**3.1 Translational research by the analysis of entire cancer genomes using BAC arrays**

The development of high-resolution microarray-based comparative genomic hybridization (aCGH) using cDNA of BACs makes it possible for translational research to analyze the entire cancer genome in a single experiment. Well-designed aCGH studies will increase our understanding of the genetic basis of cancer, help to identify novel predictive and prognostic biomarkers for cancer, and molecular therapeutic targets in cancer. Compared to oligonucleotide arrays, BAC arrays have some specific features. BACs have been widely used in aCGH studies (Pinkel and Albertson 2005; Lockwood, Chari et al. 2006; Ylstra, van den Ijssel et al. 2006). The vast majority of array CGH data available today has been generated using BAC CGH arrays. BACs probes vary in length from 150 to 200 kb (Pinkel and Albertson 2005). The probe of genome-wide BAC arrays range from 2,400 to 32, 000 unique elements in tiling path array, where each BAC overlaps with its contiguous BACs. The resolution (the distance between each DNA target represented on the array) of each BAC array is defined by the number of unique probes it contains (Tan, Lambros et al. 2007). BAC tiling path arrays provide a resolution of up to 50 kb (Tan, Lambros et al. 2007). The development of a whole-genome BAC tiling path approach has improved resolution of CGH by using overlapping clones (Ishkanian, Malloff et al. 2004; Lockwood, Chari et al. 2006). These platforms provide sufficiently strong signals to detect single-copy change, and are able to accurately define the boundaries of genomic aberrations, which can possibly be utilized in archival formalin-fixed, paraffin-embedded (FFPE) tissue (Johnson, Hamoudi et al. 2006; Little, Vuononvirta et al. 2006).

High amounts of high-quality BAC DNA are needed to obtain good array performance (Ylstra, van den Ijssel et al. 2006). BACs DNA yield is generally low when isolated from *E. coli* (Pinkel and Albertson 2005). Because of the low yields of DNA from isolated BAC clones, DNA amplification is required to generate sufficient quantities of adequately pure BAC DNA for the assay. Therefore a tiling path array is costly and highly labor intensive. In addition, as BAC probes are representative of the human genome, they also contain repetitive sequences, which can result in nonspecific hybridization (Tan, Lambros et al. 2007).
