MOPOP - Chapter 17


Biotechnology and Medicinal Inventions

Table of Contents

Endnotes for Chapter 17


17.01
Scope of this Chapter – March 2016

This chapter provides guidance on Office practice particularly as it pertains to patent applications concerning inventions residing in the diverse field of "biotechnology", as well as "medicinal inventions". 

The field of biotechnology can be thought of as encompassing "any technological application that uses biological systems, living organisms, or derivatives thereof, to make or modify products or processes for specific use"Endnotes 1. Medicinal inventions, by their very nature, also interact with biological systems and encompass chemical compounds or compositions (and the preparation thereof) relating to or having therapeutic properties. It is important to note that although these descriptions offer a convenient means to label an invention, an invention may simultaneously exist in more than one field of technology.

In reading this chapter, it should be borne in mind that its purpose is to clarify, through elaboration, the application of the more generic teachings of other chapters to the examination of particular subject-matter common to biotechnology and medicinal inventions.

Nothing in this chapter should be interpreted as providing exceptions to any practice of general applicability set out in any other chapter.

17.02
Living matter – March 2016

The following subsections provide guidance for determining whether claims featuring living matter define statutory subject-matter within the scope of section 2 of the Patent Act. section 2 requires the subject-matter of an invention to fall within one of the categories of invention, i.e., an art, process, machine, manufacture, composition of matter, or an improvement in one of the preceding categories [see Chapter 12 of this manual].

17.02.01
Higher and lower life forms – March 2016

For the purposes of section 2 of the Patent Act, life forms have in view of the jurisprudenceEndnotes 1 been divided into lower life forms (statutory) and higher life forms (non-statutory), with the distinction being, in general, whether the life form is unicellular (lower) or multicellular (higher). Lower life forms are generally deemed to fall within the scope of section 2 as being either "manufactures" or "compositions of matter" since they can be produced en masse (bearing similarity to how chemical compounds are prepared) and formed in such large numbers that any measurable quantity will possess uniform properties and characteristicsEndnotes 2.

Higher life forms do not fall within the scope of section 2 of the Patent ActEndnotes 3. Further, the Office takes the position that animals at any stage of development are not statutory subject-matter eligible for patent, and consequently fertilized eggs and totipotent stem cellsEndnotes 4 are included in the higher life form proscription.

A stem cell which is embryonic, multipotent or pluripotentEndnotes 5 is not alone capable of developing into an animal and is considered to be a lower life form. Where a claim to a cell could be reasonably understood in view of the description as encompassing within its scope a fertilized egg or totipotent stem cell, this subject-matter should be expressly excluded by proviso, otherwise the claim may be construed as including matter excluded from the scope of section 2.

Note that the fact that a claimed cell could form part of a higher life form does not mean that the claim to the cell should necessarily be construed to be a claim to the higher life form. However, where, upon a purposive construction, a claim to a cell is construed to be a claim to a higher life form, the claim lacks compliance with section 2 of the Patent Act.

Where a claim is construed as an isolated cell, there is no need to specify in the claim that the cell is "as found in the laboratory" or is "in isolated form"Endnotes 6.

Lower life forms include: microscopic algae; unicellular fungi (including moulds and yeasts); bacteria; protozoa; viruses; transformed cell lines; hybridomas; and embryonic, pluripotent and multipotent stem cells.

Higher life forms include: animals, plants, mushrooms, fertilized eggs and totipotent stem cells. Plant varieties that are distinct, uniform and stable may be protected under the Plant Breeders' Rights Act, administered by the Canadian Food Inspection Agency. A plant part such as a cutting, callus, rhizome, tuber, fruit, or seed (regardless of whether the seed is coated) is also considered to be a higher life form.

A claim that is not directed to a higher life form per se but instead includes a higher life form within its scope (e.g., as a component of a composition or food product, as a use, etc.) may, depending on the essential elements as determined through a purposive construction analysis, be statutory subject-matter. For example, consider a claim to "an animal feed comprising X".  Where the claim is construed as the use of X for animal feed, the claim will likely be statutory regardless of whether X is a higher life form. When construed to be X or a product comprising X, the claim will be non-statutory if X is a higher life form. In cases where X is a higher life form that has been processed by significant chemical or physical modification, the claim may be construed as a manufacture within the definition of invention provided in section 2 of the Patent Act

Note that a statutory method or process of producing a non-statutory higher life form will not change the determination that the life form itself is non-statutory.

Example 1:

In an application for patent, the inventors identify the problem to be solved as a need to provide a plant that is resistant to herbicide Q. The specification discloses a new recombinant plant and propagation material thereof produced by a process involving the transformation of a plant cell with an expression vector comprising a bacterial nucleic acid from S. hygroscopicus (SEQ ID NO:1) that confers resistance to herbicide Q.

Claims:

  1. A plant transformed with an expression vector comprising the nucleic acid molecule depicted in SEQ ID NO:1.
  2. A plant cell comprising the nucleic acid molecule depicted in SEQ ID NO:1.
  3. The plant cell of claim 2, wherein the cell is in a plant.
  4. A plant propagation material comprising the plant cell of claim 2.
  5. A seed comprising the nucleic acid molecule depicted in SEQ ID NO:1.
  6. An artificial seed comprising:
    1. embryonic plant tissue comprising the nucleic acid molecule depicted in SEQ ID NO:1; and
    2. an alginate layer that encapsulates the embryonic plant tissue.
  7. A bacterial host cell transformed with an expression vector comprising the nucleic acid molecule depicted in SEQ ID NO:1.

Analysis: Claims 2 and 7 are each construed to be directed to statutory subject-matter within the scope of section 2 of the Patent Act. In contrast, the subject-matter defined by each of claims 1 and 3-6 is non-statutory because each claim is construed to be directed to a higher life form, which lies outside the definition of "invention" as defined in section 2 of the Patent Act. More specifically, claim 1 is construed to be directed to a plant and claims 4-6 are construed to include seeds. Although the preamble of claim 3 defines a cell, it is important to note that the claim specifies the cell is in a plant. Thus, the claim is construed to be directed to an entire plant.

Example 2:

An application describes a novel transgenic pig that produces odourless manure due to the introduction and expression of a transgene (SEQ ID NO:2) in its genome.

Claims:

  1. A fertilized porcine ovum transfected with DNA having the sequence of SEQ ID NO:2.
  2. A cell line consisting of cells transfected with DNA comprising the sequence of SEQ ID NO:2.
  3. A transgenic pig comprising cells as defined in claim 2.
  4. Use of the pig of claim 3 for producing odourless manure.

Analysis: Claims 1 and 3 are non-statutory. Claim 1 is construed as a fertilized ovum, which has the inherent ability to develop into an animal, while claim 3 is construed as a higher life form. Consequently, the subject-matter of both claims is non-statutory. In contrast, claims 2 and 4 are statutory. Claim 2 is construed as a composition of matter and claim 4 defines a statutory "art" when construed to be the use of the pig and not the pig itself.

17.02.02
Organs and tissues – March 2016

Organs and tissues (whether of plant or animal origin) are generally not considered to be manufactures or compositions of matter for the purposes of section 2 of the Patent Act. Organs and tissues are in general created by complex processes, elements of which require no human intervention, and do not consist of ingredients or substances that have been combined or mixed together.  In view of this, the Office considers that a genetically-modified organ or tissue is not statutory subject-matter.

Artificial organ-like or tissue-like structures that are distinct from true tissues and organs and that have been generated by human intervention through the combination of various cellular and/or inert components may be considered, on a case-by-case basis, to be manufactures or compositions of matter within the scope of section 2 of the Patent ActEndnotes 7. For example, functional and anatomical differences may be indicators that serve to distinguish an organ-like or tissue-like structure from a true organ or tissue.

17.02.03
Processes to produce life forms – March 2016

The patentability of a method or process is independent of whether or not the product of the method or process is statutory. Processes to produce higher life forms, organs or tissues are not, therefore, defective on the grounds that they produce non-statutory products.

An especially important consideration is the degree of human intervention embodied in the claimed process. A process which occurs essentially according to nature, with no significant human intervention, is not patentableEndnotes 8. Thus, for example, a claim construed to be directed to a process for producing a plant solely by traditional cross-breeding techniques is not patentable (even where one of the cross-bred plants is transgenic or otherwise modified). A process that is a result of both human intervention and the laws of nature, however, is patent-eligible subject-matter where at least one step of human intervention is an essential element of the claim.

Processes that are considered to include significant human intervention include: processes to produce a lower life form, processes to produce a higher life form (if more than traditional breeding techniques), processes to produce an organ or a tissue through genetic transformation; processes for the in vitro culturing or manipulation of cells; processes to separate cells; and processes to generate mutants using a chemical or physical agent.

Example 1:

An application discloses a need for a new insect-resistant cotton plant. The description discloses a process for producing an insect-resistant transgenic plant, which requires the transformation of plant cells with a Bt toxin gene from a bacterium. Although transformation techniques were part of the common general knowledge of the person skilled in the art, it was not well known that insect resistance in cotton could be conferred by transforming plant cells with a Bt toxin gene.

Claims:

  1. A process to produce an insect resistant cotton plant, comprising:
    1. transforming a plant cell with an expression vector carrying a nucleic acid sequence encoding a Bt toxin gene;
    2. generating a transgenic parent plant from said transformed cell;
    3. crossing the plant of step b) with a plant of cotton variety B;
    4. selecting progeny of said cross that have insect resistance; and
    5. backcrossing the selected progeny with the transgenic parent plant.
  2. A transgenic plant produced by the process of claim 1.

Analysis: The problem to be solved by the invention is determined to be a need to produce a new insect-resistant cotton plant. In this case, the solution is a process that relies on the transformation of a plant cell with a Bt toxin gene to generate a transgenic plant, which is followed by steps of traditional breeding that ultimately produce an insect resistant plant. Given that steps a) through e) provide the identified solution, these steps are all considered essential elements of claim 1. Thus, claim 1 defines statutory subject-matter since step a), which involves significant human invention, is an essential element of the claim. The fact that the process yields a non-statutory product (a plant) has no effect on the patentability of the process. 

It should be emphasized that a proper assessment for patentability must be based on a purposive construction of the claim and not simply on a literal interpretation of the claim. For example, consider a different scenario in which it was common general knowledge that insect-resistant cotton plants are produced by transforming plant cells with a Bt toxin gene. In this scenario, the inventor discovered that the existing process, which uses transgenic Bt toxin plants, could be improved by using cotton variety B in crossbreeding. Thus, given that the person skilled in the art would recognize that transforming a cotton plant with a Bt toxin gene represents a commonly known solution to a commonly known problem, the problem would instead be viewed as a need to improve the process for producing insect-resistant cotton plants. In this case, the solution is based on the use of variety B in the breeding process, as represented by steps c) to e) of the claim. Given that the essential elements of the claim are limited to steps of traditional breeding [steps c) to e)], the claim would not define a statutory invention as defined in section 2 of the Patent Act.

Claim 2 is non-statutory. The subject-matter of the claim defines a higher life form and no degree of human intervention in its production can change the determination that it falls outside the definition of invention in section 2 of the Patent Act [see 17.02.01].

Example 2:

The description discloses a need for biological systems that can be used to screen cancer therapeutics. The description discloses a novel and inventive process for producing a skin-equivalent that is useful for screening potential anti-melanoma drugs.

Claims:

  1. A process for producing a skin-equivalent, comprising:
    1. providing a perforated biocompatible membrane;
    2. seeding said membrane with epithelial cells; and
    3. cultivating said cells thereon in vitro.
  2. A skin-equivalent produced by the process of claim 1.

Analysis: Given that the process of claim 1 requires significant human intervention, and the end result of the process, the skin equivalent (claim 2), is functionally and anatomically distinct from natural skin [see 17.02.02], the subject-matter of these claims is not excluded from the scope of section 2 of the Patent Act. Therefore, the claims are statutory.

Example 3:

An application discloses a need for a sheep breed exhibiting the desirable trait of decreased wool fibre diameter and a need for an improved breeding method to produce such sheep. The inventors screened sheep for a genetic polymorphism and disclosed that a genetic marker (BAA81) on chromosome 11 correlated to the desired trait. Marker assisted selection was performed to identify sheep having the marker. In brief, DNA primers specific to the region surrounding the BAA81 marker were created, the primers were mixed with genomic DNA isolated from a sheep and PCR was performed. Sheep selected by this process were mated to produce progeny that exhibited significantly decreased fibre diameter compared to sheep lacking the marker.

Claim:

  1. A method for producing sheep having decreased wool fibre diameter comprising:
    1. performing a marker assisted selection by identifying molecular marker BAA81 in chromosome 11;
    2. selecting a ram and ewe homozygous for BAA81; and
    3. mating to produce sheep having decreased wool fibre diameter.

Analysis: It is clear that identification of the BAA81 region on chromosome 11 was not part of the common general knowledge. Recognizing that the problem to be solved was to produce sheep that have decreased wool fibre diameter, the inventors solved the problem using an improved breeding method that relied on marker assisted selection to identify the BAA81 polymorphism (step a) and selective breeding of only those sheep having the marker (steps b and c). Hence, in this case, all the steps of the claimed method are essential to solving the problem. The claim defines statutory subject-matter within the scope of section 2 of the Patent Act since the method relies on significant human intervention (step a) and is not construed as being limited to steps of traditional breeding.

17.02.04
Bioinformatics – January 2009

Biomolecules are chemical compounds, and claims to nucleic acids, polypeptides, proteins and peptides are therefore directed to statutory matter.  Certain biomolecules, further, express information through their primary structure (i.e. their sequence).

The three-dimensional structure of a biomolecule is often of importance in understanding its biological activity and behavior.  A claim to a biomolecule, defining the molecule in terms of its atomic coordinates, is statutory.  In contrast, a claim to the three-dimensional atomic coordinates that represent the shape of the biomolecule in space is not statutory.  The coordinates themselves are simply information, which is non-statutory.

Note that the exclusion from patentability of information does not depend on whether or not the information has been recorded on a carrier, nor on the nature of the carrier.

A computer model of a biomolecule which relies on the structural information of the biomolecule is not patentable, since the model itself equates to a graphical presentation of the underlying information. This exclusion extends to include generic computer systems and/or programs that have merely been configured to generate the model.

Computer models of biomolecules can be used in, for example, in silico screening methods.  The mere presence of a computer model of a biomolecule in a method does not of itself render the method unpatentable.

Examples:

  1. A polypeptide comprising the amino acid sequence depicted in SEQ ID NO: 1. (statutory)
  2. A protein comprising the atomic coordinates set out in figure 1. (statutory)
  3. A computer readable medium having recorded thereon the sequence set forth in SEQ ID NO: 1. (non-statutory)
  4. Atomic coordinates of protein X, said coordinates depicted in figure 1. (non-statutory)
  5. A method of obtaining inhibitors of protein X, comprising the steps of:
    1. generating a three-dimensional computer model of protein X using the atomic coordinates depicted in figure 1;
    2. identifying the binding site of protein X using said model; and
    3. electronically screening a library of compounds with defined spatial coordinates in order to identify compounds which are structurally complementary to the binding site of protein X; and
    4. preparing complementary compounds as inhibitors of protein X. (statutory)

17.03
Medical and surgical methods – January 2009

17.03.01* (formerly 17.02.03a*)
Medical and surgical methods – January 2009

A method which provides a practical therapeutic benefit to a subject, even if this is not its primary or intended purpose, is considered to be a method of medical treatment and is therefore not patentable.Endnotes 1 By way of examples, surgical, medical, dental and physiotherapeutic methods of treatment are non-statutory matter.

To be considered a method of medical treatment, the method should cure, prevent or ameliorate an ailment or pathological condition, or treat a physical abnormality or deformity such as by physiotherapy or surgery. Certain natural conditions such as ageing, pregnancy, baldness and wrinkles are not considered to be pathological, and methods to treat such conditions are therefore not proscribed.

Methods that involve performing surgery on the human or animal body are excluded, whether the effect of the surgery is therapeutic or not. Methods that involve the excision of tissue, organ, or tumour samples from the body are considered to be forms of surgery, and are excluded regardless of their reproducibility. The removal of fluids from the body such as by needle or cannula is not of itself surgery.Endnotes 2 A method to remove fluids may nevertheless be proscribed if it otherwise involves surgery, such as in the placement of a cannula or stent in the body,Endnotes 3 or if it lacks utility, e.g. for not being reproducible.

