Four-color CGH: a new method for quality control of comparative genomic hybridization

Comparative genomic hybridization (CGH) has become a widely used method in molecular cytogenetics to screen for copy number aberrations in human malignancies. Although the hybridization protocol is relatively simple, the validation and quality control of CGH have remained difficult. We describe here a new modification of CGH, four-color CGH, which is based on conventional CGH with an added Cy5-labeled second reference DNA, that serves as an internal standard in every hybridization. The internal standard aids in identifying inconsistently hybridized chromosomal regions (such as 1pter, 19, 22). When using a special second reference DNA (from a sex-mismatched trisomy 13 cell line) for four-color CGH, it is possible to standardize the dynamic range of hybridization. The four-color CGH modification is simple to adopt, requiring only the addition of Cy5-labeled reference DNA to the existing hybridization protocol. The principles and the modifications of the CGH image analysis software are described in detail.