Patent Primer

American College of Medical Genetics and Genomics Intellectual Property Subcommittee
of the Committee on the Economics of Genetic Services


October 2003

Patricia D. Murphy, PhD, Chair      GeneWISE, Slingerlands, NY
Peter B. Jacky, PhD Kaiser Permanente NW, Clackamas, OR
Anne Maddalena, PhD GeneDX, Gaithersburg, MD
C. Sue Richards, PhD Oregon Health Sciences University, Portland
Bradley W. Popovich, PhD Xenon Genetics, Burnaby, BC, Canada
Reed E. Pyeritz, MD, PhD University of Pennsylvania, Philadelphia
Annette K. Taylor, MS, PhD Kimball Genetics, Inc., Denver, CO
Michael S. Watson, PhD ACMG, Bethesda, MD
Marc S. Williams, MD Gundersen Lutheran Medical Center, La Crosse, WI


Disclaimer: This patent primer is designed for educational purposes only and is not meant to be comprehensive. It is not and should not be construed to be legal advice. If you require specific legal advice about patents, licensing or any other intellectual property issue, you should contact your university's Technology Transfer/Intellectual Property Office or an attorney knowledgeable about intellectual property law.


The patent system was designed to promote the progress of science by encouraging innovation, i.e., "inventiveness." A patent or item of "intellectual property" (IP) is a contract between the inventor and the public, the latter being represented by the US Patent and Trademark Office (USPTO or PTO). In granting a patent, the government gives rights to the inventor to exclude others from "practicing" the invention for a defined and limited time. The meaning of the term "practicing" is defined in the statutes as making, using, selling, offering to sell or importing. In return for this exclusive arrangement, the inventor must fully and clearly disclose the invention in a manner that allows others to practice it. Note that the inventor is not given the right to practice the invention, but rather to prevent others from practicing (for example, a drug may be patented successfully, but the FDA may not approve its use in humans). Permission by the inventor for others to practice the invention is called a "license," which can be granted either exclusively or nonexclusively. Sometimes several patents overlap and the parties must "cross-license" all applicable IP. Licenses often have up-front fees and/or ongoing royalties.


The explosion in patents came with the development of the field of pharmacology in the early 1940s. Commercialization by companies required IP protection to give some assurance that there was a way to provide a "return on investment" (ROI) to stockholders in publicly traded companies. Indeed, in the 1950s, the AMA changed its "canon of ethics" to allow patents on devices and drugs to comply with the shifting medical environment. In the 1970s, Boyer and Cohen patented recombinant DNA technologies and revolutionized patent law. The subsequent US Supreme Court ruling (Diamond vs. Chakrabarty; 1980) allowing patents on living genetically engineered organisms (i.e., an oil-dissolving bacterium) was in the same year that the Bayh-Dole Act was passed to grant patent rights to universities and other grant recipients who used federal monies (i.e., provided for the retention of title to inventions and allowed for exclusive licensing to commercialize the invention). Prior regulations had only allowed nonexclusive license deals with the government and its scientists. Under certain circumstances, the government has "march-in" rights that may require the funding recipient to grant a license to a third party or take title itself in order to grant such a license. Post-1980s patents have been issued for a broad spectrum of inventions: recombinant DNA and proteins, transgenomic animals, PCR and other enabling technologies, cell lines, enzymes, probes, antisense and gene sequences, as well as specific mutations and polymorphisms within genes.


Patenting Authorities

In addition to the USPTO, based in the Department of Commerce, there are patent offices throughout the world. Several treaties have been completed to facilitate the issuance of consistent patents between countries. Uniform procedures in Europe were established in 1972 in order to obtain multinational protection of patent rights in member states. The Patent Cooperation Treaty (PCT) of 1978 is administered by the World Intellectual Property Organization (WIPO), one of the sixteen agencies within the United Nations.

Under current law, the term of a patent begins on the date on which the patent issues and ends 20 years from the date of filing of the patent application or from the date of application to which priority is claimed. The term may be calculated differently if certain circumstances apply. Patents that were issued prior to, or were pending on, June 8, 1995, are entitled to a term of at least 17 years from the issue date. In addition, certain patents may receive extensions of term upon application to compensate for delays in obtaining regulatory approval to market a product covered by the patent. Filing a continuing application does not restart the clock on the term; rather the term is measured from the filing of the parent application.


There are three main types of patents: "Utility" patents are directed to functional inventions, "design" patents are directed to ornamental manufactured objects, and "plant" patents are directed to asexually reproduced plants. Utility patents can have multiple claims, and each claim defines the limits of a single invention. The claims may appear in independent form or dependent form, the latter a shorthand way to incorporate language from an earlier claim. Claims cover a "process, machine, manufacture of or composition of matter." Nucleic acids are considered a composition of matter and can be covered if they have been isolated, purified or otherwise manipulated through the intervention of the "hand-of-man" (US Supreme Court, 1980; the original wording is "anything under the sun that is made by man"). A notice by the Commissioner of the PTO in 1987 extended patents to "non-naturally occurring, non-human multicellular living organisms, including animals," which directly resulted in a patent granted for the "oncomouse" in 1988.