Claims which do not involve a step of surgery or provide a practical therapeutic benefit do not form part of the method of surgery or medical treatment exclusion.Endnotes 4 Thus, certain methods of diagnosing a disease or medical condition, whether practised in vitro or in vivo,Endnotes 5 of treating an animal solely to derive an economic benefit,Endnotes 6 or for achieving a cosmetic result may be patentable.

As mentioned in subsection 11.10.02, use claims are permitted but are scrutinized closely to ensure they do not equate to a medical or surgical method, for example by the inclusion of a medical or surgical step.

Similarly, a claim which recites a dosage regime, or a prescribed dosage amount, may be directed to a method of medical treatment since dosage regimes and prescribed dosage amounts fall within the purview of a medical professional.Endnotes 7 However, dosage forms, pharmaceutical packages or kits, which may physically embody a dosage regime or prescribed dosage amount, are considered patentable subject matter.Endnotes 8

The removal of the medical aspect of a claim may render it acceptable. Inclusion of terms such as "cosmetic", "diagnostic" or "non-medical" in a claim may be taken as disclaimers to medical methods provided the description contains adequate support for such terminology and provided the claim can reasonably be understood to be directed to a non-medical method the results of which cannot reasonably be said to produce a practical therapeutic effect.

Examples:

  1. A method of preventing cervical cancer in a human subject, comprising administering a human papilloma virus peptide defined by SEQ ID NO: 1 to said subject.

    Analysis: non-statutory, since the method is self-evidently a method of medical treatment.

  2. A method of producing antibodies specific for the human papilloma virus peptide defined by SEQ ID NO: 1, comprising administering said peptide to a rodent.

    Analysis: statutory, since rodents are not susceptible to human papilloma virus and do not derive any therapeutic benefit from the administration of the peptide.

  3. A method of producing tenderized meat, comprising:
    1. injecting an animal with a proteolytic composition; and
    2. slaughtering said animal after a period of time sufficient to allow for tenderization of the meat of said animal.

    Analysis: statutory, since the animals do not obtain any therapeutic benefit from the method, and the method has clear industrial applicability.

  4. A method for detecting and localizing a breast tumour, without medically treating said tumour, which method comprises the following steps:
    1. injecting a subject with an antibody X which has been labelled with a diagnostically effective amount of a radioactive isotope;
    2. allowing said labelled antibody to localize at the site of the breast tumour; and
    3. detecting the emission of radioactivity from said radioactive isotope thereby localizing the site of the breast tumour in said subject.

      Analysis: Statutory because, in this case, there is a distinction between the concentration of the radioisotope-labelled antibody which is used for diagnosis and that which would provide a therapeutic effect. The proviso "without medically treating said tumour" therefore qualifies the amount of antibody used and restricts it to non- therapeutic concentrations.Endnotes 9

  5. A method of analyzing a sample of breast tissue to diagnose breast cancer in a subject, comprising the following steps:
    1. homogenizing said sample in extraction buffer to yield soluble and insoluble fractions;
    2. separating the soluble fraction from the insoluble fraction;
    3. reacting the soluble fraction with [novel] antibody X; and
    4. detecting specific binding of antibody X with antigen Y

      wherein specific binding of antibody X to antigen Y indicates the presence of breast cancer.

    Analysis: Statutory, since the method is clearly a diagnostic method and has been drafted in such a manner that any acts required to obtain the necessary sample of breast tissue do not form part of the claimed invention.

  6. A method of detecting breast cancer in a subject comprising the following steps:
    1. obtaining a sample of breast tissue from a subject by [novel] needle biopsy conducted under the virtual guidance of a system which generates a three-dimensional image of a putative breast tumour which has been localized in vivo by immuno-radiography with an antibody reactive with antigen Y; and
    2. detecting the presence of antigen Y in said sample,

      wherein the presence of antigen Y at an amount exceeding 125 ng/g of tissue indicates the presence of breast cancer.

    Analysis: non-statutory, since step (i) involves a step (a needle biopsy) which equates to surgery.

  7. A method of screening for a potential drug for [human] disease X, comprising:
    1. administering a plurality of test compounds to [novel] mice which have been genetically engineered by insertion of human gene Y to mimic disease X;
    2. evaluating the severity of disease progression in said mice in the presence and absence of each of the compounds; and
    3. selecting compounds which slow disease progression as potentials for treating disease X.

    Analysis: statutory, since a method wherein a disease is induced in an otherwise healthy subject is not a method of medical treatment, even if the so-induced disease is subsequently treated.

17.03.02
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17.03.03
Kits and packages – November 2017

This section focuses on the patentability of claims to kits and packages in the context of medical inventions.

A "package" is generally understood as one or more components that are contained within conventional packaging material, such as a box, paper or plastic wrapping, or the like. The person skilled in the art would understand that a package may contain a single component, a plurality of the same component, one or more different components, or any combination of these without limitation. Where appropriate, a package may be defined more particularly as, for example, a commercial package or a pharmaceutical package.

A "kit" is generally understood as a specific type of package that contains two or more components.

When a kit contains a composition, such as a unit dosage form, which is composed of two or more ingredients that are formulated together, that single formulated product is considered as one component in the kit. Thus, one unit dose would not reasonably be considered as two separate components in a kit. The skilled person would understand that there is a difference between a "composition" and a "kit", based on the plain and ordinary meaning of those terms.

When a pharmaceutical composition comprising an active ingredient is a component in a medical kit, the following is a non-exhaustive list of examples of what the second component may be: an instrument for administration, e.g., an applicator, empty syringe or graduated cup; a separate formulating excipient, adjuvant or potentiator; a separate activating agent, reagent, or buffer; an antiseptic wipe; a test strip; a separate product comprising a second active ingredient; or instructions defining the use. See 17.03.03b below for a more detailed discussion of instructions.

17.03.03a
Claims of indefinite scope or lacking clarity

The subject-matter of a claim must be defined distinctly and in explicit terms, in accordance with subsection 27(4) of the Patent Act, because the claims define the subject-matter of the monopoly. The scope of a claim must be clear and definite from the perspective of the person skilled in the art.

The terms "package" and "kit" are used interchangeably at times. In some cases this leads to a lack of clarity or creates avoidable ambiguity within a claim or set of claims, contrary to subsection 27(4) of the Patent Act.

A kit would be understood as a specific type of package comprising at least two components so, in order to comply with subsection 27(4) of the Patent Act, the term "kit" must be construed as having a minimum of two components. Where the term "kit" is construed as consisting of only one component, the claim to the kit would not comply with subsection 27(4) of the Patent Act. For instance, a subsection 27(4) defect would be identified where the application defines a kit as consisting of only one component. A subsection 27(4) defect may also be identified in cases where the application states that a kit is an embodiment of the invention but does not explicitly describe the components of said kit and the examiner construes the kit as having only one component. In contrast, no defect would be identified in cases where either the description or claim unambiguously defines the kit as containing at least two components or where the examiner construes the kit as containing at least two components.

If a package claim defines two or more components then there would be no lack of clarity even though the subject-matter could have been claimed as a kit. There are no restrictions on the number of components a package may contain.

A patent application may contain multiple independent product claims within the same claim set, such as claims to a package, a kit, and a package containing the kit, as long as the existence of the multiple product claims does not result in a lack of clarity.

Example

An application discloses that compound A, a known herbicide, has therapeutic utility for treating disease Y in humans. The description states that compositions comprising compound A may be formulated for a variety of routes of administration, but focuses on subcutaneous and intravenous injectable formulations and liquid oral formulations. In one embodiment the formulation and an empty syringe may be packaged together within a kit. The description also discloses using the formulation in combination with a second compound that also treats disease Y, and refers to a number of compounds well known for treating Y. Also described is an embodiment where compound A is packaged together with a second compound for treating disease Y.

Claims:

  1. A pharmaceutical composition comprising compound A and a pharmaceutically acceptable formulating excipient.
  2. A kit comprising the pharmaceutical composition of claim 1.
  3. The kit according to claim 2, further comprising an instrument for administering the pharmaceutical composition.
  4. A package comprising the kit of claim 2.

Analysis: Claim 1 complies with subsection 27(4) of the Patent Act. The claim is directed to a pharmaceutical composition comprising at least two ingredients, namely compound A and a pharmaceutically acceptable formulating excipient. The excipient is defined in broad terms but the nature and scope of the excipient would be clear to the skilled person based on their common general knowledge and in view of the specification as a whole, based on the terms "pharmaceutically acceptable" and "formulating".

Claim 2 complies with subsection 27(4) of the Patent Act. The claim is directed to a kit comprising the pharmaceutical composition of claim 1. The claim only explicitly defines one component of the kit, namely the composition, and there are no indications in the claim relating to the nature of a second component. However, given that there is a basis in the description for what the second component of the kit may be, e.g. a syringe or the additional compound for treating disease Y, the scope of the claim would be understood as comprising at least two components and, therefore, satisfies subsection 27(4) of the Patent Act.

Claim 3 complies with subsection 27(4) of the Patent Act. The claim is directed to a kit comprising the pharmaceutical composition of claim 1 and an instrument for administering the composition. The instrument is defined in broad terms, but the nature and scope would be clear to the skilled person, based on their common general knowledge and in view of the specification as a whole. Notably, the claim would have also complied with subsection 27(4) if the second component of the kit was defined as the additional compound for treating disease Y.

Claim 4 complies with subsection 27(4) of the Patent Act. The claim is directed to a package comprising the kit of claim 2. As discussed above for claim 2, the kit satisfies subsection 27(4). In this case, the placement of the kit within a package does not lead to a lack of clarity and, therefore, the subject-matter of claim 4 also satisfies subsection 27(4) of the Patent Act. Notably, claim 4 would also be compliant with subsection 27(4) if it referred to claim 3 instead of claim 2.

Note that the claims must still be assessed for compliance with the other requirements of patentability.

17.03.03b
Instructions

Instructions are generally understood as information printed or displayed on a substrate. In the context of medical inventions, this information often suggests actions or directions that can be taken, such as how an active agent can be administered or used in treatment.

Instructions may be claimed as a secondary component of a kit or package; however, there is no general requirement that a kit or package comprise instructions.

Where a use is defined in the preamble or body of a claim or as part of the instructions, the claim may be construed as a "kit for use" or "package for use", which is distinct from a claim to a kit or package per se. For instance, claims such as "a kit comprising A and B and instructions for using A and B to treat disease Y" and "a kit for treating disease Y comprising A and B" are both construed as "kit for use" claims.

Example

An application discloses there is a need for improved treatment of painful diabetic neuropathy in patients. The description states that the inventors have surprisingly discovered that levetiracetam and carbamazepine (known anti-epileptic drugs), when used in combination, are effective for reducing pain associated with diabetic neuropathy.

Claims:

  1. A kit comprising:
    1. a first pharmaceutical formulation comprising levetiracetam; and
    2. a second pharmaceutical formulation comprising carbamazepine.
  2. The kit of claim 1 further comprising instructions for using levetiracetam and carbamazepine to treat pain associated with diabetic neuropathy.

A search of the prior art identified patent document D1, which discloses the combined use of levetiracetam and carbamazepine in epileptic patients. An embodiment of D1 includes a kit comprising both levetiracetam and carbamazepine as well as instructions for preventing seizures in patients.

Analysis: Claims 1 and 2 comply with subsection 27(4) of the Patent Act. Claim 1 recites a kit comprising a first pharmaceutical formulation comprising levetiracetam and a second pharmaceutical formulation comprising carbamazepine. The scope of claim 1 would be understood as a kit containing at least two components, namely the first and second pharmaceutical formulations. In claim 2, the skilled person would understand that the instructions, which define the use of levetiracetam and carbamazepine, represent an additional component of the kit. In view of this, the claims satisfy subsection 27(4) of the Patent Act.

In regard to the requirement for novelty, claim 1 is anticipated by D1 because D1 discloses and enables a kit comprising both levetiracetam and carbamazepine. Recognizing that the kit of claim 2 further comprises instructions for using levetiracetam and carbamazepine to treat pain associated with diabetic neuropathy and that D1 does not disclose and enable this use, claim 2 is novel over D1. Thus claim 2 is regarded as a new use of a kit comprising levetiracetam and carbamazepine that complies with section 28.2 of the Patent Act.

Note that the claims must still be assessed for compliance with the other requirements of patentability.

17.03.04
Medical diagnostic methods – November 2017

The examination of patent applications featuring medical diagnostic method claims presents certain challenges and warrants specific guidance to ensure efficient, predictable, and reproducible examination.

A diagnostic method outlines a sequence of steps to be followed to extract diagnostic meaning from data and will often comprise steps to:

  • acquire data about an analyte Endnotes 10 (e.g., identifying, detecting, measuring, etc. the presence or quantity of X in a sample); and
  • analyze the significance of the acquired data (e.g., wherein the presence, increase/decrease of the quantity, etc. of X correlates to condition Y).

In order to determine the patentability of a diagnostic method claim, the examiner must take into account the general guidance on purposive construction in Chapter 13 of this manual, which involves a determination of the problem addressed by the application, the solution as contemplated by the inventor and the essential elements that provide the solution. It follows that an evaluation for compliance with section 2 of the Patent Act is to be made on the basis of the essential elements as determined through a purposive construction.

The guidance herein may be applicable to claims in a form such as:

  • A method of diagnosing disease Y by detecting analyte X, wherein the presence of X indicates that a patient has disease Y;
  • A method of predicting the prognosis of a subject having disease Y comprising determining the expression level of analyte X, wherein increased expression correlates to a good survival probability;
  • A method of determining if a patient will respond to treatment by measuring analyte X, wherein the patient will respond to treatment if X is below threshold value…;
  • Use of a method to diagnose disease Y, characterized in that a sample is examined for the presence of analyte X;
  • Use of analyte X to diagnose disease Y;
  • A kit for diagnosing disease Y comprising components A and B…;
  • Use of a device for determining whether a patient has disease Y, the device comprising a microarray having two or more oligonucleotides selected from A, B, C, D, E, F,… and P;
  • Use of a compound to treat a patient suffering from disease Y wherein the presence of analyte X, which indicates that the patient has disease Y, was determined;
  • a computer-implemented method for diagnosing disease Y; or
  • any claim having similar language when construed to be a claim to a diagnostic method per se.
17.03.04a
Identifying the problem

The identification of the problem and the solution provided by the invention informs the purposive construction of the claims.Endnotes 11 An identification of the problem is guided by the description and the examiner's understanding of the common general knowledge in the relevant art.

Examiners should bear in mind that an application may describe more than one problem to be solved. For diagnostic methods, it may be appropriate to consider that an inventor is generally looking to solve a data acquisition problem and/or a data analysis problem.

Where a data acquisition problem exists, the description will typically describe technical matter that goes beyond the common general knowledge (CGK) of the skilled person in the art. Factors in the description that may indicate the existence of a data acquisition problem include:

  • disclosure of a novel or non-CGK analyte;
  • disclosure of a novel or non-CGK combination of biomarkers;
  • disclosure of a novel or non-CGK means to identify or quantify an analyte (regardless of whether the analyte itself was known or CGK);
  • 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;Endnotes 12
  • disclosure that a CGK means to identify or quantify an analyte is performed within specific constraints (e.g., timing) that is not standard to that means;Endnotes 13
  • 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.

Factors in the description that may suggest that a data analysis problem exists 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 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;
  • indicators or explicit statements that, in order to acquire data about a particular analyte, it is CGK 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 is CGK.

Once the problem is identified, the examiner must determine the solution to the problem as contemplated by the inventor. In some cases, the problem may not be readily apparent and an identification of the solution may actually inform the problem addressed by the invention.

17.03.04b
Determining the solution to the identified problem

Recall from Chapter 13 that the solution is the element or set of elements that is essential to the successful resolution of the problem. If a claim includes solutions to more than one problem, examination should focus on one solution to a problem in performing the purposive construction. The initial choice of solution should be guided by the description, selecting the solution given the greatest emphasis by the inventors. If it becomes necessary to consider a different solution, the analysis should be undertaken anew.

