SELECTION PROBE AMPLIFICATION
First Claim
1. A method of enriching a complex set of nucleic acids for a set of target nucleic acids, the method comprising:
- (a) isolating the complex set of nucleic acids;
(b) amplifying the complex set of nucleic acids to produce amplified nucleic acids;
(c) exposing the amplified nucleic acids to at least about 2,000 distinct selection probes in a single reaction medium under conditions promoting annealing between the selection probes and the amplified nucleic acids that are complementary to the selection probes, wherein the selection probes have sequences complementary to the target nucleic acids;
(d) removing the amplified nucleic acids that are not strongly bound to the selection probes; and
(e) releasing annealed amplified nucleic acids from the selection probes, wherein said annealed amplified nucleic acids are said target nucleic acids, thereby enriching said complex set of nucleic acids for said set of target nucleic acids.
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Abstract
Multiple unique selection probes are provided in a single medium. Each selection probe has a sequence that is complementary to a unique target sequence that may be present in a sample under consideration. For example, each selection probe may be complementary to a sequence that includes one of the SNPs used to genotype an organism. Single-stranded selection probes anneal or hybridize with sample sequences having the unique target sequences specified by the selection probe sequences. Sequences from the sample that do not anneal or hybridize with the selection probes are separated from the bound sequences by an appropriate technique. The bound sequences can then be freed to provide a mixture of isolated target sequences, which can be used as needed for the application at hand.
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Citations
57 Claims
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1. A method of enriching a complex set of nucleic acids for a set of target nucleic acids, the method comprising:
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(a) isolating the complex set of nucleic acids; (b) amplifying the complex set of nucleic acids to produce amplified nucleic acids; (c) exposing the amplified nucleic acids to at least about 2,000 distinct selection probes in a single reaction medium under conditions promoting annealing between the selection probes and the amplified nucleic acids that are complementary to the selection probes, wherein the selection probes have sequences complementary to the target nucleic acids; (d) removing the amplified nucleic acids that are not strongly bound to the selection probes; and (e) releasing annealed amplified nucleic acids from the selection probes, wherein said annealed amplified nucleic acids are said target nucleic acids, thereby enriching said complex set of nucleic acids for said set of target nucleic acids. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35)
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36. A method of enriching a complex set of nucleic acids for a set of target nucleic acids, the method comprising:
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(a) amplifying the complex set of nucleic acids to produce amplified nucleic acids; (b) exposing the amplified nucleic acids to at least about 2,000 distinct selection probes in a single reaction medium under conditions promoting annealing between the selection probes and the amplified nucleic acids that are complementary to the selection probes, wherein the selection probes have sequences complementary to the target nucleic acids; (c) removing the amplified nucleic acids that are not strongly bound to the selection probes; (d) releasing annealed amplified nucleic acids from the selection probes, wherein said annealed amplified nucleic acids are said target nucleic acids; and (e) sequencing at least some of the target nucleic acids released in (d). - View Dependent Claims (37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48)
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49. A method of enriching a complex set of nucleic acids for a set of target nucleic acids, the method comprising:
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(a) amplifying the complex set of nucleic acids to produce amplified nucleic acids; (b) exposing the amplified nucleic acids to at least about 2,000 distinct selection probes in a single reaction medium under conditions promoting annealing between the selection probes and the amplified nucleic acids that are complementary to the selection probes, wherein the selection probes have sequences complementary to the target nucleic acids; (c) removing the amplified nucleic acids that are not strongly bound to the selection probes; and (d) releasing annealed amplified nucleic acids from the selection probes, wherein said annealed amplified nucleic acids comprise less than about 3% of the sample. - View Dependent Claims (50, 51, 52, 53, 54, 55, 56)
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57. A kit for isolating target nucleic acid fragments from non-target nucleic acid fragments, the kit comprising:
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the set of selection probes comprising between about 104 and 105 distinct selection probes in a common medium, each selection probe having a sequence complementary to a distinct target sequence; sequencing reagents comprising a sequencing primer, a DNA polymerase, ATP sulfurylase, luciferase, apyrase, adenosine 5′
-phosphosulfate, and luciferin; anda solid substrate comprising a surface feature for binding with the moiety on the selection probes and thereby facilitating immobilization of the selection probes on the substrate.
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Specification