Experimental design and data analysis for array comparative genomic hybridization

Array comparative genomic hybridization (aCGH) is a technique for measuring chromosomal aberrations in genomic DNA. With the availability of high-resolution microarrays, detailed characterization of the cancer genome has become possible. In this review, we discuss several issues in the generation and interpretation of aCGH data, including array platforms, experimental design, and data analysis. Due to the complexity of the data, application of appropriate statistical methods is crucial for avoiding false positive findings. We also describe integration of copy number data with other types of data to identify functional significance of observed aberrations.