Comparative genomic hybridization (CGH)
First Claim
1. A method of detecting a chromosomal abnormality in a suspected bladder cancer test sample by detecting an amplification of a unique sequence at at least one position selected from the group consisting of q21 on human chromosome 8, q31-qter on human chromosome 13, p15-pter on human chromosome 7, q24-qter on human chromosome 8, cen-p13 on human chromosome 11 and q13-qter on human chromosome 9, in the test sample, said method comprising the steps of:
- (a) labelling nucleic acids from the test sample and from a control sample with different labels;
(b) contacting said labelled nucleic acids from each sample with a plurality of target nucleic acids, wherein either the labelled nucleic acids or the target nucleic acids, or both, have had repetitive sequences, if initially present, blocked and/or removed; and
(c) comparing the intensities of the signals from labelled nucleic acids hybridized to each target nucleic acid, thereby allowing detection of the presence or absence of the amplification in the test sample.
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Abstract
Disclosed are new methods comprising the use of in situ hybridization to detect abnormal nucleic acid sequence copy numbers in one or more genomes wherein repetitive sequences that bind to multiple loci in a reference chromosome spread are either substantially removed and/or their hybridization signals suppressed. The invention termed Comparative Genomic Hybridization (CGH) provides for methods of determining the relative number of copies of nucleic acid sequences in one or more subject genomes or portions thereof (for example, a tumor cell) as a function of the location of those sequences in a reference genome (for example, a normal human genome). The intensity(ies) of the signals from each labeled subject nucleic acid and/or the differences in the ratios between different signals from the labeled subject nucleic acid sequences are compared to determine the relative copy numbers of the nucleic acid sequences in the one or more subject genomes as a function of position along the reference chromosome spread. Amplifications, duplications and/or deletions in the subject genome(s) can be detected. Also provided is a method of determining the absolute copy numbers of substantially all RNA or DNA sequences in subject cell(s) or cell population(s).
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Citations
53 Claims
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1. A method of detecting a chromosomal abnormality in a suspected bladder cancer test sample by detecting an amplification of a unique sequence at at least one position selected from the group consisting of q21 on human chromosome 8, q31-qter on human chromosome 13, p15-pter on human chromosome 7, q24-qter on human chromosome 8, cen-p13 on human chromosome 11 and q13-qter on human chromosome 9, in the test sample, said method comprising the steps of:
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(a) labelling nucleic acids from the test sample and from a control sample with different labels;
(b) contacting said labelled nucleic acids from each sample with a plurality of target nucleic acids, wherein either the labelled nucleic acids or the target nucleic acids, or both, have had repetitive sequences, if initially present, blocked and/or removed; and
(c) comparing the intensities of the signals from labelled nucleic acids hybridized to each target nucleic acid, thereby allowing detection of the presence or absence of the amplification in the test sample. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 30, 31, 32)
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10. A method of detecting a chromosomal abnormality in a suspected bladder cancer test sample by detecting a deletion of a unique sequence at at least one position selected from the group consisting of q34 on human chromosome 9, p22-pter on human chromosome 8, the p arm of human chromosome 17, p21 on human chromosome 3, the p arm of human chromosome 9, q26 on human chromosome 10, q23-qter on human chromosome 12, p 12-pter on human chromosome 16, the p arm of human chromosome 3, p16 on human chromosome 4, the p arm of human chromosome 5, q21-q22 on human chromosome 6, q11-q13 on human chromosome 15, p15 on human chromosome 11, q23-qter on human chromosome 11, q11-qter on human chromosome 15 and p13.1-pter on human chromosome 19, in the test sample, said method comprising the steps of:
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(a) labelling nucleic acids from the test sample and from a control sample with different labels;
(b) contacting said labelled nucleic acids from each sample with a plurality of target nucleic acids, wherein either the labelled nucleic acids or the target nucleic acids, or both, have had repetitive sequences, if initially present, blocked and/or removed; and
(c) comparing the intensities of the signals from labelled nucleic acids hybridized to each target nucleic acid, thereby allowing detection of the presence or absence of the deletion in the test sample. - View Dependent Claims (11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35)
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36. A method for detecting a copy number variation in a suspected bladder cancer sample by detecting an amplification of a unique sequence at q21 on human chromosome 8, said method comprising:
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contacting a probe that binds selectively to a target polynucleotide sequence of q21 on human chromosome 8 with a nucleic acid sample prepared, directly or indirectly, from said suspected bladder cancer sample, wherein said nucleic acid sample comprises said target polynucleotide sequence and said probe is contacted with said sample under conditions in which said probe forms a stable hybridization complex with said target nucleic acid sequence; and
detecting said hybridization complex. - View Dependent Claims (37, 38, 39, 40, 41)
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42. A method for detecting a copy number variation in a suspected bladder cancer sample by detecting a deletion of a unique sequence at at least one position selected from the group consisting of q23-qter on human chromosome 12, p12-pter on human chromosome 16, p16 on human chromosome 4, q11-q13 on human chromosome 15, q11-qter on human chromosome 15, and p13.1-pter on human chromosome 19, said method comprising:
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contacting a probe that binds selectively to a target polynucleotide sequence of at least one position selected from the group consisting of q23-qter on human chromosome 12, p12-pter on human chromosome 16, p16 on human chromosome 4, q11-q13 on human chromosome 15, q11-qter on human chromosome 15, and p13.1-pter on human chromosome 19 with a nucleic acid sample prepared, directly or indirectly, from said suspected bladder cancer sample, wherein said nucleic acid sample comprises said target polynucleotide sequence and said probe is contacted with said sample under conditions in which said probe forms a stable hybridization complex with said target nucleic acid sequence; and
detecting said hybridization complex. - View Dependent Claims (43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53)
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Specification