The U.S. Patent and Trademark Office’s Board of Patent Appeals and Interferences (BPAI) affirmed an examiner’s rejection of the claims of U.S. App. Ser. No. 09/563,817 (the ’817 application) as both lacking utility under 35 U.S.C. §101 and non-obviousness under 35 U.S.C. §103. The ’817 application claimed computer-based systems of screening gene fragments and, as such, the BPAI’s decision spoke both to the patentability of biotechnical and software/database inventions. Ex parte Nehls et al., Appeal No. 07-1823, (BPAI), (Jan. 28, 2008) (Grimes, APJ; Green, APJ and Adams, APJ, concurring-in-part).

The claim at issue before the BPAI was directed at a computer-based system for identifying DNA fragments of the genome comprising a data storage means having about 1,000 DNA gene-trapped sequences (GTSs), a searching means for comparing a target sequence to each GTS in the storage means and a retrieval means for obtain the GTS homologous to the target sequence. The BPAI held that the utility of the claimed system depended on the utility of the GTSs because if the sequences lacked utility, then so did a system for identifying them.

The BPAI held that the GTSs disclosed by Nehls et al. were gene fragments not accompanied by a persuasive explanation that they were anything other than research intermediates or had any uses that distinguished them from any other human gene fragment. As such, the claimed system did not have substantial or specific utility similar to the expressed sequence tags (ESTs) in the Federal Circuit’s utility decision in In re Fisher.

The BPAI also upheld the examiner’s rejection of the claimed system as obvious over Altschul et al.—a well-known reference describing the popular computer DNA sequence analysis software referred to as the Basic Local Alignment Search Tool (BLAST). Even though the claimed system specifically required a data storage means comprising 1000 unique GTSs not disclosed in Altschul, the examiner argued that the content of the data storage means does not alter how the claimed BLAST-like computer system functions. As such, the examiner reasoned that this claim recitation merely provided “non-functional descriptive material.”

The BPAI indicated that the relevant case law for this analysis stemmed from cases and computer-related inventions involving “printed matter,” which must be functionally related to the substrate on which it is printed to provide patentable weight. For “data structures” to patentably distinguish computer-related inventions, they must be functionally related to the computer’s operation.

In applying the law to the ’814 application, the BPAI held that the 1,000 unique GTSs did not affect, enhance or otherwise change the process of comparing a target sequence to a database of other sequences as shown by Altschul. The BPAI opined that the claimed data storage means comprising 1,000 unique GTSs and the computer system were independent of one another. The BPAI also opined that a claim to a computer system for searching a phone book placed in a database or a database of MP3s would similarly not be patentable absent some novel and non-obvious characteristic of the computer hardware or search tools. The BPAI was further unconvinced by Nehls et al.’s arguments that the claimed 1,000 GTSs are limiting functional descriptive material because nucleic acids are patentable. The BPAI countered that although nucleic acids are patentable, their digitized sequence or “abstract representation” in a database as claimed, is not.