US Appeal Board Rejects Method and Program for Cluster Analysis in Bioinformatics (Ex parte Kelkar)

[part of a heat map of gene expression value; from Wikimedia] In Ex parte Kelkar, claims were directed to a method for determining similarity between portions of gene expression profiles or genes (independent claim 1) and a program product having computer readable code stored on a recordable media for determining similarity between portions of gene expression profiles or genes (independent claim 10). Illustrative claim 1 reads: 1. A method for determining similarity between portions of gene expression profiles in a computer comprising the steps of: processing a number of gene expression profiles with a similar sequences algorithm that is a time and intensity invariant correlation function to obtain a data set of gene expression profile pairs and a match fraction for each gene expression profile pair; listing gene expression profile pairs in clusters by their match fractions; removing a first gene expression profile from a cluster when another cluster has another gene expression profile with a higher match fraction with the first gene expression profile, unless the another gene expression profile requires a larger number of subsequences to achieve similarity with the first gene expression profile; repeating the removing step until all gene expression profiles are listed in only one cluster providing output of the listing of clusters of gene expression profiles. Parallel to claim 1, program product claim 10 comprises "programmed means" for each of the steps as defined by claim 1. The assesment of patentability by the Board of Appeals was based on the following observations: The method according to claim 1 is performed "in a computer"; The specification teaches that "[t]he present invention may also be used in any digital computer architectures, including personal, minicomputer and mainframe computer environments, and in local area and wide area computer networks"; Claim 1 "does not transform any physical object or article"; The specification teaches that a preferred embodiment "uses a time and intensity-invariant correlation function such as that described by R. Agrawal. [...] Specifically, we employ the similar sequence algorithm embodiment of the above described correlation function in Intelligent Miner for Data [...] which was designed for business intelligence, against time varying gene expression data." In a first examination stage, the Board determined that the claimed method fails the machine-or-transformation test since, allegedly, it neither is limited to a particular machine (cf. observations 1, 2), nor do the method steps of claim 1 transform a particular article into a different state or thing (cf. observation 3). In a second examination stage, the Board then analysed claim 1 under the Supreme Court’s precedents on the unpatentability of abstract ideas (see earlier posting). It found that "claim 1 applies the mathematical manipulation of data to determine the similarity between portions of gene ex…