High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays

Abstract

Gene 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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Figure 1: Comparison of the fluorescence intensity ratio on λ DNA targets to the ratio of λ DNA in model test and reference genomes.
Figure 3: Analysis of breast cancer cell line BT474.
Figure 2: Precision and accuracy of human copy number measurements.
Figure 4: Copy number variation on chromosome 20 in four breast tumours.

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Acknowledgements

Work supported by NIH grants HD 17665, CA 45919 and P50 CA 58207; by U.S. DOE DE-AC03-76SF00098; California BCRP grants 1IB-003 and 2RB-0225; NIST ATP 94-05-0021; and Vysis. S.C. was supported by a postdoctoral fellowship from the U.S Army DAMD 17-96-1-6165 and Y.Z. received postdoctoral support from NIH training grant CA 09215. We thank U.J. Kim for the Xq26.1 clones.

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Correspondence to Daniel Pinkel.

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Pinkel, D., Segraves, R., Sudar, D. et al. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 20, 207–211 (1998). https://doi.org/10.1038/2524

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