Rapid analysis of variations in a genome
First Claim
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1. A method for determining a sequence of a locus of interest, said method comprising:
- (a) amplifying a locus of interest on a template DNA using a first and second primers, each of the first and second primers comprising a 3′
annealing region that anneals to the template DNA, wherein the second primer contains a recognition site for a restriction enzyme such that digestion with the restriction enzyme generates a 5′
overhang containing the locus of interest, and wherein the melting temperature of the 3′
annealing region of the first primer is greater than the melting temperature of the 3′
annealing region of the second primer, and further wherein the annealing temperature for cycle 1 of the amplification is at about the melting temperature of the 3′
annealing region of the second primer, the annealing temperature for cycle 2 of the amplification is at about the melting temperature of the 3′
annealing region of the first primer, and the annealing temperature for cycle 3 is at about the melting temperature of the entire second primer, and wherein the annealing temperatures for cycle 2 and cycle 3 are greater than the annealing temperature for cycle 1;
(b) digesting the amplified DNA with the restriction enzyme that recognizes the recognition site on the second primer;
(c) incorporating a nucleotide into the digested DNA of (b) by using the 5′
overhang containing the locus of interest as a template; and
(d) determining the sequence of the locus of interest by determining the sequence of the DNA of (c) containing the incorporated nucleotide.
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Abstract
The invention provides a method useful for determining the sequence of large numbers of loci of interest on a single or multiple chromosomes. The method utilizes an oligonucleotide primer that contains a recognition site for a restriction enzyme such that digestion with the restriction enzyme generates a 5′ overhang containing the locus of interest. The 5′ overhang is used as a template to incorporate nucleotides, which can be detected. The method is especially amenable to the analysis of large numbers of sequences, such as single nucleotide polymorphisms, from one sample of nucleic acid.
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Citations
54 Claims
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1. A method for determining a sequence of a locus of interest, said method comprising:
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(a) amplifying a locus of interest on a template DNA using a first and second primers, each of the first and second primers comprising a 3′
annealing region that anneals to the template DNA, wherein the second primer contains a recognition site for a restriction enzyme such that digestion with the restriction enzyme generates a 5′
overhang containing the locus of interest, and wherein the melting temperature of the 3′
annealing region of the first primer is greater than the melting temperature of the 3′
annealing region of the second primer, and further wherein the annealing temperature for cycle 1 of the amplification is at about the melting temperature of the 3′
annealing region of the second primer, the annealing temperature for cycle 2 of the amplification is at about the melting temperature of the 3′
annealing region of the first primer, and the annealing temperature for cycle 3 is at about the melting temperature of the entire second primer, and wherein the annealing temperatures for cycle 2 and cycle 3 are greater than the annealing temperature for cycle 1;
(b) digesting the amplified DNA with the restriction enzyme that recognizes the recognition site on the second primer;
(c) incorporating a nucleotide into the digested DNA of (b) by using the 5′
overhang containing the locus of interest as a template; and
(d) determining the sequence of the locus of interest by determining the sequence of the DNA of (c) containing the incorporated nucleotide. - 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49)
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50. A method for determining a sequence of a locus of interest, said method comprising:
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(a) amplifying a locus of interest on a template DNA using a first and second primers, each of the first and second primers comprising a 3′
annealing region that anneals to the template DNA, wherein the second primer contains a recognition site for a restriction enzyme such that digestion with the restriction enzyme generates a 5′
overhang containing the locus of interest, and wherein the melting temperature of the 3′
annealing region of the first primer is greater than the melting temperature of the 3′
annealing region of the second primer, and further wherein the annealing temperature for cycle 1 of the amplification is at about the melting temperature of the 3′
annealing region of the second primer, and the annealing temperature for a cycle of amplification subsequent to the first cycle of amplification is at about the melting temperature of the 3′
annealing region of the first primer, and wherein the annealing temperature for said cycle of amplification subsequent to the first cycle of amplification is greater than the annealing temperature for cycle 1;
(b) digesting the amplified DNA with the restriction enzyme that recognizes the recognition site on the second primer;
(c) incorporating a nucleotide into the digested DNA of (b) by using the 5′
overhang containing the locus of interest as a template; and
(d) determining the sequence of the locus of interest by determining the sequence of the DNA of (c) containing the incorporated nucleotide. - View Dependent Claims (51)
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52. A method for determining a sequence of a locus of interest, said method comprising:
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(a) amplifying a locus of interest on a template DNA using a first and second primers, each of the first and second primers comprising a 3′
annealing region that anneals to the template DNA, wherein the second primer contains a recognition site for a restriction enzyme that cuts DNA at a distance from the recognition site and digestion with the restriction enzyme generates a 5′
overhang containing the locus of interest, wherein the first primer contains a recognition site for a restriction enzyme that is different from the recognition site for the restriction enzyme on the second primer, and contains a tag at the 5′
end, and wherein the melting temperature of the 3′
annealing region of the first primer is greater than the melting temperature of the 3′
annealing region of the second primer, and further wherein the annealing temperature for cycle 1 of the amplification is at about the melting temperature of the 3′
annealing region of the second primer, the annealing temperature for cycle 2 of the amplification is at about the melting temperature of the 3′
annealing region of the first primer, and the annealing temperature for cycle 3 is at about the melting temperature of the entire second primer, and further wherein the annealing temperatures for cycle 2 and cycle 3 are greater than the annealing temperature for cycle 1;
(b) digesting the amplified DNA with the restriction enzyme that recognizes the recognition site on the second primer;
(c) incorporating a labeled nucleotide into the digested DNA of (b) by using the 5′
overhang containing the locus of interest as a template;
(d) digesting the DNA of (c) with the restriction enzyme that recognizes the recognition site on the first primer; and
(e) determining the sequence of the locus of interest by determining the sequence of the digested DNA of (d) containing the labeled nucleotide. - View Dependent Claims (53)
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54. A method for determining a sequence of a locus of interest, said method comprising:
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(a) amplifying a locus of interest on a template DNA using a first and second primers, each of the first and second primers comprising a 3′
annealing region that anneals to the template DNA, wherein the second primer contains a recognition site for a restriction enzyme such that digestion with the restriction enzyme generates a 5′
overhang containing the locus of interest, wherein the 5′
region of the second primer does not anneal to the template DNA, and wherein the annealing temperature for cycle 1 of the amplification is at about the melting temperature of the 3′
annealing region of the second primer, and the annealing temperature for a cycle of amplification subsequent to the first cycle of amplification is at about the melting temperature of the entire second primer, and wherein the annealing temperature for said cycle of amplification subsequent to the first cycle of amplification is greater than the annealing temperature for cycle 1;
(b) digesting the amplified DNA with the restriction enzyme that recognizes the recognition site on the second primer;
(c) incorporating a nucleotide into the digested DNA of (b) by using the 5′
overhang containing the locus of interest as a template; and
(d) determining the sequence of the locus of interest by determining the sequence of the DNA of (c) containing the incorporated nucleotide.
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Specification