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A biological patent is a patent relating to an invention or discovery in biology. It can be a composition of matter, a method for obtaining or using one or more thereof, or a product combining such things. As with all utility patents in the U.S, the patent provides the patent holder with the right to exclude others from making, using, selling, or importing the claimed invention for a limited period of time - for patents filed after 1998, twenty years from the filing date. Natural biological substances themselves can be patented (apart from any associated process or usage) in the United States if they are sufficiently "isolated" from their naturally occurring states. Prominent historical examples of such patents on isolated products of nature include adrenaline, insulin, vitamin B12, and gene patents.
The United States has been patenting chemical compositions based upon human products for over 100 years. The first patent for a human product was granted on March 20, 1906, for a purified form of adrenaline. It was challenged and upheld in Parke-Davis v. Mulford  Judge Hand argued that natural substances when they are purified are more useful than the original natural substances.
The 1970s marked the first time when scientists patented methods on their biotechnological inventions with recombinant DNA. It wasn’t until 1980 that patents for whole-scale living organisms were permitted. In 1980, the U.S. Supreme Court, in Diamond v. Chakrabarty, upheld the first patent on a newly created living organism, a bacterium for digesting crude oil in oil spills. The patent examiner for the United States Patent and Trademark Office had rejected the patent of a living organism, but Chakrabarty appealed. As a rule, raw natural material is generally rejected for patent approval by the USPTO. The Court ruled that as long as the organism is truly "man-made," such as through genetic engineering, then it is patentable. Because the DNA of Chakrabarty's organism was modified, it was patentable.
Since that 1980 court case, there has been much patenting of genetically modified organisms. This includes bacteria (as just mentioned), viruses, seeds, plants, cells, and even non-human animals. Isolated and manipulated cells - even human cells - can also be patented. In 1998, the U.S. Patent and Trademark Office (PTO) issued a broad patent claiming primate (including human) embryonic stem cells, entitled "Primate Embryonic Stem Cells" (Patent 5,843,780). On 13 March 2001, a second patent (6,200,806) was issued with the same title but focused on human embryonic stem cells. In another example, a genetically modified mouse, dubbed the Oncomouse, that is useful for studying cancer, was patented by Harvard University as U.S. Patent 4,736,866
New plants and seeds are also patentable. There are two ways that new plants can be protected. One is a "plant patent" that protects Plant breeders' rights when new plants are bred as opposed to be genetically created. These rights are different from those provided by the more commonly considered patent rights under the utility model. In one example of a utility patent on a genetically modified seed and the plants that come from it, the biotechnology company Monsanto developed and patented a glyphosate-resistant gene for the canola plant which has the effect of producing canola that is resistant to their Roundup brand of herbicide. Monsanto has enforced this patent against farmers who used the seed without paying Monsanto—see Monsanto Canada Inc. v. Schmeiser.
Gene patents 
A gene patent is a patent on a specific isolated gene sequence, its chemical composition, the processes for obtaining or using it, or a combination of such claims. With respect to subject matter, gene patents may be considered a subset of the broader category of biological patents.
Gene patents may claim the isolated natural sequences of genes, the use of a natural sequence for purposes such as diagnostic testing, or a natural sequence that has been altered by adding a promoter or other changes to make it more useful. In the United States, patents on genes have only been granted on isolated gene sequences with known functions, and these patents cannot be applied to the naturally occurring genes in humans or any other naturally occurring organism.
The "Chakrabarty patent", owned by General Electric, was filed in 1972 and issued in 1981 after the Supreme Court decision discussed above. While not commercially important, this patent and the Supreme Court case "opened the floodgates for protection of biotechnology-related inventions and helped spark the growth of an industry."
In 1978 University of California filed a patent application for the cDNA encoding human growth hormone, which issued in 1982 as US Patent 4,363,877 and listed Howard M. Goodman, John Shine, and Peter H. Seeburg as inventors. University of California licensed its patent to Lilly, leading to extended litigation among University of California, Lilly, and Genentech; each of Lilly and Genentech had introduced recombinant human growth hormone drugs, which were among the first biotech drugs brought to market.
The "Cohen/Boyer patents" were invented by Stanley Cohen of Stanford University and Herbert Boyer of University of California, San Francisco. The patents cover inventions for splicing genes to make recombinant proteins that are foundational to the biotechnology industry. Stanford managed the patents and licensed them nonexclusively and broadly, earning over $200 million for the universities.
The "Axel Patents" were invented by Richard Axel, Michael H. Wigler, and Saul J. Silverstein of Columbia University. These patents covered cotransformation, a form of transformation, another foundational method of biotechnology; Columbia licensed these patents nonexclusively and broadly and earned about $790 million.
