Patent ID: 7803541
Filing Date: 2010-09-28
Classification: C12Q

Abstract:
1. A method of detecting ten or more different target nucleic acids of interest, the method comprising: providing a sample comprising or suspected of comprising the ten or more different target nucleic acids of interest, which ten or more different target nucleic acids comprise different polynucleotide sequences and are different molecules; providing a pooled population of particles, the population comprising ten or more subsets of particles, a plurality of the particles in each subset being distinguishable from a plurality of the particles in every other subset, and the particles in each subset having associated therewith a capture probe, which capture probe comprises a polynucleotide sequence C-2 that is different from subset to subset of particles; providing ten or more subsets of n capture extenders, wherein n is at least two, and wherein each capture extender comprises a polynucleotide sequence C-1 and a polynucleotide sequence C-3, wherein one subset of n capture extenders is provided for each of the target nucleic acids of interest, and wherein, in the subset of n capture extenders provided for each given target nucleic acid of interest, i) the polynucleotide sequences C-3 of the different capture extenders in the subset are complementary to nonoverlapping sequences in the given target nucleic acid, and ii) the polynucleotide sequences C-1 of the capture extenders in the subset are complementary to one of the polynucleotide sequences C-2, wherein C-1 is different from subset to subset of capture extenders, whereby hybridization of the capture extenders to the capture probe comprising the complementary sequence C-2 associates each subset of n capture extenders with a selected subset of the particles; contacting the sample, the pooled population of particles, and the subsets of n capture extenders; hybridizing any of the ten or more different target nucleic acids of interest present in the sample to its complementary subset of n capture extenders and hybridizing the subset of n capture extenders to its complementary capture probe, wherein the n capture extenders provided for a given target nucleic acid of interest hybridize to nonoverlapping sequences in that target nucleic acid, whereby the hybridizing the target nucleic acid of interest to the n capture extenders and the n capture extenders to the capture probe stably captures the target nucleic acid on the subset of particles with which the capture extenders are associated, wherein the hybridizing the subset of n capture extenders to the complementary capture probe is performed at a hybridization temperature which is greater than a melting temperature T determining which subsets of particles have a target nucleic acid of interest captured on the particles, thereby indicating which of the ten or more different target nucleic acids of interest were present in the sample, by i) hybridizing one or more label extenders and a label probe system comprising a label to any target nucleic acid of interest captured on the particles and ii) identifying at least a portion of the particles from each subset and detecting the presence or absence of the label on those particles.