Patent ID: 7914981

Claim:
A method for identifying a plurality of sequences differing by one or more single-base changes, insertions, deletions, or translocations, said method comprising: providing a sample potentially containing target nucleotide sequences differing by one or more single-base changes, insertions, deletions, or translocations; providing a plurality of oligonucleotide probe sets, each set characterized by (a) a first oligonucleotide probe, having a target-specific portion and an addressable array-specific portion and (b) a second oligonucleotide probe, having a target-specific portion and a detectable reporter label; providing a ligase; blending the sample, the plurality of oligonucleotide probe sets, and the ligase to form a mixture; subjecting the mixture to one or more ligase detection reaction cycles to form a ligated product sequence containing (a) the addressable array-specific portion, (b) the target-specific portions, and (c) the detectable reporter label, if their respective target nucleotide is present in the sample; providing a solid support with capture oligonucleotides immobilized at particular sites, wherein the capture oligonucleotides, each having greater than 16 nucleotides, have nucleotide sequences complementary to the addressable array-specific portions with the capture oligonucleotides hybridizing to their complementary addressable array specific portion under uniform hybridization conditions, wherein adjacent capture oligonucleotides on the solid support which are complementary to the addressable array-specific portions corresponding to single-base changes, insertions, deletions, or translocations at different locations in the target nucleotide sequences differ in their nucleotide sequences, when aligned to each other, by at least 25% of the nucleotides to minimize cross hybridization between non-complementary capture oligonucleotides and addressable array-specific portions, and, wherein the solid support and the capture oligonucleotides form an addressable array; contacting the mixture, after said subjecting, with the solid support under conditions effective to hybridize the addressable array-specific portions to the capture oligonucleotides in a base-specific manner, thereby capturing the addressable array-specific portions on the solid support at the site with the complementary capture oligonucleotide; and detecting and distinguishing the reporter labels of ligated product sequences captured to the solid support at particular sites, thereby indicating the presence of target nucleotide sequences in the sample, wherein the oligonucleotide probe sets are configured so that the addressable array-specific portion is comprised of a nucleotide sequence which is distinct from that of the target-specific portions, in order to prevent hybridization between the target-specific portions and the capture oligonucleotides as well as between the target nucleotide sequence and the addressable array-specific portion.