The DNA present in an individual's genome is called genomic DNA.
`
`GDX1025, 22.
`
`29. A gene sequence encodes (i.e., contains information necessary to
`
`produce) a protein. A protein is produced after a) transcription of the gene into an
`
`mRNA (or messenger ribonucleic acid) molecule and, b) translation of the mRNA
`
`molecule into a protein molecule. Only some regions of a gene, called exons,
`
`encode a protein, and are present in the transcribed mRNA. GDX1025, 6-7. Other
`
`gene parts, called introns, which are interspersed between the exons, do not encode
`
`a protein and introns are processed out of mature mRNA by cellular mechanisms.
`
`Id.
`
`30. An individual's germline DNA sequence or germline sequence is
`
`inherited from the individual's parents and is consequently present in all nucleated
`
`cells types in the body. GDX1025, 22. Normal (non-disease causing) alterations or
`
`variations can exist in a gene sequence within a population. GDX1025, 18-19.
`
`Thus, some alterations are not linked to a disease or a risk of developing a disease.
`
`Such non-disease linked alterations are called polymorphisms. However, other
`
`alterations are linked to a disease or a risk of developing a disease and are called
`
`mutations. Id. A germline mutation is present in genomic DNA of all cells and is
`
`inherited by an individual from his or her parents, and can be passed on to an
`
`
`
`- 14 -
`
`GeneDX 1002, pg. 17
`
`

`

`
`
`
`individuals progeny. GDX1025, 22. In contrast, a somatic mutation is present in
`
`Inter Partes Review of USPN 6,051,379
`Declaration of Madhuri Hegde, Ph.D, FACMG (Exhibit GDX1002)
`
`the genomic DNA of only certain cells and is not passed on to progeny. Id. In
`
`cancer genetics, somatic mutations are generally thought to arise in specific cells as
`
`a result of random chance or as a result of environmental factors. GDX1025, 8.
`
`31. Because of alterations in its sequence, a gene can exist in alternative
`
`forms within a population. Alternate forms of a gene are called alleles. The most
`
`common nucleotide sequence not linked to increased disease risk is often referred
`
`to as a wild-type sequence. GDX1025, 18-19.
`
`32. Prior to September 23, 1997, a POSA was able to extract DNA,
`
`mRNA, or proteins from cells using conventional methods. Such methods allowed
`
`a POSA to isolate a specific segment of genomic DNA, such as a gene or a part of
`
`a gene for further study or use. GDX1025, 10. Such conventional methods allowed
`
`a POSA to synthetically create DNA or RNA. Before September 23, 1997,
`
`conventional protocols allowed a POSA to synthesize DNA or RNA, or a DNA
`
`complementary to the natural (native) mRNA. GDX1025, 14-15, 21.
`
`33. Prior to September 23, 1997, disease-associated genes were routinely
`
`identified by positional cloning and then routinely screened for mutations. Before
`
`BRCA2, "[p]ositional cloning [had] been used effectively [to isolate] several
`
`important human disease genes such as cystic fibrosis, familial adenomatous
`
`polyposis, and Huntington's disease." GDX1006, 6:1 to 6:2; GDX1025, 6. A
`
`
`
`- 15 -
`
`GeneDX 1002, pg. 18
`
`

`

`
`
`
`disease gene is first localized by determining a chromosomal region associated
`
`Inter Partes Review of USPN 6,051,379
`Declaration of Madhuri Hegde, Ph.D, FACMG (Exhibit GDX1002)
`
`with inheritance of the disease in affected families in a process called mapping.
`
`GDX1006, 3:2. After the disease-linked chromosomal region is sufficiently
`
`narrowed by mapping, the gene can be identified and characterized by other
`
`standard molecular biology techniques. Id., 3:2.
`
`34. Normally, positional cloning starts with physically mapping the gene
`
`location on a chromosome by linkage analysis. See GDX1006, 3:2. Linkage
`
`analysis aims to find the location of a gene of interest on a chromosome relative to
`
`a marker DNA sequence, whose position on the chromosome is already known.
`
`"Linkage analysis relies on the identification of a marker or markers that segregate
`
`[in families] with disease predisposition." Id., 3:2. In other words, by identifying
`
`the presence of certain markers in family members with disease, and the absence of
`
`the same marker in individuals without disease, researchers can determine that a
`
`certain genetic region correlates with the disease.
`
`35. Physically mapping genes was routine before September 23, 1997.
`
`And markers spanning the entire human genome had been identified and were
`
`routinely being used. Researchers were able to perform multiple rounds of linkage
`
`analysis, with each round finding genetic markers that are incrementally closer to
`
`the gene location. Using this mapping approach, a gene can be located to a
`
`
`
`- 16 -
`
`GeneDX 1002, pg. 19
`
`