Key methods to manipulate DNA to create monoclonal antibodies are covered by a thicket of patents, including the "Winter patent" was invented by Gregory P. Winter of the Medical Research Council which covers methods to make chimeric, humanized antibodies and has been licensed to about fifty companies. Abgenix owned a patent on methods of making transgenic mice lacking endogenous heavy chains. The "Boss patent" was owned by Celltech and covered methods of making recombinant antibodies and antibody fragments, together with vectors and host cells useful in these processes. Genentech owned the "Old Cabilly" patent that covered altered and native immunoglobulins prepared in recombinant cell culture, as well as the "New Cabilly" patent that covers artificial synthesis of antibody molecules. Medarex owned a patent that covered high affinity human antibodies from transgenic mice. These patents have been broadly licensed and have been the subject of litigation among patent holders and companies that have brought monoclonal antibody drugs to market.
A patent application for the isolated BRCA1 gene and cancer-cancer promoting mutations, as well as methods to diagnose the likelihood of getting breast cancer, was filed by the University of Utah, National Institute of Environmental Health Sciences (NIEHS) and Myriad Genetics in 1994; over the next year, Myriad, in collaboration with investigators from Endo Recherche, Inc., HSC Research & Development Limited Partnership, and University of Pennsylvania, isolated and sequenced the BRCA2 gene, and the first BRCA2 patent was filed in the U.S. by Myriad and other institutions in 1995. Myriad is the exclusive licensee of these patents and has enforced them in the US against clinical diagnostic labs. This means that legally all testing must be done through Myriad's lab or by a lab which it had licensed. This business model led from Myriad being a startup in 1994 to being a publicly traded company with 1200 employees and about $500M in annual revenue in 2012; it also led to controversy and the Association for Molecular Pathology v. Myriad Genetics lawsuit mentioned below. The patents expire, starting in 2014.
Controversy over biological patents occurs on many levels, driven by, for example, concern over the expense of patented medicines or diagnostics tests (against Myriad Genetics with respect to their breast cancer diagnostic test), concerns over genetically modified food which comes from patented genetically modified seeds as well as farmer's rights to harvest and plant seeds from the crops (for both issues see Monsanto article).
Each nation has its own patent law, and what is patentable in some countries is not allowed to be patented in others. Stem cells derived from humans are a good example of these differences. In the United States, isolated stem cells are patentable subject matter. However, a challenge against some US stem cell patents is being litigated by two non-profit organizations: The Foundation for Taxpayer & Consumer Rights and Public Patent Foundation along with molecular biologist Jeanne Loring of the Burnham Institute. The European Patent Office has ruled that certain stem cell lines, derived from destruction of human embryos, were not to be granted a European patent.
In the United States, biological material derived from humans can be patented if it has been sufficiently transformed. In litigation that was famous at the time, a cancer patient, John Moore, sued the University of California. Cancer cells had been removed from Moore as part of his medical treatment; these cells were studied and manipulated by researchers. The resulting cells were "immortalized" and were patented by the university as U.S. Patent 4,438,032 and have become widely used research tools. The subject of the litigation was the financial gain that the university and researchers achieved by additionally charging money to companies by licensing the cell line.
Michael Heller and Rebecca Eisenberg are academic law professors who believe that biological patents are creating a "tragedy of the anticommons," "in which people underuse scarce resources because too many owners can block each other." Others claim that patents have not created this "anticommons" effect on research, based on surveys of scientists.
Professional societies of pathologists have criticized patents on disease genes and exclusive licenses to perform DNA diagnostic tests. In the 2009 Myriad case, doctors and pathologists complained that the patent on BRCA1 and BRCA2 genes prevented patients from receiving second opinions on their test results. Pathologists complained that the patent prevented them from carrying out their medical practice of doing diagnostic tests on patient samples and interpreting the results.
Another example is a series of lawsuits filed by the Alzheimer’s Institute of America (AIA) starting in 2010, concerning a gene patent it controls. The patent covers a genetic mutation that predisposes to Alzheimer's, and more importantly, it applies to transgenic mice carrying the mutation. These mice are widely used in Alzheimer's research, both by academic scientists doing basic research and by companies that use the mice to test products in development. Two of these suits are directed to companies that were started based on inventions made at universities (Comentis and Avid), and in each of those cases, the university has been sued along with the company. While none of the suits target universities that are conducting basic research using the mice, one of the suits is against Jackson Labs, a nonprofit company that provides transgenic mice to academic and commercial researchers and is an important repository of such mice.
While there is some controversy concerning the patenting of isolated genes and the way those patents are used, and there is controversy concerning patents on the diagnostic uses of genes (the real source of dispute in the Myriad court case), it is difficult to find controversy surrounding patents on genes that are used to manufacture therapeutic proteins (for an example of patents on therapeutic proteins, the drug candidate that is the subject of the early part of the movie 'Extraordinary Measures' was covered in part by a classic gene patent, US Patent 6,770,468.) There is also little controversy concerning the role of gene patents in the chemical industry—for instance in the manufacture of enzymes used in consumer products or industrial processes.
Myriad Genetics case 
Association for Molecular Pathology v. Myriad Genetics is a case challenging the validity of gene patents in the United States, specifically challenging certain claims in issued patents owned or controlled by Myriad Genetics that cover isolated DNA sequences, methods to diagnose propensity to cancer by looking for mutated DNA sequences, and methods to identify drugs using isolated DNA sequences.
