J Lung Cancer.  2011 Dec;10(2):77-86. 10.6058/jlc.2011.10.2.77.

Array-based Comparative Genomic Hybridization and Its Application to Cancer Genomes and Human Genetics

• Cho EK

• KMID: 2005738
• DOI: http://doi.org/10.6058/jlc.2011.10.2.77

Abstract

Microarray comparative genomic hybridization (CGH) has proven to be a specific, sensitive, and rapid technique, with considerable advantages compared to other methods used for analysis of DNA copy number changes. Array CGH allows for the mapping of genomic copy number alterations at the sub-microspecific level, thereby directly linking disease phenotypes to gene dosage alterations. The whole human genome can be scanned for deletions and duplications at over 30,000 loci simultaneously by array CGH (~40 kb resolution). Array CGH can be used for analysis of DNA copy number aberrations that cause not only cancer and human genetic disease, but also normal human variation. This review gives the various array CGH platforms and their applications in cancer and human genetics.

Keyword

Comparative genomic hybridization; Neoplasms; Human genetics

MeSH Terms

Coat Protein Complex I
Comparative Genomic Hybridization
DNA
DNA Copy Number Variations
Gene Dosage
Genetics, Medical
Genome
Genome, Human
Humans
Phenotype
Coat Protein Complex I
DNA

Figure

• 

  Fig. 1. Array comparative genomic hybridization. (A) Sample and reference DNAs are differentially labeled with fluorescent dyes (typically, cyanine-3 and cyanine-5), combined, and co-hybridized to cloned DNA fragments, which are spotted on a glass slide. The sample and reference competitively bind to the spots and fluorescence intensity ratios resulting from hybridization of both DNAs are reflected by their relative quantities. (B) To reduce the false-positive error rate, the two profiles of a dye-swap experiment are compared. Data are normalized so that the ratio is set to some standard value, typically 1.0 on a linear scale or 0.0 on a logarithmic scale. Each dot on the graph represents a clone spotted on the array. Blue values to the left and red values to the right of the ‘1’ line indicate a loss of a genomic region, blue values to the right and red values to the left indicate a gain or amplification, and blue and red values at ‘1’ indicate no copy number change. A value of 0.5 as seen in this figure indicates a homozygous deletion.

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