The sands of patentable subject-matter are shifting around the world, and Canada is no exception. On 29 June 2015, the Canadian Intellectual Property Office (“CIPO”) released a Practice Notice

(Patent Notice: Examination Practice Respecting Medical Diagnostic Methods – PN 2015-02) providing guidance on the examination of medical diagnostic method claims. Since the release of these guidelines, there has been an influx of examiner’s reports from the CIPO rejecting patent applications featuring certain types of diagnostic method claims.

Consistent with the most recent guidance on the examination of computer-implemented inventions in view of the decision of the Federal Court of Appeal in Amazon.com, Inc. v. Canada (Attorney General), 2011 FCA 328, Practice Notice PN 2015-02 provides that the patentability of diagnostic method claims is determined by a purposive construction of the words of the claims. On a purposive construction, the essential elements of the claims will be identified. The Practice Notice instructs that in order to construe the claims, the examiner is to first identify the problem that the inventors set out to solve (in view of the description of the patent application and the examiner’s understanding of the common general knowledge) and the solution disclosed. The Practice Notice contemplates two different types of problems for diagnostic methods: a “data acquisition problem” and a “data analysis problem.  As can be seen from the discussion below, the CIPO will consider a diagnostic method claim to be directed to patentable subject- matter where the problem solved by the invention is a “data acquisition problem”. In contrast, the CIPO will not consider a diagnostic method claim to be directed to patentable subject -matter where the problem solved by the invention is a “data analysis problem”.

Differentiating “Data Acquisition” and “Data Analysis” Problems

Practice Notice PN 2015-02 describes a “data acquisition problem” as being solved by an invention which pertains to a novel structure or method in order to be able to physically acquire data (e.g., an invention that is directed to using novel methods of acquiring data on a known biomarker or one that is directed to the discovery of a new biomarker). Indicia that the problem to be solved is a “data acquisition problem” in the Practice Notice include:

• disclosure of an analyte[1] that does not form part of the common general knowledge, and a method of identifying or quantifying the analyte;

• explicit statements that a specific problem or solution relates to how to identify or quantify a particular analyte;

• a significant level of detail devoted to describing the technical details of how data about a particular analyte is acquired; and/or

• an emphasis on the challenges or deficiencies of prior means to identify or quantify a particular analyte.

In contrast, a “data analysis problem” is solved by an invention which pertains to the analysis of the significance of the acquired data (e.g., the invention is directed to a natural correlation between a medical condition and a biomarker where conventional techniques are used to detect a known biomarker). Indicia that the problem to be solved is a “data analysis problem” in the Practice Notice include:

• explicit statements suggesting the problem to be solved is a “data analysis problem”, or something other than a “data acquisition problem”;

• placing an emphasis on the discovery of a new correlation between a condition and an analyte that forms part of the common general knowledge, with a relative absence of technical details pertaining to how to acquire the data about the analyte;

• indicators or explicit statements that, in order to acquire data about a particular analyte, it is common general knowledge to apply the means contemplated by the application; and/or

• an absence of any explicit indication in the application that any practical problems were overcome relating to how to acquire data about an analyte that forms part of the common general knowledge.

Thus, unless the invention involves a novel molecule, or a new way of detecting or quantifying a new or known molecule, it appears that the CIPO will consider the claimed invention to be directed to a “data analysis problem”.

Practice Notice PN 2015-02 also instructs that if a claim includes a solution to more than one problem, examination should focus on only one solution in performing purposive construction. The effect of this approach as it is currently being applied is to classify all diagnostic claims as being directed to either a “data acquisition problem” or a “data analysis problem”, and to treat these categories as mutually exclusive.

Determination of the Essential Elements of a Diagnostic Method Claim

Under the approach to purposive construction applied by the CIPO pursuant to its previous Practice Notice PN 2013-02, the examiner is to determine the essential elements of a claim as the “element or set of elements that is essential to the successful resolution of the problem”. The CIPO will only consider a diagnostic method claim to define patentable subject- matter if a physical step of data acquisition can be identified as an essential element of the claim.

Where the examiner concludes that the problem solved by the invention is a “data acquisition problem”, the Practice Notice instructs that the solution is provided by those elements that provide a means to acquire data about an analyte. Exemplary data acquisition steps given in the Practice Notice include:

• detecting protein X in a subject sample;

• measuring the concentration of substrate X;

• determining the expression levels of genes A, B and C;

• contacting a urine sample with antibody A and determining optical density; or

• incubating a sample with a nucleic acid probe consisting of SEQ ID NO:1 and detecting hybridization between the probe and target sequence Z.

