Comparative genomic hybridization has been adapted to the microarray format with the GenoSensor™ system, which consists of a unique chromium-coated chip surface, multi-colour fluorescent hybridization chemistry and a wide-field, non-scanning, CCD-based imaging system. In genomic assays differentially labelled test (green) and reference (red) DNA are co-hybridized to the chip in the presence of Cot-1 DNA (to suppress repeat sequences). Custom software determines the green/red ratios for each pixel under each target spot to deduce sequence gains or losses. The combination of these features provides for high sensitivity and a linear dose response over several orders of magnitude in model systems. For applications to oncology research we have developed the AmpliOnc™ I array, which contains 3 spots for each of over 50 target loci (mostly oncogenes) that have been shown to be potentially amplified in tumour tissues. In hybridizations of normal female (green) against normal male (red) total human DNA, the spots containing the androgen receptor (X chromosome) revealed a green/red ratio significantly higher than the ratios of all other loci (>99% confidence level). This suggests sufficient sensitivity for single copy-change detection. In tests with defined tumour cell lines, the expected ratios were obtained for multiple amplifications with more than 95% confidence on each chip. Multiple tumour cell lines and primary tumours have been analysed with the AmpliOnc™ chip. In all cases known oncogene amplifications were confirmed, and in some instances additional and so far unknown amplifications were discovered.
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