Patent ID: 6897023

Claim:
A method for determining the relative abundance of a nucleic acid sequence between first and second nucleic acid populations, comprising: (a) contacting a reference library which comprises multiple copies of a selected nucleic acid sequence with: a first probe, derived from a first nucleic acid population, having a sequence which is complementary to said selected sequence and a terminal first sample ID (SID) sequence, and a second probe, derived from a second nucleic acid population, having a sequence which is complementary to said selected sequence and a terminal second sample ID (SID) sequence; wherein said first and second probes are present in relative amounts proportional to the relative abundance of the selected nucleic acid sequence in the first and second nucleic acid populations, respectively, whereby, upon said contacting, (i) said first and second probes competitively hybridize with said selected sequence in said reference library, such that; the ratio of duplexes formed by the first probe with said selected sequence to duplexes formed by the second probe with said selected sequence is proportional to the ratio of the amount of the selected sequence in the first nucleic acid population to the amount of the selected sequence in the second nucleic acid population, and said first and second SID sequences are present as single stranded extensions on said duplexes; and (ii) said first SID sequences on said duplexes formed by the first probe with said selected sequence and said second SID sequences on said duplexes formed by the second probe with said selected sequence hybridize with each other in a 1:1 ratio; and further comprising (b) detecting the presence of unhybridized first SID sequences and/or unhybridized second SID sequences, as an indication of the relative amounts of hybridized first probe and hybridized second probe.