# Association for Molecular Pathology v. United States Patent & Trademark Office

> District Court, S.D. New York · April 5, 2010 · 702 F. Supp. 2d 181

URL: https://www.frixlaw.com/law-library/cases/2252138

## Case

- **Full name:** ASSOCIATION FOR MOLECULAR PATHOLOGY, Et Al., Plaintiffs, v. UNITED STATES PATENT AND TRADEMARK OFFICE, Et Al., Defendants
- **Court:** District Court, S.D. New York
- **Decided:** April 5, 2010
- **Citations:** 702 F. Supp. 2d 181; 2010 WL 1233416
- **Precedential status:** Published
- **Opinion:** Opinion by Sweet
- **Judges:** Sweet
- **Cited by:** 9 later opinions in the Frix Law Library

## Citator (automated)

- No negative treatment found by the automated citator. That is not the same as a confirmation that the case is good law; read the citing cases.
- Full citator and citing cases: https://www.frixlaw.com/law-library/cases/2252138

## How later opinions describe it (automated extraction)

- noting that genes, which are composed of segments of DNA, "contain[ ] the information used by the body” to produce proteins

## Opinion text

OPINION
SWEET, District Judge.
TABLE OF CONTENTS
I. PRIOR PROCEEDINGS..................................................186
II. THE PARTIES AND AMICI..............................................186
III. THE FACTS ............................................................192
*184
A. The Development of Genetics as a Field of Knowledge.....................192
B. Molecular Biology and Gene Sequencing ................................193
1. DNA............................................................193
2. Extracted and purified DNA.......................................196
3. RNA............................................................197
4. cDNA...........................................................198
5. DNA sequencing.................................................199
C. The Development of the Patents-in-Suit.................................200
D. Application of the Patents-in-Suit.......................................203
1. Myriad’s
BRCAl/2
testing.........................................203
2. Funding for Myriad’s
BRCAl/2
tests................................203
3. Myriad’s enforcement of the patents-in-suit..........................204
E. Disputed Issues......................................................206
1. The impact of Myriad’s patents on
BRCAl/2
testing...................206
2. The impact of gene patents on the advancement of science and medical treatment..............................................207
TV. THE PATENTS .........................................................211
A. Summary of the Patents ..............................................211
B. Construction of the Claims ............................................214
1. Legal standard...................................................214
2. Resolution of the disputed claim terms ..............................216
a. “DNA” and “isolated DNA”....................................216
b. “BRCA1” and “BRCA2”.......................................217
V. CONCLUSIONS OF LAW................................................217
A. The Summary Judgment Standard.....................................217
B. 35 U.S.C. § 101 and Its Scope .........................................218
C. The Composition Claims Are Invalid Under 35 U.S.C. § 101 ...............220
1. Consideration of the merits of Plaintiffs’ challenge is appropriate.....220
2. Patentable subject matter must be “markedly different” from a product of nature...............................................222
3. The claimed isolated DNA is not “markedly different” from native DNA..........................................................227
D. The Method Claims are Invalid Under 35 U.S.C. § 101 ....................232
1. The claims for “analyzing” and “comparing” DNA sequences are invalid under § 101.............................................233
2. The claim for “comparing” the growth rate of cells is invalid under § 101 .........................................................237
E. The Constitutional Claims Against the USPTO Are Dismissed.............237
VIII. CONCLUSION..........................................................238
Plaintiffs Association for Molecular Pathology, et al. (collectively “Plaintiffs”) have moved for summary judgment pursuant to Rule 56, Fed.R.Civ.P., to declare invalid fifteen claims (the “claims-in-suit”) contained in seven patents (the “patents-in-suit”) relating to the human
BRCAl
and
BRCA2
genes (Breast Cancer Susceptibility Genes 1 and 2) (collectively,
“BRCAl/2”)
under each of (1) the Patent Act, 35 U.S.C. § 101 (1952), (2) Article I, Section 8, Clause 8 of the United States Constitution, and (3) the First and Fourteenth Amendments of the Constitution because the patent claims cover products of nature, laws of nature and/or natural phenomena, and abstract ideas or basic human knowledge or thought. The defendant United States Patent and Trademark Office (“USPTO”) issued the patents-in-suit which are held by defendants Myriad Genetics and the University of Utah Research Foundation (“UURF”) (collectively “Myriad” or the “Myriad Defendants”). Myriad has cross-
*185
moved under Rule 56, Fed.R.Civ.P., for summary judgment dismissing Plaintiffs’ complaint, and the USPTO has cross-moved under Rule 12(c), Fed.R.Civ.P., for judgment on the pleadings. Based upon the findings and conclusions set forth below, the motion of Plaintiffs to declare the claims-in-suit invalid is granted, the cross-motion of Myriad is denied, and the motion of the USPTO is granted.
As discussed
infra
in greater detail, the challenged patent claims are directed to (1) isolated DNA containing all or portions of the
BRCAl
and
BRCA2
gene seqüence and (2) methods for “comparing” or “analyzing” BRCAl and
BRCA2
gene sequences to identify the presence of mutations correlating with a predisposition to breast or ovarian cancer. Plaintiffs’ challenge to the validity of these claims, and the arguments presented by the parties and amici, have presented a unique and challenging question:
Are isolated human genes and the comparison of their sequences patentable?
Two complicated areas of science and law are involved: molecular biology and patent law. The task is to seek the governing principles in each and to determine the essential elements of the claimed biological compositions and processes and their relationship to the laws of nature. The resolution of the issues presented to this Court deeply concerns breast cancer patients, medical professionals, researchers, caregivers, advocacy groups, existing gene patent holders and their investors, and those seeking to advance public health.
The claims-in-suit directed to “isolated DNA” containing human
BRCAl/2
gene sequences reflect the USPTO’s practice of granting patents on DNA sequences so long as those sequences are claimed in the form of “isolated DNA.” This practice is premised on the view that DNA should be treated no differently from any other chemical compound, and that its purification from the body, using well-known techniques, renders it patentable by transforming it into something distinctly different in character. Many, however, including scientists in the fields of molecular biology and genomics, have considered this practice a “lawyer’s trick”
1
that circumvents the prohibitions on the direct patenting of the DNA in our bodies but which, in practice, reaches the same result. The resolution of these motions is based upon long recognized principles of molecular biology and genetics: DNA represents the physical embodiment of biological information, distinct in its essential characteristics from any other chemical found in nature. It is concluded that DNA’s existence in an “isolated” form alters neither this fundamental quality of DNA as it exists in the body nor the information it encodes. Therefore, the patents at issue directed to “isolated DNA” containing sequences found in nature are unsustainable as a matter of law and are deemed unpatentable subject matter under 35 U.S.C. § 101 .
Similarly, because the claimed comparisons of DNA sequences are abstract mental processes, they also constitute unpatentable subject matter under § 101.
The facts relating to molecular biology are fundamental to the patents at issue and to the conclusions reached. Consequently, in the findings which follow, the discussion of molecular biology precedes the facts concerning the development, application, and description of the patents. Following those facts are the conclusions which compel the partial grant of summary
*186
judgment to the Plaintiffs, the denial of Myriad’s cross-motion, and the grant of the USPTO’s motion for judgment on the pleadings.
1. PRIOR PROCEEDINGS
The complaint in this action was filed on May 12, 2009, alleging violations of 35 U.S.C. § 101 ; Article I, Section 8, Clause 8 of the United States Constitution; and the First and Fourteenth Amendments to the Constitution.
Defendants moved to dismiss the complaint which motion was denied by the opinion of November 1, 2009.
See Assoc. for Molecular Pathology v. U.S. Patent and Trademark Office,
669 F.Supp.2d 365 (S.D.N.Y.2009). Plaintiffs were found to have the necessary standing to assert their declaratory judgment claims against the Myriad Defendants and the USPTO, and specific personal jurisdiction was found to exist over the Directors of the UURF by virtue of acts performed in their official capacity that were directed to the state of New York. It was also determined that this Court possessed the necessary subject matter jurisdiction to hear Plaintiffs’ constitutional claims against the USPTO and that the complaint satisfied the pleading requirements set forth in
Ashcroft v. Iqbal,
— U.S. -, 129 S.Ct. 1937 , 173 L.Ed.2d 868 (2009).
Plaintiffs’ motion for summary judgment and the cross-motions for summary judgment and judgment on the pleadings were heard and marked fully submitted on February 4, 2010.
II. THE PARTIES AND AMICI
Plaintiff Association for Molecular Pathology (“AMP”) is a not-for-profit scientific society dedicated to the advancement, practice, and science of clinical molecular laboratory medicine and translational research based on the applications of genomics and proteomics. AMP members participate in basic and translational research aimed at broadening the understanding of gene/protein structure and function, disease processes, and molecular diagnostics, and provide clinical medical services for patients, including diagnosis of breast cancer. Sobel Decl. ¶¶ 2, 4-5.
2
Plaintiff the American College of Medical Genetics (“ACMG”) is a private, nonprofit voluntary organization of clinical and laboratory geneticists. The Fellows of the ACMG are doctoral level medical geneticists and other physicians involved in the practice of medical genetics. With more than 1300 members, the ACMG’s mission is to improve health through the practice of medical genetics. In order to fulfill this mission, the ACMG strives to define and promote excellence in medical genetics practice and the integration of translational research into practice; promote and provide medical genetics education; increase access to medical genetics services and integrate genetics into patient care; and advocate for and represent providers of medical genetics services and their patients. Watson Decl. ¶¶ 2, 4-5.
Founded in 1922, plaintiff the American Society for Clinical Pathology (“ASCP”) is the largest and oldest organization representing the medical specialty of pathology and laboratory medicine. ASCP is a not-for-profit entity organized for scientific and educational purposes and dedicated to patient safety, public health, and the practice of pathology and laboratory medicine and has 130,000 members working as pathologists and laboratory professionals. ASCP members design and interpret the tests that detect disease, predict outcome,
*187
and determine the appropriate therapy for the patient. The ASCP is recognized for its excellence in continuing professional education, certification of laboratory professionals, and advocacy. Ball Decl. ¶¶ 2, 5.
Plaintiff the College of American Pathologists (“CAP”) is a national medical society representing more than 17,000 pathologists who practice anatomic pathology and laboratory medicine in laboratories worldwide. The College’s Commission on Laboratory Accreditation is responsible for accrediting more than 6,000 laboratories domestically and abroad, and approximately 23,000 laboratories are enrolled in CAP’s proficiency testing programs. It is the world’s largest association composed exclusively of board-certified pathologists and pathologists in training worldwide and is widely considered the leader in laboratory quality assurance. CAP is an advocate for high quality and cost-effective medical care. Scott Decl. ¶¶ 2, 4-5.
Plaintiff Haig Kazazian, M.D. (“Dr. Kazazian”), is the Seymour Gray Professor of Molecular Medicine in Genetics in the Department of Genetics at the University of Pennsylvania School of Medicine. He is a human genetics researcher and the previous chair of the Department. Dr. Kazazian and plaintiff Arupa Ganguly, Ph.D. (“Dr. Ganguly”), designed tests to screen the
BRCAl
and
BRCA2
genes in their lab and provided screening to approximately 500 women per year starting in 1996. Drs. Kazazian and Ganguly ceased their
BRCAl/2
testing in response to cease-and-desist letters from Myriad relating to the patents-in-suit. Kazazian Decl. ¶¶ 1-5.
Plaintiff Dr. Ganguly is an Associate Professor in the Department of Genetics at the Hospital of the University of Pennsylvania. Dr. Ganguly’s work previously included
BRCAl/2
screening for both research and clinical purposes. She ceased
BRCAl/2
screening following her receipt of cease-and-desist letters from Myriad accusing her lab of violating the patents-in-suit. Ganguly Decl. ¶¶ 1, 3-5.
Plaintiff Wendy Chung, M.D., Ph.D. (“Dr. Chung”), is an Associate Professor of Pediatrics and the Herbert Irving Professor of Pediatrics and Medicine in the Division of Molecular Genetics at Columbia University. Dr. Chung is a human geneticist whose current research includes research on the
BRCAl
and
BRCA2
genes. Because of the patents-in-suit, Dr. Chung currently cannot tell research subjects in her studies the results of their
BRCAl/2
tests and cannot offer clinical
BRCAl/2
testing services. Chung Decl. ¶¶ 1-9, 11-13,16.
Plaintiff Harry Ostrer, M.D. (“Dr. Ostrer”), is a Professor of Pediatrics, Pathology and Medicine and Director of the Human Genetics Program in the Department of Pediatrics at New York University School of Medicine. Dr. Ostrer’s work has focused on understanding the genetic basis of development and disease, including disorders of sexual differentiation and genetic susceptibility to breast and prostate cancer and malignant melanoma. Dr. Ostrer is actively engaged in identifying genes that convey risk of breast cancer and that may mitigate the effects of mutations in the
BRCAl
and
BRCA2
genes. Dr. Ostrer is also the Director of the Molecular Genetics Laboratory of NYU Medical Center, one of the largest academic genetic testing laboratories in the United States. Because of the patents-in-suit, Dr. Ostrer currently cannot tell research subjects in his studies the results of their
BRCAl/2
tests and cannot offer clinical
BRCAl/2
testing services. Ostrer Decl. ¶¶ 1-4.
Plaintiff David Ledbetter, Ph.D. (“Dr. Ledbetter”), is a Professor of Human Genetics and Director of the Division of Medical Genetics at the Emory University
*188
School of Medicine. Research in his laboratory focuses on the molecular characterization of human developmental disorders. Dr. Ledbetter directs the Emory Genetics Laboratory which provides testing services for individuals with or at risk for genetic diseases. Because of the patents-in-suit, Dr. Ledbetter cannot offer comprehensive
BRCAl/2
genetic testing to patients. Led-better Decl. ¶¶ 1-8,16.