Where a data acquisition problem has been identified, the solution is provided by those elements that provide a means to acquire data about an analyte. The means by which the data is acquired may be represented by either a single step or by multiple steps within the diagnostic claim.

For example, elements relating to data acquisition may be represented by steps such as:

  • 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 the optical density at 450 nm; 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.

Where a data analysis problem has been identified, the solution is provided by those elements that relate to the analysis of acquired data for the purpose of providing diagnostic meaning.

For example, elements relating to data analysis may be represented by steps such as:

  • 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;
  • wherein if the sample has a value greater than 0.24 then disease Y is suspected; or
  • wherein hybridization of the probe to a target is indicative of the presence of disease Y.
17.03.04c
Purposive construction

Having identified the problem and solution, a purposive construction of the claims involves:

  • interpreting the meaning of the various terms used therein; and
  • determining whether elements in the claims are essential (provide the solution to the identified problem) or non-essential (do not provide the solution to the identified problem).

Recognizing 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 vice versa), the data acquisition elements and data analysis elements in the diagnostic method claim likely have a relationship reflecting an aggregation rather than a combination. Thus, the solution to a problem will be provided by either data acquisition elements or data analysis elements, but not both.

Where a data acquisition problem exists, the essential element or set of essential elements providing the solution is the means to acquire data about an analyte. If the identified problem does not relate to data acquisition then it will presumably relate instead to a data analysis problem. Where this is the case, the essential elements will include steps relating to the mental analysis and/or intellectual significance of the data and will likely not include any steps to acquire the data since the way the data is acquired does not change the nature of the solution (e.g., how X is detected or measured in a sample will not change the intellectual significance of its presence).

17.03.04d
Determining whether a claim defines statutory subject-matter

A diagnostic claim construed as being limited to essential elements that are disembodied (e.g., mental process, lacking physicality, no practical application, etc.) will be identified as defective for not complying with section 2 of the Patent Act because the subject-matter does not fall within a category of invention as defined in section 2. This would generally apply to situations where the identified solution is only provided by an element or set of elements associated with the analysis or significance of the acquired data (e.g., correlation of a marker to a disease).

By contrast, data acquisition elements likely define statutory subject-matter since they usually relate to tangible (non-disembodied) practical steps which fall within a category of invention as defined in section 2. Thus, where such a data acquisition element is identified as an essential element of the construed claim, the claimed subject-matter will likely be statutory unless the claim includes excluded subject-matter, such as a method of medical treatment.

17.03.04e
Examples

Example 1:

The following background information is applicable to all scenarios within Example 1. Each scenario will provide separate additional information about the prior art and/or CGK.

The specification describes a method of diagnosing whether a patient is at risk for developing thyroid cancer.

  • The description states there is a need to identify a biomarker associated with thyroid cancer.
  • It is disclosed that the presence of mutation A, corresponding to the presence of nucleotide A at position 123 of gene XYZ, correlates to a thyroid cancer risk.
  • The steps required to identify mutation A in a biological sample are detailed in the description.
  • Human gene XYZ was well known in the prior art as an important signalling pathway gene and the full-length of its nucleotide sequence was available in public gene databases prior to the claim date.
  • The prior art does not disclose a correlation between gene XYZ and thyroid cancer.

Claim:

1. A method of diagnosing whether a human subject is at risk for developing thyroid cancer comprising:

  1. providing a biological sample from the subject;
  2. analysing the sample of step a) to determine the identity of the nucleotide at position 123 of gene XYZ; and
  3. wherein the subject is at risk for thyroid cancer if the identity of the nucleotide at position 123 is nucleotide A.

Scenario 1A:

  • A mutation at position 123 within gene XYZ
    • was not CGK, and
    • was not specifically identified in any of the prior art.

Analysis:

Person of ordinary skill in the art (POSITA)

The POSITA is a team including an oncologist, an endocrinologist, a geneticist, a molecular biologist and a medical technologist.

Common general knowledge (CGK)

The CGK of the POSITA included knowledge of cancer treatment and diagnosis as well as conventional genotyping techniques. At the claim date, gene XYZ was a well-known signaling pathway gene and the gene, as well as data available in public databases about the gene, were CGK to the POSITA. In this scenario, mutation A in gene XYZ was not CGK to the POSITA.

The Problem

It is clear from the description and CGK that there is more than one problem to be solved by this invention. Given that the application discloses a need to identify a biomarker that correlates to thyroid cancer risk, this is suggestive that a data analysis problem exists. The description also makes apparent that the inventors are proposing a solution to a data acquisition problem since a mutation at position 123 of gene XYZ was not CGK to the POSITA and, by extension, methods of detecting and specifically acquiring data about the nucleotide at position 123 were also not CGK. Recognizing that means for specifically detecting the nucleotide at position 123 of gene XYZ were not CGK and that the description details how this is detected, a purposive construction will be based on the data acquisition problem: a need to detect and identify the nucleotide at position 123 of gene XYZ in a human subject.

The Solution

The identified data acquisition problem is solved by the provision of a method that, when practised:

  1. provides means for detecting the identity of the nucleotide at position 123 of gene XYZ within a biological sample, and
  2. specifically acquires data about the identity of the nucleotide at position 123.

What are the essential elements?

As the solution to the data acquisition problem is provided by steps (a) and (b) of the claimed method, these steps are essential elements of claim 1.

Statutory subject-matter – section 2

Claim 1, as construed, is statutory because the essential elements of the claim define subject-matter that falls within a category of invention as defined in section 2 of the Act.

Novelty – subsection 28.2(1)

Although the full nucleotide sequence of gene XYZ was known in the prior art, the prior art did not specifically disclose means to detect the nucleotide at position 123 in known gene XYZ in a biological sample from a human subject and specifically acquire data about the identity of the nucleotide at position 123. Therefore, the claim is novel because there is no single prior art disclosure that discloses and enables the essential elements of the claim.

Obviousness – section 28.3

Based on a reading of the specification as a whole from the perspective of the POSITA, in light of their CGK, the inventive concept of the claim includes a method that provides both a means for detecting the identity of the nucleotide at position 123 of gene XYZ within a biological sample, and the specific acquisition of data about the identity of the nucleotide at that position. Considering the prior art, it is apparent that genotyping techniques were well known at the claim date and the full length nucleotide sequence of gene XYZ (including position 123) was available to the POSITA from public databases. However, the difference between the prior art and the inventive concept is that the prior art did not disclose looking specifically at position 123 of gene XYZ in order to acquire data about the identity of the nucleotide at that position. The difference does not constitute a step that would have been obvious to the POSITA. Therefore, the construed claim is inventive.

Regarding claim 1 in scenario 1A:

  • Statutory subject-matter s2: Y
  • Novel 28.2(1): Y
  • Non-obvious 28.3: Y

As the claim meets all of the requirements of patentability the claim is allowable.

Scenario 1B:

  • D1 discloses that nucleotide position 123 of gene XYZ has been determined to be a mutational hotspot across a population of tumour samples. Methods used to specifically identify a mutation at this position are also described. This information was not CGK to the POSITA.

Analysis:

Since neither the description nor the CGK have changed relative to Scenario 1A, the POSITA, CGK, problem, solution and essential elements remain as they were stated in that scenario. The analysis below takes into consideration the disclosure of prior art document D1.

Statutory subject-matter – section 2

Claim 1, as construed, is statutory because the essential elements of the claim define subject-matter that falls within a category of invention as defined in section 2 of the Act.

Novelty – subsection 28.2(1)

The claim lacks novelty in view of D1 because D1 discloses and enables the essential elements of claim 1, namely means for the identification of the nucleotide at position 123 of gene XYZ in a biological sample and the acquisition of specific data about the identity of the nucleotide at that position. It should be noted that, in this case, the actual identity of the nucleotide at position 123 (e.g., whether it is A, T, C or G) is not part of the claim or the essential elements.

Further, although D1 did not disclose that a mutation at said position correlates to thyroid cancer risk, the claim is anticipated because this correlation is not an essential element of the data acquisition problem.

Obviousness – section 28.3

The claim is obvious in view of D1 because it was already determined that the claim is anticipated by D1 (see MOPOP 15.02.02d). For the sake of completeness, the examiner determines that the inventive concept of the claim includes a method that provides both a means for identifying the nucleotide at position 123 of gene XYZ within a biological sample, and the specific acquisition of data about the identity of the nucleotide at that position. D1 discloses means for identifying the nucleotide at position 123 of gene XYZ in a biological sample and acquiring specific data about the identity of the nucleotide at that position. It is evident that there is no difference between the inventive concept of the claim and D1 and, therefore, the POSITA would not have required any degree of invention to arrive at the inventive concept.

It should be noted that the data analysis elements do not form part of the inventive concept as the examiner has determined that a data acquisition problem was solved.

Regarding claim 1 in scenario 1B:

  • Statutory subject-matter s2: Y
  • Novel 28.2(1): N
  • Non-obvious 28.3: N

The claim is not allowable as it does not meet all of the requirements of patentability

Scenario 1C:

  • Each of D2-D8 independently discloses testing human subjects for prostate cancer by determining the identity of the nucleotide at position 123 and looking at whether mutation A exists at that position. The examiner has determined that both the means for determining the identity of the nucleotide at position 123 in a biological sample from a human subject and the link between mutation A and prostate cancer were CGK.

Analysis:

Person of ordinary skill in the art (POSITA)

The POSITA is a team including an oncologist, an endocrinologist, a geneticist, a molecular biologist and a medical technologist.

Common general knowledge (CGK)

The CGK of the POSITA included knowledge of cancer treatment and diagnosis as well as conventional genotyping techniques. At the claim date, gene XYZ was a well known signaling pathway gene and the gene, as well as data available in public databases about the gene, were CGK to the POSITA. In this scenario, both mutation A in gene XYZ and the means of determining whether this mutation was present in gene XYZ at nucleotide position 123 in a sample were CGK to the POSITA (see D2-D8). Further, the link between mutation A at position 123 and prostate cancer was CGK.

The Problem

Considering the specification as a whole and the background of the CGK in the relevant field, the examiner has determined that a problem related to data analysis exists. More particularly, the problem appears to be related to a need to correlate a particular genotype in a human subject with a risk of developing thyroid cancer. Although the specification also describes methods for acquiring data about the mutation at nucleotide position 123 of gene XYZ, it is apparent that the inventors are not proposing a solution to a data acquisition problem of how to determine the sequence at position 123 of gene XYZ because its solution already existed in the CGK (see D2-D8).

The Solution

The solution to the identified data analysis problem was arrived at by the discovery of a correlation between the presence of a mutation at position 123 of gene XYZ and thyroid cancer.

What are the essential elements?

As the solution to the data analysis problem is represented by step (c) of the claimed method, the essential element of the claim relates to the correlation between mutation A at position 123 and the risk of thyroid cancer.

Statutory subject-matter – section 2

Claim 1, as construed, is not statutory because the essential element of the claim defines subject-matter that is disembodied and does not fall within a category of invention as defined in section 2 of the Act.

Novelty – subsection 28.2(1)

The claim is novel because there is no single prior art disclosure that discloses and enables the essential element of the claim, namely the correlation between mutation A at position 123 and the risk of thyroid cancer.

It should be noted that although each of D2-D8 independently discloses and enables a method for identifying the nucleotide at position 123 of gene XYZ in a biological sample, the claim is not anticipated by any of D2-D8 because the data acquisition steps in the claim that correspond to the means of detection are not essential elements of the data analysis problem.

Obviousness – section 28.3

Based on a reading of the specification as a whole from the perspective of the POSITA, in light of their CGK, the inventive concept of the claim is the correlation between the presence of mutation A at position 123 of gene XYZ and thyroid cancer. Taking into consideration the information disclosed in D2-D8 and the CGK, it is apparent that mutation A at position 123 of gene XYZ was associated with prostate cancer. However, the prior art does not disclose an association with thyroid cancer. The examiner has concluded, in this case, that the POSITA would not have considered the association between mutation A at position 123 of gene XYZ and thyroid cancer to have been obvious at the claim date. Therefore, the construed claim is inventive.

Regarding claim 1 in scenario 1C:

  • Statutory subject-matter s2: N
  • Novel 28.2(1): Y
  • Non-obvious 28.3: Y

The claim is not allowable as it does not meet all of the requirements of patentability.

It should be noted that if the applicant argues that a data acquisition problem (not a data analysis problem) was solved by their invention, the examiner would provide an alternative data acquisition problem analysis in a subsequent report.

Example 2:

The specification describes an improved method for diagnosing disease P, which is a lysosomal storage disease.

  • The background of the invention discloses that methods for diagnosing disease P were well known in the art and involved measuring enzyme E activity within cultured skin samples wherein the patient is diagnosed as having disease P when the activity of enzyme E is lower than the control.
  • According to the description, the diagnostic method of the invention is an improvement over existing methods of diagnosing disease P because enzyme E activity is measured from dried blood samples. The method is advantageous since it is less invasive and faster than methods of the prior art.
  • The description details the steps of the improved method.
  • D1 discloses a method of diagnosing disease P which involves measuring enzyme E activity in cultured skin cells from patients.
  • D2 discloses a method of measuring enzyme activities in three lysosomal storage diseases related to disease P (but not including disease P) using tandem mass spectrometry on samples of dried blood obtained from patients. D2 states that it is advantageous to carry out the determination of enzyme activity on dried blood samples rather than on conventional skin cell samples.
  • The prior art does not disclose enzyme E activity measurement on blood samples.

Claim:

1. A method of diagnosing disease P in a subject comprising:

  1. providing a dried blood sample from said subject;
  2. measuring the activity of enzyme E in the sample, wherein enzyme E activity is detected by mass spectrometry; and
  3. 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.

Analysis:

Person of ordinary skill in the art (POSITA)

The POSITA is a team including a medical practitioner, a biochemist, and a medical technologist.

Common general knowledge (CGK)

The CGK of the POSITA included knowledge of disease P and other lysosomal storage diseases, as well as existing biochemical assays for diagnosing such diseases. In this example, it was CGK to diagnose disease P by carrying out enzyme assays on skin samples. It was not CGK to measure enzyme E activity in blood samples.

The Problem

Considering the specification as a whole and the background of the CGK of the POSITA in the relevant field, the examiner has determined that the problem relates to data acquisition. Specifically, the identified problem is a need for an improved method of measuring enzyme E activity in a biological sample from a human subject. This conclusion was based on the fact that the instant description details an improved assay method dependent on sample selection which represents a solution that did not exist in the CGK prior to the invention.

The Solution

The identified data acquisition problem is solved by the provision of an improved method that, when practised:

  1. provides means for measuring enzyme E activity by carrying out the measurement by mass spectrometry using a sample of dried blood; and
  2. specifically acquires data about enzyme E activity.

What are the essential elements?

As the solution to the data acquisition problem is provided by steps (a) and (b) of the claimed method, these steps are essential elements of claim 1.

Statutory subject-matter – section 2

Claim 1, as construed, is statutory because the essential elements of the claim define subject-matter that falls within a category of invention as defined in section 2 of the Act.

Novelty – subsection 28.2(1)

The claim is novel because there is no single prior art disclosure that discloses and enables the essential elements of the claim.

Obviousness – section 28.3

Based on a reading of the specification as a whole from the perspective of the POSITA, in light of their CGK, the inventive concept of the claim includes an improved method which includes steps for measuring enzyme E activity by carrying out the measurement by mass spectrometry on a sample of dried blood and specifically acquiring data about the activity of enzyme E. With respect to the prior art, D1 is considered the closest prior art and discloses a method of measuring enzyme E activity. The method of claim 1 differs from D1 in that D1 discloses that the enzyme assay was carried out on cultured skin cells while the instant method uses dried blood samples. This difference, however, does not amount to an inventive step in view of D2. The POSITA would have come directly and without difficulty to measure enzyme E activity in dried blood samples using mass spectrometry given that D2 disclosed that the use of such samples exhibited an advantage over the use of cultured skin cells in assays for other enzymes implicated in related lysosomal storage diseases. Therefore, the claim is obvious in view of a D1 when combined with D2.

Regarding claim 1 in Example 2:

  • Statutory subject-matter s2: Y
  • Novel 28.2(1): Y
  • Non-obvious 28.3: N

The claim is not allowable as it does not meet all of the requirements of patentability.

