Comparative genomic hybridization

• US 7,537,895 B2
• Filed: 05/08/2006
• Issued: 05/26/2009
• Est. Priority Date: 03/04/1992
• Status: Expired due to Fees

• Current Assignee: Regents of the University of California (University of California)
• Original Assignee: Regents of the University of California (University of California)
• Inventors: Pinkel, Daniel J., Waldman, Frederic, Gray, Joe W, Kallioniemi, Anne, Kallioniemi, Olli-Pekka
• Primary Examiner(s): Horlick; Kenneth R.
• Assistant Examiner(s): Tung; Joyce
• Application Number:
  US11/431,094
• Publication Number:
  US 20060292608A1
• Time in Patent Office: 1,114 Days
• Field of Search: 435/4, 435/6, 435/5, 435/91.1, 435/91.2, 536/23.1, 536/24.32, 536/24.33
• US Class Current: 435/6.14
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6841 In situ hybridisation
• CPC Class Codes: C12Q 1/6853 using modified primers or templates
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2525/151 repeat or repeated sequences, e.g. VNTR, microsatellite, concatemer
• CPC Class Codes: C12Q 2537/143 Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis
• CPC Class Codes: C12Q 2545/113 with an external standard/control, i.e. control reaction is separated from the test/target reaction
• CPC Class Codes: C12Q 2545/114 involving a quantitation step
• CPC Class Codes: C12Q 2563/107 fluorescence
• CPC Class Codes: C12Q 2600/158 Expression markers

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).

Claims

1. A method of surveying all chromosomes in a human genome for the presence of a copy number variation in one or more unique DNA sequence(s), said method comprising:

(a) labeling DNA comprising unique sequences from each chromosome from a sample with a label;

(b) contacting the labeled DNA with a plurality of target nucleic acids comprising unique sequences from each chromosome under conditions that permit non-saturating hybridization of target nucleic acids, wherein either the labeled DNA or the target nucleic acids, or both, have been treated so as to block or remove repetitive sequences, if initially present, without blocking or removing unique sequences; and

(c) comparing the intensities of the signals from the labeled DNA hybridized to each target nucleic acid to determine the copy number of at least one unique sequence in the hybridized labeled DNA relative to the copy numbers of one or more different unique sequences in the hybridized labeled DNA.

2. The method of claim 1, wherein the labeled DNA comprises total cellular DNA.

3. The method of claim 1, wherein the labeled DNA comprises DNA amplified from total genomic DNA.

4. The method of claim 1, wherein the target nucleic acids comprise a genome or portion thereof.

5. The method of claim 1, wherein the target nucleic acids are immobilized on a substrate.

6. The method of claim 5, wherein the target nucleic acids comprise a metaphase chromosome spread.

7. The method of claim 1, wherein the labeled DNA is contacted with the target nucleic acids in the presence of additional DNA comprising unique sequences from each chromosome, wherein the additional DNA is unlabeled.

8. The method of claim 1, wherein repetitive sequences in the labeled DNA are blocked.

9. The method of claim 1, wherein repetitive sequences in the target nucleic acids are blocked.

10. The method of claim 1, wherein repetitive sequences in the labeled DNA are removed;

and unique sequences in the labeled DNA are retained.

11. The method of claim 1, wherein repetitive sequences in the target nucleic acids are removed;

and unique sequences in the target nucleic acids are retained.

12. The method according to claim 1, wherein the hybridization is done in situ, the target nucleic acids comprise reference metaphase chromosomes, and the intensities of signals from labeled DNA are compared as a function of position on the metaphase chromosomes.

13. The method of claim 1, wherein the DNA is labeled with a fluorochrome.

14. The method of claim 1, wherein the copy number variation comprises an amplification or a deletion of one or more unique DNA sequences.

15. The method of claim 14, wherein the amplification or deletion comprises an amplification or deletion, respectively, of more than 2 hundred kilobases and less than 20 megabases.

16. The method of claim 1, wherein a chromosomal amplification is detected at a locus on chromosome 1.

17. The method of claim 1, wherein a chromosomal amplification is detected at a locus on chromosome 8.

18. The method of claim 1, wherein a chromosomal amplification is detected at a locus on chromosome 17.

19. The method of claim 1, wherein a chromosomal amplification is detected at a locus on chromosome 20.

20. A method of surveying all chromosomes in a human genome for the presence of a copy number variation in one or more unique DNA sequence(s), said method comprising:

(a) labeling DNA comprising unique sequences from each chromosome from a sample with a label;

(b) contacting the labeled DNA with a plurality of target nucleic acids comprising unique sequences from each chromosome under conditions that permit hybridization of target nucleic acids, wherein either the labeled DNA or the target nucleic acids, or both, have been treated so as to block or remove repetitive sequences, if initially present; and

(c) comparing the intensities of the signals from the labeled DNA hybridized to each target nucleic acid to determine the relative copy numbers of unique sequences in the hybridized labeled DNA.