Patent ID: 7550266

Claim:
A method for comparing gene expression profiles of two or more samples, said method comprising: (a) synthesizing a plurality of first strand cDNAs from a first sample using a mixture of first-strand primers comprising [5′-(sample-specific sequence tag A) 20-24 T 12-16 AN-3′, 5′-(sample-specific sequence tag A )20-24 T 12-16 CN-3′, and 5′-(sample-specific sequence tag A) 20-24 T 12-16 GN-3′], wherein N is any of G, A, T or C; (b) synthesizing a plurality of first strand cDNAs from a second sample using a mixture of first-strand primers comprising [5′-(sample-specific sequence tag B) 20-24 T 12-16 AN-3′, 5′-(sample-specific sequence tag B) 20-24 T 12-16 CN-3′, and 5′-(sample-specific sequence tag B) 20-24 T 12-16 GN-3′], wherein N is any of G, A ,T, or C and wherein said sample-specific sequence tag A is different from said sample-specific tag B; (c) mixing first-strand cDNAs from said first sample with first-strand cDNAs from said second sample to form a single reaction mixture; (d) co-amplifying said cDNAs in said reaction mixture of step (c) using a mixture of primers comprising a primer common to both samples, a primer specific for said sequence tag A, and a primer specific for said sequence tag B, wherein said co-amplifying permits selectively amplifying at least a subset of said cDNA so as to generate one or more sample-specific amplified products; (e) detecting the abundance of one or more said sample-specific amplified products, wherein said abundance determines an expression profile of one or more genes in said first and said second sample; and (f) comparing the expression profile of said one or more genes in said first sample with an expression profile of said one or more genes in said second sample, wherein a difference in the expression profile indicates differential expression of said one or more genes in said first and second samples.