Simultaneous analysis of multiple genomes
First Claim
1. A method of simultaneously analyzing a plurality of genomes to obtain sequence information at one or more loci in each genome, the method comprising the steps of:
- providing for each genome a set of probes, each probe within a set being specific for a locus of the genome;
separately hybridizing each set of probes with its respective genome to form probe-genome complexes in separate reaction mixtures;
combining the separate reaction mixtures and enzymatically treating the probe-genome complexes to form amplifiable probes;
amplifying and labeling the amplifiable probes to form labeled probes, so that for each different locus of each different genome there is a unique labeled probe; and
specifically hybridizing the labeled probes to their respective complements on a microarray so that the presence or absence of a labeled probe specifically hybridized to the microarray is indicative of sequence information of each of the one or more loci of each genome in the plurality.
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Abstract
The invention provides methods for multiplexing readouts from multiple hybridization-based assays that each comprise one or more hybridization or annealing steps and one or more enzymatic processing steps. In one aspect, the invention permits simultaneously analysis of a plurality of genomes by separately hybridizing a set of probes with the different genomes to form sets of probe-genome complexes in separate reaction mixtures that are combined and enzymatically treated to form amplifiable probes. From such amplifiable probes, labeled probes are produced so that for each different locus of each different genome there is a unique labeled probe, which are then specifically hybridized to their respective complements on a microarray. In another aspect, labeled oligonucleotide tags are produced from amplifiable probes. The invention is useful in applications of multiplexed hybridization-based assays for measuring characteristics of genomic samples taken from many different individuals. By conducting hybridization steps separately on samples different individuals then combining them for enzymatic processing, one takes advantage of natural reaction rate differences between hybridization reactions and enzymatic reactions to enable analysis of products of multiple assays on a single readout platform.
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Citations
13 Claims
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1. A method of simultaneously analyzing a plurality of genomes to obtain sequence information at one or more loci in each genome, the method comprising the steps of:
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providing for each genome a set of probes, each probe within a set being specific for a locus of the genome;
separately hybridizing each set of probes with its respective genome to form probe-genome complexes in separate reaction mixtures;
combining the separate reaction mixtures and enzymatically treating the probe-genome complexes to form amplifiable probes;
amplifying and labeling the amplifiable probes to form labeled probes, so that for each different locus of each different genome there is a unique labeled probe; and
specifically hybridizing the labeled probes to their respective complements on a microarray so that the presence or absence of a labeled probe specifically hybridized to the microarray is indicative of sequence information of each of the one or more loci of each genome in the plurality. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12)
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13. A method of simultaneously analyzing a plurality of samples to determine the presence or quantity of one or more analytes, the method comprising the steps of:
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providing for each sample a set of probes including at least one probe for each analyte, each probe within a set being specific for at least one of the analytes and each probe within a set having an oligonucleotide tag attached;
separately reacting each set of probes with its respective sample to form probe-analyte complexes in separate reaction mixtures;
combining the separate reaction mixtures and enzymatically treating the probe-analyte complexes to form amplifiable probes;
amplifying and labeling the amplifiable probes to form labeled oligonucleotide tags, so that for each different analyte of each different sample there is a unique labeled oligonucleotide tag; and
specifically hybridizing the labeled oligonucleotide tags to their respective complements on a microarray so that the presence or absence of a labeled oligonucleotide tag specifically hybridized to the microarray is indicative of the presence or quantity of each of the one or more analytes of each sample in the plurality.
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Specification