Identification of rearrangements in nucleic acid molecules
First Claim
1. A method for identifying a chromosomal rearrangement in a test nucleic acid, the method comprising:
- providing a substrate having attached thereto a first nucleic acid comprising the sequence of all or a portion of a first chromosome;
contacting said substrate with a test nucleic acid under conditions that permit a first portion of the test nucleic acid to hybridize to all or a portion of said first nucleic acid;
contacting the test nucleic with a second nucleic acid under conditions that permit hybridization of all or a portion of the second nucleic acid to a second portion of the test nucleic acid, wherein the second nucleic acid comprises the sequence of all or a portion of a second chromosome; and
detecting hybridization of said test nucleic acid to each of said first nucleic acid and said second nucleic acid as an indication that the test nucleic acid comprises a chromosomal rearrangement.
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Accused Products
Abstract
Disclosed are methods and compositions for detecting a chromosomal rearrangement in a sample of nucleic acids. In an exemplary method, a first nucleic acid comprising a portion of a first chromosome, which may be detectably labeled, is attached to a substrate; a first portion of a test nucleic acid is hybridized to the first nucleic acid; a second nucleic acid comprising all or a portion of a second chromosome, which may be detectably labeled, is hybridized to a second portion of the test nucleic acid, thereby forming a trimolecular sandwich, and the hybridization of the test nucleic acid to both of the first and second nucleic acids is detected as an indication that the test nucleic acid comprises a chromosomal rearrangement. In particular embodiments, the first and second nucleic acids are derived from the same chromosome. In a related method, the test nucleic acid is used as a template for nucleic acid synthesis, and primers derived from a first and a second chromosome or from the same chromosome, which are distinctly labeled with first and second labels, respectively, are used to prime nucleic acid synthesis. A synthesized nucleic acid comprising each of the first and second primers is detected as an indication that the test nucleic acid comprises a chromosomal rearrangement. Also disclosed are kits for detecting chromosomal rearrangements. Such methods and kits can be used, for example, in the diagnosis or identification of disease-associated chromosomal rearrangements, e.g., cancers such as leukemia.
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Citations
63 Claims
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1. A method for identifying a chromosomal rearrangement in a test nucleic acid, the method comprising:
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providing a substrate having attached thereto a first nucleic acid comprising the sequence of all or a portion of a first chromosome;
contacting said substrate with a test nucleic acid under conditions that permit a first portion of the test nucleic acid to hybridize to all or a portion of said first nucleic acid;
contacting the test nucleic with a second nucleic acid under conditions that permit hybridization of all or a portion of the second nucleic acid to a second portion of the test nucleic acid, wherein the second nucleic acid comprises the sequence of all or a portion of a second chromosome; and
detecting hybridization of said test nucleic acid to each of said first nucleic acid and said second nucleic acid as an indication that the test nucleic acid comprises a chromosomal rearrangement. - 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)
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29. A trimolecular sandwich comprising:
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a substrate;
a first nucleic acid comprising the sequence of all or a portion of a first chromosome, wherein said first nucleic acid is attached to said substrate;
a test nucleic acid, wherein a first portion of said test nucleic acid is hybridized to all or a portion of said first nucleic acid; and
a second nucleic acid, wherein all or a portion of the second nucleic acid is hybridized to a second portion of the test nucleic acid, and wherein the second nucleic acid comprises the sequence of all or a portion of a second chromosome. - View Dependent Claims (30, 31, 32, 33)
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34. A method for identifying a test nucleic acid comprising a chromosomal rearrangement, the method comprising:
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providing a test nucleic acid as a template for nucleic acid synthesis;
contacting said test nucleic acid with each of (i) a population of first primers, wherein substantially all of said first primers are detectably labeled with a first label and wherein said population of first primers is randomly generated, and wherein each of said first primers hybridizes to a portion of a first chromosome and (ii) a population of second primers, wherein substantially all of said second primers are detectably labeled with a second label and wherein said population of second primers is randomly generated, and wherein each of said second primers hybridizes to a portion of a second chromosome, and further wherein said second label is distinct from said first label;
synthesizing a nucleic acid complementary to said test nucleic acid, wherein said test nucleic acid serves as a template for nucleic acid synthesis and one of said first primers and one of said second primers prime synthesis of the synthesized nucleic acid; and
detecting a synthesized nucleic acid comprising each of said first and said second labels as an indication that the test nucleic acid comprises a chromosomal rearrangement. - View Dependent Claims (35, 36)
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37. A kit comprising:
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(i) a substrate, the substrate having attached thereto a first nucleic acid comprising all or a portion of a first chromosome, wherein the first nucleic acid is detectably labeled with a first label; and
(ii) a second nucleic acid comprising all or a portion of a second chromosome, wherein the second nucleic acid is detectably labeled with a second label and wherein said second label is distinct from said first label. - View Dependent Claims (38, 39)
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40. A kit comprising:
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(i) a substrate (ii) a nucleic acid comprising all or a portion of a chromosome, and (ii) instructions for using said substrate and said nucleic acid to detect a chromosomal rearrangement. - View Dependent Claims (41, 42, 43, 44, 45)
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46. A method for identifying a chromosomal rearrangement in a test nucleic acid, the method comprising:
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providing a substrate having attached thereto a first nucleic acid comprising the sequence of a first portion of a chromosome;
contacting said substrate with a test nucleic acid under conditions that permit a first portion of the test nucleic acid to hybridize to all or a portion of said first nucleic acid;
contacting the test nucleic with a second nucleic acid under conditions that permit hybridization of all or a portion of the second nucleic acid to a second portion of the test nucleic acid, wherein the second nucleic acid comprises the sequence of a second portion of said chromosome; and
detecting hybridization of said test nucleic acid to each of said first nucleic acid and said second nucleic acid as an indication that the test nucleic acid comprises a chromosomal rearrangement. - View Dependent Claims (47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58)
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59. A method for comparing a test nucleic acid with a reference nucleic acid, the method comprising:
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providing a substrate having attached thereto a first nucleic acid comprising the sequence of a first portion of a first chromosome;
contacting said substrate with a test nucleic acid under conditions that permit a first portion of the test nucleic acid to hybridize to all or a portion of said first nucleic acid;
contacting the test nucleic with a second nucleic acid under conditions that permit hybridization of all or a portion of the second nucleic acid to a second portion of the test nucleic acid, wherein the second nucleic acid comprises the sequence of (i) a second portion of said chromosome or (ii) a portion of a second chromosome;
detecting hybridization of said test nucleic acid to each of said first nucleic acid and said second nucleic acid; and
comparing the ability of said test nucleic acid to hybridize to each of said first nucleic acid and said second nucleic acid with the ability of said reference nucleic acid to hybridize to each of said first nucleic acid and said second nucleic acid. - View Dependent Claims (60, 61, 62, 63)
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Specification