Plaintiff Stephen T. Warren, Ph.D. (“Dr. Warren”), is the William Patterson Timmie Professor of Human Genetics, Chairman of the Department of Human Genetics, and Professor of Biochemistry and Professor of Pediatrics at Emory University. He is a past President of the American Society of Human Genetics. Dr. Warren supervises genetic research at Emory and is responsible for the laboratories at the Emory Genetics Laboratory. These laboratories would offer
BRCAl/2
genetic testing but for the patents-in-suit. Ledbetter Decl. ¶¶ 1,16.
Plaintiff Ellen Matloff, M.S. (“Ms. Matloff’), is Director of the Yale Cancer Genetic Counseling Program. Ms. Matloff advises women on the desirability of obtaining an analysis of their genes to determine if the women have the genetic mutations that correlate with an increased risk of breast and/or ovarian cancer. If she determines that such an analysis is warranted and the individual woman concurs, Ms. Matloff arranges for the analysis and then advises the woman of the significance of the results. Ms. Matloff would like to have the option to send patient samples to laboratories other than Myriad Genetics for
BRCAl/2
sequencing. Matloff Decl. ¶¶ 1-4,11.
Plaintiff Elsa W. Reich, M.S. (“Ms. Reich”), is a Professor in the Department of Pediatrics at New York University. She is a genetic counselor. She helps women decide whether to be tested for mutations in the
BRCAl
and
BRCA2
genes. If they need testing, she sends samples to Myriad and explains the results for the women. Ms. Reich would like to have the option to send patient samples to laboratories other than Myriad for
BRCAl/2
sequencing. Reich Decl. ¶¶ 1-3, 8.
Plaintiff Breast Cancer Action (“BCA”) is a national organization of approximately 30,000 members based in San Francisco, California. BCA is dedicated to representing the voices of people affected by breast cancer in order to inspire and compel the changes necessary to end the breast cancer epidemic. Its members include breast cancer survivors, family members of people diagnosed with breast cancer and other people affected by or concerned about breast cancer. BCA advocates for policy changes directed at achieving prevention, finding better treatments, and reducing the incidence of breast cancer, provides information about breast cancer to anyone who needs it via newsletters, web sites, e-mail and a toll-free number, and organizes people to get involved in advocacy to advance its policy goals. Brenner Decl. ¶¶ 1-3.
Plaintiff Boston Women’s Health Book Collective, doing business as Our Bodies Ourselves (“OBOS”), is a nonprofit, public interest women’s health education, advocacy, and consulting organization. OBOS provides information about health, sexuality and reproduction from a feminist and consumer perspective. OBOS advocates for women’s health and provides information to members of the public about genetic analysis. Norsigian Decl. ¶¶ 1-4.
Plaintiff Lisbeth Ceriani (“Ms. Ceriani”) is a 43-year-old single mother who was diagnosed with cancer in both breasts in May 2008. Ms. Ceriani is insured through MassHealth, a Medicaid insurance program for low-income people. Her oncolo
*189
gist and genetic counselor recommended that she obtain
BRCAl
and
BRCA2
genetic testing because she may need to consider further surgery in order to reduce her risk of ovarian cancer. However, Myriad will not accept the MassHealth coverage, and Ms. Ceriani is unable to pay the full cost out-of-pocket. Ceriani Deck ¶¶ 1-6.
Plaintiff Runi Limary (“Ms. Limary”) is a 32-year-old Asian-Ameriean woman who was diagnosed with aggressive breast cancer in 2005. Ms. Limary obtained
BRCAl/2
testing through Myriad and received the following result: “genetic variant of uncertain significance.” Because of Myriad’s patents, she is unable to pursue alternative testing options. Limary Deck ¶¶ 1-5.
Plaintiff Genae Girard (“Ms. Girard”) is a 39-year-old woman who was diagnosed with breast cancer in 2006. Shortly after her diagnosis, she obtained
BRCAl/2
genetic testing from Myriad and tested positive for a deleterious mutation on the
BRCA2
gene. She sought a second opinion of that test result but learned that Myriad is the only laboratory in the country that can provide full
BRCAl/2
sequencing. Girard Deck ¶¶ 1-6.
Plaintiff Patrice Fortune (“Ms. Fortune”) is a 48-year-old woman who was diagnosed with breast cancer in February 2009. Ms. Fortune is insured through Medi-Cal. Her oncologist and genetic counselor recommended that she obtain
BRCAl/2
genetic testing, including the supplemental testing that is offered by Myriad separate from its standard test, but told her that Myriad would not accept her insurance. Ms. Fortune is unable to pay the full cost out-of-pocket. Fortune Deck ¶¶ 1-5.
Plaintiff Vicky Thomason (“Ms. Thomason”) is a 52-year-old woman who was diagnosed with ovarian cancer in 2006. She obtained
BRCAl/2
genetic testing from Myriad in 2007 and was found to be negative for mutations covered by that test. Her genetic counselor advised her about additional
BRCAl/2
genetic testing offered by Myriad that looks for other large genetic rearrangements that are not included in Myriad’s standard full sequencing test, but informed her that her insurance would not cover the full cost of that test. Ms. Thomason is unable to afford the extra cost. Thomason Deck ¶¶ 1-8.
Plaintiff Kathleen Raker (“Ms. Raker”) is a 41-year-old woman whose mother and maternal grandmother died from breast cancer. She obtained
BRCAl/2
genetic testing from Myriad in 2007 and was found to be negative for mutations covered by that test. Her genetic counselor advised her about additional
BRCAl/2
genetic testing offered by Myriad that looks for other large DNA rearrangements that are not included in Myriad’s standard full sequencing test, but informed her that it was unclear whether her insurance would cover the full cost of that test. Ms. Raker is unable to afford the extra cost. Raker Deck ¶¶ 1-9.
Defendant USPTO is an agency of the Commerce Department of the United States with its principal office in Alexandria, Virginia. USPTO Answer ¶ 27.
Defendant Myriad is a for-profit corporation incorporated in Delaware with its principal place of business in Salt Lake City, Utah. Myriad is the former co-owner of several of the patents-in-suit and the current exclusive licensee of the patents-in-suit. Myriad is the sole provider of full sequencing of
BRCAl
and
BRCA2
genes in the United States on a commercial basis. Myriad Answer ¶ 28.
The University of Utah Research Foundation, whose directors are named as defendants in their official capacity, is an
*190
owner or part-owner of each of the patents-in-suit. Myriad Answer ¶ 29.
Amici curiae American Medical Association, American Society of Human Genetics, American College of Obstetricians and Gynecologists, American College of Embryology, and The Medical Society of the State of New York are non-profit organizations representing physicians and medical students throughout the United States, including New York; professionals in the field of human genetics, including researchers, clinicians, academicians, ethicists, genetic counselors and nurses whose work involve genetic testing; women’s health care professionals; and embryologists. These amici contend that the patents-in-suit are directed to unpatentable natural phenomena in violation of Article I, Section 8, Clause 8 of the Constitution, and 35 U.S.C. § 101 , are unnecessary to promote innovation in genetic research, and violate medical and scientific ethics.
Amici curiae March of Dimes Foundation, Canavan Foundation, Claire Altman Heine Foundation, Breast Cancer Coalition, Massachusetts Breast Cancer Coalition, National Organization for Rare Disorders, and National Tay-Sachs £ Allied Diseases Association are non-profit organizations dedicated to advancing the treatment of a variety of genetic diseases, including breast cancer, Tay-Sachs, Spinal Muscular Dystrophy, Canavan disease, and other rare genetic disorders. These amici contend that Myriad’s patents represent patents on natural phenomena and laws of nature, thereby restricting future research and scientific progress.
Amici curiae National Women’s Health Network, Asian Communities for Reproductive Justice, Center for Genetics and Society, Generations Ahead, and Pro-Choice Alliance for Responsible Research are non-profit organizations seeking to improve the health of women; promote reproductive justice; encourage responsible use and governance of genetic, reproductive and biomedical technologies; promote policies on genetic technologies that protect human rights; promote accountability, safety, and social justice in biomedical research from a women’s rights perspective. These amici contend that isolated DNA constitutes an unpatentable product of nature whose patenting harms women by stifling innovation and interfering with patient access to medical testing and treatment. These amici also contend that human genes and the information contained therein constitute part of the common heritage of humanity, and patenting human gene sequences is contrary to both international law and treatises as well as the public trust doctrine.
Amici curiae The International Center for Technology Assessment, Indigenous People Council on Biocolonialism, Greenpeace, Inc., and Council for Responsible Genetics are non-profit organizations dedicated to assisting the public and policy makers in understanding how technology affects society, protecting the cultural heritage and genetic materials of indigenous peoples; addressing global environmental problems; and protecting the public interest and fostering public debate about the social, ethical, and environmental implications of genetic technologies. These amici contend that the patents-in-suit claim unpatentable products of nature and that gene patents have significant negative consequences, including privatization of genetic heritage in violation of fundamental precepts of common heritage, public domain, and the public trust doctrine; creation of private rights of unknown scope and significance; facilitate the exploitation of indigenous peoples; and violation of patients’ rights to informed consent.
Amicus curiae Biotechnology Industry Organization (“BIO”) is the country’s larg
*191
est biotechnology trade association, representing over 1200 companies, academic institutions, and biotechnology centers in all 50 states. BIO members are involved in the research and development of biotechnological healthcare, agricultural, environmental, and industrial products. BIO member companies range from start-up businesses and university spin-offs to large Fortune 500 corporations. BIO contends that patents directed to isolated DNA fall within the categories of patent-eligible subject matter because they differ “in kind” from naturally-occurring DNA. The BIO also contends that patents such as the ones in dispute here provide incentives for investment in biotechnology that promotes the advancement of science.
Amicus curiae Boston Patent Law Association (“BPLA”) is a non-profit association of attorneys and other intellectual property professionals. BPLA’s members serve a broad range of clients who rely on the patent system, including independent investors, corporations, investors, and nonprofit and academic institutions, such as universities and research hospitals. BPLA contends that patents, including patents on gene-related inventions, promote innovation by protecting investments in the innovation process. It further contends that the patents-in-suit satisfy the requirements of 35 U.S.C. § 101 as well as the Constitution.
Amicus curiae Generic Alliance (“GA”) is a not-for-profit, tax-exempt health advocacy organization founded in 1986 (as the Alliance for Genetic Support Groups). It brings together diverse stakeholders that create novel partnerships in advocacy. By integrating individual, family, and community perspectives to improve health systems, Genetic Alliance seeks to revolutionize access to information to enable translation of research into services and individualized decision-making. GA contends that the wholesale abolition of patents on isolated DNA molecules and isolated purified natural substances is legally untenable and undesirable as public policy, because it would diminish the promise of genetic research for patients and negatively affect other areas of medicine.
Amicus curiae Rosetta Genomics, Inc. is a wholly owned subsidiary of amicus curiae Rosetta Genomics, Ltd., a molecular diagnostics company that provides diagnostic tests for cancer and which owns several patents claiming isolated nucleic acid sequences. Amicus curiae George Mason University (“George Mason”) is a public university located in Virginia. Research conducted at George Mason has been incorporated into patent applications covering cancer diagnostics. These amici contend that the question of patentability of human gene sequences is appropriately left to Congress; that the patents-in-suit promote, rather than hinder innovation; and that the challenged patents are lawful under 35 U.S.C. § 101 and the Constitution.
Amicus curiae BayBio is an independent, nonprofit 501(c)(6) trade association serving the life sciences industry in Northern California, and represents more than 330 companies involved in the research and development of treatments, cures, and diagnostics. Amicus curiae Celera Corporation is a manufacturer of diagnostic products that include gene-based products used in genetic testing. Amicus curiae The Coalition for 21st Century Medicine represents some of the world’s most innovative diagnostic technology companies, clinical laboratories, researchers, physicians, venture capitalists, and patient advocacy groups that share a common mission to develop advanced diagnostics that improve the quality of healthcare for patients. Amicus curiae Genomic Health, Inc., is a life sciences company committed to im
*192
proving the quality of cancer treatment decisions through genomics-based clinical laboratory services and currently offers the Oncotype DX breast cancer assay, which predicts the likelihood of the recurrence of specific types of breast cancer and whether a patient will benefit from certain treatment strategies. Amicus curiae Qiagen, N.V. is a leading provider of innovative sample and assay technologies and products which are considered standard for use in molecular diagnostics, applied testing, and academic and pharmaceutical research and development. Amicus curiae Target Discovery, Inc. discovers, validates, and utilizes protein isoforms to improve clinical diagnosis and management of disease. Amicus curiae XDx, Inc., is a molecular diagnostics company focused on the discovery, development and commercialization of non-invasive gene expression testing in the areas of transplant medicine and autoimmunity through the use of modern genomics and bioinformatics technology. These amici contend that patent exclusivity is required for the development of personalized medicine and that the challenged patents satisfy the requirements of 35 U.S.C. § 101 and the Constitution. In addition, the amici contend that the harm alleged by Plaintiffs can be redressed through traditional judicial remedies and do not require a finding that isolated DNA constitutes unpatentable subject matter.
Amicus curiae Kenneth Chahine, Ph.D. (“Professor Chahine”), is a Visiting Professor of Law at S.J. Quinney College of Law at the University of Utah. Professor Chahine contends that the scope of the claims-in-suit are sufficiently limited to avoid claiming products of nature and that the claims directed to isolated DNA and diagnostic process satisfy the requirements of patentable subject of 156 matter under 35 U.S.C. § 101 .
Amicus curiae Kevin E. Noonan, Ph.D. (“Dr. Noonan”), is a patent attorney with McDonnell Boehnen Hulbert & Berghoff LLP. Dr. Noonan contends that isolated human DNA constitutes patentable subject matter and that a ban on patenting isolated human DNA would negatively affect the development of human therapeutics, the development of personalized medicine, and the scientific research in general.
III. THE FACTS
The facts as set forth in this section are taken from the parties’ respective statements and counterstatements pursuant to Local Civil Rule 56.1 and the affidavits submitted by the parties and amici and are not in dispute except where noted.
