Array comparative genomic hybridization (array CGH) enables the genome-wide detection of genomic copy number variations between test and reference samples. Genomic DNA from test and reference samples are differentially labeled with fluorochromes and cohybridized to DNA probes immobilized onto a glass slide. By analyzing the fluorescent intensity ratio on the targets, chromosomal imbalances across the genome can be quantified and defined positionally. The resolution of array CGH depends on the size of the genomic fragments as well as their density. In addition to detecting pathological copy number changes, the technology can be applied to any research question that involves comparing copy number differences between two samples. In this chapter, we present our standard labeling and hybridization protocol for BAC arrays. The troubleshooting guide that is included should allow newcomers in the field to avoid pitfalls and overcome some of the difficulties we have painstakingly tackled over the years.