`

`
`
`
`relatively narrow region on a chromosomal region bound by the two closest
`
`Inter Partes Review of USPN 6,051,379
`Declaration of Madhuri Hegde, Ph.D, FACMG (Exhibit GDX1002)
`
`markers. GDX1006, 7:2.
`
`36. Then, once the location of a gene had been genetically refined to
`
`chromosomal region, it was recognized that "the only viable approach [] to
`
`obtaining the gene is to capture the linked region physically, search for all the
`
`genes within it, and see which is altered consistently in linked families …."
`
`GDX1006, 7:2. Capturing and determining the disease gene involves: 1) physically
`
`placing the genetic region of interest into laboratory host organisms, such as yeast
`
`and bacteria in a commonly used process known as cloning; 2) screening the host
`
`organisms to identify the ones carrying candidate disease-causing genes; and 3)
`
`screening the candidate genes for mutations that cause the disease. GDX1006, 7:2
`
`to 2:1.
`
`37. Prior to September 23, 1997, yeast artificial chromosomes (YACs),
`
`bacterial artificial chromosomes (BACs), P1 phages, and cosmids were commonly
`
`used laboratory tools to clone (amplify) specific segments of genomic DNA.
`
`GDX1006, 7:2. Clones were then used to screen cDNA libraries from appropriate
`
`tissue to identify the cDNAs corresponding to the candidate gene located within
`
`the region. Id., 8:2 to 11:1. The commonly used approaches include: direct
`
`hybridization, exon trapping, CpG island trapping, and zooblots. Id., 10:1 to 11:1.
`
`
`
`- 17 -
`
`GeneDX 1002, pg. 20
`
`

`

`
`
`
`Each of these approaches could be used to thoroughly screen a cDNA library to
`
`Inter Partes Review of USPN 6,051,379
`Declaration of Madhuri Hegde, Ph.D, FACMG (Exhibit GDX1002)
`
`identify a candidate gene.
`
`38. Candidate genes and gene sequences were routinely analyzed for the
`
`presence of mutations that co-segregate with disease, for example, by detecting
`
`whether any sequence variation was present in the gene of individuals with disease
`
`as compared to individuals without disease in the same family. GDX1006, 11:1 to
`
`12:2. And various methods for screening genes for sequence variations were well-
`
`known and routinely used prior to September 23, 1997. Such routine methods
`
`included hybridization (e.g., allele-specific hybridization using allele-specific
`
`oligonucleotide (ASO) probes) and sequencing methods. GDX1006, 11:1 to 12:2;
`
`GDX1020, 11-12; GDX1029, 20:25-28; GDX1030, 1-5; GDX1021, 1-82;
`
`GDX1026, 1:2, 4:1, 5:2; GDX1023, 2-3.
`
`39. Hybridization methods detect an alteration in a nucleic acid (called
`
`target or template) by sequence-specific binding (based on complementarity) of the
`
`
`2 GDX1021 has an online publication date of May 1, 2001, but corresponds
`
`to the printed publication date of August 1995, as indicated at the bottom of page 1
`
`of the document, which states “Current Protocols in Human Genetics (1995) 9.4.1-
`
`9.4.8.” See GDX1021, 1. And, the ‘379 patent cites to the 1995 publication. See
`
`GDX1001, 9:15:52-54.
`
`
`
`- 18 -
`
`GeneDX 1002, pg. 21
`
`

`

`
`
`
`target nucleic acid with another nucleic acid (called a probe). The allele-specific
`
`Inter Partes Review of USPN 6,051,379
`Declaration of Madhuri Hegde, Ph.D, FACMG (Exhibit GDX1002)
`
`hybridization assay utilized in the ‘379 patent was one such routine method.
`
`GDX1001, 8:13:5-10, 9:15:52-54. In the allele-specific hybridization assay, a
`
`target sequence, such as a gene or gene fragment from an individual, is probed
`
`with ASO probes that can distinguish even single-base changes in a DNA sequence
`
`by specific hybridization. GDX1030, 1:1; GDX1029, 20:25-28; GDX1021, 1, 6:2.
`
`These ASO probes are designed to have sequences that are exactly complementary
`
`to either a mutant sequence or a wild-type sequence. GDX1030, 1:Abstract and
`
`2:Table 1. An ASO probe that is complementary to a mutant sequence will not
`
`hybridi