Example 3:

The specification describes a method of diagnosing gastrointestinal infections based on the presence of combinations of markers in stool samples.

  • According to the description, there is a need for a new diagnostic test for gastrointestinal infections.
  • The description details the steps of the detection method and discloses that the presence of two of more protein markers selected from G, U, T and S in stool samples are indicative of the presence of pathogenic bacteria that correlate to gastrointestinal infections.
  • D1 discloses that each of protein markers G and U are uniquely associated with bacterial strain, X1. Each marker was separately identified in stool samples from human subjects. There is no evidence in D1 that G and U were looked for in combination within the same sample. Further, the link between the combination of G and U and bacterial strain X1 was not CGK to the POSITA.

Claim:

1. A method of screening for pathogenic bacteria comprising:

  1. providing a stool sample from a subject;
  2. detecting a combination of two or more protein markers in the sample selected from G, U, T and S; and
  3. wherein the presence of the two or more markers in the sample indicates that the subject is likely to have a gastrointestinal infection.

Person of ordinary skill in the art (POSITA)

The POSITA is a team including a medical practitioner, a microbiologist, and a medical technologist.

Common general knowledge (CGK)

The CGK of the POSITA included knowledge of gastrointestinal infections and associated pathogenic bacteria. Means for detecting two or more of markers selected from G, U, T and S together in a stool sample were not CGK to the POSITA.

The Problem

Considering the specification as a whole and the background of the CGK of the POSITA in the relevant field, the examiner has determined that the problem relates to data acquisition. Specifically, the identified problem relates to the detection of combinations of two or more of markers G, U, T and S in a sample.

The Solution

The identified data acquisition problem is solved by the provision of a method that provides means for detecting combinations of two or more markers selected from G, U, T and S within the same stool sample; and that specifically acquires data about the presence of these markers.

What are the essential elements?

As the solution to the data acquisition problem is provided by steps (a) and (b) of the claimed method, these steps are essential elements of claim 1.

Statutory subject-matter – section 2

Claim 1, as construed, is statutory because the essential elements of the claim define subject-matter that falls within a category of invention as defined in section 2 of the Act.

Novelty – subsection 28.2(1)

The claim is novel. D1 does not anticipate the construed claim because it does not disclose the detection of a combination of two or more of markers within the same stool sample.

Obviousness – section 28.3

Based on a reading of the specification as a whole from the perspective of the POSITA, in light of their CGK, the inventive concept of the claim is a method that provides means for detecting combinations of two or more markers selected from G, U, T and S within the same stool sample and specifically acquiring data about their presence in the sample. D1 represents the closest prior art and discloses the specific association of each of markers G and U with bacterial strain X1, as well as methods for separately detecting each of the two markers in stool samples. D1 does not disclose that the methods provide steps for detecting the combination of the two markers in the same sample. However, this difference does not constitute an inventive step. In view of D1, the POSITA would have been aware that both proteins G and U act as markers for the same strain and the POSITA would have come directly and without difficulty to the method of detecting the combination of both G and U within the same stool sample. Therefore, the examiner determines that, in this case, the claim is obvious in view of D1 and the CGK of the POSITA.

Regarding claim 1 in Example 3:

  • Statutory subject-matter s2: Y
  • Novel 28.2(1): Y
  • Non-obvious 28.3: N

The claim is not allowable as it does not meet all of the requirements of patentability.

Example 4:

The specification describes a method for determining the risk of developing diabetes associated with exposure to persistent organic pollutants (POPs).

  • According to the description, the inventors wanted to investigate whether there was a correlation at the molecular level between diabetes and POP exposure.
  • The description discloses that the expression levels of five genes were consistently upregulated in patients that had both diabetes and high industrial exposure to POPs as compared to diabetic patients with low POP exposure.
  • The description details the steps required for measuring the expression levels of the five upregulated genes in blood samples obtained from patients which included the use of a commercial DNA microarray.
  • D1 discloses a commercial DNA microarray (the same as that exemplified in the instant application) and a summary of the probe sets included on the microarray. Probes for genes T, O, X, I and C were among the 22,000 probe sets on the array.
  • D2-D8 disclose case studies observing that people exposed to POPs have a higher incidence of diabetes than the general population. Thus, the general link between POPs and diabetes is CGK.

Claims:

1. A method for determining the risk of developing persistent organic pollutant (POP)-associated diabetes, comprising:

  1. 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
  2. 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.

2. Use of a microarray to determine the risk of developing POP-associated diabetes by measuring 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.

3. A microarray comprising 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.

Purposive construction for claims 1 and 2:

A purposive construction analysis is set out below for claims 1 and 2 because these claims include both data acquisition and data analysis elements related to medical diagnoses.

As the examiner has determined that claim 3 is not a diagnostic method and defines statutory subject-matter, a purposive construction analysis has not been set out for claim 3. Only the examiner's conclusions as to novelty and inventiveness are provided below for claim 3.

Person of ordinary skill in the art (POSITA)

The POSITA is a team including a medical practitioner, a toxicologist, an endocrinologist and a medical technologist. Further, the POSITA is skilled in gene expression analysis using microarrays.

Common general knowledge (CGK)

The CGK of the POSITA included knowledge of POPs and the health effects associated with POP exposure and bioaccumulation, as well as knowledge of insulin-related metabolic diseases. The link between POP exposure and diabetes was also CGK but the CGK did not include any knowledge of associated genetic markers. The CGK also included the use of commercial microarrays to simultaneously measure the expression levels of a plurality of genes. As admitted in the description, each of genes T, O, X, I and C were represented, amongst thousands of other genes, on a single commercial microarray. It was not CGK, however, to both 1) specifically measure the expression levels of genes T, O, X, I, and C and 2) specifically acquire the data about the expression levels of T, O, X, I and C (while disregarding the levels of all other genes).

The Problem

Considering the specification as a whole and the background of the CGK of the POSITA in the relevant field, the examiner has determined that a problem the inventors set out to address relates to data acquisition. Specifically, the identified problem relates to the determination of the expression levels of only genes T, O, X, I and C in a patient's sample.

The Solution

The identified data acquisition problem is solved by the provision of a method that both 1) specifically measures the expression levels of genes T, O, X, I and C, and 2) specifically acquires data about the expression levels of only these genes.

What are the essential elements?

As the solution to the data acquisition problem is provided by step (a) of claim 1, this step is an essential element of claim 1.

In claim 2, elements of the claim that provide means to acquire data about the expression levels of genes T, O, X, I and C are essential because they give the solution to the identified data acquisition problem. However, the use of the microarray to determine the risk of developing POP-associated diabetes is not an essential element of claim 2 because it provides the solution to a data analysis problem.

Statutory subject-matter – section 2

Claims 1 and 2, as construed, are statutory because the essential elements of the claims define subject-matter that falls within a category of invention as defined in section 2 of the Act.

Novelty – subsection 28.2(1)

Claims 1 and 2 are novel. The prior art does not anticipate the construed claim because no single document discloses the essential element of the claims. Although D1 discloses a microarray that is capable of measuring the expression levels of thousands of genes, including T, O, X, I and C, D1 does not anticipate claim 1 or 2 because the data set acquired from D1 is not specific to data about the expression levels of genes T, O, X, I and C alone and D1 does not teach looking specifically at these particular genes.

Claim 3 lacks novelty in view of D1, which discloses and enables a microarray comprising 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.

It should be noted that if the term "comprising" in claim 3 was replaced by the term "consisting", claim 3 would be novel if a microarray consisting solely of oligonucleotide capture probes that are complementary to nucleic acids corresponding to T, O, X, I and C was not disclosed in the prior art.

Obviousness – section 28.3

Based on a reading of the specification as a whole from the perspective of the POSITA, in light of their CGK, the inventive concept of claims 1 and 2 is specifically measuring the expression levels of genes T, O, X, I and C in a patient's sample using a microarray comprising 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 specifically acquiring data about the expression levels of these genes. Considering the prior art, it is apparent that the use of commercial microarrays to simultaneously measure the expression levels of a plurality of genes was well known at the claim date. Further, microarrays comprising oligonucleotide capture probes that are complementary to nucleic acids corresponding to T, O, X, I and C were known from D1. However, the difference between the prior art and the inventive concept is that the prior art did not disclose that expression level data about only T, O, X, I and C was specifically acquired and D1 did not disregard data about the expression levels of the remaining 22,000 genes on the array. The difference does not constitute a step that would have been obvious to the POSITA. Therefore, claims 1 and 2 are inventive.

Claim 3 is obvious in view of D1 because it was already determined that the claim was anticipated by D1 (see MOPOP 15.02.02d). For the sake of completeness, the examiner determines that the inventive concept of claim 3 is a microarray comprising 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. Prior art document D1 also discloses and enables a microarray comprising 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. It is evident that there is no difference between the inventive concept of claim 3 and D1 and, therefore, the POSITA would not have required any degree of invention to arrive at the inventive concept.

Regarding claim 1 in Example 4:

  • Statutory subject-matter s2: Y
  • Novel 28.2(1): Y
  • Non-obvious 28.3: Y

Regarding claim 2 in Example 4:

  • Statutory subject-matter s2: Y
  • Novel 28.2(1): Y
  • Non-obvious 28.3: Y

Regarding claim 3 in Example 4:

  • Statutory subject-matter s2: Y
  • Novel 28.2(1): N
  • Non-obvious 28.3: N

The application is not allowable as claim 3 does not meet all of the requirements of patentability.

17.04
Sufficiency of the description – January 2009

Closely related to the question of utility is that of sufficiency. subsection 27(3) of the Patent Act requires (inter alia) that the description "correctly and fully describe the invention and its operation or use as contemplated by the inventor".  Thorson P. summarized the requirements for sufficient specification in Minerals Separation North American Corp v Noranda Mines, Ltd, and later described this "onus of disclosure" as "a heavy and exacting one". Endnotes 1

The description must be correct; this means that it must be both clear and accurate.  It must be free from avoidable obscurity or ambiguity and must be as simple and distinct as the difficulty of description permits.  It must not contain erroneous or misleading statements calculated to deceive or mislead the persons to whom the specification is addressed and render it difficult for them without trial and experiment to comprehend in what manner the invention is to be performed.  It must not, for example, direct the use of alternative methods of putting it into effect if only one is practicable, even if persons skilled in the art would be likely to choose the practicable method.  The description of the invention must also be full; this means that its ambit must be defined, for nothing that has not been described may be validly claimed. Endnotes 2

As was noted in section 12.04.03c, the description must contain sufficient information to support a sound prediction of the utility of the invention.  Further, it must set out the invention such that a person skilled in the art can practice it having reference only to the description itself and to common general knowledge.

In Consolboard, Dickson J. noted that "the inventor must, in return for the grant of a patent, give to the public an adequate description of the invention with sufficiently complete and accurate details as will enable a workman, skilled in the art to which the invention relates, to construct or use that invention when the period of the monopoly has expired". Endnotes 3   The description must be able to answer the questions "What is your invention?: How does it work?" Endnotes 4 such that "when the period of the monopoly has expired the public will be able, having only the specification, to make the same successful use of the invention as the inventor could at the time of his application". Endnotes 5

A description sufficient to allow the public (in the form of a person skilled in the art) to practice the invention is said to be enabling.  Since the person skilled in the art is the addressee of the description, it is not necessary for common knowledge to be comprehensively disclosed.  A known assay technique does not need, for example, to be taught in full.  Merely referring to this technique is sufficient for the person skilled in the art to know how to practise it.

When an examiner has reason to believe that a description is deficient for not having correctly and fully described the claimed invention, an objection is raised under subsection 27(3).  This might be the case, for example, when a broad claim is supported only by its own verbatim language.

It is important to bear in mind that the specification must be sufficient to allow the full scope of the claimed invention to be practised without the need for the person skilled in the art to exercise their inventive ingenuity.  If the person skilled in the art is called on to solve problems in such a manner that an inventive step would be present, the description is insufficient (and the attendant claims are unsupported).

17.05
Nucleic acids and proteins – March 2016

The following subsections relate to issues regarding nucleic acids, polynucleotides, peptides, polypeptides and proteins and the disclosure of their sequences in a sequence listing.

17.05.01
Defining by structure

Generally a product may be defined by its structure, in terms of the process by which it is made, or in terms of its physical or chemical properties. Often the most explicit and definite manner in which to define a chemical compound is by its structure.

For a biomolecule such as a nucleic acid molecule or protein, the structure is typically represented by the nucleotide or amino acid sequence, e.g., "a polypeptide consisting of the amino acid sequence MARNDCQEGHILKFPSTWYV".

For greater clarity, the claim should be explicitly directed to a biomolecule defined by reference to a sequence listing identifier that points to the corresponding sequence in the sequence listing [see 17.05.07], e.g., "a nucleic acid consisting of the nucleotide sequence represented by SEQ ID NO:1" or "a protein comprising the amino acid sequence set forth in SEQ ID NO:2". A claim simply directed to a sequence listing identifier, however, may be interpreted as a claim to mere information (i.e., to the string of letters depicted in the sequence listing), which is not compliant with section 2 of the Patent Act, rather than a claim to the biomolecule itself.  A claim directed to "SEQ ID NO:8", for example, would be unacceptable but a claim to "DNA encoding the protein comprising amino acids 1-260 of SEQ ID NO: 8" would be unambiguous (assuming the reference sequence is clearly defined – see below).

Note that even where a claim to a biomolecule is defined by reference to a sequence within the sequence listing it is not an assurance that the claimed biomolecule will be adequately defined by structure. For example, where a biomolecule is defined in a claim by reference to a sequence that contains a number of variable symbols such as "Xaa" or "n", the claimed subject-matter may not be defined in distinct and explicit terms and may fail to comply with subsection 27(4) of the Patent Act.

In the case of a nucleic acid molecule defined by the protein it encodes, the provision of a partial amino acid sequence of the protein is not taken as an adequate description of a nucleic acid molecule which is capable of encoding the entire proteinEndnotes 1.

17.05.02
Defining by functional limitation

Functional language is generally used to provide breadth to a claim. In certain cases, language that defines specific functional or biological activity may be used to further distinguish a claimed biomolecule from biomolecules of the prior art. Although the use of functional language does not make a claim defective per se, if it is used then the entire scope of the claim must be clear and fully supported by the description [see Chapter 9 of this manual for more information].

In general, the use of functional language in a claim is acceptable if the person skilled in the art would not need to resort to inventive ingenuity to practise the full scope of the claim. For example, consider a claim to "a plant transformation vector comprising a gene of interest; a transposon; and a marker gene positioned within the transposon, wherein the marker gene induces abnormal cellular differentiation in plant tissue". Assuming that representative marker genes are adequately supported in the description and are well known in the prior art by persons skilled in the art, it is acceptable in this case to define the marker gene in functional terms.

On the other hand, where the use of functional language requires the person skilled in the art to exert an inventive effort to practise the full scope of the claim or, likewise, the use of the language causes the scope of the claim to be overly-broad, the claim is likely defective in view of section 84 of the Patent Rules. Where the examiner determines that the description is insufficient to support the breadth of the claim, depending on the facts, a defect could be identified under subsection 27(3) of the Patent Act. Where knowledge of the structure of the protein or nucleic acid is needed to realize the full scope of the claim, the claim may also lack compliance with subsection 27(4) of the Patent Act if the nucleic acid or protein is not further defined by the structure that provides the functional activity.

In the case where, for example, the structure of a protein (or a nucleic acid encoding a protein) is defined in terms of a percent identity to a reference sequence, the claim should additionally specify that the protein has the same biological activity as that described in the application in order to comply with subsection 27(4) of the Patent Act– e.g., "a nucleic acid comprising a sequence that is at least 90% identical to SEQ ID NO:1 which encodes a protein having alpha-amylase activity".

Example:

An application describes a novel polypeptide depicted in the sequence listing as SEQ ID NO:2 that has xylanase activity and is shown to be particularly effective in processes for making biofuels. The description does not describe any variants of the polypeptide having xylanase activity. A search of the prior art revealed that xylanases are generally known. A search for the amino acid sequence of SEQ ID NO:2 identified prior art documents D1 and D2. D1 discloses a polypeptide having 82% sequence identity to SEQ ID NO:2 but lacking xylanase activity while D2 discloses a xylanase having 92% sequence identity with SEQ ID NO:2.