A. The Development of Genetics as a Field of
Knowledge
The field of genetics — the science of heredity and variation in living organisms— and the concept of units of heredity that could be transmitted from one generation to another originated in the 19th century from experiments with pea plants conducted by Gregor Mendel. Mendel showed that certain traits are passed on from parent to offspring as discrete entities and do not appear blended in the offspring. He hypothesized that it was the plant’s genotype, or assortment of hereditary factors, that determined the plant’s phenotype, or appearance. Mason Deck ¶ 8. In 1909, this unit of inheritance was termed a “gene.” Yet the gene remained an abstract concept until 1915, when it was shown that genes corresponded to physical spans of chromosomal material. Mason Deck ¶ 9.
In 1944, scientists determined that the chemical compound known as deoxyribonucleic acid, or DNA,
3
served as the carri
*193
er for genetic information by demonstrating that DNA extracted from one strain of bacteria and transferred to another strain could transfer certain characteristics found in the first strain. Oswald Theodore Avery, et al.,
Studies on the Chemical Nature of the Substance Inducing Transformation of Pneumococcal Types: Induction of Transformation by a Desoxyribonucleic Acid Fraction Isolated from Pneumococcus Type III,
79 J. Exp. Med. 137-158 (1944).
On April 25, 1953, James Watson and Francis Crick published their determination of the famous double-helix structure of DNA in the journal Nature. James D. Watson & Francis H.C. Crick,
A Structure for Deoxyribose Nucleic Acid,
171 Nature 737-38 (1953). Dr. Crick subsequently contributed to the decryption of the genetic code and proposed “the central dogma” of molecular biology: (1) information is encoded in a segment of DNA, i.e., a gene; (2) transmitted through a molecule called RNA; and then (3) utilized to direct the creation of a protein, the building block of the body. Mason Decl. ¶ 10.
Our understanding of the DNA contained within our cells has since grown at an exponential rate and has included the landmark completion of the first full-length sequence of a human genome, containing 25,000 genes, as a result of the work performed by the Human Genome Project from 1990 to 2003. Sulston Decl. ¶¶ 11, 22. Access to the information encoded in our DNA has presented expansive new possibilities for future biomedical research and the development of novel diagnostic and therapeutic approaches. How this genomic information is best harnessed for the greater good presents difficult questions touching upon innovation policy, social policy, medical ethics, economic policy, and the ownership of what some view as our common heritage.
B.
Molecular Biology and Gene Sequencing
An understanding of the basics of molecular biology is required to resolve the issues presented and to provide the requisite insight into the fundamentals of the genome, that is, the nature which is at the heard of the dispute between the parties. What follows represents the standard undisputed knowledge of those in the field of molecular biology as set forth in the parties’ 56.1 Statements and expert declarations. Citations are also made to two established texts in the field: Bruce Alberts, et al.,
Molecular Biology of the Cell
(4th ed. 2002)
(“The Cell”)
and James Watson, et al.,
Molecular Biology of the Gene
(6th ed. 2008) (“The Gene”).
1. DNA
DNA is a chemical molecule composed of repeating chemical units known as “nucleotides” or “bases.” DNA is composed of four standard nucleotides: adenine, thymine, cytosine, and guanine. As shorthand, scientists denote nucleotides by the first letter of the names of their bases: “A” for adenine; “G” for guanine; “T” for thymine; and “C” for cytosine. These nucleotide units are composed of several chemical elements, namely carbon, hydrogen, oxygen, nitrogen, and phosphorus, and are linked together by chemical bonds to form a strand, or polymer, of the DNA molecule. Kay Decl. ¶¶ 14, 125; Linck Decl. ¶ 70. Although it can exist as a single strand of nucleotides, DNA typically exists as a “double helix”
4
consisting of
*194
two intertwined strands of DNA that are chemically bound to each other. This structure is possible because of a property of DNA known as “base pair complementarity” or “base pairing,” in which adenine on one strand of DNA always binds to thymine on the other strand of DNA, and guanine on one strand always bind to cytosine on the other strand. Kay Decl. ¶ 129. For example, if a portion of one strand of DNA has the nucleotide sequence ACTCGT, the corresponding section of DNA on the complementary strand will have the nucleotide sequence TGAGCA.
Genes are basic units of heredity found in all living organisms and are responsible for the inheritance of a discrete trait. Sulston Decl. ¶ 11. In molecular terms, a gene is composed of several, typically contiguous, segments of DNA. Kay Decl. ¶ 142. Each gene is typically thousands of nucleotides long and usually “encodes” one or more proteins, meaning it contains the information used by the body to produce those proteins. Some of the segments of DNA within a gene, known as “exons” or “coding sequences,” contain sequences necessary for the creation of a protein, while other segments of DNA, known as “in-trons,” are not necessary for the creation of a protein.
5
See
Mason Decl. ¶ 11; Kay Decl. ¶ 151; Schlessinger Decl. ¶ 14. DNA encodes proteins by way of three nucleotide combinations, termed “codons,” that correspond to one of twenty amino acids that constitute the building blocks of proteins. Sulston Decl. ¶¶ 14-15. For example, the codon adenine-thymine-guanine (ATG) encodes the amino acid methionine. Kay Decl. ¶ 158. However, because there are only twenty different amino acids but 64 possible codons that can be derived from combinations of the four DNA nucleotides, most amino acids are encoded by more than one DNA codon.
The Gene
at 37 & Table 2-3.
Together, the approximately 25,000 genes in the human body make up the human genome.
6
The genome, and the genes within it, are contained within almost every cell in the human body and define physical traits such as skin tone, eye color, and sex, in addition to influencing the development of conditions such as obesity, diabetes, Alzheimer’s disease, and bipolar disorder. Mason Decl, ¶¶ 4-5; Sulston Decl. ¶¶ 10-11.
The linear order of DNA nucleotides that make up a polynucleotide, such as a gene, is referred to as the “nucleotide sequence,” “DNA sequence,” or “gene sequence.”
7
Kay Decl. ¶ 126; Schlessinger Decl. ¶ 19; Linck Decl. ¶ 45; Sulston Decl. ¶ 16; Mason Decl. ¶ 13; Chung Decl. ¶ 10. Gene sequences constitute biological information insofar as they describe the structural and chemical properties of a particular DNA molecule and serve as the cellular “blueprint” for the production of proteins. Sulston Decl. ¶ 16; Kay Decl. ¶ 126; Schlessinger Decl. ¶ 19; Linck Decl. ¶¶ 45, 46. Genes and the information represented by human gene sequences are products of nature universally present in each individual, and the information content of a human gene sequence is fixed. While many inventive steps may be necessary to allow scientists to extract and read a gene sequence, it is undisputed that the ordering of the nucleotides is determined by
*195
nature. Sulston Decl. ¶ 10, 17; Ostrer Decl. ¶ 14; Chung Decl. ¶ 25; Ledbetter Decl. ¶ 27; Leonard Decl. ¶ 15.
Scientists often use the term “wild-type” to refer to the “normal” human gene sequence, i.e. the sequence of a gene without any variations,
8
against which individuals’ gene sequences are compared. Mason Decl. ¶ 17; Grody Decl. ¶ 46. Variations in the human genome are very common: aside from identical twins, the genomes of any two individuals are estimated to have one to five nucleotide differences for every 1000 nucleotides. Mason Decl. ¶ 14; Sulston Decl. ¶ 12.
Variations in the human genome, also known as “mutations,” can occur at different scales. Small scale variations can be manifested as slight sequence differences between the same genes in different individuals. Thus, for example, if the wild-type sequence of a portion of a gene is represented by GACTCG, a variation of that sequence might omit the first C (resulting in GATCG) or contain an extra C at that point (resulting in GACCTCG) or reverse the order of two of the letters (e.g., GCATCG). Mason Decl. ¶16. Alternatively, there can be large scale variations, such as the addition or deletion of substantial chromosomal regions. Thus, a particular gene may omit several hundred letters at one point or may add several hundred letters where they do not normally exist in the wild-type gene sequence. Even larger variations, known as structural variants, also can occur, involving the deletion or duplication of up to millions of nucleotides. Extra copies or missing copies of the genome that are larger than 1000 nucleotides are called “copy number variants” (“CNVs”). Mason Decl. ¶ 15, 18.
Some of these mutations have little or no effect on the body’s processes, while other mutations, including those that appear to correlate with an increased risk of particular diseases, do interfere with the body’s processes.
9
There are also variants of uncertain significance (“VUS”): variants whose effect on the body’s processes, if any, is currently unknown. Mason Decl. ¶ 19; Sulston Decl. ¶ 18; Kay Decl. ¶ 76.
DNA as it is found in the human body— “native DNA” or “genomic DNA” — is packaged, along with proteins, into complex structures known as chromosomes, which contain the vast majority of the genes located in the cells of the human body. Kay Decl. ¶ 131; Schlessinger Decl. ¶ 12. This mixture of DNA and proteins that makes up chromosomes is also referred to as chromatin.
See The Gene
at 135. Genes are organized on forty-six chromosomes (twenty-three of which are inherited from the mother, and twenty-three of which are inherited from the father) which together constitute the vast majority of the human genome.
10
Mason Decl. ¶ 5. The proteins within the chromosomes are bound
11
to the DNA molecules
*196
and modulate the structure and function of the DNA molecules to which they are associated. Kay Decl. ¶ 131; Schlessinger Decl. ¶ 12;
The Cell
at 198, 208, Fig. 4-24. This interaction between chromosomal proteins and native DNA is one method by which the body establishes which genes are inactive, which genes are active, and the level of activity. Kay Decl. ¶ 132. Some DNA in the body also undergoes chemical modifications, such as methylation,
12
which can affect the level of activity of a gene, but does not affect the nucleotide sequence of the gene. Kay Decl. ¶ 132; Mason Supp. Decl. ¶ 22.
2. Extracted and purified DNA
Native DNA may be extracted from its cellular environment, including the associated chromosomal proteins, using any number of well-established laboratory techniques. Grody Decl. ¶ 13; Leonard Decl. ¶ 33. A particular segment of DNA, such as a gene, contained in the extracted DNA may then be excised from the genomic DNA in which it is embedded to obtain the purified DNA of interest. Kay Decl. ¶¶ 133, 137. DNA molecules may also be chemically synthesized in the laboratory. Kay Decl. ¶¶ 17,133,137.
Although the parties use the term “isolated DNA” to describe DNA that is separated from proteins and other DNA sequences, the term “isolated DNA” possesses a specific legal definition reflecting its use in the patents-in-suit. To avoid any confusion for purposes of this fact recitation, the term “extracted DNA” will be used to refer to DNA that has been removed from the cell and separated from other non-DNA materials in the cell (e.g., proteins); “purified DNA” will be used to refer to extracted DNA which has been further processed to separate the particular segment of DNA of interest from the other DNA in the genome; and “synthesized DNA” will be used to refer to DNA which has been synthesized in the laboratory.
As noted above, native DNA, unlike purified or synthesized DNA, is not typically found floating freely in cells of the body, but is packaged into chromosomes. Kay Decl. ¶¶ 131, 148. However, when DNA is copied, or replicated, in preparation for cell division, short segments of DNA are dissociated from the chromosomal proteins, although they are still contained within the cell. Similarly, when a particular portion of DNA is transcribed into RNA, segments of DNA exist dissociated from the proteins normally bound to it. Mason Supp. Decl. ¶ 23.
Purified or synthesized DNA may be used as tools for biotechnological applications for which native DNA cannot be used. Kay Decl. ¶¶ 134, 138; Schlessinger Decl. ¶ 27. For example, unlike native DNA, purified or synthesized DNA may be used as a “probe,”
13
which is a diagnostic tool that a molecular biologist uses to target and bind to a particular segment of DNA, thus allowing the target DNA sequence to be detectable using standard
*197
laboratory machinery. Kay Decl. ¶ 135; Schlessinger Decl. ¶ 29. Purified or synthesized DNA can also be used as a “primer”
14
to sequence a target DNA, a process used by molecular biologists to determine the order of nucleotides in a DNA molecule, or to perform polymerase chain reaction (“PCR”) amplification, a process which utilizes target-DNA specific primers to duplicate the quantity of target DNA exponentially. Critchfield Decl. ¶ 40; Kay Decl. ¶ 184.
During this process, the DNA molecule being used as a probe or a primer binds, or “hybridizes,” to a specific nucleotide sequence of a DNA target molecule, such as the
BRCAl
or
BRCA2
gene. This sequence-specific binding of two strands of DNA results from the same base-pairing phenomenon which allows two complementary strands of DNA to form the double helix structure. As a result, a strand of isolated DNA being used as a primer with the sequence ATGTCG, for example, will bind specifically to the portion of the target DNA molecule containing the nucleotide sequence TACAGC. The hybridization of a primer or probe to a DNA target, such as
BRCAl
or
BRCA2,
results in the formation of a “hybridization product” that either acts as a substrate for the enzymes used in the sequencing or amplification reaction or permits the detection of the target DNA.
See
Kay Decl. ¶¶ 138, 183; Schlessinger Decl. ¶ 30;
The Gene
at 105-06; 113-15.
The utility of purified
BRCAl/2
DNA molecules as biotechnological tools therefore relies on their ability to selectively bind to native or isolated
BRCAl/2
DNA molecules, which ability is a function of the isolated DNA’s nucleotide sequence. Kay Decl. ¶ 138.
3. RNA
Ribonucleic acid (“RNA”) is another nucleic acid found in cells. Like DNA, an RNA molecule is composed of a combination of four different nucleotides, three of which are the same bases incorporated into DNA: adenine, cytosine, and guanine. Unlike DNA, however, RNA utilizes uracil as the fourth nucleotide base, rather than thymine. In addition, the sugar-phosphate backbone in RNA is chemically different from the sugar-phosphate backbone of DNA. Kay Decl. ¶ 170.
