Detection of chromosoal abnormalities associated with breast cancer
First Claim
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1. A method of detecting an amplification or gain of unique sequences at at least one chromosomal region selected from the group consisting of:
- on human chromosome 1,about position p22 to the centromere;
the q arm;
the centromere to about position p32;
about position q31 to qter;
about position q32;
about position q32 to qter;
on human chromosome 2,the p arm;
on human chromosome 3,about position p14;
about position p14 to qter;
about position p22 to pter;
about position q26 to qter;
on human chromosome 4,the p arm;
about position q32 to about position q34;
on human chromosome 5,the p arm;
about position q31 to qter;
about position q32 to qter;
on human chromosome 6,the p arm;
the centromere to about position p21;
about position p23 to pter;
the centromere to about position q21;
about position q12 to about position q13;
about position q21;
about position q21 to about position q22;
on human chromosome 7,the p arm;
the centromere to about position p12;
about position p21;
pter to about position q31;
the q arm;
about position q22 to about position q32;
on human chromosome 8,about position p12;
the q arm;
about position q21;
about position q21 to about position q23;
about position q21 to qter;
about position q22 to about position q23;
about position q22 to qter;
about position q23 to about position q24;
about position q23 to qter;
about position q24;
on human chromosome 10,the p arm;
the centromere to about position q21;
about position q22;
on chromosome 11,about position p15;
the q arm;
about position q13;
on human chromosome 12,the p arm;
the q arm;
about position q14 to about position q15;
about position q21;
about position q21 to about position q23;
about position q24;
on human chromosome 13,about position 22 to qter;
about position q31 to qter;
on human chromosome 14,the q arm;
about position q24 to qter;
about position q31;
about position q31 to qter;
on human chromosome 15,about position q21 to qter;
about position q24;
about position q25;
about position q26;
entire human chromosome 16;
on human chromosome 16,the p arm;
the q arm;
about position q23 to about position q24;
on human chromosome 17,the centromere to about position q24;
about position q12;
about position q21 to qter;
about position q22 to about position q23;
about position q22 to about position q24;
about position q22 to qter;
about position q24 to qter;
on human chromosome 18,the p arm;
on human chromosome 19,the q arm;
about position q13;
about position q13 to qter;
entire human chromosome 20;
on human chromosome 20,the p arm;
the q arm;
about position q12 to about position q13;
about position q13;
about position q13 to qter;
about position q34;
qter;
entire chromosome 21;
entire chromosome 22;
on the human X chromosome,the p arm,in a test sample, said method comprising;
(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 gain or 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).
45 Citations
29 Claims
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1. A method of detecting an amplification or gain of unique sequences at at least one chromosomal region selected from the group consisting of:
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on human chromosome 1, about position p22 to the centromere; the q arm; the centromere to about position p32; about position q31 to qter; about position q32; about position q32 to qter; on human chromosome 2, the p arm; on human chromosome 3, about position p14; about position p14 to qter; about position p22 to pter; about position q26 to qter; on human chromosome 4, the p arm; about position q32 to about position q34; on human chromosome 5, the p arm; about position q31 to qter; about position q32 to qter; on human chromosome 6, the p arm; the centromere to about position p21; about position p23 to pter; the centromere to about position q21; about position q12 to about position q13; about position q21; about position q21 to about position q22; on human chromosome 7, the p arm; the centromere to about position p12; about position p21; pter to about position q31; the q arm; about position q22 to about position q32; on human chromosome 8, about position p12; the q arm; about position q21; about position q21 to about position q23; about position q21 to qter; about position q22 to about position q23; about position q22 to qter; about position q23 to about position q24; about position q23 to qter; about position q24; on human chromosome 10, the p arm; the centromere to about position q21; about position q22; on chromosome 11, about position p15; the q arm; about position q13; on human chromosome 12, the p arm; the q arm; about position q14 to about position q15; about position q21; about position q21 to about position q23; about position q24; on human chromosome 13, about position 22 to qter; about position q31 to qter; on human chromosome 14, the q arm; about position q24 to qter; about position q31; about position q31 to qter; on human chromosome 15, about position q21 to qter; about position q24; about position q25; about position q26; entire human chromosome 16; on human chromosome 16, the p arm; the q arm; about position q23 to about position q24; on human chromosome 17, the centromere to about position q24; about position q12; about position q21 to qter; about position q22 to about position q23; about position q22 to about position q24; about position q22 to qter; about position q24 to qter; on human chromosome 18, the p arm; on human chromosome 19, the q arm; about position q13; about position q13 to qter; entire human chromosome 20; on human chromosome 20, the p arm; the q arm; about position q12 to about position q13; about position q13; about position q13 to qter; about position q34; qter; entire chromosome 21; entire chromosome 22; on the human X chromosome, the p arm, in a test sample, said method comprising; (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 gain or amplification in the test sample. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17)
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18. A method of detecting a deletion of unique sequences at at least one chromosomal region selected from the group consisting of:
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on human chromosome 9, the p arm; on human chromosome 16, the q arm; about position q22; on human chromosome 17, the p arm; in a test sample, said method comprising; (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 (19, 20, 21, 22, 23)
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24. A method for detecting a copy number variation in a suspected breast cancer sample by detecting an amplification of unique sequences from the chromosomal region on chromosome 17, position q22 to position q24, wherein the unique sequences comprise a target polynucleotide sequence hybridizable with a probe specific for chromosome 17, q22 to q24,
said method comprising: -
(a) contacting a probe that binds selectively to said target polynucleotide sequence of said region with a nucleic acid sample prepared, directly or indirectly, from said suspected breast 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 polynucleotide sequence; and (b) detecting said hybridization complex. - View Dependent Claims (25, 26, 27, 28, 29)
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Specification
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Current AssigneeRegents of the University of California (University of California)
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Original AssigneeRegents of the University of California (University of California)
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InventorsKallioniemi, Ollie-Pekka, Kallioniemi, Anne, Sakamoto, Masaru, Waldman, Frederic, Pinkel, Daniel, Gray, Joe W.
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Primary Examiner(s)FREDMAN, JEFFREY NORMAN
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Application NumberUS09/912,818Publication NumberTime in Patent Office1,855 DaysField of Search435/6, 435/91.2, 536/22.1, 536/231, 536/24.3US Class Current435/6.14CPC Class CodesC12Q 1/6809 Methods for determination o...C12Q 1/6841 In situ hybridisationC12Q 1/6886 for cancer immunoassay for ...C12Q 2537/157 A reaction step characteris...C12Q 2545/114 involving a quantitation stepC12Q 2600/156 Polymorphic or mutational m...G06F 15/025 adapted to a specific appli...Y10S 436/813 Cancer