Claims:

  1. A recombinant polypeptide having xylanase activity.
  2. A recombinant polypeptide comprising an amino acid sequence that is at least 80% identical to SEQ ID NO:2.

Analysis: claim 1 is defective. The claimed polypeptide is defined broadly by a functional description of its activity rather than by its structural features. The description discloses with particularity only one polypeptide; this polypeptide is described as having the structural features depicted in SEQ ID NO:2 and the desired xylanase activity. Given that the claim defines more than the description supports, the claim is defective in view of section 84 of the Patent Rules. Where the examiner determines that the description is insufficient to support the breadth of the claim, depending on the facts a defect could be identified under subsection 27(3) of the Patent Act. The subject-matter of the claim also lacks novelty in view of D2 (in effect, the claim would be anticipated by any earlier public disclosure of a polypeptide having the desired activity). D1, on the other hand, would not be anticipatory to claim 1 since D1 does not disclose a polypeptide having the specified activity. Furthermore, if, having regard to the claim and description, it is not clear to the skilled person what is being claimed then a defect under subsection 27(4) of the Patent Act may also be identified.

Claim 2 is defective on multiple grounds. The polypeptide is defined in terms of its structure and, more particularly, to the minimum threshold of percent identity of the structure to the amino acid sequence of SEQ ID NO:2. In this case the claim defines more than the description supports and does not comply with section 84 of the Rules. Given that claim 2 does not define the functional activity of the polypeptide, the claim potentially encompasses polypeptides that lack xylanase activity and/or have unknown function. Identification of a defect under subsection 27(4) of the Patent Act may be warranted where it is unclear whether what is being claimed has the same functional activity as the polypeptide of the application. In addition, the claim is defective for lacking novelty in view of either D1 or D2, which each disclose and enable a polypeptide comprising an amino acid sequence that is "at least 80% identical to SEQ ID NO:2". Had claim 2 included a functional limitation to xylanase activity then D1 would not have been anticipatory.

17.05.03
Nucleic acid and amino acid terminology

Nucleotide or amino acid sequences referred to as being "substantially identical" to a target sequence are not adequately defined since there is no accepted convention in the art as to what is encompassed by the term "substantially" and since the scope of a claim may vary depending on what one considers to be a "substantially" identical sequence.

A nucleotide or amino acid sequence may be defined by a threshold percentage limit as compared to a target sequence – e.g., a nucleic acid molecule comprising a nucleotide sequence that is at least 95% identical to the sequence of SEQ ID NO: 7. If the term "homology" is used to describe the relationship between the sequence and the target then the claim is considered indefinite since the term implies an evolutionary relationship which either exists or does not existEndnotes 2. Applicants are generally permitted to replace the term "homology" with the term "identity" for greater clarity. A defect under subsection 27(4) of the Patent Act may also be identified where a claim includes the term "similarity" and there is no clear definition of what the applicant considers to be similar residues.

17.05.04
Hybridizing nucleic acids

Nucleic acids are often defined as sequences that hybridize to a particular target sequence under various reaction, or stringency, conditions. Given that there is no clear consensus as to what conditions are best used in a given hybridization reaction and that different reaction conditions will capture different nucleic acids, a claim may be held to be indefinite for failing to define the particular parameters to be used during the hybridization reaction and ensuing washings.

Where the target itself is solely defined as being any member of a large family of nucleic acids, e.g., a family of degenerate nucleic acids or variants encoding the same amino acid sequence (including nucleic acids defined as having less than 100% identity), the scope of a claim to a nucleic acid molecule that hybridizes to such a target becomes unclear. In such cases, the target is not limited to a single clearly-defined nucleic acid but instead encompasses a vast number of possible combinations of hybridizing and target nucleic acids.

Where a claim suggests that a nucleic acid molecule, which hybridizes to a target sequence encoding a functional polypeptide, is itself also capable of encoding a functional polypeptide, the claim may be held to be defective under subsection 27(4) of the Patent Act since hybridizing nucleic acids may either not encode a polypeptide, or encode a polypeptide having a different function than that encoded by the target. For greater clarity, such claims should indicate that the nucleic acid molecule hybridizes to the complement of the target sequence.

17.05.05
Sequence alignment methods

Whenever a sequence is identified as having a certain percent identity to a reference sequence, it is necessary to define in the claim whether the percent identity is relative to the full length of the reference sequence or is a partial alignment (such as a BLAST alignmentEndnotes 3).

For the sake of clarity, alignment of the sequence over the full length of the reference sequence is greatly preferred when making the comparison.

17.05.06
Considerations respecting obviousness

In accordance with section 28.3 of the Patent Act, an invention as claimed cannot be obvious or, equivalently, must be the result of ingenuityEndnotes 4) [see Chapter 15 of this manual for further guidance].

If given the amino acid sequence of a polypeptide, the entire class of nucleic acids encoding it can be generated through simple deduction;i.e., by using the genetic code to back-translate from the amino acid sequence. Therefore, where protein X is known in the prior art, a broad claim to "a nucleic acid encoding the amino acid sequence of protein X", for example, is considered obvious.

The opposite is also considered obvious. An amino acid sequence encoded by a known nucleic acid can be directly derived through the translation of the known coding nucleotide sequence provided the correct reading frame has been identified or is obvious.

Given that the class of nucleic acids encoding any particular polypeptide is astronomically large, the identification of a species of the class which has unexpected or advantageous properties can be inventive. Such claims should be analyzed in the context of a selection [see Chapter 15 of this manual].

Example:

An application discloses that a nucleic acid molecule (SEQ ID NO:7) is particularly advantageous for expression in plant tissue and encodes a peptide having the amino acid sequence set forth in SEQ ID NO:8. Prior art document D1 discloses the amino acid sequence of peptide G, which is identical to SEQ ID NO:8, but was derived through Edman degradation. There are no indications in D1 that recombinant techniques were used nor is there an explicit disclosure of a nucleic acid molecule which encodes peptide G. Review Article D2 discusses methods and codon usage tables that may be used in order to achieve enhanced expression of heterologous genes in plant tissues.

Claims:

  1. A nucleic acid encoding the peptide identified by SEQ ID NO:8.
  2. A nucleic acid which has been optimized for expression in plant tissue and which encodes the peptide identified by SEQ ID NO:8.
  3. A nucleic acid comprising the sequence identified by SEQ ID NO: 7 which has been optimized for expression in plant tissue and which encodes the peptide identified by SEQ ID NO: 8.

Analysis: Although it is recognized that obviousness inquiries should follow a four-step approach,Endnotes 5  the analysis has been simplified for the purposes herein.

Claim 1 is obvious in view of D1. Firstly, the claim does not refer to any nucleic acid in particular and merely reflects the general idea of having a nucleic acid molecule which is capable of encoding the peptide; an idea that a person of skill in the art would readily appreciate in view of D1. Second, D1 provides the amino acid sequence of the peptide making it a simple matter of deduction for the person of skill in the art to generate a nucleotide sequence capable of encoding the peptide. Therefore, claim 1 fails to satisfy section 28.3 of the Patent Act in view of the teachings of D1.

Claim 2 is obvious in view of D1 in combination with D2. The claim does not refer to any nucleic acid in particular and merely reflects, albeit in a somewhat more restricted sense, the general idea of having a nucleic acid molecule which has been optimized for expression in plant tissue; an idea that a person of skill in the art would readily be able to put into practical effect by deducing an appropriate encoding sequence from D1 in view of the more specific guidance offered by D2.

Claim 3 is not obvious since neither D1 nor D2 discloses nor suggests the particular sequence referred to in the claim (SEQ ID NO:7). Given that it is disclosed that the sequence has a substantial advantage, the claim represents the selection of nucleic acids having a particular sequence from amongst the genus of all possible nucleic acids encoding the peptide and from amongst the subgenus of all possible nucleic acids employing plant optimized codons.

17.05.07
Sequence listings

An application that discloses a nucleotide or amino acid sequence, other than one that belongs to the prior art, must contain a sequence listing. In some cases, the provision of a sequence listing may be needed to satisfy administrative requirements (e.g., sections 94 and 111 of the Patent Rules), and to "correctly and fully describe the invention and its operation or use as contemplated by the inventor" (i.e., subsection 27(3) of the Patent Act).

The following subsections apply to applications filed on or after June 2, 2007. For applications filed prior to that date, the applicant may substitute the requirements of sections 111 to 131 of the Patent Rules as they read immediately prior to the coming into force of the current rules for the requirements of current section 111 of the Patent Rules. Similarly, the requirements of section 62 as it read immediately prior to the coming into force of the current rules may be substituted for the requirements of current section 94 of the Patent Rules.

17.05.07a
Requirements for a sequence listing

In accordance with subsection 111(1) of the Patent Rules, if an application discloses "a nucleotide or amino acid sequence other than a sequence identified as forming a part of the prior art, the description shall contain, in respect of that sequence, a sequence listing in electronic form, and both the sequence listing and the electronic form shall comply with the PCT sequence listing standard".

When this is the case, the provision of the sequence listing is a requirement for completion of the application (whether or not the application is a PCT national phase application). section 94 of the Patent Rules requires that the sequence listing be provided to the Office within the later of twelve-months from filing or three months from the date of receipt of a notice requisitioning its provision. An applicant may not request the sequence listing from another application be brought forward and recorded against the application since the Office does not consider that such a request satisfies the requirements of section 94 and subsection 111(1) of the Patent Rules.

The applicant must provide any required sequence listing within "the applicable time" to avoid the payment of the fee set out in item 2 of Schedule II. For an application other than a PCT national phase application, the applicable time is 15 months from the earliest priority date or, where no priority is claimed, 15 months from the filing date. For a PCT national phase application, the applicable time is 3 months from payment of the requisite fees for national entry and provision of a copy of the application and/or a translation of the application if applicable (i.e., the requirements of subsections 58(1) and 58(2) of the Patent Rules).

When a sequence listing submitted in accordance with subsection 111(1) of the Patent Rules is of record in the Office, it is not permissible for a paper copy of the sequence listing to be of record. Applicants will be requisitioned to withdraw any paper copy of a sequence listing for which a PCT sequence listing standard-compliant electronic sequence listing has been made of record.

In accordance with subsection 111(2), if a sequence listing is added to an application originally filed without a sequence listing, "the applicant shall file a statement to the effect that the listing does not go beyond the disclosure in the application as filed".

17.05.07b
The PCT sequence listing standard

The term "PCT sequence listing standard" refers to the Standard for the Presentation of Nucleotide and Amino Acid Sequence Listings in International Patent Applications Under the PCT. This standard is provided in annex C of the Administrative Instructions under the PCT and is available via the World Intellectual Property Organization (WIPO) website.

As per subsection 111(3) of the Patent Rules, if an application as filed contains a sequence listing that does not comply with the PCT sequence listing standard and the applicant replaces the non-compliant sequence listing with one that does comply with that standard, the applicant shall file a statement to the effect that the replacement listing does not go beyond the disclosure in the application as filed.

17.05.07c
Correction of a sequence listing

If a sequence listing is found to contain errors, any correction of the listing must comply with the requirements of subsection 38.2(2) of the Patent Act. That is, no new matter may be added to the specification or drawings as originally filed and any correction made to a sequence listing must be reasonably inferable from the specification or drawings as filed. Where the correct sequence could only be determined by, for example, re-sequencing a sample, the correction is not reasonably to be inferred.

17.05.07d
Identification of a sequence listing

In accordance with subsection 86(3) of the Patent Rules, the claims may refer to sequences represented by sequence listings by the sequence identifier and preceded by "SEQ ID NO:". The sequence identifier can simply be an Arabic numeral, such that the first sequence identified in the description could be identified as SEQ ID NO:1, the second as SEQ ID NO:2, etc.

17.05.07e
Variable symbols in a sequence listing

The use of the symbols "n" (or "N") and "Xaa" to define "unknown or modified" bases and amino acids, respectively, is discussed in paragraphs 10 and 18 of the PCT sequence listing standard. When these symbols are used in a sequence listing, they can represent only a single residue (nucleotide or amino acid, respectively) at a specific position in the sequence.

The Office considers that the residues represented by the symbols "n" (or "N") and "Xaa" may be defined in the "Features" section as being either present or absent, and that these symbols may also be used to define that a standard nucleotide or amino acid residue is either present or absent. Similarly, these symbols can be used, through the definitions given in the "Features" section, to represent alternate residues at a given position.

Note that since such symbols represent only a single residue, a sequence of variable length must be presented by using a sufficient number of discrete symbols to represent the maximum length of the sequence. Symbols used in such a presentation may then be qualified in the "Features" section to be either present or absent.

The foregoing discussion relates only to the manner in which the foregoing symbols may be used as a matter of nomenclature. During examination, an examiner must consider whether or not the use of such symbols contravenes the Patent Act and/or Rules, for example on the basis of clarity or support [see 17.05.01].

17.06
Deposits of biological materials – March 2016

Deposits of biological material are addressed in the Patent Act at subsections 38.1(1) and (2). Note that for the purposes of section 38.1, the term "biological material" may include bacteria, bacteriophages, cells in culture, hybridomas, filamentous fungi, yeasts, plant seeds, viruses, purified nucleic acid molecules, plasmids, and replication-defective cells.

Subsection 38.1(1) of the Patent Act provides that:

Where a specification refers to a deposit of biological material and the deposit is in accordance with the regulations, the deposit shall be considered part of the specification and, to the extent that subsection 27(3) cannot otherwise reasonably be complied with, the deposit shall be taken into consideration in determining whether the specification complies with that subsection.

Subsection 38.1(2) of the Patent Act provides that:

For greater certainty, a reference to a deposit of biological material in a specification does not create a presumption that the deposit is required for the purpose of complying with subsection 27(3).

Where a specification refers to a deposit, the deposit shall be considered part of the specification if it is in accordance with the regulations. Sections 103 to 110 of the Patent Rules regulate deposits of biological material. In particular, subsection 104(1) requires the deposit to be made by the applicant with an international depositary authority on or before the filing date of the application. Before the application is open to public inspection, the applicant must inform the Commissioner of the name of this authority and the accession number given to the deposit as per subsection 104(2). The description must include this information and the date of the original deposit with the authority. Further practical aspects of the Patent Rules are covered in Appendix 1 of this chapter.

17.06.01
Considerations respecting sufficiency of disclosure

Bearing in mind that a specification must both adequately describe and enable an invention in order to satisfy subsection 27(3) of the Patent Act so that "when the period of the monopoly has expired the public will be able, having only the specification, to make the same successful use of the invention as the inventor could at the time of his application",Endnotes 1 sufficiency must be considered where the specification refers to a biological deposit. The considerations respecting sufficiency of disclosure as a requirement for patentability are more fully addressed in Chapter 9 of this manual.

A deposit of biological material may be made whether or not it is necessary to enable the invention as required per subsection 27(3) of the Patent Act. However, where the invention cannot be enabled in the absence of access to a biological material, the deposit is a necessary element to make the description sufficient unless the required material is publicly known and reliably available to the person skilled in the art. A biological material is considered to be reliably available if it can be obtained commercially or can be reproducibly prepared or isolated from available materials using established procedures and without undue experimentation. In the case of plant seeds, the Office considers a seed to be reliably available where it enables one to obtain, in a reproducible manner, a homogeneous population of plants that are identical to the plant of the invention.

The fact that a biological deposit has been made does not of itself mean that an invention has been adequately describedEndnotes 2. A claim to a desired product does not merit protection simply because reference is made to where the product can be found. Thus, if it is possible to define the product in clear and explicit terms, a deposit is not considered a substitute for a full and correct description of the product itself and, in view of subsection 38.1(1) of the Patent Act, would not of itself meet the requirements of subsection 27(3) of the Patent Act.

Whenever possible, it is preferable that both methods of disclosure should be usedEndnotes 3 (i.e., disclosures relating to both the deposit of biological material and a clear and explicit description of the product or process of making the product).

Example:

The specification as filed describes both a new mutant strain of bacteria, which is useful for treating gastrointestinal disorders, and a nucleic acid molecule isolated from the strain. The description includes the dates of the original deposits with the international depositary authority and the corresponding accession numbers of both the strain and plasmid comprising the nucleic acid molecule.

