Patent ID: 7371519

Claim:
A method for comparing the expression profiles of at least two distinct samples, said method comprising: (a) enzymatically generating: (i) a first population of oligonucleotide tagged nucleic acids of differing sequence from an mRNA sample derived from a first sample, wherein each oligonucleotide tagged nucleic acid of said first population comprises a same first oligonucleotide tag; and (ii) a second population of oligonucleotide tagged nucleic acids of differing sequence from an mRNA sample derived from a second sample, wherein each oligonucleotide tagged nucleic acid of said second population comprises a same second oligonucleotide tag that differs from said first oligonucleotide tag; (b) hybridizing said first and second populations of oligonucleotide tagged target nucleic acids to an array of probe nucleic acids stably associated with the surface of a solid support, wherein said hybridizing occurs in the presence of: (i) first labeled oligonucleotide complementary to said first oligonucleotide tag of said first population; and (ii) second labeled oligonucleotide complementary to said second oligonucleotide tag of said second population; whereby hybridized complexes comprising said oligonucleotide tagged target nucleic acids, probe nucleic acids and labeled oligonucleotides are produced on the surface of said array; (c) detecting the presence of said hybridized complexes on said array surface; (d) deriving an expression profile for each of said samples from said detected hybridized complexes; and (e) comparing the derived expression profiles of each of said samples; whereby the expression profiles of said at least two distinct samples are compared.