Method and nucleic acids for the analysis of a colon cell proliferative disorder

Abstract

The present invention relates to modified and genomic sequences, to oligonucleotides and/or PNA-oligomers for detecting the cytosine methylation state of genomic DNA, as well as to a method for ascertaining genetic and/or epigenetic parameters of genes for use in the differentiation, diagnosis, treatment and/or monitoring of colon cell proliferative disorders, or the predisposition to colon cell proliferative disorders.

What is claimed is: 
     
         1 . A method for detecting colorectal cancer or colon adenomas or risk thereof in a human subject, comprising:
 a) contacting genomic DNA in a biological sample obtained from the subject comprising colorectal DNA, with a reagent or series of reagents comprising at least one of bisulfite, hydrogen sulfite or disulfite;   b) comparing the nucleic acid sequence of untreated genomic DNA as set forth in SEQ ID NO: 54 to corresponding nucleic acid sequence derived from SEQ ID NO: 54 by bisulfite treatment according to method step a) based on the differential base-pairing properties of uracil and cytosine;   c) determining the methylation status of one or more CpG dinucleotides within the genomic region defined in method step b) by detecting unconverted cytosine bases in this region; and   d) detecting colorectal cancer or colon adenomas or risk thereof in the human subject by comparing the methylation state of at least one CpG position within the nucleic acid sequence of method step b) to the methylation state of the same CpG position or positions in genomic DNA derived from a human control subject not suffering from colorectal cancer or colon adenomas, wherein a higher degree of CpG methylation in the sample, compared to that of the control, indicates a presence or an increased likelihood of colorectal cancer or colon adenomas.   
     
     
         2 . The method of  claim 1 , wherein in method step c) a portion or fragment of the treated DNA derived from SEQ ID NO: 54 is amplified by means of a polymerase chain reaction (PCR) to provide an amplificate. 
     
     
         3 . The method of  claim 2 , wherein at least 10 different fragments, each fragment having a length of 10 to 200 base pairs, are amplified. 
     
     
         4 . The method of  claim 2 , wherein the amplification step is carried out using one or more sets of primer oligonucleotides suitable to amplify a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 239, 240, 367 and 368 and amplifiable portions thereof. 
     
     
         5 . The method of  claim 2 , wherein determining the methylation status of at least one CpG dinucleotide comprised by SEQ ID NO: 54 comprises hybridization of the amplificate to oligonucleotides or peptide nucleic acid (PNA) oligomers. 
     
     
         6 . The method of  claim 2 , wherein the amplificates are labeled with a fluorescent label. 
     
     
         7 . The method of  claim 1 , wherein the method differentiates between normal colon tissue and a tissue selected from the group consisting of colon adenoma tissue and colon carcinoma tissue.