Patent ID: 8003329

Claim:
A method of determining relative amounts of a plurality of target polynucleotides in a sample, the method comprising the steps of: combining in a reaction mixture the plurality of target polynucleotides and a plurality of different nucleic acid probes each specific for a different target polynucleotide so that selectable nucleic acid probes are formed, such that the selectable nucleic acid probes are in substantially the same relative amounts as the plurality of target polynucleotides and are resistant to at least one nuclease activity, wherein each different nucleic acid probe comprises a different oligonucleotide tag; treating the reaction mixture with one or more nuclease activities so that substantially all nucleic acid probes that do not form selectable probes are digested; amplifying the selectable nucleic acid probes in an emulsion amplification reaction, the emulsion amplification reaction comprising micelles that each comprise on average one or fewer selectable nucleic acid probes, amplification reaction components, and a signal generating component specific for each different oligonucleotide tag, such that an optical signal specific for such oligonucleotide tag is generated whenever a selectable nucleic acid probe containing such oligonucleotide tag is amplified; and determining numbers of micelles having optical signals specific for each different oligonucleotide tag in a sample of the emulsion amplification reaction to determine the relative amounts of the plurality of target polynucleotides.