Claims:

  1. A Bifidobacterium sp. strain having probiotic activity for treating gastrointestinal disorders, which is deposited under ATCC-8888.
  2. An isolated nucleic acid molecule selected from the group consisting of:
    1. the DNA insert of the plasmid deposited under ATCC-9999; and
    2. the DNA included in the strain of claim 1.

Analysis: claim 1 features a bacterium strain, which is partly defined by reference to its biological deposit number. In this case, recognizing that it is not always possible to describe the matter in terms of its structure and/or physical characteristics, a description of the biological deposit in the description provides a sufficient disclosure of the claimed strain and, therefore, satisfies subsection 27(3) of the Patent Act.

Claim 2 is directed to an uncharacterized nucleic acid molecule defined by reference to biological deposits containing the molecule. Given that it is possible to define the nucleic acid molecule in clear and explicit terms (e.g., by its DNA sequence) and despite the fact that the skilled person in the art may be able to isolate the molecule from the deposit and characterize it (e.g., determine its sequence), the mere inclusion of the deposit information in the specification is not a substitute for a full and correct description of the molecule itself. In the absence of a disclosure of the DNA sequence of the molecule in the specification, subsection 27(3) of the Patent Act is not satisfied. The claim may also be considered non-compliant with subsection 27(4) of the Act since the claimed subject-matter is not defined in distinct and explicit terms.

17.06.02
Considerations respecting anticipation

Where an invention cannot be enabled without requiring access to a biological material associated with the invention, a description may lack sufficiency unless a deposit of this material was made [see 17.06.01]. This requirement extends to an allegedly anticipatory disclosure relevant under section 28.2 of the Patent Act [see Chapter 15 for further guidance]. Consequently, if a prior art disclosure requires access to a biological material in order for the matter described therein to be practised, the biological material must necessarily have been reliably available to the person skilled in the art before the claim date in order for the disclosure to be anticipatory.

Example 1:

An application claims a mutant strain of Citrobacter sp. that is able to effectively remove mercury from wastewater. The description provides details of the biological deposit of the strain with an international depositary. A search of the prior art reveals document D1, which discloses an isolated bacterial strain of Citrobacter sp. that has an ability to degrade mercury but does not describe a biological deposit or how to otherwise obtain the strain.

Claims:

  1. A biologically pure culture of a strain of Citrobacter sp. having mercury-degrading activity.
  2. The culture of claim 1 wherein the strain is deposited under NCIMB Accession No. 24601.

Analysis: prior art document D1 discloses a strain that falls within the scope of claim 1; however, D1 is not enabling since the strain is not reliably available to the person skilled in the art. The strain is further defined in claim 2 by reference to a particular biological deposit, which is neither disclosed nor enabled in D1. Thus, the subject-matter of the claims is not anticipated by D1. It is noted that the examiner may additionally determine that the claims are defective in view of section 84 of the Rules and/or subsection 27(4) of the Act.

Example 2:

An application discloses plasmid Y and provides details of its biological deposit with an international depositary. Prior art document D2 describes "plasmid X", which was constructed from various known genetic elements using known methods. Plasmid X was not deposited but the genetic elements used to construct it were all freely available to the public.

Claim:

  1. Plasmid Y [which has the same elements and arrangement as prior art plasmid X] deposited as IDAC 314159-26.

Analysis: the claim is anticipated since claimed plasmid Y is indistinguishable from known plasmid X.  Further, a person of skill in the art would be enabled to construct plasmid Y using known, freely available, genetic elements and methods.  The fact that the plasmids do not share the same name does not negate the finding of anticipation.

17.07
Antibodies - November 2017

Antibodies, as a class of chemical compounds, have been structurally and functionally well-characterized. The structure of an antibody relates directly to its biological function, including its binding specificity and affinity to its target antigen. Structurally, each antibody is composed of light and heavy polypeptide chains where each chain has variable and constant regions. The variable regions comprise subregions involved in antigen binding, which are known as the complementarity determining regions (CDRs).

It is well established in the art that the formation of an intact antigen binding site generally requires the association of the complete heavy and light chain variable regions of a given antibody, each of which consists of three CDRs which provide the majority of the contact residues for the binding of the antibody to its target epitope. Given that the sequences of the CDRs are responsible for the specific binding of the antibody to its antigen, small changes to those sequences may significantly and unpredictably alter binding specificity and affinity. Therefore, it is generally expected that all of the heavy and light chain CDRs in their proper order and in the context of framework sequences which maintain their required conformation, are required in order to produce an antibody and that proper association of heavy and light chain variable regions is required in order to form functional antigen binding sites.

It is known that, in general, immunization of a mammal with an antigen results in the production of an antiserum containing a heterogeneous mixture of antibodies in which individual antibodies bind to different regions displayed on the surface of the immunizing antigen (i.e., an epitope or antigenic determinant). Thus, antiserum comprises an entire family of antibodies capable of binding to different epitopes on an antigen.

An antibody is often defined in functional terms by its specific binding to a particular target antigen. A claim directed to “an antibody which specifically binds to antigen X” typically represents a generic group of structurally different antibodies having common binding specificity to the antigenic target. This contrasts with a claim to a particular antibody which has been defined in terms of a property of the antibody itself rather than merely by what it binds (for example, the particular antibody is defined in terms of its encoding DNA/protein sequence, or by reference to a biological deposit that was made in accordance with the Patent Rules). Thus a claim to “an antibody which specifically binds to antigen X” is considered to be a claim to a generic group of structurally different antibodies having said binding specificity. Conversely,  a claim to “an antibody which specifically binds to antigen X wherein said antibody has a heavy chain encoded by a nucleic acid of SEQ ID NO: 1 and a light chain encoded by a nucleic acid of SEQ ID NO:2” or a claim to “an antibody which specifically binds to antigen X and is produced by a hybridoma having accession number ABC-123”, encompasses only the particular antibody, i.e. is not a claim to a generic antibody.

A claim to an antibody, as with a claim to any other subject-matter, must be supported by a specification that satisfies subsection 27(3) of the Patent Act. In the case of antibodies, this means that at the relevant date, which is deemed to be the filing dateEndnotes 1, the specification must:

  • correctly and fully describe the antibody invention and its operation or use as contemplated by the inventor; and
  • set out clearly the various steps in a process, or the method of making or using the antibody, in such full, clear, concise and exact terms as to enable any person skilled in the relevant art to make or use it.   

Generally, a claim to an antibody specific for antigen X will be considered supported by a specification provided:

  1. antigen X itself has been fully characterized; and
  2. either antiserum has been prepared, or where antiserum has not been prepared, there is neither anything peculiar about the antigen nor any indications that would lead a person of skill in the art to question the likelihood of success if that person desired to produce an antibody to the antigen.

The claims must also distinctly and explicitly define subject-matter that is novel, non-obvious, useful and statutory.

If antigen X is known or obvious in view of the prior art then an antibody reactive with that antigen would generally be considered obvious.  

Where the prior art discloses and enables antibodies reactive with a close structural relative of antigen X, then a claim to an antibody reactive with antigen X (e.g. an antibody “capable of binding” or “that specifically binds” to antigen X) will be anticipated if the claim, upon a purposive construction, is construed to encompass cross-reacting antibodies of the prior art.

An antibody invention must also be useful. An inventor need not expressly set out the utility of the antibody in the specification; however, if the invention’s utility is questioned, then it must be demonstrated or soundly predicted as of the application’s filing date in order to comply with section 2 of the Patent Act  (for further guidance see 17.07.05).

Example:

The description discloses a novel protein that has utility as a diagnostic target for detecting a disease caused by a pathogenic bacterium. Also disclosed are the amino acid sequence of the protein (SEQ ID NO:2), methods of purifying the protein using recombinant techniques, and reference to routine methods of preparing antibodies to a protein by immunizing a suitable mammalian host. The description is silent as regards the production of any antibodies and lacks any working examples of an antibody specific to the protein.

Claim:

  1. An antibody that specifically binds to a protein consisting of the amino acid sequence set forth in SEQ ID NO:2.

Scenario 1

A search of the prior art for the sequence depicted in SEQ ID NO:2 reveals that the closest structural relative to the protein is 20% identical with no common domains of any significance.

Analysis: the claim is fully supported by a specification that satisfies subsection 27(3) of the Patent Act because the specification is enabling with respect to preparing antibodies and the scope of the claim in respect of the antigenic target is limited to the fully characterized protein of SEQ ID NO:2 which serves as a correct and full description of the corresponding antibody that specifically binds to it. Recognizing that the antigenic protein (SEQ ID NO:2) is not disclosed in the prior art, it follows that the claimed antibody, which specifically binds this protein, is novel and non-obvious. The protein (SEQ ID NO:2) itself has utility as a diagnostic target and antibodies that bind the protein serve a specific useful purpose. Further, the subject-matter of the claim is defined in distinct and explicit terms. Therefore, the claim complies with the Patent Act and Rules.

Scenario 2

A search of the prior art for the sequence depicted in SEQ ID NO:2 reveals that the protein is a low-molecular-weight member of a class of known proteins. Prior art document D1 teaches that antibodies to this class of proteins have never been prepared despite several attempts.

Analysis: the description is silent as regards the successful production of antibodies against the protein of SEQ ID NO:2. Considering that D1 discloses that, despite several attempts, antibodies have never been raised against proteins of a similar type, the person skilled in the art would not regard the instant specification as sufficient to enable the production of the claimed antibody. Thus, paragraph 27(3)(b) of the Patent Act is not satisfied. It is noted that the antibody of claim 1 is otherwise correctly and fully described by way of the disclosure of the fully characterized antigen to which it specifically binds.

17.07.01
Polyclonal antibodies – January 2017

Polyclonal antibodies can be thought of as a generic group that is representative of the entire family of antibodies in antiserum capable of binding a target antigen. Polyclonal antibodies share specificity to the target antigen yet each individual antibody can differ in regard to which epitope on the antigen it specifically binds.

Methods for preparing polyclonal sera are well known in the art and a specification generally does not need to describe in detail any of these methods to be enabling with respect to paragraph 27(3)(b) of the Patent Act.

With respect to a correct and full description of the invention pursuant to paragraph 27(3)(a) of the Patent Act, an antibody, like any other chemical compound, can be described in terms of its chemical structure; however, polyclonal antibodies are not described this way. Rather, it has become accepted practice to describe polyclonal antibodies in terms of the fully characterized antigen to which they specifically bind, e.g., “an antibody that specifically binds to antigen X”. Recognizing that an antigen is implicitly understood to carry many epitopes, a fully characterized antigen is representative of the collective of epitopes carried on the target antigen and therefore provides a correct and full description of the corresponding polyclonal binding partners.

For the purposes of paragraph 27(3)(a) of the Patent Act, a disclosure of an antigen’s chemical structure may be enough to fully characterize the antigen. Where the antigen is a protein, for instance, a description of its complete amino acid sequence is likely adequate. In some cases, a description of the antigen in other terms, such as formula, chemical name, physical properties or by biological deposit, may be adequate provided that the person skilled in the art understands the scope of the antibody claim through the unique physical or chemical properties of the antigen.

If antigen X is known or obvious in view of the prior art then polyclonal antibodies reactive with that antigen would generally be considered obvious.  

A polyclonal antibody invention must also be useful  (for further guidance see 17.07.05).

17.07.02
Monoclonal antibodies – January 2017

A monoclonal antibody binds to a specific epitope or antigenic determinant carried on an antigen. A monoclonal antibody can be viewed as one member of the family of polyclonal antibodies contained in antiserum produced by an immunizing antigen. For specific guidance respecting humanized and chimeric monoclonal antibodies, see 17.07.03.

17.07.02a
Sufficiency of the disclosure

As with claims to polyclonal antibodies, a claim to a monoclonal antibody must be supported by a specification that is both enabling and includes a correct and full description of the antibody invention. Sufficiency of disclosure is based on a fact-specific determination.Endnotes 2

The common general knowledge of the person skilled in the art is an important factor for assessing whether the specification of an application is sufficient to enable the skilled person to practise the invention. Generally, the specification need not set out a detailed procedure for producing a monoclonal antibody since the core steps for preparing a monoclonal antibody are now well known to a skilled person in the art.  A description of a detailed step-by-step protocol would be necessary, however, if the invention resides, at least in part, in an applicant having inventively adapted known procedures to overcome some difficulty in making a monoclonal antibody to a particular antigen.

Although each application will be considered on its own merits, the following non-exhaustive list of factors should be considered by examiners when determining whether claims to monoclonal antibodies are enabled by a specification:

  • whether the applicant actually prepared a monoclonal antibody;
  • where a monoclonal antibody had not been prepared,
    • whether the target antigen to which the monoclonal antibody specifically binds was fully characterized,
    • the availability and/or ease of production of the antigen,
    • whether there is an absence of any indications that the applicant was unable to produce a monoclonal antibody or that one of skill in the art would be unable to reproducibly make a monoclonal antibody to the target antigen, or
    • whether there is an absence of any indications that undue experimentation or undue adaption of known core steps would be necessary for preparing a monoclonal antibody;
  • whether the scope of an antibody claim in respect to the antigen is appropriate.

Thus, the enablement requirement of paragraph 27(3)(b) of the Patent Act is satisfied in cases where a person skilled in the art, in view of their common general knowledge and having only the specification and the fully characterized antigen, would be enabled to produce a monoclonal antibody specific to that antigen without displaying inventive ingenuity or undertaking undue experimentation.

A specification must not only be enabling with respect to a claimed monoclonal antibody but also must provide a correct and full description of the antibody to satisfy paragraph  27(3)(a) of the Patent Act.

Although each application will be considered on its own merits, the following non-exhaustive list of factors should be considered by examiners when determining whether a specification provides acorrect and full descriptionof a monoclonal antibody:

  • whether there was a full characterization of the target antigen to which the monoclonal antibody specifically binds;
  • if not, whether the applicant actually prepared the monoclonal antibody and provided a full characterization thereof;
  • if not, whether the applicant prepared a monoclonal antibody and deposited a hybridoma which produces the antibody, in accordance with the Patent Rules, on or before the filing date of the application [see 17.06]; and
  • whether the scope of an antibody claim with respect to the antigen is appropriate.

As outlined above, paragraph 27(3)(a) may be satisfied in respect of monoclonal antibodies described through reference to the fully characterized antigen to which they specifically bind.Endnotes 3  Depending on the facts of the particular case, a full characterization of the antigen can entail a disclosure of its structure, formula, chemical name, or physical properties. In many cases, the disclosure of the complete amino acid sequence of an antigenic polypeptide may indicate possession of all the putative epitopes carried by the polypeptide and, by extension, serve to correctly and fully describe the genus of the corresponding generic monoclonal antibodies.Endnotes 4

Cases in which more detailed support may be required to provide a full characterization of the antibody invention include:

  • where the applicant is claiming a particular monoclonal antibody reciting particular functional characteristics that go beyond the simple interaction with the target antigen binding, e.g., where the monoclonal antibody is asserted to have agonist, antagonist or neutralizing activity, specificity for a particular epitope, or a remarkably high affinity constant;Endnotes 5
  • the target antigen is complex;
  • despite the target antigen being novel, the full characterization of the antigen identified the presence of substructures or epitopes that are common to a known antigen; and/or
  • monoclonal antibodies immunoreactive with the novel target antigen could be either inherently known, by virtue of cross-reactivity with the novel antigen, or obvious.Endnotes 6

Depending on the facts of the particular case, this detailed support may come, for example, in the form of a disclosure of a representative embodiment of the antibody, a biological deposit, or an explicit description of the amino acid sequences of the binding regions of the monoclonal antibody, the epitope and/or the binding pocket of the target antigen essential to its function.

17.07.02b
Other patentability requirements

In order to be patentable, a claimed monoclonal antibody must be novel and non-obvious in accordance with sections 28.2 and 28.3 of the Patent Act, respectively. Please see Chapter 15  of this manual for a general discussion of anticipation and obviousness.

The Office considers that where the description includes a full characterization of a novel and inventive antigen X, a claim to the corresponding monoclonal antibody having specific binding to X would be novel and non-obvious.