The creation of proteins, which do the work of the body, comprises two steps: transcription and translation. Transcription is the process by which a temporary copy of a particular DNA sequence, in the form of an RNA molecule, is generated. Mason Decl. ¶¶ 11-12; Kay Decl. ¶¶ 149, 150. During transcription, a discrete segment of DNA unwinds itself inside the cell and the bases of the DNA molecule act as “clamps” that hold the bases of the newly forming RNA molecule in place while the chemical bonds of its sugar-phosphate backbone are formed. Kay Decl. ¶ 150. Each nucleotide in the DNA strand corresponds to a nucleotide to be incorporated into the newly forming RNA molecule: adenine on the DNA molecule binds to and thereby acts as a clamp for RNA nucleotide uracil, thymine for adenine, guanine for cytosine, and cytosine for guanine. Kay Decl. ¶ 150. This newly generated RNA is termed “pre-messenger RNA” or “pre-mRNA” and, like the DNA from which it was generated, contains both in-trons and exons. In a process known as “splicing,” the introns are physically cut out of the pre-mRNA by the cell and the remaining RNA segments containing the exons are rejoined, or “ligated,” together in consecutive order to form the final
*198
“messenger RNA,” or “mRNA.” Mason Decl. ¶ 11; Kay Decl. ¶ 151; Schlessinger Decl. ¶ 14. Pre-mRNAs can also undergo a process known as “alternative splicing,” in which different combinations of exons from the same pre-mRNA molecule are ligated together to yield different final mRNA products.
15
Kay Decl. ¶ 152; Schlessinger Decl. ¶ 14.
During translation, an mRNA molecule serves as a template for the assembly of a protein. Kay Decl. ¶ 157. In a process that parallels the transcription of DNA, the mRNA bases, along with other proteins in the cell, serve as clamps to hold the corresponding amino acids in place while the chemical bonds between the individual amino acids are formed. Kay Decl. ¶ 157. The three-nucleotide codons originally found in DNA and copied into mRNA determine which amino acids are incorporated into the protein and the order in which they are incorporated. Kay Decl. ¶ 157.
4. cDNA
Complementary DNA, or “cDNA,” is a type of DNA molecule generated from mRNA during a process known as “reverse transcription” which is catalyzed by a protein known as “reverse transcriptase.” cDNA derives its name from the fact that it is “complementary” to the mRNA from which it is produced — that is, each base in the cDNA can bind to the corresponding base in the mRNA from which it is generated. Kay Decl. ¶ 161. Because it is derived from mRNA, a cDNA molecule represents an exact copy of one of the protein coding sequences encoded by the original genomic DNA. Leonard Decl. ¶ 75. In this respect, cDNA contains the identical protein coding informational content as the DNA in the body, even though differences exist in its physical form. Mason Decl. ¶ 32.
During reverse transcription, each base of the mRNA serves as a clamp for its complementary nucleotide to be incorporated into the new cDNA molecule while the chemical bonds between the nucleotides of the cDNA strand are formed. Much like transcription, uracil on the mRNA binds to and thereby acts as a clamp for the nucleotide adenine, adenine for thymine, guanine for cytosine, and cytosine for guanine. Kay Decl. ¶ 165. The synthesis of cDNA from very long mRNA molecules, such as
BRCAl
and
BRCA2,
often does not result in a cDNA strand that is as long as the mRNA chain. Kay Decl. ¶ 166.
cDNA is typically generated by scientists in a laboratory. Kay Decl. ¶ 164, Linck Decl. ¶ 48. However, naturally occurring cDNAs, known as “pseudogenes,” exist in the human genome and are structurally, functionally, and chemically identical to cDNAs made in the laboratory. Mason Supp. Decl. ¶¶ 18-21; Nussbaum Decl. ¶¶ 41-42.
cDNA possesses certain structural and functional differences from native DNA. In contrast to most forms of native DNA, cDNA does not contain non-coding intronic sequences because it is derived from mRNA in which the introns have been removed. As a result, the production of proteins from cDNA does not require RNA splicing, in contrast to the production
*199
of proteins from native DNA as described above. Some cDNAs cannot be used to produce proteins without the addition of certain regulatory sequences, although other cDNAs possess some of the necessary regulatory sequences. cDNAs also usually contain nucleotides corresponding to the so-called “poly A tail” sequence found in mRNA, which native DNA does not possess. In addition, as mentioned above, native DNA is often (although not always) chemically modified in the body, e.g., by methylation, while cDNA generated in the laboratory is not so modified. Kay Decl. ¶¶ 168, 169; Mason Supp. Decl. ¶¶ 18-22; Nussbaum Decl. ¶¶ 41-42. cDNA also differs from mRNA in that it is a more stable compound and requires both transcription and translation to produce protein, rather than simply translation, as is the case with mRNA. Kay Decl. ¶ 171.
Much like purified DNA, cDNA can be used as a tool for biotechnological and diagnostic applications for which native DNA cannot be used. Kay Decl. ¶ 162. In addition, a scientist seeking to learn more about a protein of interest may transfer a cDNA encoding the protein into a recipient cell that does not normally express that protein. If the cDNA is operatively linked to particular “promoter” sequences that initiate transcription from the cDNA, the recipient cell will then express the protein of interest. Kay Decl. ¶ 163.
5. DNA sequencing
DNA sequencing is the process by which one “reads,” or determines the ordering of the nucleotides within a DNA molecule. Sulston Decl. ¶ 20; Kay Decl. ¶ 138. In the context of a gene or a portion of the genome, sequencing is designed to illuminate the information that nature has dictated in that person’s genome, and the sequencing process, by design, does not alter the information content of the native DNA sequence. Sulston Decl. ¶ 27; Mason Decl. ¶ 32. In that respect, sequencing is analogous to examining something through a microscope insofar as it makes visible something that exists in nature but is too small to be seen otherwise. Mason Decl. ¶ 23. Gene sequencing is used in diagnostic testing, such as Myriad’s tests, to determine whether a gene contains mutations that have been associated with a particular condition. Sulston Decl. ¶ 24; Chung Decl. ¶ 10; Swisher Decl. ¶¶ 23-26; Mason Decl. ¶ 21. These mutations, along with any association with a propensity to develop a particular disease, are caused by nature. Chung Decl. ¶ 10; Mason Decl. ¶ 20; Sulston Decl. ¶¶ 19, 27; Ledbetter Decl. ¶ 26. Therefore, the significance of any person’s gene sequence, including its relationship to any disease, is dictated by nature. Mason Decl. ¶ 32.
Sequencing is often used to identify single nucleotide substitutions or the insertion or deletion of a small number of nucleotides in a gene. Swisher Decl. ¶23; Kay Decl. ¶ 180. However, even full sequencing of an entire gene can miss large genomic rearrangements in which whole sections of the gene have been deleted or moved to a different part of the genome. Other tests have been developed that better detect these large rearrangements. Swisher Decl. ¶ 24; Ledbetter Decl. ¶¶ 16-17.
Sequencing native DNA first requires that cells of a tissue sample
16
be broken open to permit extraction of the DNA contained within the cells. Sulston Decl. ¶ 25. The extracted DNA of the entire genome
*200
contains over three billion nucleotides, of which the gene of interest comprises a very small portion. Kay Decl. ¶ 178.
BRCAl/2
sequencing by Myriad follows the typical process for sequencing extracted genomic DNA, which begins with obtaining a sufficient quantity of the
BRCAl/2
genomic DNA to permit its sequencing. Critchfield Decl. ¶ 40.
Under the current state of the art, the only practical way to obtain a sufficient amount of
BRCAl/2
genomic DNA for mutation detection purposes is to PCR amplify the genomic DNA in segments. Critchfield Decl. ¶ 40. In order to design the necessary primers to PCR amplify the correct region of the genome, at least a portion of the sequence of the target DNA molecule must be known. Kay Decl. ¶ 184. Typically, each exon of the
BRCAl/2
genes, including a small adjacent portion of the flanking introns, is separately amplified by PCR into one or more amplified DNA fragments, also called “amplicons.” The
BRCAl
and
BRCA2
genes have a total of 48 coding exons containing over 15,700 nucleotide base pairs. More than 50 amplicons are typically produced as part of Myriad’s
BRCAl/2
testing. Critchfield Decl. ¶ 40.
Following PCR amplification of the target DNA, a sequencing reaction is performed to determine the nucleotide sequence of the amplieon. Kay Decl. ¶ 183. As with PCR, at least some of the target sequence must be known in order to design a primer specific to the target DNA to be sequenced. Kay Decl. ¶¶ 177, 179, 183. For this reason, primers that bind only to specific DNA sequences in the
BRCAl
and
BRCA2
genes permit the analysis of a patient’s native DNA sequence to determine if the nucleotide composition is the same or different from the nucleotide composition of the normal
BRCAl
and
BRCA2
gene. Kay Decl. ¶ 187. Gene sequencing also sometimes utilizes cDNA as the DNA template. Leonard Decl. ¶ 75.
The techniques required for gene sequencing are well-known and understood by scientists skilled in molecular biology, and scientists and clinicians sequence and analyze genes literally every day. Chung Decl. ¶¶ 10-11; Mason Decl. ¶ 22; Hegde Decl. ¶¶ 6-7. However, because sequencing requires knowledge of the sequence of a portion of the target sequence, some ingenuity and effort is required for the initial sequencing of a target DNA.
See
Kay Decl. ¶ 183; Klein Decl. ¶ 32-34.
C.
The Development of the Patents-in-Suit
Breast cancer is the most frequently diagnosed cancer worldwide and is the leading cause of cancer death for women in Britain and the second leading cause of cancer death for women in the United States. Parthasarathy Decl. ¶ 8.
17
Ovarian cancer is the eighth most common cancer in women and causes more deaths in the Western world than any other gynecologic cancer. Swisher Decl. ¶ 10.
Throughout the 1980s, organizations dedicated to breast cancer awareness began efforts to increase public and governmental awareness of the breast cancer epidemic. In 1991, the U.S. Department of Defense created a research program devoted to breast cancer research. Over the years this funding has grown from less
*201
than $90 million during the fiscal year 1990 to more than $2.1 billion during the fiscal year 2008. Parthasarathy Decl. ¶ 10.
Throughout the 1980s, scientists from the United States, England, France, Germany, Japan, and other countries sought to be the first to identify DNA nucleotide sequences associated with breast cancer. Parthasarathy Decl. ¶ 11. In 1989, various European and American research laboratories participated in the International Breast Cancer Linkage Consortium (the “Consortium”), and in 1990, a group of researchers led by Mary-Claire King (“Dr. King”) at the University of California, Berkeley, published a landmark paper demonstrating for the first time that a gene linked to breast cancer, whose sequence was unknown but which was later designated Breast Cancer Susceptibility Gene 1 (BRCAl), was located on a region of chromosome 17.
See
Jeff M. Hall, et al.,
Linkage of Early-Onset Familial Breast Cancer to Chromosome 17q21,
250 Science 1684-89 (1990); Parthasarathy Decl. ¶ 11. Soon afterwards, research intensified as teams around the world, including groups led by Dr. King, Dr. Mark Skolnick (“Dr. Skolnick”) (co-founder of Myriad), and Dr. Michael Stratton (“Dr. Stratton”) (Institute for Cancer Research, London (“ICR”)), focused in on this region of the genome in an attempt to be the first to determine the DNA sequence of
BRCAl.
Parthasarathy Decl. ¶ 11.
Dr. Skolnick, a 1968 economics graduate of the University of California, Berkeley, had become interested in the application of demography to the study of genetics while doing research for his Ph.D. in genetics, which he received from Stanford University in 1975. While reconstructing genealogies in Italy, he met three Mormons who were microfilming parish records and from whom he learned of the resources of the Utah Genealogical Society in Salt Lake City. Thereafter, in 1973, after an inquiry from the organizers of a cancer center at the University of Utah, Dr. Skolnick suggested linking the Utah Mormon Genealogy with the Utah Cancer Registry. To further this effort, a familial cancer screening clinic was established and a program for mapping genes was developed. Skolnick Decl. ¶¶ 7,11,12.
Following publication of the King group’s study relating to
BRCAl
in the fall of 1990, Dr. Skolnick and his collaborators concluded that additional resources would be required to compete with the team of Dr. Francis Collins, which had received a substantial grant from the National Institutes of Health (“NIH”), Skolnick Decl. ¶¶ 13, 14, and in 1991 Myriad was founded by Dr. Skolnick and a local venture capital group interested in genetics. Myriad received 55 million in funding in 1992, $8 million in 1993, and 59 million in 1994. Skolnick Decl. ¶ 16.
Locating the
BRCAl
gene relied on the use of linkage analysis, in which correlations between the occurrence of cancer and the inheritance of certain DNA markers among family members were used to identify, or “map,” the physical location of, the BRCAl gene within the human genome.
See
'282 patent, col. 7:39-52. Once the physical location had been narrowed down to a sufficiently small region of the genome, Myriad was able to directly analyze the sequence of the DNA in this region and identify the nucleotides comprising the
BRCAl
gene.
See
'282 patent, col. 7:53-8:7. Successful linkage analysis requires large and genetically informative families, or kindreds, and detailed family information, such as detailed genealogical records, are an important component to this analysis. Shattuck Decl. ¶¶ 10, 13; '282 patent, col. 8:16-29.
In September 1994, the group at Myriad, along with researchers from the Na
*202
tional Institute for Environmental Health Sciences (“NIEHS”) (a subdivision of the NIH), the University of Utah, McGill University, and Eli Lilly and Company announced that they had sequenced the BRCAl gene.
See
Yoshio Miki, et ah,
A Strong Candidate for the Breast and Ovarian Cancer Susceptibility Gene BRCAl,
266 Science 66-71 (1994). In addition to funding the six NIEHS researchers who participated -in the identification of BRCAl, the NIH had also provided approximately $2 million in funding to the University of Utah.
18
See id.
at 71 n. 52; Parthasarathy Decl. ¶ 18. According to one analysis, the NIH contributed one-third of the funding for the identification of
BRCAl.
Parthasarathy Decl. ¶ 18.
