Claims at issue

There are eight independent claims in the ‘179 patent, but five of them (Claims 19, 24, 25, 33, and 36) are drawn to methods specific to the MHC locus of humans and will not be discussed. Independent claims 1 and 26 are analysed here as key claims; independent claim 9 is touched upon in this analysis where appropriate.

Claim 1 of the US ‘179 patent recites:
A method for detection of at least one coding region allele of a multi-allelic genetic locus comprising:

(a) amplifying genomic DNA with a primer pair that spans a non-coding region sequence, said primer pair defining a DNA sequence which is in genetic linkage with said genetic locus and contains a sufficient number of non-coding region sequence nucleotides to produce an amplified DNA sequence characteristic of said allele; and

(b) analyzing the amplified DNA sequence to detect the allele

Claim 9 is written in very nearly the same language as Claim 1. In the preamble (the initial statement prior to the word “comprising”), the method is recited as “for detection of at least one allele…”, in step (a), the DNA sequence is in “genetic linkage with said allele”, and in step (b), the amplified DNA is analysed to “determine the presence of a genetic variation in said amplified sequence to detect the allele.” As discussed below, these appear to be differences without a distinction – meaning that the claims may have identical interpretations.

Claim 26 recites:

A DNA analysis method for determining coding region alleles of a multi-allelic genetic locus comprising identifying sequence polymorphisms characteristic of the alleles, wherein said sequence polymorphisms characteristic of the alleles are present in a non-coding region sequence, said non-coding region sequence being not more than about two kilobases in length.

Meaning of the claims

In the United States, what the claims mean is a matter for the court (a judge) to decide 20. In determining the meaning of claim terms, the focus is an objective test of what one of ordinary skill in the art at the time of the invention would have understood the term to mean. The written text of the patent may define the terms. Furthermore, the prosecution history (the back and forth negotiations between the patent applicant and the patent office) are considered as well. Like the specification, the prosecution history is used to ascertain or inform the meaning of the claim terms and is not used to enlarge or decrease the scope of the claims. Although a judge has the option to use other sources to help establish the true meaning of the claims, only the specification and prosecution are used in this report.

Before construing the claims, it may be helpful to the reader to review some special terms found in the claims whose meaning is commonly understood in patent law.

“Comprising” means that all that follows is the minimum of what is claimed. Thus, if a method “comprises” steps A and B, a person performing the method using steps A, B, and C is infringing the claim. The indefinite article “a” or “an” means one or more.

Claims 1 and 9

As an initial step to interpreting and understanding the meaning of claims, it is wise to pay close attention to the definitions within a patent. Conveniently, the drafter of the patent text put definitions of most of the key terms in a section entitled “Definitions”, which can be found in columns 5 and 6 of the patent. Other definitions of terms are found in the prosecution history. For our purposes, only a few of these definitions are important. They are reproduced here and used below to help interpret the claims.[add a comment]

“Allele” – a genetic variation associated with a coding region; … an alternative form of the gene. (In an Amendment 22, “allele” is further defined as “associated with a change in an exon sequence rather than a change in the sequence of the encoded protein or in non-coding regions of the gene sequence.”)

“Haplotype” – a region of genomic DNA on a chromosome which is bounded by recombination sites such that genetic loci within a haplotypic region are usually inherited as a unit.

“Intron 23” (“non-coding region sequence”) – untranslated DNA sequences between exons, together with 5’ and 3’ untranslated regions associated with a genetic locus, as well as intergenic spacing sequences (“junk DNA”).

“Genetic locus” – the region of the genomic DNA that includes the gene that encodes a protein including any upstream or downstream transcribed non-coding regions and associated regulatory regions.

“Genetic linkage” – regions of genomic DNA that are inherited together 24.

In plain English and in outline form, claims 1(and 9) can be written:

  • A method for detection of at least one allele of a gene
    • the gene is multi-allelic (has two or more variant sequence)
  • first amplify genomic DNA using a primer pair that amplifies non-coding DNA
    • the non-coding DNA is genetically and physically linked to the gene,
  • then analyse the amplified DNA for a polymorphism
    • the polymorphism is indicative of a particular allele.

In other words, detection of the polymorphism in the amplified non-coding DNA acts as a surrogate for detecting the polymorphism in the coding DNA that is linked to the non-coding DNA.

Preamble

Turning now to interpreting the claims, and claims 1 and 9 in particular, the plain language of the claim read in context of the definitions set forth in the specification and the prosecution history reveal the likely meaning and scope of the claim. To illustrate how the interpretation is arrived at, we look first at what each term means.

Preamble: According to the specification, an “allele” is a genetic variation associated with a coding region. While this definition does not require per se that the variation is in a coding region, and the specification 25 contemplates other locations, both the claim language and the prosecution history support the conclusion that the only location of the variation is in a coding region. In the preamble (the part of the claim before “comprising”) of claim 1, the allele is specifically limited to a “coding region allele”. Notwithstanding the axiom that preambles do not import limitations onto the claim, in this case the use of “allele” in step (a) refers back to the preamble and as such would likely be found to be limited in the same way. Furthermore, during prosecution of the patent, the Applicant made the bald statement that “allele” is “associated with a change in an exon sequence” and not with a change in the non-coding regions of the gene sequence. With such a statement, the Applicant affirms that his view of the invention entails detection of a coding region allele.

