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 (Infinium® assay) (18). The technology was further developed to use allele-specific single-base extension in a two colour labelling method (19). This modification allows the generation of more genotypes from each array, when compared to the single colour system, as a single-bead type is sufficient to represent one SNP. Furthermore, this high-throughput method couples hybridization and primer extension, thus achieving higher specificity. It has been recently demonstrated that the bead array platform using the Infinium® assay is able to detect copy number alterations (20).