A dispute subsequently arose between Myriad and the NIH over the NIEHS scientists’ exclusion as co-inventors on the
BRCAl
patents. Parthasarathy Decl. ¶ 19. The NIH maintained that its scientists had conducted some of the most important work leading up to the sequencing of the gene, including identifying the sequences of two of the BRCAl gene fragments and assembling the complete BRCAl sequence.
Id.
Myriad agreed to include the names of the NIEHS researchers as inventors on its patent application and pay inventors’ royalties, although no payments appear to have been made as of 2005.
Id.
Following the isolation of
BRCAl,
scientists continued to search for a second gene also believed to be linked with breast and ovarian cancer.
19
Parthasarathy Decl. ¶ 12. Myriad collaborated with several research groups, including scientists at the University of Laval in Quebec, Canada, the Hospital for Sick Children in Toronto, Canada, and the University of Pennsylvania in their search for this second gene. It also collaborated with a team of researchers led by Dr. Stratton at the ICR which, in November 1995, identified a mutation in breast cancer patients that appeared to be located in the as-yet unpublished
BRCA2
gene. Dr. Stratton ended the collaboration with Myriad upon learning of Myriad’s plans to patent the
BRCA2
gene sequence. Sulston Decl. ¶ 30.
On December 21, 1995, Myriad filed for patents on the
BRCA2
gene in both the U.S. and Europe. Tavtigian Decl. ¶ 5. The next day, the Stratton group published its identification of the
BRCA2
gene in the journal Nature, and Myriad submitted the sequence of
BRCA2
to GenBank, an international depository of gene sequence information. Parthasarathy Decl. ¶ 12; Tavtigian Decl. ¶ 9; Richard Wooster, et al.,
Identification of the Breast Cancer Susceptibility Gene BRCA2,
378 Nature 789-92 (1995). Subsequent analysis of the
BRCA2
sequence from the Stratton group indicated that while they had correctly sequenced the primary portion of the
BRCA2
gene, their published sequence had errors in both ends of the
BRCA2
gene. Tavtigian Decl. ¶¶ 7-10. Nonetheless, the consensus among the scientific community is that the Stratton group, rather than Myriad, was the first to sequence the
BRCA2
gene. Parthasarathy Decl. ¶ 13.
The isolation of the
BRCAl/2
genes required considerable effort on the part of Myriad and its collaborators as well as ingenuity in overcoming technical obstacles associated with the isolation process. However, the process and techniques used were well understood, widely used, and
*203
fairly uniform insofar as any scientist engaged in the search for a gene would likely have utilized a similar approach. Parthasarathy Decl. ¶ 19; Tavtigian Decl. ¶ 13.
D.
Application of the Patents-in-Suit
Mutations in the
BRCAl/2
genes correlate with an increased risk of breast and ovarian cancer. Women with BRCA1 and
BRCA2
mutations face up to an
85%
cumulative risk of breast cancer, as well as up to a 50% cumulative risk of ovarian cancer. Love Decl. ¶ 10; Parthasarathy Decl. ¶ 9. In addition, among the 10-15% of ovarian cancer cases that are inherited genetically, 80% of women diagnosed under the age of 50 carry mutations in their BRCA1 genes and 20% carry mutations in their
BRCA2
genes. The women with inherited BRCA1 mutations have a 40-52% cumulative risk of ovarian cancer by the time they reach 70 years old. For women with inherited
BRCA2
mutations, the risk is approximately 15-25%. Swisher Decl. ¶ 11. Male carriers of mutations are also at an increased risk for breast and prostate cancer. Love Decl. ¶ 10.
The existence of
BRCAl/2
mutations is therefore an important consideration in the provision of clinical care for breast and/or ovarian cancer. A patient will not only learn of her risk for hereditary breast and ovarian cancer, but also can gain information that may be useful in determining prevention and treatment options. This information is useful for women who are facing difficult decisions regarding whether or not to undergo prophylactic surgery, hormonal therapy, chemotherapy, and other measures. Swisher Decl. ¶ 12; Love Decl. ¶ 11. Testing results for the
BRCAl/2
genes can be an important factor in structuring an appropriate course of cancer treatment, since certain forms of chemotherapy can be more effective in treating cancers related to
BRCAl/2
mutations. Swisher Decl. ¶ 13; Love Decl. ¶ 18.
1. Myriad’s
BRCAl/2
testing
Myriad offers multiple forms of
BRCAl/2
testing to the general public. Its standard test, called Comprehensive BRACAnalysis, originally only consisted of the full sequencing of the
BRCAl/2
genes. Swisher Decl. ¶¶ 29-30; Reich Decl. ¶ 10; Parthasarathy Decl. ¶ 26; Critchfield Decl. ¶ 49. In 2002, Myriad supplemented its full sequencing analysis with a large rearrangement panel (“LRP”) for detecting five common large rearrangement mutations which is now included in the Comprehensive BRACAnalysis. Critchfield Decl. ¶¶ 49, 51. In 2006, Myriad began offering a supplemental test to Comprehensive BRACAnalysis called the BRACAnalysis Rearrangement Test (“BART”), which, according to Myriad, can detect virtually all large rearrangement mutations in the
BRCAl
and
BRCA2
genes.
20
Swisher Decl. ¶¶ 29-30; Reich Decl. ¶ 10; Parthasarathy Decl. ¶ 26; Critchfield Decl. ¶ 51.
2. Funding for Myriad’s
BRCAl/2
tests
The Myriad tests are available to clinicians and patients at a cost of over $3000 per test. In 2008, the total cost to Myriad of providing these tests was $32 million with resulting revenues of $222 million.
See
Myriad Genetics, Inc., Annual Report (Form 10-K), at 27 (Aug. 28, 2008). In Ontario, where the regional public healthcare plan is ignoring Myriad’s patent, the testing for breast cancer is performed for a third of Myriad’s cost.
See
CBC News, Ontario to Offer New Genetic Test for Breast, Ovarian Cancer (Jan. 8, 2003),
*204
available at http: //www.ebc.ca/health/story/ 2003/01/06/test_denetic030106.html.
Plaintiffs have noted several instances where women have been unable to obtain funding for all of Myriad’s testing services. For example, Myriad refused to process Ms. Ceriani’s sample because it did not accept coverage by Ms. Ceriani’s insurance carrier. Unable to pay for Myriad’s tests, and unable to find scholarship programs to fund her testing, Ms. Ceriani has not been tested. Ceriani Decl. ¶¶ 5-7. Ms. Fortune’s insurance carrier is not accepted by Myriad, and Ms. Fortune is also unable to pay the full out-of-pocket cost of Myriad’s test. Fortune Decl. ¶ 5.
Myriad’s BART test is not covered by a number of insurers, and unless a patient is one of a limited number of “high risk patients” who meet certain clinical criteria established by Myriad, a patient must pay an extra fee for BART testing. Swisher Decl. ¶¶ 29-30; Reich Decl. ¶ 10; Parthasarathy Decl. ¶ 26; Critchfíeld Decl. ¶ 52. As a result of the cost of BART testing, the test is unavailable to women who would otherwise choose to utilize the test. Swisher Decl. ¶¶ 30-31; Reich Decl. ¶ 10. For example, Ms. Raker is unable to afford the extra cost for BART testing and has not been tested for large genomic rearrangements, despite the advice of her genetic counselor. Raker Decl. ¶¶ 7-11. Similarly, Ms. Thomason has been unable afford the BART testing recommended by her genetic counselor. Thomason Decl. ¶¶ 6-9.
Myriad has pursued Medicaid coverage for years, but has been unable to secure “participating provider” status in 25 states which would allow it to offer testing to that state’s Medicaid patients. Myriad also has a financial assistance program which provides free testing to low-income and uninsured patients who meet certain economic and clinical requirements. In addition, Myriad provides free testing to independent non-profit institutions. In particular, Ms. Ceriani may be eligible to receive BRACAnalysis testing at no charge through the non-profit organization Cancer Resource Foundation, for which Myriad has provided free testing since 2009. Ruseoni Decl. ¶¶ 4-6; Critchfíeld Decl. ¶ 33; Ogaard Decl. ¶¶ 4-6. Currently, 90% of the tests Myriad performs are covered by insurance at over 90% of the test cost. Critchfíeld Decl. ¶¶ 32, 33, 52, 53.
A number of researchers, clinicians, and molecular pathologists have the personnel, equipment, and expertise
to
sequence and analyze genes, including the
BRCAl
and
BRCA2
genes, at a lower cost than Myriad’s testing. Kazazian Decl. ¶¶ 8, 11; Matloff Decl. ¶ 12; Ostrer Decl. ¶¶ 8-9; Ledbetter Decl. ¶¶ 16-18. For example, the
BRCAl/2
testing previously conducted by the Yale DNA Diagnostics Laboratory and the University of Pennsylvania Genetic Diagnostic Laboratory (“GDL”) cost less than what Myriad charges, and testing by OncorMed, a one-time competitor, was cheaper than Myriad’s testing. Matloff Decl. ¶ 7; Kazazian Decl. ¶ 8; Parthasarathy Decl. ¶ 24. However, on a “cost per exon” basis, Myriad’s BRACAnalysis test costs less than testing for other genes performed by the GDL at the University of Pennsylvania and Drs. Ledbetter and Warren at Emory University.
See infra;
Critchfíeld Decl. ¶ 35.
3. Myriad’s enforcement of the patents-in-suit
During the mid-to-late-1990s, Drs. Kazazian and Ganguly offered, for a fee, screening services for
BRCAl
mutations through the GDL at the University of Pennsylvania. Kazazian Decl. ¶ 4; Ganguly Decl. ¶ 3. The screening methodology utilized by Drs. Kazazian and Ganguly differed from the testing method used by Myriad, but involved using isolated DNA
*205
encoding
BRCAl
or
BRCA2.
Kazazian Decl. ¶ 9; Parthasarathy Decl. ¶ 23. At some point during this period, Dr. Skolnick advised Dr. Kazazian that Myriad planned to stop the
BRCAl/2
testing being conducted at the GDL. Kazazian Decl. ¶ 6. On May 29,1998, Myriad offered Dr. Kazazian a collaborative license in connection with the '473, '999, '001, '282, and '441 patents. Ganguly Decl. Ex. 2. However, the license covered only single mutation tests and multiple mutation panels of up to four mutations to allow for testing of patients of Ashkenazi Jewish descent. Ganguly Decl. ¶5. Myriad subsequently sent cease and desist letters to Dr. Kazazian and the University of Pennsylvania. On August 26, 1998, OMelveny
&
Myers LLP gave notice to Dr. Kazazian of infringement in the absence of a license. Ganguly Decl. Ex. 3. Myriad subsequently sued the University of Pennsylvania in November 1998 for infringement of the patents-in-suit.
See Myriad Genetics v. Univ. of Pennsylvania,
2:98-ev-00829 (D.Utah) (filed November 19, 1998). On June 10, 1999, Myriad’s general counsel, Christopher Wright, sent a letter to the University of Pennsylvania seeking written assurances that Dr. Kazazian and the University of Pennsylvania had ceased
BRCAl/2
clinical testing. Ganguly Decl. Ex. 4. This demand was repeated in a September 22,1999 letter from Myriad to the University of Pennsylvania. Ganguly Decl. Ex. 6.
As a result of Myriad’s efforts to enforce its patents against the University of Pennsylvania, the GDL no longer conducts
BRCAl/2
screening for research or as part of its clinical practice. Kazazian Decl. ¶ 5; Ganguly Decl. ¶¶ 8-9; Parthasarathy Decl. ¶ 28. However, sometime between 1999 and 2000, Dr. Critchfield, on behalf of Myriad, informed Dr. Kazazian that he is free to conduct academic research on the
BRCAl/2
genes, including sequencing the genes and detecting mutations in the genes. Critchfield Decl. ¶ 22.
In May 1998, Myriad offered Dr. Ostrer a license agreement to conduct diagnostic
BRCAl/2
genetic testing. The proposed license would permit Dr. Ostrer to conduct single mutation tests and multiple mutation panels (up to four mutations) for patients of Ashkenazi Jewish descent only. Dr. Ostrer declined the offer as too narrow to allow him to perform any meaningful
BRCAl/2
testing. Ostrer Decl. ¶ 7.
On September 15, 1998, Myriad also notified Dr. Barbara Weber (“Dr. Weber”), a principal investigator on the Cancer Genetics Network Project (“CGNP”) sponsored by the National Cancer Institute (“NCI”), that Myriad’s patent position might impact research sponsored by NCI. As a result of that letter, the GDL at the University of Pennsylvania ceased conducting
BRCAl/2
analysis for Dr. Weber. Ganguly Decl. ¶ 12, Ex. 7. According to Myriad, the GDL’s involvement in CGNP was to provide DNA testing on
BRCAl/2
genes for a fee, similar to the activity of any commercial core lab. Critchfield Decl. ¶ 21. In September 1999, Myriad also requested that Georgetown University, one of the other cancer centers participating in the CGNP, to cease sending genetic samples to the GDL for
BRCAl/2
analysis. Ganguly Decl. ¶ 13.
In December 2000, the director of the Yale DNA Diagnostics Lab received a cease and desist letter concerning
BRCAl/2
genetic testing being conducted by the lab. As a result of the letter, the lab ceased
BRCAl/2
genetic testing. Matloff Decl. ¶ 7. In 2005, Dr. Matloff sought permission from Myriad for the Yale DNA Diagnostics Lab to conduct screening for mutations caused by large rearrangements, which Myriad was not conducting at the time. Her request was denied. Matloff Decl. ¶ 8.
*206
Myriad was also involved in a series of lawsuits in the late 1990s against Oncormed, another company undertaking BRCA-related testing, regarding patents that covered various aspects of the
BRCAl
gene sequence. Parthasarathy Decl. ¶ 27. Myriad eventually purchased Oncormed’s patents and testing services in 1998.
Id.
E.
Disputed Issues
1. The impact of Myriad’s patents on
BRCAl/2
testing
According to Plaintiffs, Myriad’s patents and its position as the sole provider of
BRCAl/2
testing has hindered the ability of patients to receive the highest-quality breast cancer genetic testing and has impeded the development of improvements to
BRCAl/2
genetic testing. Plaintiffs first note deficiencies in the genetic testing services offered by Myriad, alleging that in the several years prior to the addition of the LRP, the testing done by Myriad did not reveal all known mutations in the
BRCAl/2
genes or utilize known methodologies that would have revealed these additional mutations.
