The USPTO has just published Interim Examination Guidelines to assist examiners in determining whether certain claimed subject matter is eligible to be patented. The guidelines follow the Federal Circuit's en banc In re Bilski decision, that imposed a "machine or transformation" test as the starting point for determining patent eligibility under 35 U.S.C. §101, and include a flow chart to assist examiners in evaluating method claims for compliance with this test.

Recent caselaw suggests that courts have begun to question the patent eligibility of diagnostic methods, but neither the Bilski test nor these Guidelines directly discuss diagnostic methods. While the Supreme Court has agreed to review the Bilski decision and the new guidelines are explicitly "Interim," those responsible for diagnostic method inventions would do well during this interim period to consider how this decision and these guidelines impact patent preparation and prosecution.

Section 101, considered a threshold for patentability, requires that claimed material be useful and directed to eligible subject matter. Subject matter eligibility means that the claims must fall within a statutory class (process, machine, manufacture, composition) and not cover material within a judicially-created exception to patentability. Judicially-created exceptions include abstract ideas, mental processes, laws of nature, natural phenomena, scientific principles, and disembodied mathematical formulas.

According to the guidelines, to satisfy the machine branch of Bilski's machine or transformation test, the claims must make clear that the machine implements the method and is not merely an object upon which the method operates, and the claims must ensure the machine is particular to the method. Where the method relies on a computer to implement the method, the guidelines suggest that general purpose computers are acceptable, but the claims must specify that the computer is programmed to perform specific steps to satisfy the particularity requirement. In other words, the claims should recite that a specifically programmed computer carries out one or more steps.

To satisfy the transformation branch, it must be apparent that a particular article has changed to a different article or state, and not simply changed locations. Mathematical operations in and of themselves do not constitute a transformation, but electronic transformation of data is acceptable if the data changes to have a different function or a different use.

The guidelines further explain that the machine or transformation must also impose a meaningful limitation on claim scope, and must not be an insignificant extra solution activity. The guidelines do not elaborate on these two corollaries, but suggest that a meaningful limitation imposes boundaries on the scope of the claims, and suggest that extra solution activities are those that are not central to the purpose of the method.

In general, process claims filed in biotechnology applications will satisfy the machine or transformation test on their face. But, certain methods, including methods of diagnosis, may give the USPTO pause.

Diagnostic methods typically include the basic steps of gathering data from a patient sample, comparing the data with a standard, and generating information about or diagnosing the patient based on the comparison. A survey of published claims in diagnostic method applications reveals that few claims tie any of these steps to a particular machine, and the claims do not result in any transformation as the USPTO has interpreted this term.

Although the guidelines do not specifically discuss diagnostic methods, they counsel examiners to reject such claims if they do not tie at least one step to a particular machine, or they do not confer a different function or use on the data they manipulate. Thus, section 101 may become a significant obstacle to patentability of diagnostic method claims if they do not meet these criteria.

One possible solution for addressing a section 101 subject matter eligibility rejection of a diagnostic method claim may be to amend the claim to specify that the comparing step is carried out using a computer programmed to compare the gathered data with the standard. Amending the claim to specify that the data gathering is carried out using a machine may be acceptable, but such an amendment may not impose a meaningful limitation on the claim, for example, if the only way to gather the data is with the specified machine.

A possible alternative solution may be to amend the claim to include a step of treating a specific condition in the patient consistent with the diagnosis. This treatment step may serve as a transformation because of the change in the state of the patient.

Time will show how the USPTO will apply these guidelines to biotechnology claims generally, and to diagnostic method claims specifically. And, depending on the Supreme Court's decision in Bilski, the law of subject matter eligibility under section 101 may further change directions. Until a clear path for presenting diagnostic method claims emerges, applicants may benefit from adding particular machine and transformation fallback provisions into their specifications in advance of filing.

The USPTO is requesting public comment on these interim guidelines. To ensure consideration, written comments must be received by the USPTO on or before September 28, 2009. Comments should be sent by electronic mail message to AB98.Comments@uspto.gov. Comments may also be submitted by facsimile to (571) 273-0125, marked to the attention of Caroline D. Dennison.