Methods for detecting genetic haplotypes by interaction with probes
First Claim
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1. A method for determining genetic haplotype comprising:
- (a) identifying a target nucleic acid molecule or gene fragment, said nucleic acid molecule or gene fragment comprising a haplotype of interest, by;
(i) hybridizing a primer recognizing a first genetic variant, said variant correlating to a haplotype, to the target nucleic acid molecule or gene fragment and wherein a labeled primer dependent transcript is generated from the target nucleic acid or gene fragment; and
(1) hybridizing at least one labeled probe, said probe recognizing a second genetic variant downstream from the primer, to the primer dependent transcript, or (2) hybridizing at least one unlabeled probe, said probe recognizing recognizing a second genetic variant downstream from the primer, to the primer dependent transcript; and
(b) detecting at least one parameter displayed by one of the primer-dependent transcript, the at least one probe, or a primer-dependent transcript/probe complex, thereby correlating the displayed parameter to the haplotype.
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Abstract
The present invention provides methods for determining genetic haplotype comprising identifying target nucleic acids or gene fragments, said nucleic acids or gene fragments comprising a haplotype of interest, and detecting at least one parameter displayed by one of a primer-dependent transcript, a probe, or a primer-dependent transcript/probe complex. Further provided are methods for determining genetic haplotype comprising labeling nucleic acids or gene fragments with a least one probe, and detecting the velocity of the nucleic acid molecule or gene fragment by sequentially measuring at least one parameter displayed by the probes.
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Citations
82 Claims
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1. A method for determining genetic haplotype comprising:
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(a) identifying a target nucleic acid molecule or gene fragment, said nucleic acid molecule or gene fragment comprising a haplotype of interest, by;
(i) hybridizing a primer recognizing a first genetic variant, said variant correlating to a haplotype, to the target nucleic acid molecule or gene fragment and wherein a labeled primer dependent transcript is generated from the target nucleic acid or gene fragment; and
(1) hybridizing at least one labeled probe, said probe recognizing a second genetic variant downstream from the primer, to the primer dependent transcript, or (2) hybridizing at least one unlabeled probe, said probe recognizing recognizing a second genetic variant downstream from the primer, to the primer dependent transcript; and
(b) detecting at least one parameter displayed by one of the primer-dependent transcript, the at least one probe, or a primer-dependent transcript/probe complex, thereby correlating the displayed parameter to the haplotype. - View Dependent Claims (2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13)
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6. The method of claim A, wherein the labeled nucleic acid or gene fragment is separated from unlabeled nucleic acids by sieving the labeled nucleic acid in an electric field.
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14. A method for determining genetic haplotype comprising:
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(a) identifying a target nucleic acid molecule or gene fragment, said nucleic acid molecule or gene fragment comprising a haplotype of interest, by;
(i) hybridizing a primer recognizing a first genetic variant, said variant correlating to a haplotype, to the target nucleic acid molecule or gene fragment and wherein a primer dependent transcript is generated from the target nucleic acid or gene fragment; and
(1) hybridizing at least one labeled probe, said probe recognizing a second genetic variant downstream from the primer, to the primer dependent transcript, or (2) hybridizing at least one unlabeled probe, said probe recognizing a second genetic variant downstream from the primer, to the labeled primer dependent transcript; and
(b) detecting at least one parameter displayed by one of the labeled primer-dependent transcript, the at least one probe, or a primer-dependent transcript/probe complex, thereby correlating the displayed parameter to the haplotype. - View Dependent Claims (15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26)
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27. A method for determining genetic haplotype comprising:
(a) labeling a nucleic acid molecule or gene fragment with at least two probes, each probe recognizing a different genetic variation that defines a. haplotype; and
(b) detecting the nucleic acid molecule or gene fragment by measuring a sequential change in a single parameter displayed by the probes, thereby rendering the genetic haplotype determinable. - View Dependent Claims (28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39)
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40. A method for determining genetic haplotype comprising:
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(a) labeling a nucleic acid molecule or gene fragment with at least two probes, each probe recognizing a different genetic variation that defines a haplotype; and
(b) detecting the nucleic acid molecule or gene fragment by measuring a sequential change in at least two parameters displayed by the probes, thereby rendering the genetic. haplotype determinable. - View Dependent Claims (41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52)
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53. A method for determining genetic haplotype comprising:
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(a) labeling a nucleic acid molecule or gene fragment with at least two probes, each probe recognizing a different genetic variation that defines a haplotype; and
(b) detecting the nucleic acid molecule or gene fragment by simultaneously measuring the parameters displayed by the probes, wherein the parameter is not cooperative hybridization, thereby rendering the genetic haplotype determinable. - View Dependent Claims (54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65)
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66. A method for determining genetic haplotype comprising:
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(a) labeling a nucleic acid molecule or gene fragment with at least two probes, each probe recognizing a different genetic variation that defines a haplotype; and
(b) detecting the nucleic acid molecule or gene fragment by simultaneously measuring at least two parameters displayed by the probes, wherein the parameter is not cooperative hybridization, and further wherein the probe is bound to a molecule selected from the group consisting of a microsphere, nanosphere and bar code particle, thereby rendering the genetic haplotype determinable. - View Dependent Claims (67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78)
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79. A method for determining genetic haplotype comprising:
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(a) labeling a nucleic acid molecule or gene fragment with at least one probe, each probe recognizing a different genetic variation that defines a haplotype; and
(b) detecting the velocity of the nucleic acid molecule or gene fragment by measuring the difference in time the probe displays a parameter measured by a first detector at a first position and a second detector at a second position, wherein the probe is bound to a molecule selected from the group consisting of a microsphere, nanosphere, bar code particle, and nanocrystal, thereby rendering the genetic haplotype determinable. - View Dependent Claims (80)
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81. A method for determining genetic haplotype comprising:
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(a) labeling a nucleic acid molecule or gene fragment with a first probe and a second probe, said first probe and second probe recognizing a different genetic variation that defines a haplotype; and
(b) detecting the velocity of the nucleic acid molecule or gene fragment by sequentially measuring a first parameter displayed by the first probe and a second parameter displayed by the second probe, wherein the first or second probe is bound to a molecule selected from the group consisting of a microsphere, nanosphere, bar code particle, and nanocrystal, thereby rendering the genetic haplotype determinable. - View Dependent Claims (82)
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Specification