Chapter 16
Comparative Genomic Hybridization
BURT G. FEUERSTEIN, YUICHI HIROSE, MALGORZATA PELLARIN,
and GREGG MAGRANE
Introduction
Comparative genomic hybridization (CGH) allows the entire genome of an
organism to be scanned for relative changes in DNA copy number (copy
number aberrations) (1-3) in a single experiment. Standard CGH can detect aneuploidies, deletions, and unbalanced translocations at a resolution
of 5-10 megabases. This is particularly useful in cases where DNA is unstable and where changes in copy number occur. Thus, tumors are often
analyzed by CGH, but other applications could include diagnosis of other
chromosome based illnesses.
The method typically uses targets that consist of normal metaphase
spreads. The targets are hybridized with unlabeled CoT-l DNA to block
repeat sequences in the targets and with DNA from a test sample (usually
tumor) labeled with one tag and DNA from a reference sample (usually
normal DNA) labeled with a second tag. The ratio of the amounts of test
and reference DNAs hybridizing to each location on the metaphase targets
indicates the relative copy number of the test DNA at that location.
Since CGH only measures relative imbalances of genetic material, any
chromosome aberration that does not result in a gain or loss of genetic
~ Burt G. Feuerstein, University of California, San Francisco, Department of
Neurological Surgery and Brain Tumor Research Center, Box 1631, San Francisco, CA,
94143-0808, USA (phone +415-353-9666;fax +415-353-9699; e-mail feuer@cc.ucsf.edu),
University of California, San Francisco, Department of Laboratory Medicine, and
Cancer Genetics Program; UCSF Cancer Center, San Francisco, CA, 94143-0808, USA
Yuichi Hirose, University of California, San Francisco, Department of Neurological
Surgery and Brain Tumor Research Center, Box 1631, San Francisco, CA, 94143-0808,
USA
Malgorzata Pellarin, University of California, Brain Tumor Research Center, San
Francisco, CA, 94143-0808, USA
Gregg Magrane, University of California, Department of Laboratory Medicine, and
Cancer Genetics Program, UCSF Cancer Center, San Francisco, CA, 94143-0808, USA
PROTOCOL
Comparative Genomic Hybridization
BURT G. FEUERSTEIN, YUICHI HIROSE, MALGORZATA PELLARIN,
and GREGG MAGRANE
Introduction
Comparative genomic hybridization (CGH) allows the entire genome of an
organism to be scanned for relative changes in DNA copy number (copy
number aberrations) (1-3) in a single experiment. Standard CGH can detect aneuploidies, deletions, and unbalanced translocations at a resolution
of 5-10 megabases. This is particularly useful in cases where DNA is unstable and where changes in copy number occur. Thus, tumors are often
analyzed by CGH, but other applications could include diagnosis of other
chromosome based illnesses.
The method typically uses targets that consist of normal metaphase
spreads. The targets are hybridized with unlabeled CoT-l DNA to block
repeat sequences in the targets and with DNA from a test sample (usually
tumor) labeled with one tag and DNA from a reference sample (usually
normal DNA) labeled with a second tag. The ratio of the amounts of test
and reference DNAs hybridizing to each location on the metaphase targets
indicates the relative copy number of the test DNA at that location.
Since CGH only measures relative imbalances of genetic material, any
chromosome aberration that does not result in a gain or loss of genetic
~ Burt G. Feuerstein, University of California, San Francisco, Department of
Neurological Surgery and Brain Tumor Research Center, Box 1631, San Francisco, CA,
94143-0808, USA (phone +415-353-9666;fax +415-353-9699; e-mail feuer@cc.ucsf.edu),
University of California, San Francisco, Department of Laboratory Medicine, and
Cancer Genetics Program; UCSF Cancer Center, San Francisco, CA, 94143-0808, USA
Yuichi Hirose, University of California, San Francisco, Department of Neurological
Surgery and Brain Tumor Research Center, Box 1631, San Francisco, CA, 94143-0808,
USA
Malgorzata Pellarin, University of California, Brain Tumor Research Center, San
Francisco, CA, 94143-0808, USA
Gregg Magrane, University of California, Department of Laboratory Medicine, and
Cancer Genetics Program, UCSF Cancer Center, San Francisco, CA, 94143-0808, USA
PROTOCOL