The term “multi-allelic genetic locus” can be parsed in the following way. By the definition in the text of the patent, a “genetic locus” includes all sequence found in a primary transcript (the exons and introns of a gene sequence and upstream and downstream transcribed non-coding regions), as well as regulatory regions. While promoter sequences initially spring to mind as a regulatory region, other sequences, which may be located at some distance from the transcribed region, are probably also part of the genetic locus as defined. The breadth of this term is not overly significant in the view of the author because the term allele has been limited to coding regions. “Multi-allelic” means two or more alleles, without counting the normal or wild-type sequence as an allele. This interpretation comes not from the specification, which does not define the term, but from the prosecution history. To “further distinguish” the invention from a disclosure journal article (Kan et al.) that taught a RFLP associated with an allele of β-globin 26 gene, the Applicant added the limitation “multi-allelic” and commented that the cited article only discussed a “bi-allele”. Presumably the Applicant meant that there was only either the mutation that caused the disease or the normal gene. From this then, “multi-allelic” has to mean two or more variants in coding regions as compared to the normal sequence.

Step(a) – Primer Pair

Step (a): The next phrase that can cause some difficulty in interpretation is a “primer pair that spans a non-coding region sequence”. What the plain language of the claim doesn’t say is where precisely are the sequences that the primer pair anneals to. The definitions in the specification do define the term “intron 27-spanning primers” as a “primer pair that amplifies at least a portion of one intron.” Furthermore, the primers can be located in (or more accurately – anneal to) conserved regions of the intron or in exon sequences that are “adjacent, upstream or downstream.” What the difference is between “adjacent” and “upstream or downstream” exons is an interesting question, but the answer is not likely to significantly impact, if at all, the ultimate interpretation of the claim. Suffice it to say that the primers can anneal to either exon or non-coding sequences .

Two further limitations on the DNA sequence defined by the primer pair are: (i) that it is in genetic linkage with the genetic locus; and (ii) that it contains a sufficient number of non-coding region nucleotides to produce an amplified sequence characteristic of the allele.

First the DNA sequence located between the primers must be in genetic linkage with the genetic locus. “Genetic linkage” was defined by the Applicant during prosecution as “regions of genomic DNA that are inherited together.” In the case when the DNA sequence between the primers is found within the genetic locus, this limitation is nonsensical. In the cases when the DNA sequence between the primers is located outside the boundaries of the genetic locus, then it must be sufficiently close that the sequence and the locus are inherited together. In fact, the inventors prefer that the amplified DNA be in a non-coding region that is adjacent to an exon, and particularly next to a “variable exon”, which is one that has allelic variants. If the amplified DNA sequence does not include non-coding sequence next to a variable exon, the sequence must be sufficiently close to the variable exon to exclude recombination. Thus, the claims seem to require that the DNA sequence between the primers be associated, and very tightly linked, with a coding region variant (allele).

Linkages to Genes

Second, the DNA sequence between the primers must contain a sufficient number of non-coding region nucleotides to produce an amplified sequence characteristic of the allele. What this basically means is that the characteristic that signifies an allele is found in the non-coding region portion of the amplified fragment. The difficulty with understanding the meaning of the limitation is the term “characteristic of”. The Examiner also took issue with this term, contending that it was vague. In response, the Applicant recited a dictionary definition 31, which, in our opinion, did not illuminate much as to the meaning in the context of the claim. Further on, a bit more insight (or confusion) is provided when the Applicant states that sequences characteristic of an allele are “DNA sequences present in only one allele of a genetic locus.” This statement appears to be nonsensical (because alleles are coding region variants according to the Applicant).

When the whole application is taken together with the prosecution history, the most likely interpretation is that the non-coding portion of the amplified sequence has at least one distinguishing nucleotide that is present when a particular coding region allele is present. Types of characteristic sequences include “change in the length of the sequence, gain or loss of a restriction site or substitution of a nucleotide. “32 Relevant to this clause in the claims, the length of the non-coding region that is needed to distinguish alleles is varies according to how many alleles there are. The more alleles, the longer the non-coding region that needs to be assessed.

Finally, the claim requires “analysing the amplified DNA sequence to detect the allele.” This is pretty much a throw-away statement, because without analysis to find the “characteristic sequence” that denotes a particular allele this claim has little value.

Claim 1 in Plain Terms

In plain terms, Claim 1 protects a method for detecting a coding region polymorphism or mutant (allele) of a genetic locus that has at least two alleles (other than the normal gene). The method comprises starting with genomic DNA and amplifying non-coding region DNA that is located close enough to the allele that the allele and the non-coding region DNA are co-inherited. Furthermore, the length of non-coding region DNA needs to be long enough to contain a sequence variation that correlates with a particular allele. Finally, when a sequence variation is found, then the presence of the correlated allele is proven.

The differences in claim 9 do not dramatically change the meaning from that of claim 1. It may be possible that claim 9 applies to bi-allelic loci, that is genetic loci that have a normal and a polymorphic or mutant allele. As discussed above, “genetic linkage with said allele” makes more sense than the phrase used in claim 1, but does not likely alter meaning. Finally, the “characteristic” is more or less specified in clause (b) as a “genetic variation”, which is what the interpretation of “characteristic” was in claim 1.

Possibly more important than what the claim means is what types of non-coding region polymorphisms appear to be excluded from the claims. In the opinion of the author, such polymorphisms include those that are randomly situated (i.e., polymorphisms not linked to a particular gene), those that may map near a known gene but the gene does not exhibit allelic variants (e.g., a SNP that is located near or within an invariant gene), and those associated with a phenotype but not associated with a protein. Moreover, from the prosecution history (discussed above), some other methods that exploit noncoding region polymorphisms are explicitly excluded. These methods are those that rely on family data; “identifying a marker which could be used as a site of polymorphism to determine inheritance in family studies”; “sites of polymorphism in non-coding regions to attempt to track inheritance of disease genes in family studies”; classical RFLP analyses; and use of VNTR sequences as markers, such as for paternity testing and forensic applications.