Patentable Subject Matter In Bioinformatics After USPTO’s January Guidance: Easier To Obtain, But Harder To Keep

August 5, 2019

Contributed Commentary by Paul Liu and Ashley Barton

August 5, 2019 | Bioinformatics is an interdisciplinary field between high technology and life science in which software and computing are applied to biological data. This growing field has vast practical applications, including designing new drug therapies, performing large-scale genetic censuses, improving crops and analyzing forensics.

Title 35, section 101 of the United States Code (35 U.S.C. § 101) statutorily defines patentable subject matter. Section 101 has been interpreted as generally defining certain abstract ideas as patent subject matter ineligible. Over the past few years, the courts (e.g., the Court of Appeals for the Federal Circuit (CAFC)) have entered into a trend of interpreting bioinformatics innovations as pure computational techniques that are part of the patent subject matter ineligible abstract idea category. Based on this recent trend, patentable subject matter rejections at the United States Patent and Trademark Office (USPTO) has increased significantly for bioinformatics patent applications.

However, the USPTO released new guidance earlier this year that appears to have somewhat reversed this trend of increased patentable subject matter ineligibility for bioinformatics patent applications. At a high level, a USPTO examiner under this new guidance would first determine whether a bioinformatics patent application is directed at an abstract idea within three subject matter groupings: a mathematical concept, a method of organizing human activity or a mental process. If not, then the application is eligible for patent. If the idea does fall within one of these categories, the examiner would then decide whether the abstract idea is "integrated into a practical application." Being integrated into a practical application may include, for example, an element of a patent claim that "reflects an improvement in the functioning of a computer"; "effect[s] a particular treatment or prophylaxis"; is used with "a particular machine or manufacture that is integral to the claim"; effects "a transformation or reduction of a particular article to a different state of thing"; or is applied in "some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment." This new guidance is based off CAFC decisions that have used similar logic to support their finding that a bioinformatics innovation is patent subject matter eligible by showing ingenuity, creating a new application or modifying existing concepts.

Accordingly, an applicant for a bioinformatics patent should consider drafting patent claims that incorporate bioinformatics innovations into a concrete system to show that the bioinformatics innovations are not abstract ideas. Furthermore, the applicant may draft patent claims and/or argue that their patent claims do not fall within one or more of the three specific subject matter groupings (i.e., a mathematical concept, a method of organizing human activity or a mental process). Additionally, the applicant may draft patent claims and/or argue that their claims are integrated into a practical application, which may be bolstered by citations to the patent application's specification.

However, even if the USPTO processes a patent application to grant as a patent, the CAFC can later declare a patent invalid due to patent subject matter ineligibility since USPTO guidance is not binding to the CAFC. For example, in Cleveland Clinic Foundation v. True Health Diagnostics LLC (Fed. Cir. 2019), the CAFC stated they are not bound by USPTO's guidance. Some have argued that the CAFC's judicial decisions have been conflicting and do not allow stakeholders to reliably predict patent subject matter eligibility.

Perhaps in response to this uncertainty, a bicameral group of legislators released a draft bill that significantly revises 35 U.S.C. § 101. The bill, which has not yet been passed, defines exceptions to patent eligible subject matter, prohibits the courts from expanding the exceptions, and abrogates the exceptions that have already been delineated by courts. It also defines the term "useful" and removes considerations of whether the limits of a claim are conventional or routine—the state of art at the time of invention—separating the 35 U.S.C. § 101 requirements from those of 35 U.S.C. sections 102, 103 and 112. Legislators hope that the bill will respond to calls for consistency and the need to balance eligibility concerns with promoting investment and innovation.

Accordingly, the landscape of patent subject matter eligibility appears to have taken a recent turn to more widely deem bioinformatics innovations as patent subject matter eligible. However, this new guidance released by the USPTO, and possibly the patents recently granted, should still be evaluated in view of CAFC precedent until further clarification can be made to the landscape of patent subject matter eligibility.

Paul Liu is an intellectual property attorney at the international law firm of Duane Morris LLP. He also holds an appointment as adjunct professor of law at the Thomas Jefferson School of Law in San Diego, California, where he is a USPTO-certified Law School Faculty Clinic Supervisor. Liu previously managed bioinformatics patent portfolios at Illumina, a leading S&P 500 biotechnology company. He can be reached at

Ashley Barton was a 2019 summer associate at Duane Morris LLP. She is completing her final year of law school at the University of San Diego School of Law, where she is a member of the Intellectual Property Law Association. She received the Qualcomm Intellectual Property Scholarship as an entering law student with a background in STEM and a demonstrated interest in intellectual property law.