To evaluate the potential of the BeadArray™ platform for CNV mapping, we determined the coverage for different BeadArray™ platforms with regard to CNV events currently present in the public CNV database (Supplementary Table S3). It is clear that the current Infinium®-based array platforms are not offering extensive coverage of known CNVs, both in terms of the number of SNPs that map to each event and the number of events with SNPs. Despite this, a QuantiSNP analysis of the data is robust in the detection of CNV to as few as 5 SNPs per event, thus increasing the utility of these platforms for detection of up to 40% of previously identified events (Supplementary Table S3). Thanks to the potential for customization of the Infinium®-based BeadArrays™, future platforms or custom design arrays could be complemented for CNV detection by interrogating SNPs (or invariant nucleotide positions) mapping in the genomic region of interest. It is conceivable that the same approach could be used to generate BeadArrays™ with a biased distribution of oligonucleotides for CNV discovery, as well as other mapping applications (ChIP on
