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.[add a comment]

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.[add a comment]

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.[add a comment]

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