Patent ID: 7399584

Claim:
A method of comparing a target nucleic acid with a reference sequence comprising a predetermined sequence of nucleotides, the method comprising: (a) hybridizing a sample comprising the target nucleic acid to an array of oligonucleotide probes immobilized on a solid support, the array comprising: (1) a first probe set comprising a plurality of different probes, each probe exactly complementary to a subsequence of the reference sequence, the probe including a single interrogation position complementary to a corresponding nucleotide in the reference sequence, wherein the reference sequence is at least 50 bases, and the different probes of the first probe set are overlapping probes spanning the reference sequence; (2) a second probe set comprising a corresponding probe for each of the different probes in the first probe set, the corresponding probe in the second probe set being identical to the corresponding probe from the first probe set that includes the interrogation position, except that the one interrogation position is occupied by a different nucleotide in each of the two corresponding probes from the first and second probe sets; wherein the first probe set comprises at least three different interrogation positions corresponding to respective nucleotides in the reference sequence, the respective nucleotides forming at least three continguous nucleotides in the reference sequence, and (b) detecting a hybridization pattern of the oligonucleotide probes to the target nucleic acid and determining from the hybridization pattern whether a nucleotide in the target sequence is the same or different from the corresponding nucleotide in the reference sequence.