Patent ID: 7642055

Claim:
A method for quantifying a small target polynucleotide in each of two samples comprising; providing a first reaction mixture comprising a small target polynucleotide from a first sample, and a first linker probe, wherein the first linker probe comprises a 3′ target-specific portion, a stem, and a loop, wherein the 3′ target-specific portion base pairs with the 3′ end of the target polynucleotide; providing a second reaction mixture comprising a small target polynucleotide from a second sample, and a second linker probe, wherein the second linker probe comprises a 3′ target-specific portion, a stem, and a loop, wherein the 3′ target-specific portion base pairs with the 3′ end of the target polynucleotide, wherein the small target polynucleotide in the first reaction mixture is the same species as the small target polynucleotide in the second reaction mixture; hybridizing the first linker probe to the small target polynucleotide in the first reaction mixture to form a first target-linker probe complex, and extending the first linker probe to form a first extension product; hybridizing the second linker probe to the small target polynucleotide in the second reaction mixture to form a second target-linker probe complex, and extending the second linker probe to form a second extension product; combining the first extension reaction product and the second extension reaction product to form a pooled reaction mixture; PCR amplifying the first extension reaction product and the second extension reaction product in the presence of a first detector probe and a second detector probe to form an amplified first extension reaction product and an amplified second extension reaction product, wherein the first detector probe corresponds to the amplified first extension reaction product and the second detector probe corresponds to the second amplified second extension reaction product, wherein the stem of the first linker probe comprises a first sample identifying portion and the stem of the second linker probe comprises a second sample identifying portion, and the first detector probe hybridizes to the corresponding sample identifying portion of the amplified first extension reaction product and the second detector probe hybridizes to the corresponding sample identifying portion of the amplified second extension reaction product during the amplification reaction, wherein at least one of the first detector probe and the second detector probe further hybridizes to sequence corresponding to the small target polynucleotide during the amplification reaction; and, detecting the quantity of the small target polynucleotide in the two samples by comparing the first detector probe and the second detector probe.