This article discusses challenges in prosecuting bioinformatics patent applications before the United States Patent and Trademark Office (USPTO). Bioinformatics generally refers to an interdisciplinary field in which computer science techniques are applied to biological data to solve biological problems. Because bioinformatics patent applications are oftentimes tied to computer software, they are subject to restrictions on software-focused applications and associated subject-matter eligibility hurdles. The USPTO determines the subject-matter eligibility of bioinformatics patent applications based on Alice, Mayo, and its progeny. Four points of concern and consideration related to the subject-matter eligibility of bioinformatics patent applications in the United States are discussed below.
First, the USPTO may incorrectly reject a bioinformatics patent claim as being directed to an abstract idea, such as a mathematical concept or a mental process. For example, in its abstract idea analysis, the USPTO may fail to consider the claim as a whole. But, it is not enough for a portion of the claim to involve an abstract idea; rather, the abstract idea would need to apply to the entire claim. Patent applicants can rebut such incomplete abstract idea analysis during prosecution.
Second, the USPTO may conclusory argue that one or more claim features necessary to solve the biological problem at the heart of the bioinformatics invention are routine and conventional. In response, patent applicants can rebut such conclusory statements by arguing that the USPTO failed to provide sufficient objective evidence to support that the claim features are routine and conventional.
Third, the USPTO may overlook bioinformatics patent applications that improve an existing technological process, which is considered patent-eligible subject matter. While a bioinformatics patent application may not improve the mechanical and/or electrical operations of a computer, the application may improve an existing technological process — namely (1) enabling an existing manual process to be run on a computer, or (2) improving the accuracy and effect provided by the computer. Patent applicants can argue that the improvement to the existing technological process can be in terms of improving the result provided by the computer, such as providing a particular step or data structure that enables a manual process to be run on the computer or improving the accuracy and effect provided by the computer.
Fourth, the USPTO may incorrectly reject a bioinformatics patent claim merely because the claim involves a diagnostic method. For example, a bioinformatics patent claim may be directed to a method for diagnosing whether a particular genetic variant is benign or pathogenic. Such a diagnostic method claim is generally patent ineligible. But, the USPTO may fail to distinguish between diagnostic claims that recite a natural law and means for detection (which are generally considered patent ineligible) and claims directed to the application of natural laws (which are generally considered patent eligible). One way patent applicants can argue that its claims are directed to the application of natural laws is to recite a treatment step that; for example, the claims can recite the effects of a particular treatment or prophylaxis. Patent applicants should be cognizant of reciting a treatment step in its claims because of potential divided infringement issues, especially for bioinformatics patent applications having clinical applications.
 Alice Corp. v. CLS Bank International, 573 U.S. 208 (2014).
 Mayo v. Prometheus, 566 U.S. 66 (2012).
 Berkheimer v. HP Inc., 881 F.3d 1360, 1369 (Fed. Cir. 2018).
 McRO, Inc. v. Bandai Namco Games Am. Inc., 837 F.3d 1299, 1313 (Fed. Cir. 2016).
 McRO, Inc. v. Bandai Namco Games Am. Inc., 837 F.3d 1299, 1314 (Fed. Cir. 2016).
 Athena Diagnostics, Inc. v. Mayo Collaborative Servs., LLC, 915 F.3d 743, 750 (Fed. Cir. 2019).
 Athena Diagnostics, Inc. v. Mayo Collaborative Servs., LLC, 915 F.3d 743, 751 (Fed. Cir. 2019).