An enabling prior art disclosure of a monoclonal antibody specific to antigen X would anticipate a claim to a generic monoclonal antibody specific to antigen X. In cases where antigen X is disclosed and enabled by the prior art, a claim to a generic monoclonal antibody that binds antigen X would be obvious in view of the prior art. However, a claim to an antibody that binds antigen X may be novel and non-obvious where the claimed antibody is additionally defined in the claim by properties that distinguish the antibody from both generic and prior art antibodies, which may include:

  • its structure, i.e., nucleotide or amino acid sequences;
  • reference to a novel hybridoma which produces the claimed antibody and which was deposited in accordance with the Patent Rules (see 17.06); and/or
  • a specific and supported binding activity, such as an affinity that exceeds the threshold affinity that is expected from a generic antibody.

A monoclonal antibody invention must also be useful (for further guidance see 17.07.05).

Where an application claims nucleic acids or polypeptides relating to antibodies of the invention (e.g., light and heavy chains, variable regions, CDRs, etc.), the nucleic acids and polypeptides must be fully supported by the description (for further guidance see 17.05).

17.07.02c
Examples

The following hypothetical examples are provided to help clarify the foregoing.

Example 1:

An application discloses a novel tyrosine kinase protein, its complete amino acid sequence (SEQ ID NO:2) and corresponding nucleic acid sequence (SEQ ID NO:1). According to the description, enhanced activity of the protein is associated with pulmonary fibrosis. An embodiment of the invention includes monoclonal antibodies that specifically bind and inhibit the protein although no working examples of an antibody are described. A search of the prior art failed to identify any proteins with significant identity over the full length of the amino acid sequence depicted in SEQ ID NO:2 or any corresponding nucleic acid molecules.

Claims:

  1. A protein comprising the amino acid sequence of SEQ ID NO:2.
  2. A monoclonal antibody which specifically binds to the protein of claim 1.

Analysis: in this case, the examiner determined that claim 1 is compliant with the Patent Act and Rules (see 17.05 for further guidance on subject-matter related to this claim). The claimed subject-matter is novel and non-obvious because the prior art does not disclose or suggest any protein having an amino acid sequence with significant identity to SEQ ID NO:2. Further, the matter is fully supported by a specification that satisfies subsection 27(3) of the Patent Act because the specification is enabling with respect to preparing the protein and includes a full characterization of this protein (i.e., through the disclosure of its complete amino acid sequence). The claim also complies with subsection 27(4) of the Act as the subject-matter is distinctly and explicitly defined.

Regarding claim 2, novelty and inventiveness is acknowledged because the antigenic target of the claimed monoclonal antibody (i.e., the protein of SEQ ID NO:2) is novel and non-obvious. The scope of claim 2 in respect of the antigenic target is limited to the fully characterized protein of SEQ ID NO:2 and the examiner considers that this provides a correct and full description of the corresponding claimed monoclonal antibodies. In this case, the person skilled in the art is also enabled to produce the monoclonal antibody at the filing date of the application. Therefore, the claimed monoclonal antibody is fully supported by a specification that satisfies subsection 27(3) of the Patent Act. The claim also complies with subsection 27(4) of the Act as the subject-matter is distinctly and explicitly defined.

Example 2:

The description discloses the production of murine monoclonal antibody, M1, specific for the RF protein for use in diagnosing Rheumatoid arthritis. Also disclosed are details of a biological deposit of the hybridoma that produces the antibody. A further embodiment includes monoclonal antibodies that compete with M1 although a working example of competing antibodies is not disclosed. A search of the prior art identified the murine RF protein and its full amino acid sequence.

 Claims:

  1. An antibody selected from an anti-RF monoclonal antibody and an antigen-binding fragment thereof.
  2. A monoclonal antibody that specifically binds to RF wherein the antibody is produced by the hybridoma having accession number IDAC 022612-11.
  3. An antibody that competes for specific binding to RF with monoclonal antibody M1 produced by the hybridoma having accession number IDAC 022612-11.
  4. An isolated polynucleotide encoding the variable light chain or heavy chain of the antibody of claim 2.

Analysis: claim 1 is obvious. The scope of the claim encompasses any monoclonal antibody that is specific to the antigenic RF protein. Given that techniques for preparing monoclonal antibodies were well established as of the claim date of the application, in this case, no inventive ingenuity is required on the part of the person skilled in the art to prepare a monoclonal antibody, or antigen-binding fragment thereof, with specific binding to the known RF protein. Therefore, the claim is not in accordance with section 28.3 of the Patent Act. It is noted that the subject-matter of the claim is otherwise novel, defined in distinct and explicit terms and supported by a specification that satisfies subsection 27(3) of the Act. The scope of claim 1 in respect of the target antigen is limited to the known and fully characterized antigenic RF protein and the examiner considers that this provides a correct and full description of the corresponding monoclonal antibodies and fragments thereof. In this case, the person skilled in the art, in view of their common general knowledge of routine antibody methods and having only the specification and the fully characterized antigen, would be enabled to produce an antibody (and fragments thereof) specific to RF without displaying inventive ingenuity or undertaking undue experimentation.

Claim 2 defines the antibody by reference to a deposit of the hybridoma that produces it. The claim is novel since the prior art does not describe or enable the antibody (or antigen-binding fragment thereof) obtained from the hybridoma and is non-obvious because, unlike claim 1 to a generic antibody, claim 2 is limited to the particular antibody produced by the hybridoma having accession number IDAC 022612-11. Further, claim 2 is supported by a specification that satisfies subsection 27(3) of the Patent Act because it is enabling with respect to the particular antibody claimed and, assuming that the hybridoma which produces M1 was deposited in accordance with the Patent Rules, the provision of the deposited hybridoma serves to provide a correct and full description of the M1 antibody. Therefore, the claim fully complies with the Patent Act and Rules.

In claim 3, the antibody is distinctly and explicitly defined as one that competes with monoclonal antibody M1 for specific binding to the RF protein and, thus, satisfies subsection 27(4) of the Act. As noted above, the M1 antibody produced by the hybridoma having accession number IDAC 022612-11 is novel and non-obvious and it follows that an antibody that competes for specific binding with that particular antibody is also novel and non-obvious. Appreciating that the person skilled in the art could identify competing antibodies without undertaking undue experimentation or the need to exercise inventive ingenuity (e.g., by using routine competition binding assays), the subject-matter of claim 3 is enabled. Assuming that the hybridoma which produces M1 was deposited in accordance with the Patent Rules, the provision of the deposited hybridoma serves to provide a correct and full description of the M1 antibody and antibodies in general that specifically bind the same epitope, i.e., competing antibodies. Therefore, the claim is supported by a specification that satisfies subsection 27(3) of the Patent Act and complies fully with the Patent Act and Rules.

Claim 4 is not compliant with the Patent Act and Rules. The description discloses details of a biological deposit of the hybridoma that produces the antibody but does not disclose the full nucleotide or amino acid sequences of the antibody itself.  Therefore, the polynucleotide of claim 4 lacks compliance with paragraph 27(3)(a) of the Act. It is noted that a deposit of biological material is not a substitute for a full and correct description of the polynucleotide molecule itself (see 17.06.01 for further guidance). Further, the claim lacks compliance with subsection 27(4) of the Act because the polynucleotide is not distinctly and explicitly defined in the claim.

17.07.03
Humanized and chimeric monoclonal antibodies – January 2017

Advances in genetic engineering techniques have permitted the production of therapeutic humanized and chimeric monoclonal antibodies that combine non-human (e.g., mouse) and human amino acid sequences. The antibodies retain the non-human antigen binding characteristics conferred by the non-human sequences but beneficially elicit less antibody immunogenicity in human recipients as compared to a fully non-human monoclonal antibody.

A humanized monoclonal antibody is a “CDR-grafted” antibody meaning that only the non-human complementarity determining regions (CDRs) of the variable light and heavy chains and selected variable region framework residues have been transferred or “grafted” onto a human antibody template.

A chimeric monoclonal antibody is considered by the person skilled in the art to be a monoclonal antibody in which the non-human constant regions have been replaced with human constant regions. Chimeric antibodies are generally understood to exclude CDR-grafted antibodies.

A determination of whether a specification complies with subsection 27(3) of the Act in relation to humanized and chimeric monoclonal antibodies will generally rely on the same considerations as for monoclonal antibodies (see 17.07.02a).

Recall that compliance with paragraph 27(3)(b) of the Act requires the person skilled in the art to be enabled to make or use the antibody invention. Although core steps for preparing humanized and chimeric antibodies are now well established in the state of the art, the examiner must carefully consider, on a case-by-case basis, whether the skilled person, in view of their common general knowledge in the relevant art and the teachings of the specification, was enabled to prepare a humanized or chimeric antibody specific for the target antigen without having to undertake undue experimentation or display inventive ingenuity at the filing date.

Thus, paragraph 27(3)(b) may be satisfied in cases where, at the filing date, a person skilled in the art, in view of their common general knowledge and having only the specification and a fully characterized target antigen would not have to undertake undue experimentation or display inventive ingenuity to produce a generic humanized or chimeric monoclonal antibody specific to the target antigen.

Recall also that in order to satisfy paragraph 27(3)(a) of the Act, the specification must correctly and fully describe the antibody invention. When determining whether a humanized or chimeric antibody is correctly and fully described, the examiner may rely on the same considerations as for monoclonal antibodies as outlined in 17.07.02a. In brief, depending on the facts surrounding a particular case, a humanized or chimeric antibody may be correctly and fully described through reference to, for example:

  • the fully characterized antigen to which the antibody specifically binds (e.g., the complete amino acid sequence of the target antigenic protein);
  • a structural description of the humanized or chimeric antibody (i.e., the nucleotide or amino acid sequences which minimally encompass the non-human CDRs or the specific monoclonal antibody from which the antibody is derived);
  • a hybridoma that produces the monoclonal antibody from which the humanized or chimeric antibody is derived and which was deposited in accordance with the Patent Rules on or before the filing date of the application [see 17.06]; or
  • a structural description of the epitope to which the humanized or chimeric antibody binds.

In some cases a correct and full description of a claimed humanized or chimeric antibody may require more detailed support (see 17.07.02a).

Even where subsection 27(3) of the Act is satisfied, a claim to a humanized or chimeric antibody may not be patentable if the antibody lacks novelty or inventiveness. For instance, a claim to a generic humanized monoclonal antibody may be anticipated and/or obvious in view of an enabling prior art disclosure of: the fully characterized antigenic target to which the claimed antibody binds; monoclonal antibodies (including  humanized or chimeric monoclonal antibodies) specific to the same antigenic target; or nucleotide or amino acid sequences corresponding to the CDRs of the claimed antibody.

A humanized or chimeric monoclonal antibody invention must also be useful (for further guidance see 17.07.05).

Example:

An application discloses a Sonic Hedgehog (Shh) protein homolog and its complete amino acid sequence (SEQ ID NO:2). According to a working example in the description, a murine monoclonal antibody was prepared using conventional methods and was shown to have high affinity to the homolog in vitro with no cross-reactivity to other Shh proteins. The specification does not include any details of either the structure of the antibody or any hybridoma clone. The description further states that the invention encompasses antibodies specific to the Shh homolog including polyclonal, monoclonal, chimeric and humanized antibodies as well as antigen binding fragments (Fab, Fab’, F(ab’)2, scFV and diabodies), which can be obtained using routine techniques known to persons skilled in the art.   

Claim:

  1. An isolated antibody or antibody fragment thereof that specifically binds to a Sonic Hedgehog protein homolog comprising the amino acid sequence of SEQ ID NO:2, wherein the antibody or antibody fragment thereof is selected from the group consisting of polyclonal, Fab, Fab’, F(ab’)2, monoclonal, chimeric, scFV, diabody and humanized.

Analysis: claim 1 encompasses polyclonal antibodies, monoclonal antibodies, chimeric monoclonal antibodies, humanized monoclonal antibodies and antibody fragments (Fab, Fab’, F(ab’)2, scFv or diabody).

With respect to enablement pursuant to paragraph 27(3)(b) of the Patent Act, all of the antibodies and fragments encompassed by claim 1 are enabled since core methods for preparing these were well known to the person skilled in the art at the filing date of the application. The description also confirms that conventional methods were sufficient to at least make a monoclonal antibody specific to the homolog. A correct and full description of the subject-matter pursuant to paragraph 27(3)(a) of the Patent Act over the entire scope of claim 1 is provided by virtue of the fully characterized target antigen to which the antibodies and fragments specifically bind. In this case, the complete amino acid sequence (SEQ ID NO:2) serves to fully characterize the antigen, and by extension, the corresponding antibodies and antigen binding fragments thereof.

The examiner also determines that the target antigen is novel, non-obvious and useful and, therefore, the claimed antibodies and antigen binding fragments that specifically bind this antigen are likewise novel, non-obvious and useful. The claim also complies with subsection 27(4) of the Act as the subject-matter is distinctly and explicitly defined.

In view of the above, claim 1 complies with the Patent Act and Rules.

17.07.04
Fully human monoclonal antibodies – January 2017

Unlike chimeric and humanized monoclonal antibodies (see 17.07.03), human antibodies are derived entirely from human genes and, in view of this, are more desirable for use in therapeutic and diagnostic applications in humans.

A determination of whether a specification complies with subsection 27(3) of the Act in relation to human monoclonal antibodies will generally rely on the same considerations as for monoclonal antibodies (see 17.07.02a).

Recall that compliance with paragraph 27(3)(b) of the Act requires the person skilled in the art to be enabled to make or use the antibody invention. Although core methodologies, such as phage display technologies and transgenic-mouse technologies, are now routinely practised by persons skilled in the art to prepare fully human monoclonal antibodies to desired antigenic targets, the examiner must carefully consider, on a case-by-case basis, whether the skilled person, in view of their common general knowledge in the relevant art and the teachings of the specification, was enabled to prepare an antibody without having to undertake undue experimentation or display inventive ingenuity at the filing date. See also 17.07.02a.

Thus, the enablement requirement of paragraph 27(3)(b) of the Patent Act is satisfied in cases where a person skilled in the art, in view of their common general knowledge and having only the specification and the fully characterized antigen would be enabled to produce the antibody specific to that antigen without displaying inventive ingenuity or undertaking undue experimentation.

Recall also that in order to satisfy paragraph 27(3)(a) of the Act, the specification must correctly and fully describe the antibody invention. When determining whether a human monoclonal antibody is correctly and fully described, the examiner may rely on the same considerations as for monoclonal antibodies as outlined in 17.07.02a.

Even where subsection 27(3) of the Act is satisfied, a claim to a human monoclonal antibody may not be patentable if the antibody lacks novelty or inventiveness. For instance, a claim to a generic human monoclonal antibody may be anticipated by an enabling prior art disclosure, or may be obvious in view of an enabling prior art disclosure of: the fully characterized antigenic target to which the claimed antibody binds; monoclonal antibodies specific to the same antigenic target; or nucleotide or amino acid sequences corresponding to the CDRs of the claimed antibody.

A human monoclonal antibody invention must also be useful (for further guidance see 17.07.05).

17.07.05
Antibodies and utility – November 2017

An antibody invention must also be useful in order to satisfy section 2 of the Patent Act. The utility does not need to be expressly set out in the specification; however, if the invention’s utility is questioned, utility must be demonstrated or soundly predicted as of the application’s filing date. The threshold that must be proven to establish utility is generally quite low;Endnotes 7 a “mere scintilla” of utility will suffice.Endnotes 8

The skilled person in the art would generally accept that if an antigen itself has a practical utility then antibodies that bind the antigen would have at least some utility (e.g., for in vitro applications such as immunohistochemistry, flow cytometry and Western blotting). Where the subject-matter of the invention is directed to an antibody that is useful for an in vivo therapeutic application, the therapeutic utility would need to be either demonstrated or soundly predicted in order to satisfy section 2 of the Patent Act.

In cases where the utility requires the antibody to possess not only binding capacity to the target antigen but also functional activities, such as antagonist (i.e., blocking), agonist (i.e., activating) or neutralizing activity, the description would likely require more than a disclosure of the binding capacity to the target antigen to establish utility. The provision of a working example of the claimed antibody and in vitro or in vivo data showing the antibody has the required activity may be sufficient to demonstrate utility. In the absence of demonstration, the applicant must be in a position to soundly predict the additional functional activity necessary for the utility.