21
Chung Deck ¶ 19; Matloff Deck ¶ 8; Swisher Deck ¶ 26; Ledbetter Deck ¶ 16; Parthasarathy Deck ¶ 29. As a result, Myriad’s test may have reported false negative results during this period. Plaintiffs also cite a study published in 2006 in the Journal of the American Medical Association that concluded that 12% of those from high risk families with breast cancer and with negative test results from Myriad carried cancer-predisposing genomic deletions or duplications in one of those genes. Swisher Deck ¶¶ 25-26. Plaintiffs also note that the sensitivity and specificity of the BART test has not been validated by comparing the results of BART testing with Multiplex Ligation Dependent Probe Amplification (“MLPA”) testing commonly used by researchers. Swisher Deck ¶¶ 32, 33.
According to Plaintiffs, other labs are in a position to offer more comprehensive testing than Myriad’s standard testing services and would use newer testing methods with improved testing quality and efficiency. These labs would also include large rearrangement testing after a negative test result is received from full sequencing. Ledbetter Deck ¶¶ 17-18; Chung Deck ¶ 18; Ostrer Deck ¶ 9. In addition, labs would perform genetic testing on tumor specimens preserved in paraffin from deceased family members, which Myriad does not regularly perform even though, according to Plaintiffs, such testing can often provide valuable genetic information for living relatives and is often necessary for accurate test interpretation. Chung Deck ¶ 24.
According to Myriad, however, its full sequencing test has been recognized as the “gold standard” for
BRCAl/2
mutation testing, and it continues to improve its testing process. Critchfield Deck ¶ 37. Myriad contends that it researched and developed a commercially viable high quality test for detecting large rearrangements as soon as it and the research community recognized the need for such testing, and continues work towards a test capable of detecting all large rearrangement mutations, including extremely rare ones. Critchfield Deck ¶¶ 49, 50. According to Myriad,
BRCAl/2
studies conducted by outside researchers confirmed that the BART test exhibited superior performance over other methods for mutation detection, including the MLPA kit often used by
*207
academic researchers.
22
Critchfield Decl. ¶ 51.
According to Plaintiffs, the lack of independent
BRCAl/2
analysis also undermines the ability of the scientific community to determine the meaning of VUS results, which are reported disproportionately for members of minority groups, and whose significance would be more extensively analyzed by other labs. Chung Decl. ¶ 20-21; Ostrer Decl. ¶ 12; Matloff Decl. ¶ 9. Myriad, however, asserts that it has undertaken significant efforts to determine the clinical importance of VUSs by establishing an in-house review committee for variant classification and developing a systematic approach to providing clinical interpretations for detected sequence variants based on generally accepted scientific data and analysis of its own database. In addition, clarification of any VUS previously reported to a patient is immediately provided to the patient and her doctor. According to Myriad, the VUS reporting rate has decreased markedly, with a 50% decrease in major ethnic groups between 2002 and 2006, and a total of 850 VUSs for about 21,000 patients have been clarified, including 502 VUSs for 13,127 patients since the beginning of 2008. Myriad also asserts that it has made critical data available to researchers to assist in the analysis of VUSs and which have the potential of improving the diagnostic testing for other genes. Critchfield Decl. ¶¶ 57-59.
Plaintiffs contend that as a result of the patents-in-suit,
BRCAl/2
genetic testing is one of the very few tests performed as part of breast cancer care and prevention for which a doctor or patient cannot get a second confirmatory test done through another laboratory. Love Decl. ¶ 12. In particular, women who receive a positive result cannot confirm the lab’s findings or seek a second opinion on the interpretation of those results.
23
Ledbetter Decl. ¶23; Ostrer Decl. ¶ 11. According to Myriad, absent any doubts regarding the accuracy of the original test, resequencing the patient’s genes by another laboratory would be an unnecessary waste of resources, and Myriad has never prohibited a second interpretation of the results of its diagnostic tests. Critchfield Decl. ¶ 64; Reilly Decl. ¶¶ 54, 55. In addition, there are multiple laboratories available to conduct confirmatory
BRCAl/2
testing pursuant to patent licenses granted by Myriad, including both the University of Chicago Genetic Services Laboratories and Yale DNA Diagnostic Laboratories. Critchfield Decl. ¶ 62. That confirmatory testing, however, is limited to the confirmation of certain, specific positive test results; the remaining types of positive test results as well as all negative test results are excluded from such testing services. Matloff Decl. ¶¶ 9, 10.
Whether the patents at issue impact the testing for
BRCAl/2
mutations favorably or unfavorably is an issue of factual dispute not resolvable in the context of the instant motions.
2. The impact of gene patents on the advancement of science and medical treatment
There exists a deep disagreement between the parties concerning the effects of
*208
gene patents on the progression of scientific knowledge.
According to Plaintiffs, data sharing is the key to the future of genetic discoveries and bioinformatics, and gene patents impede research aimed at identifying the role of genes in medical conditions. Sulston Decl. ¶¶ 36, 38. Plaintiffs assert that this understanding has wide acceptance, noting that from the beginning of the Human Genome project,
24
most scientists and even some private companies recognized the importance of keeping the genome freely available to all. For example, in 1994, the pharmaceutical company Merck funded a massive drive to generate gene sequences and place them into public databases, thereby making them difficult to patent. Sulston Decl. ¶¶ 22, 29. In 1996, a group of 50 of the most prominent geneticists who were involved with the sequencing of the human genome adopted the Bermuda principles which included the mandate that all “human
genome
sequence information should be freely available and in the public domain in order to encourage research and development and to maximize its benefit to society.” Sulston Decl. ¶ 33. The proliferation of intellectual property rights directed to genetic material has also been postulated to contribute to a phenomenon dubbed “the tragedy of the anti-commons,” in which numerous competing patent rights held by independent parties prevents any one party from engaging in productive innovation.
See, e.g.,
Michael A. Heller & Rebecca S. Eisenberg,
Can Patents Deter Innovation? The Anticommons in Biomedical Research, 280
Science 698 (1998) (citing Michael A. Heller,
The Tragedy of the Anticommons: Property in the Transition from Marx to Markets,
111 Harv. L. Rev. 621 (1998)).
According to Dr. Fiona Murray (“Dr. Murray”), who received a grant to research the impact of gene patenting on scientific research and commercialization, 4382 of the 23,688 genes listed in the database of the National Center for Biotechnology Information (“NCBI”) — nearly 20% of human genes — are explicitly claimed as United States intellectual property. Murray Decl. ¶ 6. After devising a study to gauge the impact of gene patenting on public knowledge that utilized the time lag between publication of papers
on
a
gene
sequence and the issuance of a patent claiming that gene sequence, Dr. Murray concluded that the Myriad patents have negatively impacted the public knowledge of the
BRCA1
and
BRCA2
genes by 5-10%. Murray Decl. ¶¶ 7-15, 20.
Plaintiffs have cited other studies to demonstrate the chilling effect of gene patents on the advancement of both genetic research and clinical testing. A survey of laboratory directors in the United States conducted by Dr. Mildred Cho (the “Cho study”) found that 53% decided not to develop a new clinical test because of a gene patent or license, and 67% believed that gene patents decreased their ability to conduct research. Cho Decl. ¶ 10. This correlated with a study conducted by the American Society of Human Genetics that reported that 46% of respondents felt that patents had delayed or limited their research. Cho Decl. ¶ 11. The Cho study also revealed that of those who stopped performing a clinical test because of a gene patent or license, the largest number stopped doing
BRCAl
and
BRCA2
testing (with the same number having stopped Apolipoprotein E testing). Cho Decl. ¶ 16. Specifically, the survey found that nine labs had ceased performing
BRCAl/2
ge
*209
netic testing as a result of the patents-in-suit. In addition to labs that have ceased performing
BRCAl/2
genetic testing, labs have avoided or refrained from developing tests for
BRCAl
and
BRCA2
as a result of the patents held by Myriad. Ostrer Decl. ¶ 6; Ledbetter Decl. ¶¶ 14-16. Studies of other gene patents have also revealed that labs frequently stop developing or offering clinical tests for disease as a result of gene patents. For example, a purportedly valid scientific survey of labs in the United States found a 26% drop in the number of labs performing testing for hemochromatosis as a result of gene patents. Cho Decl. ¶¶ 18-20.
Researchers, clinicians, and pathologists are aware that Myriad has sent cease and desist letters in connection with the patents-in-suit and that Myriad prohibits clinical testing of the
BRCAl/2
genes. Kazazian Decl. ¶¶ 5-11; Ganguly Decl. ¶¶ 4-14; Chung Decl. ¶ 15; Hegde Decl. ¶ 10; Matloff Decl. ¶¶ 5-7; Ostrer Decl. ¶¶ 4-7; Swisher Decl. ¶ 28; Hubbard Decl. ¶¶ 7-8; Kant Decl. ¶ 4; Ledbetter Decl. ¶ 13; Reich Decl. ¶¶ 3, 5; Parthasarathy Decl. ¶¶ 28-31. Myriad also does not permit researchers to tell patients involved in research the results of their
BRCAl/2
testing, leading physicians involved in breast cancer care and research unable to meet their ethical obligations to provide genetic test results to research subjects, when requested. Ostrer Decl. ¶ 10; Chung Decl. ¶ 13, 14. In addition to the direct benefits to the patient of knowing the results of their testing, such disclosure would also provide valuable insights into patient behavior that would enhance patient care. Ostrer Decl. ¶ 10. The AMA has also expressed its belief that the “[t]he use of patents ... or other means to limit the availability of medical procedures places significant limitation on the dissemination of medical knowledge, and is therefore unethical.” American Medical Association, Opinion 9.095-The Use of Patents and Other Means to Limit Availability of Medical Procedures, (adopted June 1995), available at http://www.amaassn.org/ama/pub/ physician-resources/medical-ethics/ code-medical-ethics/opinion9095.shtml. In addition, others have argued that human genes are the common heritage of mankind whose use should not be restricted by patent grants.
See, e.g.,
Pilar A. Ossorio,
The Human Genome
as
Common Heritage: Common Sense or Legal Nonsense?,
35 J.L. Med. & Ethics 425 , 426 (2007); Melissa L. Sturges,
Who Should Hold Property Rights to the Human Genome? An Application of the Common Heritage of Humankind,
13 Am. U. Int’l L.Rev. 219, 245 (1997); Barbara Looney,
Should Genes Be Patented? The Gene Patenting Controversy: Ethical and Policy Foundations of an International Agreement,
26 Law & Pol’y Int’l Bus. 231 (1994); Hubert Curien,
The Human Genome Project and Patents,
254 Science 1710,1710-12 (1991).
According to Plaintiffs, Myriad has withheld critical data concerning genetic predisposition to breast cancer from the Breast Cancer Information Core (“BIC”), an international, open access online database that is a central repository for information about the
BRCAl/2
genes and their genetic variants. The BIC facilitates the identification of deleterious mutations (i.e. those associated with a higher risk of cancer), provides a mechanism to collect and distribute data about genetic variants, and plays an important role in helping to elucidate the significance of those variants through its collection of data. Swisher Decl. ¶¶ 15, 17, 18; Chung Decl. ¶22; Ostrer Decl. ¶ 13. Although the value of the BIC comes from the amount and quality of data provided by the scientific community, Myriad, according to Plaintiffs, has not contributed any data to BIC in the past two years. Sulston Decl. ¶ 36; Swish
*210
er Decl. ¶¶ 19-21; Ostrer Decl. ¶¶ 12-13; Chung Decl. ¶¶ 21-22; Ledbetter Decl. ¶ 20.
Plaintiffs also assert that gene patents impede the development of improved genetic testing. For example, as new sequencing technologies offer the possibility of faster and less expensive sequencing of a patient’s genes, patents on one or more genes may impede scientists’ ability to develop a comprehensive test for complex diseases or provide a person with an analysis of his or her entire genome. Sulston Deck ¶ 38; Ledbetter Deck ¶ 24. In addition, Plaintiffs assert that gene patents interfere with the ability of physicians and researchers to investigate complex diseases. For example,
BRCAl/2
may be associated with cancers other than breast and ovarian cancer, but so long as the patents on these genes remain, no one will be able to include these genes in tests for other disease predispositions. Ledbetter Deck ¶¶ 24-25. Gene patents similarly impede the development and improvement of tests for diseases by geneticists. Ledbetter Deck ¶¶ 14-15. Plaintiffs also assert that allowing only a single lab to offer testing means that the one lab dictates the standards for patient care in testing for that disease; in contrast, patient care is promoted when more than one lab offers a particular genetic test, utilizing different methodologies, since this can ensure the quality of the testing and accuracy of the test results. Chung Deck ¶ 23; Ledbetter Deck ¶ 23; Reich Deck ¶¶ 9, 11; Ostrer Deck ¶ 11; Parthasarathy Deck ¶ 31.
Plaintiffs further assert that gene patents are not necessary to create incentives for initial discoveries or the development of commercial applications, including diagnostic tests. Cho Deck ¶ 25; Leonard Deck ¶¶ 20-21. Patents have not been necessary for the rapid introduction of genetic testing, as evidenced by genetic testing that has been offered prior to the issuance of a patent. Cho Deck ¶ 21. In support of this assertion, Plaintiffs cite a study of gene patents issued in the United States for genetic diagnostics that showed that 67% of these patents were issued for discoveries funded by the U.S. government. Cho Deck ¶ 22. Similarly, another study showed that 63% of patents on gene sequences resulted from federally supported research. Leonard Deck ¶ 22. As previously noted, the NIH provided $2 million in research grants to the University of Utah, or approximately one-third of the total funding, for the identification of the
BRCAl
sequence. Parthasarathy Deck ¶ 18.