In contrast, where the examiner concludes that the problem is a “data analysis problem”, the Practice Notice instructs that the solution is provided by those elements that relate to the analysis of acquired data or the purpose of providing diagnostic meaning. Exemplary data analysis steps given in the Practice Notice include:

• relating the presence of protein X from said test sample to a diagnosis of whether the test sample is from a subject suffering from disease Y;

• comparing the expression levels of genes A, B and C to a control standard, wherein a decrease in the levels as compared to the control is indicative of disease Y; or

• wherein hybridization of the probe to a target is indicative of the presence of disease Y.

The Practice Notice asserts that how data is analyzed or interpreted in a diagnostic method generally has no material effect on how the data needs to be physically acquired (and conversely, how data is analyzed generally has no material effect on how the data is acquired). Therefore, the Practice Notice concludes that the data acquisition elements and data analysis elements in the diagnostic method claim likely have a relationship reflecting an aggregation rather than a combination. The practical effect of this analysis is that the examiner will make a determination that a claim is directed to either a “data acquisition problem” or a “data analysis problem”, and, depending on that determination, will conclude that either only the steps that solve the data acquisition problem, or only the steps that solve the data analysis problem, are essential elements of the claimed invention.

Our View of the Practice Notice

The CIPO’s approach to the analysis of the essential elements of a claim as set forth in PN 2013-02 has been soundly criticized, and is not further discussed here. However, Practice Notice PN 2015-02’s bifurcation of patentability based on whether the problem solved is a “data acquisition problem” or a “data analysis problem”, and its characterization of the relationship between the data acquisition steps and the data analysis steps in diagnostic method claims as an unpatentable aggregation, are troublesome developments.

Historically, the subject-matter of a claim has been considered to be an “aggregation” if each of the elements in the claim is known, and each element performs its own individual function as would be expected if it were used on its own[2]. By contrast, the subject-matter of a claim is considered to be a patentable “combination” if the elements in the claim cooperate to produce a unitary result . Practice Notice PN 2015-02 essentially asserts that the CIPO will not consider both the data acquisition steps and data analysis steps of a diagnostic method as a combination that cooperates to produce a unitary result[3].  This is so even though in the absence of either step, the other step cannot function and produce a useful result (or as useful a result) on its own. For example, data acquired from the acquisition step has limited utility unless such data is analyzed using the data analysis step to provide a meaningful conclusion as to the outcome of the diagnostic method. Conversely, without the data acquisition step, there is no data on which to perform an analysis, and therefore no useful information can be obtained about any particular subject who is subjected to the diagnostic method.

The CIPO’s restrictive application of the guidance in Practice Notice PN 2015-02 raises potential concerns for those attempting to obtain patent protection for diagnostic methods in Canada. Many novel diagnostic methods are directed to the discovery of a natural correlation between a medical condition and a biomarker. It is not uncommon that the description of a diagnostic method patent application mentions that the biomarker can be detected using any of a variety of conventional diagnostic techniques.

In the absence of legislative change or further court decisions, applicants seeking to obtain patent protection for a diagnostic method in Canada may need to carefully consider their patenting strategies. Where possible, any novel aspects of the molecule that is assayed or the method that is used to acquire the diagnostic data or quantify the molecule should be emphasized in the description and claims. However, in some cases where the molecule to be assayed and methods to detect and quantify that molecule were known, it may be difficult to frame the claims to conform to the analysis set forth in Practice Notice PN 2015-02. For such applications, it is anticipated that appeals to the Patent Appeal Board, and ultimately the Canadian courts, may be required to clarify the correct approach to be taken to evaluating the patentability of diagnostic methods.

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[1] Practice Notice PN 2015-02 defines the term “analyte” to mean a chemical substance or biomarker that is the subject of analysis.

[2] Crila Plastic Industries Ltd. v. Ninety-eight Plastic Trim Ltd. (1987), 18 C.P.R. (3d) 1 (F.C.A.) at pages 1 and 7 to 9, affirming 10 C.P.R. (3d) 226 (F.C.T.D.); see also Canadian Intellectual Property Office, “Manual of Patent Office Practice” (last update: March 2016) at section 15.02.04 [MOPOP].

[3] See MOPOP at section 15.02.04.