Nature Genetics
20, 207 - 211 (1998)
doi:10.1038/2524
High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarraysDaniel Pinkel1, 2, Richard Segraves1, Damir Sudar2, Steven Clark1, Ian Poole3, David Kowbel2, Colin Collins2, Wen-Lin Kuo1, Chira Chen1, Ye Zhai1, Shanaz H. Dairkee4, Britt-marie Ljung5, Joe W. Gray1, 2
& Donna G. Albertson1, 2, 61
Cancer Genetics Program, UCSF Cancer Center, University of California San Francisco, Box 0808, San Francisco, California 94143-0808, USA. 2
Life Sciences Division, E.O. Lawrence Berkeley National laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA. 3
Vysis, Inc., Downers Grove, Illinois, USA. 4
Geraldine Brush Cancer Research Institute, California Pacific Medical Center, 2330 Clay Street, San Francisco, California 94115, USA. 5
Pathology Department, University of California San Francisco, Box 0102, San Francisco, California 94143, USA. 6
MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.
Correspondence should be addressed to Daniel Pinkel pinkel@cc.ucsf.eduGene dosage variations occur in many diseases. In cancer, deletions and copy number increases contribute to alterations in the expression of tumour-suppressor genes and oncogenes, respectively. Developmental abnormalities, such as Down, Prader Willi, Angelman and Cri du Chat syndromes, result from gain or loss of one copy of a chromosome or chromosomal region. Thus, detection and mapping of copy number abnormalities provide an approach for associating aberrations with disease phenotype and for localizing critical genes. Comparative genomic hybridization3(CGH) was developed for genome-wide analysis of DNA sequence copy number in a single experiment. In CGH, differentially labelled total genomic DNA from a 'test' and a 'reference' cell population are cohybridized to normal metaphase chromosomes, using blocking DNA to suppress signals from repetitive sequences. The resulting ratio of the fluorescence intensities at a location on the 'cytogenetic map', provided by the chromosomes, is approximately proportional to the ratio of the copy numbers of the corresponding DNA sequences in the test and reference genomes. CGH has been broadly applied to human and mouse malignancies. The use of metaphase chromosomes, however, limits detection of events involving small regions (of less than 20 Mb) of the genome, resolution of closely spaced aberrations and linking ratio changes to genomic/genetic markers. Therefore, more laborious locus-by-locus techniques have been required for higher resolution studies2,
3,
4,
5. Hybridization to an array of mapped sequences instead of metaphase chromosomes could overcome the limitations of conventional CGH (ref. 6) if adequate performance could be achieved. Copy number would be related to the test/reference fluorescence ratio on the array targets, and genomic resolution could be determined by the map distance between the targets, or by the length of the cloned DNA segments. We describe here our implementation of array CGH. We demonstrate its ability to measure copy number with high precision in the human genome, and to analyse clinical specimens by obtaining new information on chromosome 20 aberrations in breast cancer.
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