Methods and compositions for the detection of chromosomal aberrations
First Claim
1. A method of detecting in a sample of chromosomes a chromosomal translocation associated with cancer, wherein the translocation results in at least one fusion chromosome, said method comprising:
- (a) preparing at least a first, a second and a third genomic nucleic acid probe, said first and second probe designed to hybridize to a fusion chromosome on one side of the fusion breakpoint region, but at different locations and said third probe is designed to hybridize to a chromosome on the other side of the breakpoint fusion region, wherein said first, second and third probes are distinctly labeled so that each is distinguishable;
(b) contacting the labeled probes in pairs wherein the third probe is a member of each pair, to the sample containing the chromosomes under conditions of appropriate stringency to allow specific hybridization of the probes to complementary sequences within the DNA of said chromosomes; and
(c) detecting the presence of label from the three probes hybridized to the chromosomes; and
(d) inferring the presence of the translocation from the label pattern.
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Abstract
This invention relates generally to methods and compositions for direct detection of specific nucleic acid flanking sequences associated with structural chromosomal aberration breakpoints, by forming hybrids between the sequences and genetic probes, and detecting the probes. In particular aspects, the invention concerns detection of nucleic acid sequences in situ in chromosomes, and more specifically in cells, including interphase cells. Compositions of probes useful for detecting chromosomal translocations, in particular those associated with human leukemias, are also disclosed. An aspect of the invention is labelled probes that, when juxtaposed by formation of an aberration, are distinguishable and provide a pattern different from that of normal cells.
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Citations
36 Claims
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1. A method of detecting in a sample of chromosomes a chromosomal translocation associated with cancer, wherein the translocation results in at least one fusion chromosome, said method comprising:
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(a) preparing at least a first, a second and a third genomic nucleic acid probe, said first and second probe designed to hybridize to a fusion chromosome on one side of the fusion breakpoint region, but at different locations and said third probe is designed to hybridize to a chromosome on the other side of the breakpoint fusion region, wherein said first, second and third probes are distinctly labeled so that each is distinguishable;
(b) contacting the labeled probes in pairs wherein the third probe is a member of each pair, to the sample containing the chromosomes under conditions of appropriate stringency to allow specific hybridization of the probes to complementary sequences within the DNA of said chromosomes; and
(c) detecting the presence of label from the three probes hybridized to the chromosomes; and
(d) inferring the presence of the translocation from the label pattern. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 21, 22, 23, 24, 25, 26)
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17. A method of dectecting a chromosomal translocation resulting in a fusion gene between BCR and ABL genes associated with cancer, said method comprising:
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(a) preparing at least three nucleic acid probes, each labeled with distinguishable label, wherein a first of said probes hybridizies to the BCR gene side of the translocation, a second of said probes hybridizes to a different part of the BCR gene than the part to which the first probe hybridized, and the third probe hybridizes to part of the ABL gene;
(b) contacting said probes in pairs, wherein the third probe is a member of each pair to chromosomes under conditions of appropriate stringency to allow specific hybridization of the probes to complementary DNA sequences in the chromosomes;
(c) detecting the presence of hybridized probes; and
(d) identifying said chromosomal translocation by the labeling pattern of the probes relative to the chromosomes;
wherein said resulting fusion gene encodes either of two proteins designated as p190 and p210. - View Dependent Claims (18, 20)
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27. A method of detecting a structural chromosomal translocation comprising:
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(a) contacting probes prepared from the inserts of MSB-1 and c-H-abl with chromosomal DNA from a human subject;
(b) contacting probes prepared from the inserts of PEM12 and c-H-abl with chromosomal DNA from the same subject;
(c) detecting the presence of probe molecules hybridized to complementary sequences within the chromosomal DNA; and
(d) identifying the specific chromosomal translocation present in the subject by the pattern of hybridization of the subject'"'"'s chromosomal DNA with said probes. - View Dependent Claims (28, 29, 30, 31, 32, 33, 34, 35)
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36. A method of detecting a chromosomal translocation resulting in a fusion gene between BCR and ABL, said fusion gene associated with cancer, said method comprising:
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(a) preparing at least two nucleic acid probes, each labeled with a distinguishable label, wherein a first of said probes hybridizes to the BCR gene side of the translocation, and the third probe hybridizes to a part of the ABL gene;
(b) contacting said probes to chromosomes under conditions of appropriate stringency to allow specific hybridization of the probes to complementary DNA sequences in the chromosomes;
(c) detecting the presence of hybridized probes; and
(d) identifying the chromosomal translocation by the labeling pattern of the probes relative to the chromosomes;
wherein said translocation results in a fusion gene that encodes either of two proteins designated as p190 and p210.
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Specification