This list is very much based on my personal experience. The purpose is to provide examples of the sorts of problems that can occur on biotech cases. This allows development of pre-empting strategies, such as making sure the application contains the appropriate fallback positions.
1. Claiming Gene and Protein Sequences Which Are Homologues Of Prior Art Sequences
Examiners are increasingly strict in allowing claims to sequences which are homologues of prior art sequences, probably due to the perception that is technically easy to obtain such sequences. Thought should be given as to why the skilled person might have thought the claimed sequence did not exist, what technical difficulties were overcome during cloning and what advantages the new sequence gives.
2. Claims That Cover Homologues Of New Gene And Protein Sequences
It has generally been the case that Examiners would allow applicants to claim sequences which had homology of 65-70% to a new gene/protein sequence as long as a functional limitation was also recited, such as ‘retaining kinase activity’. However increasingly Examiners are likely to ask for further structural descriptions of the functional sequences. Thought should therefore be given to fallbacks which specify which sequence positions need to be the same as the cloned sequence to retain activity. In addition experimental work describing the properties of homologues should be included in the application if it is available.
3.Claims To Antibodies
Examiners seem to be getting stricter on all aspects of antibody patenting, both in terms of defining the antibody and showing that it has inventive step. If possible the specific epitope sequence bound by the antibody should be given and fallbacks should be introduced which define what the antibody does not bind. In addition it would be very helpful to have data showing surprising properties of the antibody, such as high levels of affinity or specificity. If the prior art is close then bear in mind that the onus is on the applicant to show novelty and appropriate fallbacks will need to be present to define the antibody so that it is clearly novel.
4. Claims Referring To Conditions That Are Defined Functionally
Sometimes the invention is relevant to more than one disease condition in which case a functional definition is appropriate for defining the condition in the claims (e.g. a condition in which TNF-α levels are elevated). In this situation Examiners can be very strict on making sure that the specific conditions which are covered can be identified by the skilled person. In my experience limitation to specific defined conditions is often required and it is rare for Examiners to allow claims that only define a condition functionally.
5. Claims To Mutant Proteins With Specific Activities
If the invention concerns finding a mutant enzyme with a new or improved activity, then it can be difficult to claim all mutants that would have that activity. One must consider how to define equivalent mutations at the same or other positions, as well as how best to cover homologous proteins with the same mutation. Clearly having data showing activity in a range of mutants would be helpful.
6. Claims To Diagnosis By Detecting All Relevant Polymorphisms In A Gene
Where the invention concerns the finding that polymorphisms in a specific gene can be used to diagnose susceptibility to a disease condition then it can be difficult to claim all possible polymorphisms that could form the basis of the diagnostic test. Claims to detection of specific listed polymorphisms for which data is available should be possible, but claims to polymorphisms which are in linkage disequilibrium to them might not possible, though such linked polymorphisms could be identified by routine means.
7. Claims To Use Of A Crystal Structure To Design A Molecule
Where the invention concerns the deducing of a crystal structure then it should be possible to obtain claims covering use of the specific structure to design molecules bind or modulate the molecule that has been crystallised. However it can be difficult to obtain claims covering use of any crystal structure of the same molecule that can be obtained in the same way (i.e. Use of a crystal structure obtainable by [crystallisation, X-ray diffraction and computation steps] to design a modulator of protein X). Clearly claims which are limited to use of a specific set of coordinates would be very narrow.
8. Claims To A Composition Defined Functionally
Where the invention relates to a large number of compositions which cannot easily be defined by specifying the amounts of each component then a functional definition can be appropriate (e.g. A composition comprising component A and component B in synergistic amounts). Whether or not an Examiner will accept a functional definition will be decided on a case-by-case basis, and therefore the assumption should not be made that a functional definition will not be accepted.
9. Claims To A Product Which Solves More Than One Problem
Under European practice the problem solution approach is used to assess inventive step. Normally all of the claims will be analysed with reference to the same problem being solved. However given that products, such as molecules, will have more than one property they can be solutions to different problems, some of which are obvious and some which are not. As a simplistic example, if the invention concerns the discovery that adding a (novel) protein with a specific sequence to a composition causes stabilisation of the composition, and this property of the protein is not obvious, it might still not be possible to obtain a claim to the protein per se if it has homology to known proteins. Finding homologues to known proteins can be deemed to be obvious by Examiners (solving the problem of providing another protein with similar properties, say), and so claims to them can be difficult to obtain even where they turn out to have surprising properties which provide an inventive solution to a problem.
10. Claims To All Functionally Equivalent Epitope Sequences
Where the invention concerns identification of a T cell epitope sequence then it should normally be possible to cover homologues of the epitope. However it can be difficult to define a functional limitation for the homologues which is acceptable to the Examiner. A reference to a complex test, such as ‘capable of binding the same T cell receptor’ might not be acceptable. Thus thought needs to be given to providing several different functional limitations.