Comparative genomic hybridization (CGH)
First Claim
1. A method of comparing copy numbers of unique DNA sequences in a first cell or cell population relative to copy numbers of substantially identical sequences in a second cell or cell population, said method comprising the steps of:
- (a) labelling genomic DNA sequences from each cell or cell population with a different label;
(b) hybridizing said labelled DNA sequences from each cell or cell population to a reference genome under the following conditions;
(i) either the labelled DNA sequences, andr the reference genome have their repetitive sequences blocked and/or removed; and
(ii) unique DNA sequences in the labelled DNA sequences and unique DNA sequences in the reference genome are retained;
(c) comparing the intensities of the signals from the labelled DNA sequences hybridized to the reference genome.
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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
54 Claims
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1. A method of comparing copy numbers of unique DNA sequences in a first cell or cell population relative to copy numbers of substantially identical sequences in a second cell or cell population, said method comprising the steps of:
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(a) labelling genomic DNA sequences from each cell or cell population with a different label; (b) hybridizing said labelled DNA sequences from each cell or cell population to a reference genome under the following conditions; (i) either the labelled DNA sequences, andr the reference genome have their repetitive sequences blocked and/or removed; and (ii) unique DNA sequences in the labelled DNA sequences and unique DNA sequences in the reference genome are retained; (c) comparing the intensities of the signals from the labelled DNA sequences hybridized to the reference genome. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21)
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22. A method of comparing copy numbers of unique DNA sequences in a first cell or cell population relative to copy numbers of substantially identical sequences in a second cell or cell population, said method comprising the steps of:
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(a) labelling genomic DNA sequences from each cell or cell population with a different fluorochrome label; (b) hybridizing, in situ, said labelled DNA sequences from each cell or cell population to a reference genome under the following conditions; (i) either the labelled DNA sequences, and/or the reference genome have their repetitive sequences blocked and/or removed; and (ii) unique DNA sequences in the labelled DNA sequences and unique DNA sequences in the reference genome are retained; (c) comparing the intensities of the signals from the fluorochrome labelled DNA sequences hybridized to the reference genome. - View Dependent Claims (23, 24, 25, 26, 27)
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28. A method of comparing copy numbers of unique RNA sequences in a first cell or cell population relative to copy numbers of substantially identical sequences in a second cell or cell population, said method comprising the steps of:
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(a) labelling RNA sequences from each cell or cell population with a different label; (b) hybridizing said labelled RNA sequences from each cell or cell population to a reference genome under the following conditions; (i) either the labelled RNA sequences, and/or the reference genome have their repetitive sequences blocked and/or removed; and (ii) unique RNA sequences in the labelled RNA sequences and unique RNA sequences in the reference genome are retained; (c) comparing the intensities of the signals from the labelled RNA sequences hybridized to the reference genome. - View Dependent Claims (29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48)
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49. A method of comparing copy numbers of unique RNA sequences in a first cell or cell population relative to copy numbers of substantially identical sequences in a second cell or cell population, said method comprising the steps of:
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(a) labelling RNA sequences from each cell or cell population with a different fluorochrome label; (b) hybridizing, in situ, said labelled RNA sequences from each cell or cell population to a reference genome under the following conditions; (i) either the labelled RNA sequences, and/or the reference genome have their repetitive sequences blocked and/or removed; and (ii) unique RNA sequences in the labelled RNA sequences and unique RNA sequences in the reference genome are retained; (c) comparing the intensities of the signals from the fluorochrome labelled RNA sequences hybridized to the reference genome. - View Dependent Claims (50, 51, 52, 53, 54)
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Specification