Method of detecting the presence or absence of a plurality of target sequences using oligonucleotide tags

A method of detecting the presence or absence of a plurality of selected target sequences in a target polynucleotide, the method comprising the steps of:

• adding to the target polynucleotide a plurality of ligation probes, each ligation probe including a first oligonucleotide and a second oligonucleotide which are complementary in sequence to adjacent portions of a selected one of the target sequences in the target polynucleotide, the first oligonucleotide having an oligonucleotide tag attached, each ligation probe having a different oligonucletide tag having a length within the range of 12 to 60 nucleotides, and each oligonucleotide tag consisting of a plurality of subunits, each subunit consisting of an oligonucleotide of 3 to 9 nucleotides in length and each subunit being selected from a minimally cross-hybridizing set;
• hybridizing the ligation probes with the target polynucleotide;
• treating the hybridized first and second oligonucleotides under conditions effective to ligate the first and second oligonucleotides whenever the first and second oligonucleotides form perfectly match duplexes with adjacent target sequences;
• separating ligated first and second oligonucleotides from unligated first and second oligonucleotides;
• sorting the ligated first and second oligonucleotides by specifically hybridizing the oligonucleotide tags with their respective complements, the respective complements being attached as uniform populations of substantially identical oligonucleotides in spatially discrete regions on the one or more solid phase supports;
• and
• detecting the presence or absence of the selected target sequences by the presence or absence of ligated first and second oligonucleotides on the one or more solid phase supports.