Patent ID: 7115364

Claim:
An array of nucleic acid probes immobilized on a solid support, the array comprising at least two sets of probes, (1) a first probe set comprising a plurality of probes, each probe comprising a segment of at least six nucleotides exactly complementary to a subsequence of a reference sequence, the segment including at least one interrogation position complementary to a corresponding nucleotide in the reference sequence, (2) a second probe set comprising a probe for each interrogation position in the first probe set, each probe in the second probe set being identical to a sequence comprising a corresponding probe from the first probe set or a subsequence of at least six nucleotides thereof that includes the interrogation position, except that the interrogation position is occupied by a different nucleotide in each of the two corresponding probes from the first and second probe sets; wherein the probes in the first probe set collectively have at least three interrogation positions respectively corresponding to each of three contiguous nucleotides in the reference sequence; provided that the array does not consist of a complete set of probes of a given length, wherein a complete set is all permutations of nucleotides A, C, G and T/U; and wherein the reference sequence is at least 50 bases, and the first probe set comprises overlapping probes spanning the reference sequence.