Patent claims should cover the broadest expression of the ‘technical effect’ which is possible, and part of the art of a biotech patent attorney is to be able to draft claims having considered the equivalents of all the features present. Here are our favourite equivalents:
Homologues of Sequences
Whenever specific protein or nucleic acid sequences are mentioned thought should be given to homologous sequences that might be able to provide the same function. That function might not necessarily be the natural function of the sequence. For example for a vaccine invention the equivalent might have the same antibody or T cell epitopes. Homologues are normally defined by means of a minimal percentage homology to a specific sequence. In this case the specification should also give an example of an algorithm that can be used to calculate homology, though I have never come across an instance of an Examiner requiring the algorithm to be mentioned in the claims. In the example below the required function is to be able to tolerise an individual.
- A composition for use in preventing or treating allergy to ragweed by tolerisation comprising: (i) at least one original polypeptide selected from RGW03B, RGW03A or RGW03 (SEQ ID NO’s. 9, 8 or 7) or a variant thereof; (ii) at least one original polypeptide selected from RGWOl, RGWOlA or RGWOlB (SEQ ID NO’s. 1, 2 or 3) or a variant thereof; iii) at least one original polypeptide selected from RGW04 or RGW04A (SEQ ID Nos: 10 or 11) or a variant thereof; and (iv) optionally one or more original polypeptides independently selected from any of SEQ ID NO’s. 4-6 and 12-31 or variants thereof; wherein said variants are: (a) a polypeptide of length 9 to 20 amino acids that comprises a region consisting of: the equivalent original peptide sequence; or a homologous sequence which has at least 65% homology to the equivalent original peptide sequence, which sequence is capable of tolerising an individual to the equivalent original peptide sequence, or (b) a polypeptide of length 9 to 20 amino acids that comprises a region consisting of a sequence that represents either: a fragment of the equivalent original peptide sequence; or a homologue of a fragment of the equivalent original peptide sequence, which sequence is capable of tolerising an individual to the equivalent original peptide sequence and has a length of at least 9 amino acids, and wherein said homologue has at least 65% homology to any 9 contiguous amino acids in the equivalent original peptide sequence.
T cell Epitopes
Equivalents of T cell epitopes will be sequences that bind to the same T cell receptor. Examiners may not be too pleased to see sequences defined in terms of what they bind to. The example below shows the sorts of equivalents that could be considered.
- A method of diagnosing coeliac disease, or susceptibility to coeliac disease, in an individual comprising: (a) contacting a sample from the host with an agent selected from (i) the epitope comprising sequence which is: SEQ ID NO: 1 or 2, or an equivalent sequence from a naturally occurring homologue of the gliadin represented by SEQ ID NO : 3, (ii) an epitope comprising sequence comprising: SEQ ID NO : 1, or an equivalent sequence from a naturally occurring homologue of the gliadin represented by SEQ ID NO : 3, which epitope is an isolated oligopeptide derived from a gliadin protein, (iii) an analogue of (i) or (ii) which is capable of being recognised by a T cell receptor that recognises (i) or (ii), which in the case of a peptide analogue is not more than 50 amino acids in length, or (iv) a product comprising two or more agents as defined in (i), (ii) or (iii), and (b) determining in vitro whether T cells in the sample recognise the agent; recognition by the T cells indicating that the individual has, or is susceptible to, coeliac disease.
Single Nucleotide Polymorphisms (SNP’s)
SNP’s are often ‘associated’ with other SNP’s, i.e. they tend to be found together in genomes. This is termed ‘linkage disequilibrium’. Diagnostic tests that detect the presence of a particular SNP could also be based on detecting SNP’s which are in linkage disequilibrium with it, and so it is worth thinking about whether to attempt to claim those other SNP’s. See the example below. [The Trilateral Report on SNP’s (see here) provides useful guidance on how Patent Offices assess their patentability]
- A method of testing a dog to determine the likelihood that the dog is protected from liver copper accumulation, comprising detecting in a sample the presence or absence in the genome of the dog of one or more polymorphisms selected from (a) SNP ATP7a_Reg3_F_6 (SEQ ID NO: 142) and (b) one or more polymorphisms in linkage disequilibrium with (a).
Crystal Factors and Crystal Structures
Where the feature is essentially a numerical value or a set of values then careful thought may be needed as to how to cover equivalents. X-ray diffraction data (structure factors) and structural coordinates obtained by crystallography are an example of this. As can be seen from the claims below equivalents can be defined in terms of being ‘obtainable’ by the relevant crystallographic method. [The Trilateral Report on claims relating to 3D structures (see here) provides guidance on how Patent Offices will examine such subject matter]
- Use of the structure factors obtainable by subjecting a crystal comprising at least an epitope binding fragment of the SM3 antibody, bound to a peptide recognised by the epitope binding site of SM3 to X-ray diffraction measurements to identify, screen, characterise, design or modify a chemical entity.
- Use of the structural coordinates obtainable by subjecting a crystal comprising at least the epitope binding fragment of the SM3 antibody, bound to a peptide recognised by the epitope binding site of SM3 to X-ray diffraction measurements and deducing the structural coordinates from the diffraction measurements, to identify, screen, characterise, design or modify a chemical entity.
You may also wish to see related articles Top 10 Points about Gene and Protein Sequences and 10 Points on Patent Applications Directed to SNPs (single nucleotide polymorphisms).