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 Chip, DNAse protection assays on arrays, global methylation analysis). The great advantage of such custom design is the possibility to detect both potential CNV events and SNPs on the same high-throughput genotyping platform, thus saving both time and biological reagents.