Children’s Hospital of Eastern Ontario v University of Utah Research Foundation, T-2249-14 [CHEO Statement of Claim]
The Children’s Hospital of Eastern Ontario (“CHEO”) has brought an action against the University of Utah Research Foundation, Genzyme Genetics, and Yale University, which puts directly at issue the patentability of isolated DNA under Canadian law. The patents at issue have been preventing the CHEO and other hospitals from conducting on-site genetic screening for the cardiac disorder Long QT syndrome in Ontario,  and may prevent the CHEO from conducting next-generation sequencing techniques for the diagnosis of Long QT (the “Proposed Tests”).  The CHEO wishes to be able to conduct these tests freely.
The CHEO’s statement of claim is three-pronged. First, the CHEO seeks a declaration under section 60(2) of the Patent Act that the hospital’s conduct does not infringe any of the claims in the patents at issue: Canadian Patents Nos. 2,240,737, 2,336,236, 2,337,491, 2,369,812, or 2,416,545 (collectively the “Long QT Patents”). Secondly, the CHEO also seeks a declaration under section 6(1) of the Patent Act that each and every one of the isolated nucleic acid claims and testing method claims in the Long TQ Patents is invalid. Thirdly, in the alternative, the CHEO argues under section 19.1(2) of the Patent Act that the Proposed Tests constitute a public non-commercial use of the Long QT Patents. 
The Proposed Tests would involve sequencing the 13 genes associated with long QT and comparing the patient genes with known reference sequences to assess the patient’s risk of Long QT. [17-18] Five of these genes are the subject matter of the patents at issue. 
The Patents at Issue
The ‘737 Patent relates to the KVLQT1 gene, a particular gene associated with Long QT.  The types of claims include: nucleic acid, vector, host cell, polypeptide synthesis, polypeptide, testing method and transfected cell.  The ‘236 Patent relates to the genomic structure of the “HERG” gene.  All the claims in the ‘236 Patent relate to testing methods.  The ‘491 Patent relates to the KVLQT1 gene and its applications.  The types of claims include: nucleic acid, testing method, polypeptide, vector, transfected cell, and drug screening method. The ‘812 Patent relates to the KCNE2 gene and its applications.  The types of claims include: nucleic acid, polypeptide, vector, transfected cell, exon amplification method, testing method, and drug screening method. The ‘545 Patent relates to a specific mutation in the SCN5A gene.  The types of claims include: nucleic acid, testing method, polypeptide, transfected cell and vector.
An example of a claim to an isolated nucleic acid being challenged is claim 1 from the ‘545 Patent:
- An isolated DNA comprising a nucleic acid encoding the polypeptide of SEQ ID NO:4.
Two examples of a claim to a testing method being challenged is claim 11 of the ‘812 Patent:
- A method of amplifying an exon of a nucleic acid comprising a nucleotide sequence coding for the polypeptide set forth in SEQ ID NO:2 wherein said method comprises using a pair of primers.
And claim 7 of the ‘491 Patent:
- A method for diagnosing the presence of a polymorphism in human potassium voltage-gated channel Isk-related family member 1 (KCNE1) which causes long QT syndrome wherein said method is performed by means which identify the presence of said polymorphism, wherein said polymorphism is one which results in the presence of a mutated form of the KCNE1 polypeptide of SEQ ID NO:4, wherein said mutated form comprises SEQ ID NO:4 except for an amino acid change selected from the group consisting of (a) a leucine at amino acid28, (b) a histidine at amino acid 32, (c) a tryptophan at amino acid 98, (d) an alanine at amino acid 127, and (e) a threonine at amino acid 127.
Non-Infringement of Children’s Hospital’s Proposed Tests
The CHEO argues that its Proposed Tests will not infringe any of the claims to isolated nucleic acids because the Proposed Tests will not involve isolating or amplifying any of the claimed sequences, but will only isolate the patient’s exons from the genes tested. [42-43]
The CHEO further argues that its Proposed Tests will not infringe the testing method claims because the Proposed Tests will require the clinical judgment of a clinical professional, and will not be possible based on identification of the mutations alone.  Further, the Proposed Tests avoid the “screening” described in the testing method claims.  The CHEO argues a number of further more specific allegations of non-infringement. [46-49]
Finally, the CHEO argues that the Proposed Tests will not infringe any of the claims of the Long QT Patents because the Proposed Tests will be used on a non-commercial scale for a non-commercial purpose. 
Invalidity of the Nucleic Acid Claims
The CHEO argues that the claimed nucleic acids are unpatentable subject matter since they are naturally occurring, encode for naturally occurring human genes, and were discovered by extracting genetic material from human beings.  Further, the CHEO argues that the isolating the claimed nucleic acids requires trivial effort that does not constitute a sufficiently marked departure from the naturally-occurring unpatentable nucleic acids to warrant patentability. 
The CHEO also argues that each of the claims to isolated nucleic acid claims are invalid due to lack of novelty,  obviousness,  and the claims being broader than the invention made or disclosed. 
Invalidity of the Method Testing Claims
The CHEO argues that the testing method claims are unpatentable subject matter for being merely an abstract mathematical comparison between a patient genetic sequence and a reference genetic sequence which amounts to a “mere scientific principle or abstract theorem”.  The CHEO further argues that the testing method claims are unpatentable for interfering with the skill and judgment required of a skilled professional,  or, in the alternative, that the testing method claims lack utility since they require no comparison by a skilled professional, which is necessary to achieve a useful result. 
The CHEO also argues the method testing claims are invalid for obviousness  and insufficient disclosure. 
A statement of defence has yet to be filed. The case docket can be monitored here.
The arguments being put forth by the CHEO are similar to the arguments that resonated with the Supreme Court of the United States in Association for Molecular Pathology et al v Myriad Genetics, Inc, et al, 569 US 12-398 (2013), which determined that isolated DNA sequences are not patentable subject matter for being a product of nature, and were not patent eligible merely because they had been isolated (at 8-9). The Myriad case dealt with isolated genetic sequences relating to predispositions towards breast or ovarian cancer, but the claims at issue are highly similar to the claims at issue in this case. An example of a claim struck down by the Supreme Court of the United States is claims 1 and 2 of United States Patent No. 5,747,282:
- An isolated DNA coding for a BRCA1 polypeptide, said polypeptide having the amino acid sequence set forth in SEQ ID NO:2.
- The isolated DNA of claim 1, wherein said DNA has the nucleotide sequence set forth in SEQ ID NO:1.
It is interesting to note that a court in Australia has recently come to the opposite conclusion regarding the patentability of isolated DNA in D’Arcy v Myriad Genetics Inc  FCAFC 115. In that case, the Court found the claim at issue to qualify as a “manner of manufacture” and thus patentable subject matter. The claim at issue was analogous to the claims at issue in the United States decision in Myriad. The claim at issue was claim 1 of Australian Patent No. 686004:
- An isolated nucleic acid coding for a mutant or polymorphic BRCA1 polypeptide, said nucleic acid containing in comparison to the BRCA1 polypeptide encoding sequence set forth in SEQ.ID No:1 one or more mutations or polymorphisms selected from the mutations set forth in Tables 12, 12A and 14 and the polymorphisms set forth in Tables 18 and 19.
The link to the full summary of the Australian case can be found here.