Methods, kits and compositions pertaining to the suppression of the detectable probe binding to randomly distributed repeat sequences genomic nucleic acid

A method for comparing a sample of genomic nucleic acid with that of a control sample using a genomic nucleic acid reference array, said method comprising:

• a) providing a sample of genomic nucleic acid to be tested;
• b) providing a control of genomic nucleic acid, wherein the control and the sample are differentially labeled;
• c) providing a genomic nucleic acid reference array;
• d) providing a mixture of two or more non-nucleotide probes wherein one probe of the mixture comprises a nucleobase sequence that is at least ninety percent homologous to a sequence selected from the group consisting of:
• SEQ ID NO. 3, SEQ ID NO. 4, SEQ ID NO:
• 5, SEQ ID NO:
• 6, SEQ ID NO:
• 7, SEQ ID NO:
• 8, SEQ ID NO:
• 9, SEQ ID NO:
• 10, SEQ ID NO:
• 11, SEQ ID NO:
• 12, and SEQ ID NO:
• 13, and another probe of the mixture comprises a nucleobase sequence selected from the group consisting of:
• TT(k)TTTTT(k)TTTLysOLysOTTT(k)TTTTT(k)TT and AA(k)AAAAA(k)AAALysOLysOAAA(k)AAAAA(k)AA, wherein (k) is D-lysine, Lys is L-lysine, and O is 8-amino-3,6-dioxaoctanoic acid;
• e) treating the sample and control genomic nucleic acid, the array or both the sample and control genomic nucleic acid and the array with the mixture of non-nucleotide probes under suitable hybridization conditions;
• f) contacting the array with the treated mixture of sample and control genomic nucleic acid under suitable hybridization conditions;
• and
• g) comparing the intensities of the signals from the differential labels of the array to be caused by hybridization of the probes to genomic nucleic acid thereby determine one or more variations in copy numbers of sequences in the sample as compared with the relative copy numbers of substantially identical sequences in the control.