Methods and compositions for whole genome amplification and genotyping
First Claim
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1. A method of detecting typable loci of a genome, comprising the steps of:
- (a) providing an amplified representative population of genome fragments comprising said typable loci, wherein said population comprises a high complexity representation;
(b) contacting said genome fragments with a plurality of nucleic acid probes having sequences corresponding to said typable loci under conditions wherein probe-fragment hybrids are formed, wherein said probes are at most 125 nucleotides in length; and
(c) detecting typable loci of said probe-fragment hybrids.
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Abstract
This invention provides methods of amplifying genomic DNA to obtain an amplified representative population of genome fragments. Methods are further provided for obtaining amplified genomic DNA representations of a desired complexity. The invention further provides methods for simultaneously detecting large numbers of typable loci for an amplified representative population of genome fragments. Accordingly the methods can be used to genotype individuals on a genome-wide scale.
79 Citations
87 Claims
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1. A method of detecting typable loci of a genome, comprising the steps of:
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(a) providing an amplified representative population of genome fragments comprising said typable loci, wherein said population comprises a high complexity representation;
(b) contacting said genome fragments with a plurality of nucleic acid probes having sequences corresponding to said typable loci under conditions wherein probe-fragment hybrids are formed, wherein said probes are at most 125 nucleotides in length; and
(c) detecting typable loci of said probe-fragment hybrids. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 34, 35)
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18. A method of detecting typable loci of a genome, comprising the steps of:
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(a) providing an amplified representative population of genome fragments comprising said typable loci;
(b) contacting said genome fragments with a plurality of nucleic acid probes having sequences corresponding to said typable loci under conditions wherein probe-fragment hybrids are formed; and
(c) directly detecting typable loci of said probe-fragment hybrids - View Dependent Claims (19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36)
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37. A method of detecting typable loci of a genome, comprising the steps of:
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(a) providing an amplified representative population of genome fragments comprising said typable loci;
(b) contacting said genome fragments with a plurality of immobilized nucleic acid probes having sequences corresponding to said typable loci under conditions wherein immobilized probe-fragment hybrids are formed;
(c) modifying said immobilized probe-fragment hybrids; and
(d) detecting a probe or fragment modified in step (c), thereby detecting said typable loci of said genome. - View Dependent Claims (38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54)
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55-77. -77. (cancelled).
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78. A method of detecting typable loci of a genome, comprising
(a) contacting a plurality of genome fragments with a plurality of different immobilized nucleic acid probes under conditions wherein immobilized probe-fragment hybrids are formed; -
(b) modifying said immobilized probe-fragment hybrids by addition of a detection moiety to the probe, thereby forming affinity ligand-labeled probes;
(c) contacting said affinity ligand-labeled probes with a binding moiety and an amplification reagent, wherein said binding moiety has one or more sites capable of binding said ligand, and wherein said amplification reagent has affinity for said binding moiety, whereby a multimeric complexes form between said affinity ligand-labeled probe, said binding moiety and said amplification reagent; and
(d) detecting said multimeric complexes, thereby detecting typable loci of said genome fragments. - View Dependent Claims (79, 80, 81, 82, 83, 84, 85, 86, 87)
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Specification