The present invention describes a method for identifying one or more of a plurality of sequences differing by one or more single base changes, insertions, deletions, or translocations in a plurality of target
nucleotide sequences. The method includes a
ligation phase, a capture phase, and a detection phase. The
ligation phase utilizes a
ligation detection reaction between one
oligonucleotide probe, which has a target sequence-specific portion and an addressable array-specific portion, and a second
oligonucleotide probe, having a target sequence-specific portion and a detectable
label. After the ligation phase, the capture phase is carried out by hybridizing the ligated
oligonucleotide probes to a
solid support with an array of immobilized capture oligonucleotides at least some of which are complementary to the addressable array-specific portion. Following completion of the capture phase, a detection phase is carried out to detect the labels of ligated oligonucleotide probes hybridized to the
solid support. The ligation phase can be preceded by an amplification process. The present invention also relates to a kit for practicing this method, a method of forming arrays on
solid supports, and the supports themselves.