Myriad has contested these assertions and disputes the idea that patenting of isolated human DNA conflicts with the advancement of science. According to Myriad, the quid pro quo of the patent system is that inventors, in exchange for a limited period of patent exclusivity, must provide a sufficient description of the patented invention so that others may improve upon it. Reilly Deck ¶ 24; Doll Deck ¶ 44. Furthermore, according to Myriad, its policy and practice has been and still is to allow scientists to conduct research studies on
BRCAl
and
BRCA2
freely, the result of which has been the publication of over 5,600 research papers on
BRCAl
and over 3,000 research papers on
BRCA2,
representing the work of over 18,000 scientists. Critchfield Deck ¶¶ 3, 13; Li Deck ¶¶ 3-6; Baer Deck ¶¶ 3-6; Parvin Deck ¶¶ 3-6; Sandbach Deck ¶¶ 3-7.
According to Myriad, patents on isolated DNA, including the patents-in-suit, actually promote research and advance clinical development to the benefit of patients. Reilly Deck ¶¶38, 43; Critchfield Deck ¶¶ 2-18, 65, 68; Linck Deck ¶¶ 27-28, 71, 73; Tavtigian Deck ¶¶ 14-17; Doll Deck
*211
¶¶ 45-46; Schlessinger Decl. ¶¶ 31-32. Myriad has contended that gene patents are essential for obtaining capital investment in the development and commercialization of technological breakthroughs. Linck Decl. ¶¶ 27, 28; Reilly Decl. ¶ 16; Doll Decl. ¶46. In support, Myriad has cited a survey published in 2009 by the BIO of 150 biotechnology member companies in the therapeutic and diagnostic healthcare industry stating that the majority of companies (61%) generally in-licensed projects that are in the pre-clinical or Phase ¶ stage of development, and thus still require substantial R & D investment and commercialization risk by the licensee. A substantial majority (77%) of the respondents without approved products indicated that they expect to spend 5-15 years and over $100 million developing a commercial product. Myriad asserts that these expenditures dwarf any initial research funding by the federal government. Reilly Decl. ¶ 22. In particular, Myriad notes that a significant amount of private investment led to its identification of the
BRCAl
and
BRCA2
sequences, with the expectation of patent protection providing an incentive to fund the research into the determination of the gene sequences. Skolnick Decl. ¶¶ 14-16. Therefore, Myriad asserts that absent the promise of a period of market exclusivity provided by patents and the infusion of venture and risk capital derived therefrom, companies such as Myriad that capitalize on innovation simply would not be created and their products would not be brought to market or the clinic. Reilly Decl. ¶¶ 18, 34, 51, 52, 62; Critchfield Decl. ¶¶ 67, 68; Linck Decl. ¶ 73.
Myriad also notes that it has made over 20,000 submissions to the BIC database, making it the largest contributor to the database. It has also published the largest clinical series of mutation risk in the
BRCA1/2
genes based on its testing data and has tabulated and posted the data on Myriad’s website, where it is freely available to researchers throughout the world. Critchfield Decl. ¶¶ 11,12.
According to Myriad, the majority of academic researchers operating laboratories (as opposed to Clinical Laboratory Improvement Amendments (“CLIA”)— certified laboratories) do not believe that they should share test results with subjects outside of the standard clinical setting. Reilly Decl. ¶¶ 57-59.
As the declarations submitted by the parties make clear, there exists a sharp dispute concerning the impact of patents directed to isolated DNA on genetic research and consequently the health of society. As with the dispute concerning the effect of the patents-in-suit on
BRCAl/2
genetic testing, the resolution of these disputes of fact and policy are not possible within the context of these motions.
IV. THE PATENTS
A.
Summary of the Patents
The subjects of this declaratory judgment action are fifteen claims contained in seven patents issued by the USPTO:
25
claims 1, 2, 5, 6, 7, and 20 of U.S. patent 5,747,282 (the “'282 patent”); claims 1, 6, and 7 of U.S. patent 5,837,492 (the “'492 patent”); claim 1 of U.S. patent 5,693,473 (the “'473 patent”); claim 1 of U.S. patent 5,709,999 (the “'999 patent”); claim 1 of U.S. patent 5,710,001 (the “'001 patent”); claim 1 of U.S. patent 5,753,441 (the “'441
*212
patent”); and claims 1 and 2 of U.S. patent 6,033,857 (the “'857 patent”).
26
The claims-in-suit may be divided into two types of claims: composition claims and method, or process, claims. Independent claim 1 of the '282 patent is representative of the group of composition claims and claims:
An isolated DNA coding for a BRCAl polypeptide, said polypeptide having the amino acid sequence set forth in SEQ ID NO:2.
This claim is therefore directed to an isolated DNA molecule possessing a nucleotide sequence that translates into the BRCAl protein. Because most amino acids can result from the translation of more than one DNA codon, multiple DNA sequences correspond to the nucleotide sequence claimed by this claim. Claim 2 of the '282 patent is dependent on claim 1 but contains an additional limitation that identifies the specific
BRCAl
nucleotide sequence of the claimed DNA.
27
Claims 5 and 6 of the '282 patent are directed to fragments as short as 15 nucleotides of the DNA molecules claimed in claims 1 and 2 of the '282 patent.
28
Finally, claim 7 of the '282 patent and claim 1 of the '473 patent are directed to isolated DNA possessing one of the specified mutant
BRCAl
gene sequences.
29
Claims 1, 6, and 7 of the '492 patent are also composition claims covering isolated DNA molecules containing certain specified nucleotide sequences relating to the
BRCA2
gene. Claim 1 is directed to an isolated DNA molecule encoding the
BRCA2
protein.
30
Like claim 1 of the '282 patent, claim 1 of the '492 patent is directed to multiple possible DNA sequences as a result of the redundancy of the DNA codons. Claim 6 of the '492 patent, however, is considerably broader than claim 1 and is directed to any DNA nucleotide encoding any mutant
BRCA2
protein that is associated with a predisposition to breast cancer.
31
Claim 7 of the '492 pat
*213
ent depends on claim 6, but is restricted to the mutated forms of the
BRCA2
nucleotide sequence set forth in the specification,
32
As a result of the breadth of these composition claims, they reach isolated
BRCAl/2
DNA obtained from any human being.
Claim 1 of the '999 patent is representative of the group of method claims. It claims:
A method for detecting a germline alteration in a BRCAl gene, said alteration selected from a group consisting of the alterations set forth in Tables 12A, 14, 18, or 19 in a human which comprises analyzing a sequence of a BRCAl gene or BRCAl RNA from a human sample or analyzing a sequence of BRCAl cDNA made from mRNA from said human sample with the proviso that said germline alteration is not a deletion of 4 nucleotides corresponding to base numbers 4184-4187 of SEQ ID NO:l.
Thus, claim 1 of the '999 patent covers the process of identifying the existence of certain specific mutations in the
BRCAl
gene by “analyzing” the sequence of the
BRCAl
DNA, RNA, or cDNA made from
BRCAl
RNA obtained from a human sample.
Most of the remaining method claims-in-suit are similarly structured and directed to the comparison of gene sequences. Claim 1 of the '001 patent claims a method for determining whether a human tumor sample contains a mutation in the BRCAl gene by “comparing” the sequence of the BRCAl gene from the tumor with the sequence of the
BRCAl
gene from a non-tumor sample from the same person.
33
Claim 1 of the '441 patent and claim 1 of the '857 are both directed to the same process, differing only as to whether the claimed method is directed to
BRCAl
('441) or
BRCA2
('857). Both of these independent claims are directed to the process of determining whether an individual has inherited an altered
BRCAl
or
BRCA2
gene by “comparing” the individual’s
BRCAl
or
BRCA2
gene sequence with the wild-type
BRCAl
or
BRCA2
gene sequence.
34
Claim 2 of the '857 patent cov
*214
ers a method for determining whether an individual has a predisposition for breast cancer by “comparing” the individual’s
BRCA2
gene sequence with the known wild-type BR.CA2 gene sequence.
35
Finally, claim 20 of the '282 patent claims a method for determining the effectiveness of a potential cancer therapeutic comprising growing cells carrying an altered
BRCAl
gene known to cause cancer in the presence and absence of a potential cancer therapeutic, comparing the growth rates of the cells, and concluding that a slower'growth rate in the presence of the potential therapeutic indicates that it is indeed a cancer therapeutic.
36
B.
Construction of the Claims
37
1. Legal standard
Before considering the patent-eligibility of a patent claim, the disputed terms in the claims must be construed in order ensure the scope of the claims is accurately assessed.
See, e.g., Datamize, LLC v. Plumtree Software, Inc.,
417 F.3d 1342, 1354 (Fed.Cir.2005) (“[A] utility patent protects ‘any new and useful process, machine, manufacture, or composition of matter, or any new or useful improvement thereof,’ 35 U.S.C. § 101 (2000), the scope of which is defined by the patent’s written claims.”). Courts are charged with interpreting disputed claim terms as a matter of law.
Markman v. Westview Instruments, Inc.,
517 U.S. 370, 384-85 , 116 S.Ct. 1384 , 134 L.Ed.2d 577 (1996).
In interpreting the meaning of claim terms, “words of a claim are generally given their ordinary and customary meaning” to a person of ordinary skill in the art at the time of invention (i.e., the effective filing date of the patent application).
Phillips v. AWH Corp.,
415 F.3d 1303, 1312-13 (Fed.Cir.2005) (internal citations and quotation marks omitted). “Importantly, the person of ordinary skill in the art is deemed to read the claim term not only in the context of the particular claim in which the disputed term appears, but in the context of the entire patent, including the specification.”
Id.
at 1313 . Thus, the Federal Circuit has emphasized the importance of “intrinsic” evidence in claim construction: the words of the claim themselves, the written description in the patent’s specification, and, when necessary,
*215
the history of the patent application’s prosecution before the USPTO.
Id.
at 1314-17 .
The process of claim construction begins with the language of the claims themselves. The language of the claim is what the patentee chose to use to “ ‘particularly point[] out and distinctly claim[] the subject matter which the applicant regards as his invention.’ ”
Id.
at 1311-12 (quoting 35 U.S.C. § 112 , ¶ 2). Thus, “the claims themselves provide substantial guidance as to the meaning of particular claim terms.”
Id.
at 1314. In addition to the particular claim being examined, the context provided by other claims may be helpful as well. “For example, the presence of a dependent claim that adds a particular limitation gives rise to a presumption that the limitation in question is not present in the independent claim.”
Id.
at 1314-15.
Claim language must also be read in the context of the specification.
Id.
at 1315. As the Federal Circuit has made clear, “claims, of course, do not stand alone. Rather, they are part of ‘a fully integrated written instrument,’ consisting principally of a specification that concludes with the claims.”
Id.
(quoting
Markman v. Westview Instruments, Inc., 52 F.3d
967, 978 (Fed.Cir.1995)). “For that reason, claims ‘must be read in view of the specification, of which they are a part.’ ”
Id.
(quoting
Markman,
52 F.3d at 979 ). The specification “is always highly relevant to the claim construction analysis. Usually it is dispositive; it is the single best guide to the meaning of a disputed term.”
Id.
(quoting
Vitronics Corp. v. Conceptronic, Inc.,
90 F.3d 1576, 1582 (Fed.Cir.1996)). Moreover, when the patentee “act[s] as his or her own lexicographer” and includes an explicit definition of a claim term in the specification, that definition is dispositive over any ordinary meaning.
Id.
at 1319 (internal citation and quotation marks omitted);
see also Digital Biometrics, Inc. v. Identix, Inc.,
149 F.3d 1335, 1344 (Fed.Cir.1998).
In relying on the specification to interpret claim terms, the Federal Circuit has also “repeatedly warned against confining the claims” to the embodiments described in the specification.
Phillips,
415 F.3d at 1323 . The mistake of “reading a limitation from the written description into the claims” is “one of the cardinal sins of patent law.”
Id.
at 1320 (quoting
SciMed Life Sys., Inc. v. Advanced Cardiovascular Sys., Inc.,
242 F.3d 1337, 1340 (Fed.Cir.2001)).
Courts may also utilize the prosecution history which “consists of the complete record of the proceedings before the PTO and includes the prior art cited during the examination of the patent .... [T]he prosecution history can often inform the meaning of the claim language by demonstrating how the inventor understood the invention and whether the inventor limited the invention in the course of prosecution, making the claim scope narrower than it would otherwise be.”
Id.
at 1317 (internal citations omitted). However, the prosecution history “often lacks the clarity of the specification and thus is less useful for claim construction purposes.”
Id.
Lastly, courts may rely on extrinsic evidence such as dictionaries, treatises, and expert testimony, which may serve to provide a source of “accepted meaning of terms used in various fields of science and technology,” or by providing “background on the technology at issue.”
Id.
at 1317— 18. However, such “extrinsic” evidence is “less significant than the intrinsic record in determining the legally operative meaning of the claim language.”
Id.
at 1317 (internal citations and quotation marks omitted). The use of extrinsic evidence may not be
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used to contradict the meaning of the claim terms as evidenced by the intrinsic evidence.
Id.
at 1317-19;
see also Biagro W. Sales, Inc. v. Grow More, Inc.,
423 F.3d 1296, 1302 (Fed.Cir.2005).
2. Resolution of the disputed claim terms
a.
“DNA” and “isolated DNA”
The parties approach the terms “DNA” and “isolated DNA” from opposing perspectives.
38
Plaintiffs contend that the term “DNA” means “a sequence of nucleic acids, also referred to as nucleotides” and therefore constitutes a “nucleotide sequence” or a “polynucleotide.” PI. Br. at 10.
39
Myriad disputes Plaintiffs’ definition of “DNA” insofar as Plaintiffs’ definition suggests that the term “DNA” refers merely to information, that is, “a description of the linear order of nucleotide units that make up the polynucleotide.” Myriad Br. at 15. Myriad instead argues that “DNA” refers to “a real and tangible molecule, a chemical composition made up of deoxyribonucleotides linked by a phosphodiester backbone.” Myriad Br. at 14.