The case was originally heard in the United States District Court for the Southern District of New York, which ruled that all the challenged claims were not patentable subject matter. Myriad then appealed to the United States Court of Appeals for the Federal Circuit. The Circuit court overturned the previous decision in part, ruling that isolated DNA which does not exist alone in nature can be patented and that the drug screening claims were valid, and confirmed in part, finding the diagnostic claims unpatentable. The plaintiffs appealed to the Supreme Court, which granted cert and remanded the case back to the Federal Circuit. The Federal Circuit did not change its opinion, so on September 25, 2012, the American Civil Liberties Union and the Public Patent Foundation filed a petition for certiorari with the Supreme Court with respect to the second Federal Circuit Decision. As of December 2012 isolated genes remain patentable in the US.
See also 
- American Type Culture Collection (ATCC)
- Budapest Treaty
- Diamond v. Chakrabarty was a United States Supreme Court case dealing with whether genetically modified micro-organisms can be patented.
- Gene patent
- Human Genome Project
- John Moore (patent)
- Pharmaceutical patent
- Stem cell controversy
- Cook-Deegan, Robert. "Gene patents". The Hastings Center. Retrieved 10 December 2012.
- Parke-Davis & Co. v. H.K. Mulford Co., 189 F. 95 (C.C.S.D.N.Y. 1911), Learned Hand, J.
- Dutfield, Graham. "DNA Patenting: Implications for Public Health Research." Bulletin of the World Health Organization, May 2006, Volume 85, Issue 5.
- Stix, Gary. “Owning The Stuff Of Life.” Scientific American, Feb. 2006, Volume 294, Issue 2.
- "Federal Register - Utility Examination Guidelines - Comments and Responses". January 5, 2001. Retrieved April 5, 2010. See Comment 2 in which this objection is specifically raised and addressed.
- Chakrabarty - US Patent 4,259,444
- Matthew RImmer. (2002/2003) Genentech and the Stolen Gene: Patent Law and Pioneer Inventions Bio-Science Law Review 5(6):198-211
- Douglas Robinson and Nina Medlock (2005) Diamond v. Chakrabarty: A Retrospective on 25 Years of Biotech Patents. Intellectual Property & Technology Law Journal 17(10):12-15
- US Patent 4,363,877
- US Patent 4,237,224
- US Patent 4,468,464
- US Patent 4,740,470
- Feldman MP, A Colaianni and C Liu. 2007. Lessons from the Commercialization of the Cohen-Boyer Patents: The Stanford University Licensing Program. In Intellectual Property Management in Health and Agricultural Innovation: A Handbook of Best Practices (eds. A Krattiger, RT Mahoney, L Nelsen, et al.). MIHR: Oxford, U.K., and PIPRA: Davis, U.S.A. Available online at www.ipHandbook.org.
- Chris Rauber for the San Francisco Business Times. November 23, 1997. $200M patent runs out
- U.S. Patent 4,399,216
- U.S. Patent 4,634,665
- U.S. Patent 5,179,017
- U.S. Patent 5,149,636
- U.S. Patent 6,455,275
- Alessandra Colaianni and Robert Cook-Deegan (2009) Columbia University's Axel Patents: Technology Transfer and Implications for the Bayh-Dole Act Milbank Q.87(3): 683–715.
- Jennifer van Brunt (2005) The Monoclonal Maze Signals Online Magazine
- US Patent 5,225,539
- MRC Official Website Achievements and Impact: Therapeutic Antibodies
- US Patent 5,939,598
- US Patent 4,816,397
- US Patent 4,816,567
- US Patent 6,331,415
- US Patent 5,770,429
- John Schwartz for the New York Times. May 12, 2009. Cancer Patients Challenge the Patenting of a Gene
- Myriad Investor Page—see "Myriad at a glance" accessed October 2012
- See for example 2009-2010 litigation
- G2/06 WARF/Stem Cells
- Science Progress Blog
- "Association For Molecular Pathology, et al., vs. United States Patent and Trademark Office, et al." (PDF). The New York Times. March 29, 2010. Retrieved March 30, 2010.
- Patent dispute threatens US Alzheimer's research; Lawsuit could expose hundreds of scientists to property-rights litigation. Erika Check Hayden, 5 April 2011, Nature 472, 20 (2011) | doi:10.1038/472020a
- "Supreme Court Grants Myriad’s Petition for Cert.". The National Law Review. Schwegman, Lundberg & Woessner, P.A. December 3, 2012. Retrieved December 5, 2012.
- Biotechnology on the WIPO web site
- Amicus Brief by Dr. James Watson
- Genomics Law Report. Newsletter published by law firm of Robinson Bradshaw & Hinson.
- The Human Genome Project information pages
- Human Genome Project pages on Genetics and Patenting
- Bioethics and Patent Law: The Cases of Moore and the Hagahai People by Anja von der Ropp and Tony Taubman, WIPO Magazine, September 2006.
- "An Examination of the Issues Surrounding Biotechnology Patenting and its Effect Upon Entrepreneurial Companies", United States Congressional Research Service, August 31, 2000
- "Stem Cell Research and Patents: An Introduction to the Issues", United States Congressional Research Service, September 10, 2001