In the US, there is a system that allows "provisional" applications to be submitted and held on file at the PTO. These are a useful way to extend the life of a patent because they establish the "filing date" (called the "priority date") and yet they do not start the clock on the 20-year term because they are withheld from prosecution (examination) for up to one year. They are often used when there is the risk of imminent public disclosure or when it is desirable to fix the priority date for a given amount of material. Filing serves as a constructive "reduction to practice" unless the court has ruled that there is no "conception without reduction to practice," as is the case with some genetic inventions. Several provisional applications may be combined into one application that goes forward into the prosecution stage. If the one-year time period is passed, provisional applications are considered automatically abandoned. They remain confidential at the PTO and are eventually destroyed. "Continuing" applications (e.g. "continuations," "divisionals" [i.e., the original application is divided into several applications] and "continuations in part" [CIP]) are applications that claim priority to a non-provisional application. Because the new information presented in a CIP will have its own priority date (vs. the date on the original application), any filing of a CIP must be carefully evaluated.



As of March 2003 there were over 50 million published patents worldwide, with approximately 700,000 applications filed yearly (i.e., 20,000/week). Since 1980, when the US Supreme Court issued its ruling that living things (including genes) could be patented when "man-made" (see above), there have been 1800 patents issued for entire genes and several thousand applications are in active prosecution. The numbers are expected to go up exponentially with the completion of the Human Genome Project. Private companies are aggressively seeking to protect their IP by filing multitudes of applications.



In order to have a patent issued, an invention must be a new and useful "process, machine, manufacture or composition of matter." It must meet the standards of utility, novelty and non-obviousness. The invention must be something that is not in public use, published in written form or known to others in the field. To demonstrate these traits to the PTO, the body of the patent application must contain the following parts:

  • an abstract (used for patent searches with key words)
  • a specification, including a written description of the invention ("written description"), a description of the manner and process of practicing the invention without undue experimentation ("enablement"), and the "best mode" of the invention. Traditionally there are several teaching "examples" used to explain the invention to the examiners.
  • drawings, if necessary
  • at least one claim
  • gene or protein sequences, if necessary



In the case of a new organism, plant, or animal, there may be a requirement for a specimen to be deposited or held at repository during review of a patent (called the "prosecution" phase).


The claims are the most important part of any issued patent. They define succinctly the boundaries of the intellectual property. The PTO will sometimes work with (or negotiate with) the inventor and his or her attorney to obtain allowable claims that do not cover claims in other patents already issued or currently in prosecution. Since patent applications are held confidential until issued, only the PTO knows the full extent of any overlap and thus has the upper hand when revising claim language. They strive for narrow, limited claims rather than allowing broad, all-encompassing claims. The applicant is entitled to claims as broad as the prior art will allow.



Inventors are designated when the individual has contributed to the conception of the invention and it was determined that the contribution to the invention was both substantial and well documented. Joint inventors do not have to be physically working together in the same laboratory at the same time, nor do they have to contribute equally. From the patent law perspective, a joint invention is a collaborative effort to solve a particular problem or identify a particular "composition of matter." Patents can be invalidated if there has been an incorrect designation of inventors when there was "deceptive intent," but corrections are allowed even after issue when inadvertent errors have been made.


Revised Interpretive Guidelines

In January 2001, new guidelines were issued that addressed the criteria for patentability for gene sequences. Essentially outlining what needs to be met to satisfy the "utility" requirement, the PTO stated that an application must provide only a single "specific, substantial and credible" utility for each claimed invention. The PTO also requires that "a person of ordinary skill in the art would immediately appreciate why the invention is useful based on the characteristics of the invention." Whereas a gene or sequence may function a certain way while in the human body, its utility when purified away from the body (i.e., cloned) may be entirely different. An example would be a tumor antigen that is quantitatively up-regulated in a tumor cell, but is still a natural product of that type of cell, being used as a marker for the presence of malignancy (e.g., PSA) in an in vitro diagnostic test. The new interpretative guidelines also provide stricter rules for the body of the patent ("specification") in presenting the written description of the invention and providing the "best mode" for the replication by others knowledgeable in current technologies.



Infringement is judged "claim by claim" during court review. It exists only if all the features stated within a claim are practiced by another. If all the features plus some new ones (i.e., not in the original claim) are practiced, generally, this will still constitute infringement, since the original claim is being practiced. On the other hand, dropping an element of a claim will not constitute infringement. The patent office does not hold any view regarding whether a license is needed. They simply decide whether to issue patents. After issuance, one would look to what the courts have decided.


Helpful Web Sites


Additional Resources

  1. Grisham J. New rules for gene patents. Nature Biotech 2000:18:921.
  2. Agris CH. International patent filing: factors to consider in deciding when and where to file outside the United States. Nature Biotech 1998:16:479-480.
  3. Ducor P. Coauthorship and coinventorship. Science 2000:289:873-875.
  4. Amernick B. Essentials of patent law. J Natl Cancer Inst 1989: 81/19: 1450-1454.
  5. Scherer FM. The economics of human gene patents. Academic Medicine 2002: 77/12:1348-1367.