Following the completion of the human genome sequence, the emphasis has shifted towards the characterization of human genetic variation and in the last few years, thanks to novel technologies, more and more structural variation events in the genome have been identified (for review see (41)). The possibility of also using a high-throughput platform for SNP typing to reliably and accurately screen for copy number variants (CNVs) in the genome is appealing. As the resolution of these approaches improves, previously uncharacterized CNV events will become easier to detect and may hinder the optimization of CNV analytical tools, in particular with regard to the control of false positive rates. Several unknown copy number changes were identified in our analysis and 11/15 mapped to CNVs identified in other studies (http://projects.tcag.ca/variation/). Even though the further validation of all novel events was beyond the scope of this study, this overlap with other studies provides circumstantial evidence of a real event which is further strengthened by the frequency with which novel events mapped within (nested) events (9/11) from other studies. Taken together this suggests that our method can accurately identify novel CNVs if SNPs map to the region of interest.
