Methods and nucleic acids for analyses of cellular proliferative disorders

A method for detecting CpG dinucleotide methylation in genomic DNA of the Septin 9 gene from colorectal cells, comprising:

• a) extracting or otherwise isolating genomic DNA comprising colorectal cell genomic DNA comprising a Septin 9 gene from a biological sample obtained from a subject;
• b) treating the genomic DNA of a), or a fragment thereof comprising the Septin 9 gene, with one or more reagents to convert cytosine bases that are unmethylated in the 5-position thereof to uracil or to another base that is detectably dissimilar to cytosine in terms of hybridization properties;
• c) contacting the treated genomic DNA of b), or the treated fragment thereof, with an amplification enzyme and at least one oligonucleotide or peptide nucleic acid (PNA) oligomer comprising a contiguous sequence of at least 9 nucleotides that is identical to, complementary to, or hybridizes under moderately stringent or stringent conditions to a sequence selected from the group consisting of SEQ ID NOs:
• 4 to 15, and the complements thereof, wherein the treated colorectal cell genomic DNA or the fragment thereof is amplified to produce at least one amplificate, and
• d) detecting by determining a presence of, or a property of, the at least one amplificate, the methylation state or level of at least one CpG dinucleotide of the Septin 9 gene, or an average, or a value reflecting an average methylation state or level of a plurality of CpG dinucleotides of the Septin 9 gene.