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

Daniel Pinkel, Richard Segraves, Damir Sudar, Steven Clark, Ian Poole, David Kowbel, Colin Collins, Wen Lin Kuo, Chira Chen, Ye Zhai, Shanaz H. Dairkee, Britt Marie Ljung, Joe W. Gray, Donna Albertson

Research output: Contribution to journalArticle

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 hybridization (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 studies2-5. 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.

Original languageEnglish (US)
Pages (from-to)207-211
Number of pages5
JournalNature Genetics
Volume20
Issue number2
DOIs
StatePublished - 1998

Fingerprint

DNA Copy Number Variations
Comparative Genomic Hybridization
Chromosomes
Metaphase
Genome
DNA
Cri-du-Chat Syndrome
Fluorescence
Chromosomes, Human, Pair 20
Gene Dosage
Nucleic Acid Repetitive Sequences
Human Genome
Protein Sorting Signals
Tumor Suppressor Genes
DNA Sequence Analysis
Genetic Markers
Oncogenes
Cytogenetics
Chromosome Aberrations
Limit of Detection

ASJC Scopus subject areas

  • Genetics(clinical)
  • Genetics

Cite this

High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. / Pinkel, Daniel; Segraves, Richard; Sudar, Damir; Clark, Steven; Poole, Ian; Kowbel, David; Collins, Colin; Kuo, Wen Lin; Chen, Chira; Zhai, Ye; Dairkee, Shanaz H.; Ljung, Britt Marie; Gray, Joe W.; Albertson, Donna.

In: Nature Genetics, Vol. 20, No. 2, 1998, p. 207-211.

Research output: Contribution to journalArticle

Pinkel, D, Segraves, R, Sudar, D, Clark, S, Poole, I, Kowbel, D, Collins, C, Kuo, WL, Chen, C, Zhai, Y, Dairkee, SH, Ljung, BM, Gray, JW & Albertson, D 1998, 'High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays', Nature Genetics, vol. 20, no. 2, pp. 207-211. https://doi.org/10.1038/2524
Pinkel, Daniel ; Segraves, Richard ; Sudar, Damir ; Clark, Steven ; Poole, Ian ; Kowbel, David ; Collins, Colin ; Kuo, Wen Lin ; Chen, Chira ; Zhai, Ye ; Dairkee, Shanaz H. ; Ljung, Britt Marie ; Gray, Joe W. ; Albertson, Donna. / High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. In: Nature Genetics. 1998 ; Vol. 20, No. 2. pp. 207-211.
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