Matrix-CGH or Array-CGH
Dr. Bernhard Radlwimmer
Microarray-based comparative genomic hybridization (matrix-CGH or array-CGH) is a sensitive method for high-resolution analysis of genomic imbalances in tumor cell genomes (Solinas-Toldo et al., 1997). Genomic imbalances are monitored by the differential hybridization efficiencies of tumor DNA and reference DNA onto DNA sequences immobilized on glass slides in a regular array ('microarray chip') (usually bacterial artificial chromosomes, BACs).
Fig. 1:
The tumor test DNA, labeled with one fluorescence dye, and the reference DNA, labeled with another fluorescence dye, are cohybridized to these immobilized target-DNA species on the chip. Genomic imbalances are visualized by the ratio of the two fluorochromes. Data-acquisition is performed automatically by dedicated chip-readers which are equipped with adequate analysis-software for the statistical evaluation of the results.
Compared to the conventional approach of chromosomal CGH, the resolution is much improved by matrix-CGH, which allows to detect chromosomal imbalances below single-gene level.
Fig2: Genome-wide screen for chromosomal imbalances in the cell line HL60 applying matrix-CGH. Each bar represents the measured fluorescence signal ratio obtained from a spottet DNA-fragment on the microarray. The linear ratio of 1.0 indicates the balanced state, green and red circles highlight detected gains and losses of genomic material, respectively.
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A variety of microarrays have been designed. We have developed a human 8000-clone (8k) matrix-CGH chip, which includes a set of 3250 BACs (Fiegler et al., 2003), representing the whole genome with 1 Mbp resolution. Further 2000 clones are specific for known proto-oncogenes, tumor suppressor genes and genes with fundamental roles in cellular pathways, like apoptosis, cell-cycle regulation, differentiation and proliferation. Additional 3000 clones cover chromosomal regions of known or presumptive tumor-relevance. Three applications are addressed with this chip: i) genome-wide screening for DNA copy number changes at 500 kbp resolution, ii) detection of the copy number status for genes of interest in specific tumor types, iii) fine-mapping of 'hot-spots', i.e. regions frequently imbalanced in tumor cell genomes.