As its name implies, DNA, or deoxyribonucleic acid, is an acid — a tangible, chemical compound. As Myriad correctly notes, the specifications make clear that “DNA,” as used in the patents, refers to the physical manifestation of the acid, one that may be “substantially separated from other cellular components which naturally accompany a gene.” '473 patent, col. 19:8— 9; '282 patent, col. 19:10-11; '492 patent, col. 17:64-65. Despite the description of the term “DNA” set forth in the briefs, this understanding of the meaning of “DNA” is shared by both Plaintiffs’ and Myriad’s declarants.
See
Kay ¶ 125; Linck ¶ 45; Schlessinger ¶ 12; Grody ¶ 10; Leonard ¶ 30.
The term “isolated DNA” is defined by Plaintiffs as “a fragment of DNA substantially separated from other cellular components and other DNA.” PI. Br. at 10. Myriad disputes Plaintiffs’ definition insofar as it implies that fragments of DNA exist free-floating in the cell, separate from other cellular components, such as proteins and the other DNA in the chromosome. Myriad Br. at 16. The patent specifications expressly define “isolated DNA” as a DNA molecule “which is substantially separated from other cellular components which naturally accompany a native human sequence [such as] human genome sequences and proteins” and “includes recombinant or cloned DNA isolates and chemically synthesized analogs or analogs biologically synthesized by heterologous systems.” '473 patent, col. 19:6-15;
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'282 patent, col. 19:8-18; '492 patent, col. 17:62-18:5.
“Isolated DNA” is therefore construed to refer to a segment of DNA nucleotides existing separate from other cellular components normally associated with native DNA, including proteins and other DNA sequences comprising the remainder of the genome, and includes both DNA originating from a cell as well as DNA synthesized through chemical or heterologous biological means.
b.
“BRCAl” and
“BRCA2”
Plaintiffs define the term “BRCAl” as “a particular fragment of DNA found on chromosome 17 that relates to a person’s predisposition to develop breast and ovarian cancer.” PI. Br. at 11. Similarly, Plaintiffs define the term “BRCA2” as “a particular fragment of DNA found on chromosome 13 that relate[s] to a person’s predisposition to develop breast and ovarian cancer.” PI. Br. at 14. As with Plaintiffs’ proposed definition of “isolated DNA,” Myriad argues that these definitions are inconsistent with the patents’ definition of “BRCAl” and “BRCA2” as “cancer-predisposing gene[s], some alleles of which cause susceptibility to breast and ovarian cancers” because they suggest that the
BRACl
and
BRCA2
genes are not integrated into a chromosome, but are broken, detached, or otherwise easily removed from their respective chromosomes, Myriad Br. at 16.
The specifications of the patents-in-suit define the terms “BRCAl” and “BRCA2” as “a human breast cancer predisposing gene ... some alleles of which cause susceptibility to cancer, in particular breast and ovarian cancer.” '282 patent, col. 4:33-36;
see also
'282 patent, col. 1:22-23; '492 patent, col. 1:20-21, 4:28-29. Further, neither party disputes that “genes” refer to segments of DNA incorporated into chromosomes.
“BRCAl” is therefore construed to refer to a human gene, normally integrated into chromosome 17, some alleles of which cause susceptibility to breast and ovarian cancer. Similarly, “BRCA2” is construed to refer to a human gene, normally integrated into chromosome 13, some alleles of which cause susceptibility to breast and ovarian cancer.
V. CONCLUSIONS OF LAW
A.
The Summary Judgment Standard
Summary judgment is granted only where there exists no genuine issue of material fact and the moving party is entitled to judgment as a matter of law. Fed. R.Civ.P. 56(c);
see Celotex Corp. v. Catrett,
477 U.S. 317, 322-23 , 106 S.Ct. 2548 , 91 L.Ed.2d 265 (1986);
SCS Commc’ns, Inc. v. Herrick, Co.,
360 F.3d 329, 338 (2d Cir.2004). The courts do not try issues of fact on a motion for summary judgment, but, rather, determine “whether the evidence presents a sufficient disagreement to require submission to a jury or whether it is so one-sided that one party must prevail as a matter of law.”
Anderson v. Liberty Lobby, Inc.,
477 U.S. 242, 251-52 , 106 S.Ct. 2505 , 91 L.Ed.2d 202 (1986).
“The party seeking summary judgment bears the burden of establishing that no genuine issue of material fact exists and that the undisputed facts establish [its] right to judgment as a matter of law.”
Rodriguez v. City of New York,
72 F.3d 1051, 1060-61 (2d Cir.1995). In determining whether a genuine issue of material fact exists, a court must resolve all ambiguities and draw all reasonable inferences against the moving party.
See Matsushita Elec. Indus. Co. v. Zenith Radio Corp.,
475 U.S. 574, 587-88 , 106 S.Ct. 1348 , 89 L.Ed.2d 538 (1986);
Gibbs-Alfano v. Burton,
281 F.3d 12, 18 (2d Cir.2002). However, “the non-moving party may not rely
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simply on eonclusory allegations or speculation to avoid summary judgment, but instead must offer evidence to show that its version of the events is not wholly fanciful.”
Morris v. Lindau,
196 F.3d 102, 109 (2d Cir.1999) (internal quotation marks omitted).
Summary judgment is appropriate where the moving party has shown that “little or no evidence may be found in support of the nonmoving party’s case. When no rational jury could find in favor of the nonmoving party because the evidence to support its case is so slight, there is no genuine issue of material fact and a grant of summary judgment is proper.”
Gallo v. Prudential Residential Servs., L.P.,
22 F.3d 1219, 1223-24 (2d Cir.1994) (internal citations omitted).
B.
35 U.S.C. § 101 and Its Scope
Section 101 of Title 35, United States Code, provides:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefore, subject to the conditions and requirements of this title.
In interpreting this language, the Supreme Court has observed that “Congress plainly contemplated that the patent laws would be given wide scope.”
Diamond v. Chakrabarty,
447 U.S. 303, 308 , 100 S.Ct. 2204 , 65 L.Ed.2d 144 (1980);
see also J.E.M. Ag Supply, Inc. v. Pioneer Hi-Bred Int’l, Inc.,
534 U.S. 124, 131 , 122 S.Ct. 593 , 151 L.Ed.2d 508 (2001) (“[WJe are mindful that this Court has already spoken clearly concerning the broad scope and applicability of § 101.”).
However, this broad reading of § 101 and statutory patent eligibility is not without limits. “The Supreme Court has recognized that scientific principles and laws of nature, even when for the first time discovered, have existed throughout time, define the relationship of man to his environment, and, as a consequence, ought not to be the subject of exclusive rights to any one person.”
In re Meyer,
688 F.2d 789, 795 (C.C.P.A.1982) (citing
Le Roy v. Tatham,
55 U.S. (14 How.) 156, 175 , 14 L.Ed. 367 (1852)). Specifically, the Supreme Court has recognized three categories of subject-matter that fall outside the scope of § 101: “The laws of nature, physical phenomena, and abstract ideas have been held not patentable.”
Chakrabarty,
447 U.S. at 309 , 100 S.Ct. 2204 ;
see also Diamond v. Diehr,
450 U.S. 175, 185 , 101 S.Ct. 1048 , 67 L.Ed.2d 155 (1981). “The rule that the discovery of a law of nature cannot be patented rests, not on the notion that natural phenomena are not processes, but rather on the more fundamental understanding that they are not the kind of ‘discovery’ that the statute was enacted to protect.”
Parker v. Flook,
437 U.S. 584, 593 , 98 S.Ct. 2522 , 57 L.Ed.2d 451 (1978).
The exclusion of products of nature
40
as patentable subject matter under § 101 also
*219
reflects the Supreme Court’s recognition that “[pjhenomena of nature, though just discovered, mental processes, and abstract intellectual concepts are not patentable, as they are the basic tools of scientific and technological work.”
Gottschalk v. Benson,
409 U.S. 63, 67 , 93 S.Ct. 253 , 34 L.Ed.2d 273 (1972). Thus, as Justice Breyer has observed, “the reason for this exclusion is that sometimes
too much
patent protection can impede rather than ‘promote the Progress of Science and useful Arts,’ the constitutional objective of patent and copyright protection.”
Lab. Corp. of Am. Holdings v. Metabolite Labs., Inc.,
548 U.S. 124, 126-27 , 126 S.Ct. 2921 , 165 L.Ed.2d 399 (2006) (Breyer, J„ dissenting) (quoting U.S. Const., Art. I, § 8, cl. 8.) (emphasis in original). For these reasons, “manifestations of laws of nature [are] free to all men and reserved exclusively to none.”
Funk Bros. Seed Co. v. Kalo Inoculant Co.,
333 U.S. 127, 130 , 68 S.Ct. 440 , 92 L.Ed. 588 (1948).
The inquiry into an invention’s patent eligibility is a fundamental one, and as such, “[t]he obligation to determine what type of discovery is sought to be patented must precede the determination of whether that discovery is, in fact, new or obvious.”
Flook,
437 U.S. at 593 , 98 S.Ct. 2522 ;
see also In re Bilski,
545 F.3d 943, 950 (Fed.Cir.2008) (en banc),
cert.
granted, - U.S. -, 129 S.Ct. 2735 , 174 L.Ed.2d 246 (2009) (“Whether a claim is drawn to patent-eligible subject matter under § 101 is a threshold inquiry, and any claim of an application failing the requirements of § 101 must be rejected even if it meets all of the other legal requirements of patentability.”) (citing
In re Comiskey,
499 F.3d 1365, 1372 (Fed.Cir.2007));
Prometheus Labs. v. Mayo Collaborative Servs.,
581 F.3d 1336, 1343 (Fed.Cir.2009) (noting that in determining patent eligibility, “it is improper to consider whether a claimed element or step in a process is novel or nonobvious, since such considerations are separate requirements set forth in 35 U.S.C. §§ 102 and 103, respectively.” (citing
Bilski,
545 F.3d at 958 )). Consistent with this approach, the courts have rejected patent claims even when the purported invention was highly beneficial or novel, or the research and work that went into identifying it was costly or time-consuming.
See, e.g., Funk Bros.,
333 U.S. at 130 , 68 S.Ct. 440 ;
Am. Fruit Growers, Inc. v. Brogdex Co.,
283 U.S. 1, 11-13 , 51 S.Ct. 328 , 75 L.Ed. 801 (1931);
Gen. Elec. Co. v. De Forest Radio Co.,
28 F.2d 641, 642-43 (3d Cir.1928).
The distinction between the § 101 inquiry into patentable subject matter and the other requirements for patentability set forth in Title 35 is of particular importance in evaluating the authorities cited by the parties and the arguments presented. The discussion of § 101 in
In re Bergy,
596 F.2d 952 (C.C.P.A.1979) by the late Honorable Giles S. Rich, one of the authors of the 1952 Patent Act, is particularly informative in clarifying the proper scope of a § 101 analysis. There, Judge Rich stated what considerations were salient — and importantly, what considerations were not— in a § 101 analysis:
Section 101 states three requirements: novelty, utility, and statutory subject matter. The understanding that these three requirements are separate and distinct is long-standing and has been universally accepted.... Thus, the questions of whether a particular invention is
*220
novel or useful are questions wholly apart from whether the invention falls into a category of statutory subject matter.
Of the three requirements stated in § 101, only two, utility and statutory subject matter, are applied under § 101.
As we shall show, in 1952 Congress voiced its intent to consider the novelty of an invention under § 102 where it is first made clear what the statute means by “new,” notwithstanding the fact that this requirement is first named in § 101.
Id.
at 960-61 (emphasis added). Judge Rich further cautioned that “statements in the older cases must be handled with care lest the terms used in their reasoning clash with the reformed terminology of the present statute; lack of meticulous care may lead to distorted legal conclusions.”
Id.
at 959. The Supreme Court subsequently affirmed this understanding of the § 101 analysis in
Diehr ,
noting that while it had been argued that “novelty is an appropriate consideration under § 101,” “[t]he question ... of whether a particular invention is novel is ‘wholly apart from whether from whether the invention falls into a category of statutory subject matter.’ ” 450 U.S. at 189-90 , 101 S.Ct. 1048 (quoting
Bergy,
596 F.2d at 961 );
see also Bilski,
545 F.3d at 958 (“So here, it is irrelevant to the § 101* analysis whether Applicants’ claimed process is novel or non-obvious.”).
Accordingly, in considering whether the patents-in-suit comply with § 101, the proper analysis requires determining (1) whether the claimed invention possesses utility; and (2) whether the claimed invention constitutes statutory subject matter, that is, whether it is a “process, machine, manufacture, or composition of matter, or any new and useful improvement thereof,” 35 U.S.C. § 101 , or whether the claimed invention instead falls within the judicially created “products of nature” exception to patentable subject matter, i.e., “laws of nature, natural phenomenon, and abstract ideas,”
Chakrabarty,
447 U.S. at 309 , 100 S.Ct. 2204 . In contrast, the question of whether an invention is “new” or “novel” over the prior art is a question addressed by § 102 and falls outside of the scope of the present § 101 analysis. Because it is undisputed that the claimed compositions and methods possess utility, the sole task of this Court is to resolve whether the claimed compositions and methods constitute statutory subject matter or fall within the judicially created products of nature exception to patentable subject matter.
C. The Composition Claims Are Invalid Under 35
U.S.C. § 101
As noted, the issue presented by the instant motions with respect to the composition claims is whether or not claims directed to isolated DNA containing naturally-occurring sequences fall within the products of nature exception to § 101. Based upon the reasons set forth below, it is concluded that the composition claims-in-suit are excepted.
1. Consideration of the merits of Plaintiffs’ challenge is appropriate.
Myriad offers several arguments for why this Court should not engage the substance of Plaintiffs’ claims, but should instead dismiss them out of hand. Foremost among them is Myriad’s assertion that Plaintiffs’ claims should be dismissed in light of the “careful

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Source: Frix Law Library, https://www.frixlaw.com/law-library/cases/2252138. Public record. Not legal advice.