17.07.06* (formerly 17.07.02a)
Provisos and utility – January 2009

Where a proviso has been presented to avoid inoperative subject-matter, the basis upon which the utility of the remaining matter of the claim has been established must be reconsidered. Since utility will often be based on a sound prediction, a proviso to exclude a known inoperative embodiment requires that the line of reasoning upon which the utility of the remaining matter of the claim is based be reassessed.

17.07.07* (formerly 17.07.05)
Scope of claims – January 2009

In order to fulfill their public notice function, a claim must define the invention in such a manner that the person skilled in the art will understand where they may and may not go without infringing.

As Lord Loreburn noted in Natural Kinematograph Co v Bioschemes Ltd, “[t]he patent system is designed to advance research and development and to encourage broader economic activity.  Achievement of these objectives is undermined however if competitors fear to tread in the vicinity of the patent because its scope lacks a reasonable measure of precision and certainty.  A patent of uncertain scope becomes a public nuisance”.Endnotes 9

An objection to a claim for ambiguity or lack of clarity as to its limits (indefiniteness) is made under subsection 27(4) of the Patent Act.  A claim is not indefinite simply because it is broad, but rather where the precise limits of the claim are uncertain.  A claim that relies, for example, on the use of “a polyol” is not indefinite since the person skilled in the art can immediately appreciate the scope of that term.  A claim relying on “a polyol capable of <performing some function>”, however, is indefinite if the person skilled in the art would not know, or be able to reasonably predict or determine, what polyols fall within the scope of the claim.

17.07.07a* (formerly 17.07.05a)
Recourse to the description

During examination, the language of the claims is interpreted by giving each term its plain and usual meaning in the art to which the invention pertains unless it is clear from the description that a term in the claims is to be given a different meaning.

The courts have acknowledged that an applicant can act as their own lexicographer, by specifying in their description that certain terms will have particular meanings for the purposes of the application.  Whenever an applicant is desiring to act as their own lexicographer, however, it is incumbent on them to make this clear from the language of the description. Further, in so acting it is not proper to give a term having a well-known meaning a definition which is contrary to this meaning.  In such cases, uncertainty exists as to whether the term, when found in a claim, is intended to have its usual or distorted meaning.

For example, teaching that the term “up” means “down” for the purposes of the invention is only liable to cause confusion and serves no purpose.  Such a definition, when made in the description, would be objected to under subsection 27(3) of the Patent Act.  Further, the claim containing the term “up” is objected to under subsection 27(4) of the Patent Act for the lack of clarity as to whether the term is intended to actually mean “up”, or rather to mean “down” following the teachings of the description. Similarly, teaching that the symbol “P” indicates nitrogen atoms is misleading; the symbol is recognized in chemistry as designating phosphorus, and could readily be replaced by the appropriate symbol “N” to designate nitrogen.  In contrast, teaching that the term “protein”, for the purposes of the invention, has some specific but sensible meaning could be acceptable, especially where this avoids having to repeatedly include a lengthy definition in the claims.

Whenever inclusion of the definition found in the description into the claims would not be detrimental to the clarity and conciseness of the claim, however, this should be done.

It is worth noting that the courts, in construing the claims of a patent, are dealing with a document whose language is fixed.  Any deficiencies in the language of the claim can only be remedied by construing the claim in “an informed and purposive way”.  During examination, in contrast, the language of the claims may be amended so as to remove ambiguity and maximize their usefulness in serving their public notice function of defining the extent of the monopoly sought.Endnotes 10

Where a defect of clarity has been noted by an examiner in the language of a claim, it will generally be maintained in the face of a response arguing that the courts could, with the assistance of expert testimony, arrive at some construction thereof.  The purpose of the claims is to serve a public notice function, and “nothing can excuse the use of ambiguous language when simple language can easily be employed”.Endnotes 11

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17.09

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17.10
Synergistic chemical combinations – March 2016

The Office considers a synergistic combination to be one in which the combined use of two or more compounds or products generates a result that is greater than the sum of its parts and provides an unexpected advantageEndnotes 1. Please see Chapters 9 and 11 of this manual for a general discussion of combinations.

Generally, implementing the physical acts of mixing or physically combining different chemical compounds or products does not require inventive activity; however, an inventive step may be acknowledged for a synergistic combination of known components that leads to an unexpected advantage (i.e., the synergistic effect) provided the advantage was disclosed in the originally filed descriptionEndnotes 2.

To ascertain whether an unexpected advantage has been produced by a combination, it is necessary to be aware of the point of reference (the result to be expected from combining the individual components), either in view of the common general knowledge of the person skilled in the art in the relevant field or in view of the description.

The utility of a chemical combination is typically closely associated with the unexpected advantage. The utility of the combination must be established at or before the filing date of the application over the entire scope of the claim. Thus, where a synergistic effect is explicitly promised in an application, the synergistic effect must be either demonstrated or soundly predicted in order to establish utility.

In cases where a first compound has been applied to its known purpose and another compound in the combination unexpectedly enhances the result of the first compound, the enhancement effect is, in some fields, referred to as potentiation and requires similar considerations to those described above with regard to patentability.

17.11
Reach-through claims – March 2016

A "reach-through" claim seeks to encompass subject-matter extending beyond the described invention in cases where the matter has not yet been identified by the inventor but may be discovered through future use of the invention. Considering that "nothing that has not been described may be validly claimed",Endnotes 1 in a reach-through claim the subject-matter defined by the claim is not supported by the specification since the specification fails to provide an adequate written description of the matter.

To illustrate, consider an invention featuring a novel and inventive protein associated with disease Y. Claims to the protein and a method of screening for drugs that inhibit the protein may be acceptable; however, a claim to a product defined by the screening method, e.g. "a drug identified by the method of claim 2" would be considered a reach-through claim where products of the method have not yet been identified. In effect, the claim to a product identified by the method attempts to "reach through" the method in order to define a product that could be potentially identified in the future. Therefore, unidentified products of the method cannot be claimed as such a claim would fail to satisfy section 84 of the Patent Rules. Furthermore, where a product is claimed and not properly described in the specification, the disclosure and enablement requirements of subsection 27(3) of the Patent Act cannot be satisfied.

As a further example, consider an invention directed to a new and inventive method of identifying receptor ligand antagonists. Although such a method may be patent-eligible, the method cannot be legitimately extended to generally claim all antagonists which might eventually be discovered through the future use of the inventive method.

Likewise, the subsequent use of these unidentified antagonists, e.g. to treat disease, would not be patentable.

Thus, examples of reach-through claims may include:

  • product claims directed to unidentified substances defined solely in terms of either the process or method used to identify them or by their ability to modulate the biological function of a biomolecule (e.g., antagonists and agonists); and
  • process, method or use claims that use said unidentified substances.

Appendix 1
Deposits of biological material – March 2016

For the purposes of section 38.1 of the Patent Act, the term "biological material" includes material which is capable of direct or indirect self-replication. Directly self-replicating biological materials are those that replicate by themselves. Indirectly self-replicating biological materials are those that are capable of replication only in association with a directly self-replicating biological material. Bacteria, fungi (including yeast), plant seeds, cells in culture and hybridomas are representative examples of directly self-replicating materials; indirectly self-replicating materials include nucleotide sequences, plasmids, vectors, viruses, phages and replication-defective cells.

The Budapest Treaty

The Budapest Treaty on the International Recognition of the Deposit of Microorganisms for the Purposes of Patent Procedure (The Budapest Treaty) was established in 1977. The Treaty is administered by WIPO and obliges contracting states to recognize the fact and date of a deposit of biological material for patent purposes, when it is made in a depositary which has acquired official status under the Treaty. Such a depositary is known as an International Depositary Authority (IDA).  An applicant who is making multiple patent filings need only make one IDA deposit to satisfy the deposit practice in all contracting states.

The term "microorganism" is not defined in the Treaty so that it may be interpreted in abroad sense as to the applicability of the Treaty to microorganisms to be deposited under it. Whether an entity technically is or is not a microorganism matters less in practice than whether deposit of that entity is necessary for the purposes of disclosure and whether an IDA will accept it. Thus, for example, tissue cultures, plant seeds and plasmids can be deposited under the terms of the Treaty, even though they are not microorganisms in the strict sense of the word.

The Budapest Treaty came into force, with respect to Canada, on September 21, 1996.

Where to make a deposit

A list of International Depositary Authorities and their specific requirements is available at the WIPO website.

When to make a deposit

In accordance with subsection 104(1) of the Patent Rules, a deposit of biological material with an international depositary authority must be made on or before the filing date of the application.

Identifying a deposit

In accordance with subsections 104(2) and 104(3) of the Patent Rules, the applicant must inform the Commissioner, prior to publication of the application, of the name of the IDA and the accession number given by the IDA to the deposit, and must include that information in the description. Further, in accordance with section 104.1 of the Patent Rules, the applicant must include in the description the date of the original deposit with the IDA.

Term of deposit

When a sample of biological material is deposited in an IDA under the Budapest Treaty for the purposes of patent protection, the depositor undertakes not to withdraw the sample for a period of at least 30 years from the date of deposit and for at least five years from the date of the most recent request made to the depositary for the furnishing of a sample of the deposited material (Rules 6 and 9 of the Regulations under the Budapest Treaty).

New and substitute deposits

After an original sample of biological material has been deposited in an IDA (an original IDA deposit), circumstances may necessitate that a new sample of the same material be deposited in either the same or a different IDA (Article 4 of the Budapest Treaty) or that the sample be transferred to a substitute IDA (Rule 5 of the Regulations Under the Budapest Treaty).

If an IDA cannot furnish a sample of deposited material because it is no longer viable, a depositor must make a new deposit in the same IDA.

If an IDA cannot furnish a sample of deposited material because the sample must be sent abroad and this is prevented by export or import restrictions, a depositor may make a new deposit in another IDA.

To maintain an original IDA deposit date, a new deposit must be made within three months of the depositor receiving notice from an IDA that a sample is no longer viable or cannot be sent abroad, or that the IDA's status has changed. The deposit must be accompanied by a statement that the newly deposited material is the same as that originally deposited. Under subsection 106(2) of the Patent Rules, if a new deposit is not made in accordance with Article 4 of the Budapest Treaty, the application is treated as if no deposit had ever been made.

If an IDA temporarily or permanently discontinues any of the tasks required of it as an IDA such that samples of deposited biological material can no longer be provided, the defaulting IDA is required to transfer samples of deposited materials to another IDA.  The new IDA is referred to as a substitute IDA and the deposit is known as a substitute deposit.

In accordance with section 105 and subsection 106(1) of the Patent Rules, whenever a deposit of a biological material is made (or transferred) to an IDA different from the original IDA, the applicant must inform the Commissioner of the name of the new IDA and of the accession number given by the new IDA to the deposit before the expiry of the three-month period after the date of issuance of a receipt by that IDA.

Access to deposited biological material

Deposited biological material becomes available to the public once a patent application is open to inspection under section 10 of the Patent Act, or for applications filed before October 1, 1989 once a patent issues.

In accordance with subsection 104(4) of the Patent Rules, an applicant is entitled to restrict access to a deposit of biological material until such time as a patent has issued, or the application is refused, abandoned and no longer subject to reinstatement, or withdrawn, provided that they file a notice with the Commissioner before the application is open to public inspection. In such cases, any person may request that an independent expert be nominated by the Commissioner in accordance with subsection 109(1) of the Patent Rules. Once so nominated, that expert will have access to the deposit in accordance with subsection 104(4) of the Patent Rules.

In order to access a deposited biological material, a request must be made. Where a restriction has been made by the applicant and is in effect, only the independent expert may make such a request. When such a restriction is not in place, or no longer applicable, any person may request access to the deposited material.

A request for a sample of the biological material must be submitted to the Commissioner of Patents and requires, inter alia, that the requester undertake in accordance with section 108 of the Patent Rules not to make the sample, or any culture derived from the sample, available to any other person nor to use the sample, or any culture derived from the sample, for any purpose other than experiments that relate to the subject-matter of the application until such time as a patent issues, or the application is refused, abandoned and no longer subject to reinstatement, or withdrawn.

In the case of a granted patent, the request for a sample of the deposited material may be made directly to the IDA, without the need to provide a request form certified by the Commissioner of Patents unless the IDA specifically requires that a certified request form indicating that the patent has been issued be submitted.

A request form for the furnishing of a sample of deposited material will be published from time to time in the Canadian Patent Office Record (CPOR) and is also provided as Appendix 3 of the Guide to the Deposit of Microorganisms under the Budapest Treaty which may be found on the WIPO website.

Detailed procedures for obtaining samples of biological materials are provided in Appendix 2.

Nomination of an independent expert

In accordance with subsection 109(1) of the Patent Rules, the Commissioner of Patents will nominate an independent expert with the agreement of the applicant. Both the applicant and the person requesting that an expert be nominated may make suggestions as to who would be a suitable expert. In the event that the Commissioner of Patents and the applicant cannot agree on an acceptable expert within a reasonable time after a request has been made that such an expert be nominated, the applicant's notice under subsection 104(4) of the Patent Rules that access to a deposit be restricted to an expert is deemed, in accordance with subsection 109(2) of the Patent Rules, never to have been filed.

Certification

After a request has been filed with the Commissioner of Patents for the furnishing of a sample of deposited biological material, the Commissioner will, in accordance with subsection 107(2) of the Patent Rules, make the certification referred to in Rule 11.3(a) of the Regulations Under the Budapest Treaty that the deposit is referred to in an application for patent in Canada, that the requester has fulfilled all conditions for the furnishing of a sample, and that the requester has a right to a sample of the deposited material.

A copy of the request along with the certification is then sent to the requester in accordance with subsection 107(3) of the Patent Rules or in the case where the requester is an independent expert, to the applicant and to the person who requested the nomination of the expert in accordance with subsection 110(2) of the Patent Rules.


Appendix 2
Steps for obtaining samples of biological materials – March 2016

To obtain a sample of a biological material referred to in a pending application on which no restriction has been placed under subsection 104(4) or 160(4) of the Patent Rules:

  1. the requesting party completes parts I through IV of the request form;
  2. the requesting party prepares a letter of undertaking, agreeing to abide by the conditions set out in section 108 or 164 of the Patent Rules;
  3. the requesting party, under a covering letter, sends the letter of undertaking and the request form to the Commissioner of Patents, Place du Portage I, 50 Victoria St., Gatineau, Canada, K1A 0C9;
  4. the Commissioner, or a designate, completes part V of the request form, certifies it with the seal of the Patent Office and returns it to the requesting party under a covering letter;
  5. the requesting party sends the request form, a purchase order and any fee required to the IDA;
  6. the IDA sends a sample of the biological material to the requesting party.

To release a sample of a biological material referred to in a pending application, on which a restriction has been placed under subsection 104(4) or 160(4) of the Patent Rules, to an independent expert:

  1. the requesting party requests that the Commissioner of Patents nominate an independent expert for the purposes of the application;
  2. the Commissioner of Patents, with the agreement of the applicant, nominates an independent expert within a reasonable time;
  3. the independent expert completes parts I through IV of the request form;
  4. the independent expert prepares a letter of undertaking, agreeing to abide by the conditions set out in section 108 or 164 of the Patent Rules;
  5. the independent expert, under a covering letter, sends the letter of undertaking and the request form to the Commissioner of Patents, Place du Portage I, 50 Victoria St., Gatineau, Canada, K1A 0C9;
  6. the Commissioner, or a designate, completes part V of the request form, and certifies it with the seal of the Patent Office;
  7. the Commissioner sends, under covering letters, the completed request form to the requesting party, and a copy of thereof to the applicant;
  8. the requesting party sends the request form, a purchase order and any fee required to the IDA;
  9. the IDA sends a sample of the biological material to the independent expert.

To obtain a sample of a biological material referred to in an issued patent:

  1. the requesting party writes to the IDA with a purchase order giving the name and address of the requesting party;
  2. the order should include evidence, e.g., a copy of the cover page of the Canadian patent, indicating that the patent has issued and the accession number of the biological material desired;
  3. where required, the fee charged by the IDA for furnishing the sample is submitted along with the order.

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