that is in line with the lack of structural information in the data generated using microarray platforms (2). Several oligonucleotide array platforms originally developed for genotyping have also been used for copy number analysis (3–9) and oligonucleotide arrays have been specifically designed for comparative genome hybridization (CGH) applications (10,11). More recently, tiling array strategies have been successfully applied to detect copy number alterations on chromosome 22 (12). Tiling arrays offer full regional coverage and very accurate mapping however, at present multiple arrays are needed to accommodate the whole genome. There is increasing interest in the ability of SNP array platforms to detect copy number variants (CNVs), as this approach allows simultaneous profiling of copy number polymorphisms (CNPs) and SNPs, leading to a better characterization of the genetic alterations under investigation. Some of the advantages of this approach for the detection of chromosomal abnormalities have been shown for the GeneChip® technology (Affymetrix, Santa Clara, CA, USA), using 10, 100 and 500 K platforms, and a variety of statistical analysis and visualization tools have been developed for these platforms (3,4,6–9,13–17). An alternative to GeneChip® is provided by Illumina's BeadArray™ technology for high-throughput SNP genotyping, where allele-specific hybridization is coupled with primer extension
