Schematic comparative genomic hybridization for microarray setup

Schematic representation of the array CGH technique for a focused analysis of copy number imbalances along a region of interest (eg, 8q21.1). A tiling path of genomic clones (eg, BACs, PACs, PIs, cosmids) is generated to cover the region. After extraction and purification, these genomic DNA targets are arrayed onto glass slides.
Array CGH is performed by hybridizing labeled normal (Cy3) and tumor (Cy5) genomic DNA into the microarray and detected using a microarray scanner.
Each array spot, realigned in silico as a single contiguous map to correspond with the tiling path, can be analyzed by fluorescence ratio to identify the regions of copy number changes. These results may be correlated with in silico techniques to identify candidate genes of interest.