While the patent eligibility of diagnostic method claims remains questionable in the United States, the Canadian Intellectual Property Office has issued updated guidance on the types of diagnostic method claims that can–and cannot–be patented in Canada. Since most stakeholders in this field pursue patent protection internationally, it can be important to know the standards that will be applied in different jurisdictions. 

Thanks to Carmela De Luca at Bereskin & Parr for preparing this article that tipped us off to the new CIPO guidance.

The Canadian Analytical Framework

Where current U.S. jurisprudence calls for application of the two-step Mayo/Alice analytical framework (Is the claim directed to a “judicial exception”? Does the claim recite “significantly more” than the exception”), Canada applies a different two-step analysis. In Canada, a problem-solution approach is used to determine whether the claimed diagnostic method pertains to patent-eligible “data acquisition” or patent-ineligible “data analysis”:

1. Determine the problem and solution in view of common general knowledge (CGK).

2. Determine if the claimed solution to the problem involves data acquisition or data analysis.

The guidance found in Chapter 17 of CIPO’s Manual of Operating Practice illustrates disclosures that “may indicate the existence of a data acquisition problem,” including the following:

• disclosure of a novel or non-CGK analyte

• disclosure of a novel or non-CGK combination of biomarkers

• disclosure that a CGK means to identify or quantify an analyte is applied to a sample or subject population that is not standard to that means

The guidance also illustrates disclosures that “may indicate the existence of a data analysis problem,” including the following:

• an emphasis on the discovery of an allegedly new correlation between a condition and an analyte that is CGK with a relative absence of technical details pertaining to how to acquire the data about the analyte

The Canadian Diagnostic Examples

The new guidance includes four examples that apply the analytical framework to different claims based on different states of common general knowledge (CGK).

In Example 1, a diagnostic method based on detection of a novel mutation is patent-eligible, but a diagnostic method based on correlating a known mutation to a new disease is not.

Example 1. A method of diagnosing whether a human subject is at risk for developing thyroid cancer comprising:
(a) providing a biological sample from the subject;
(b) analysing the sample of step (a) to determine the identity of the nucleotide at position 123 of gene XYZ; and
wherein the subject is at risk for thyroid cancer if the identity of the nucleotide at position 123 is nucleotide A.

When the mutation is novel, the claim solves a patent-eligible data acquisition problembecause there was a need to detect and identify the nucleotide at position 123 of gene XYZ in a human subject.

When the mutation is already known to be correlated with a different cancer, the claim only solves a patent-ineligible data analysis problem relating to the correlation between the known mutation and the new condition (thyroid cancer).

In Example 2, a diagnostic method is eligible based on detection of a known analyte in a novel sample type.

Example 2. A method of diagnosing disease P in a subject comprising:
(a) providing a dried blood sample from said subject;
(b) measuring the activity of enzyme E in the sample, wherein enzyme E activity is detected by mass spectrometry; and
(c) diagnosing the subject as having disease P when the activity of enzyme E is lower than the activity of enzyme E in a control sample representative of normal subjects.

The claim solves a patent-eligible data acquisition problem because there was a need for an improved method of detecting E in biological samples.

In Example 3, a diagnostic method based on a combinations of markers is patent-eligible.

Example 3. A method of screening for pathogenic bacteria comprising:
(a) providing a stool sample from a subject;
(b) detecting a combination of two or more protein markers in the sample selected from G, U, T and S; and
wherein the presence of the two or more markers in the sample indicates that the subject is likely to have a gastrointestinal infection.

The claim solves a patent-eligible data acquisition problem of providing means for detecting combinations of two or more markers selected from G, U, T and S within the same stool sample.

In Example 4, a diagnostic method that uses a commercially available microarray chip is patent-eligible if the diagnosis is based on a novel subset of markers.

Example 4. A method for determining the risk of developing persistent organic pollutant (POP)-associated diabetes, comprising:
(a) using a microarray to measure the expression levels of genes T, O, X, I and C in a blood sample obtained from a patient, wherein the microarray comprises oligonucleotide capture probes that are complementary to nucleic acids corresponding to T, O, X, I and C and wherein each probe is attached to a solid support at a discrete position; and
(b) wherein the patient is at risk of developing diabetes if the expression levels of genes T, O, X, I and C are increased relative to the expression levels of the genes in a control sample representative of normal subjects.

The claim solves a patent-eligible data acquisition problem relating to “the determination of the expression levels of only genes T, O, X, I and C” out of the thousands that could be detected by the microarray.

(Unlike the USPTO’s Patent Eligibility examples, the guidelines also discuss novelty and non-obviousness of the example claims, which is beyond the scope of this article.)

Would Any Of These Claims Be Eligible In The U.S.?

As much as we’d like to leave this as a rhetorical question, we would be remiss if we didn’t point out that the diagnostic “wherein” clauses in the Canadian example claims might undermine the eligibility of such claims under current U.S. jurisprudence. This is highlighted by Example 29 of the USPTO’s Subject Matter Eligibility Examples for Life Sciences.