arrays. Indeed, we find that 80–85% of such missing Illumina calls overlap with SegDups (Supplementary Methods). We also find that many of the calls missed by SNP arrays but detected by CGH arrays are duplications. We ascribe this effect to a combination of differences in probe coverage and the type of reference used. Whereas SNP arrays use a population reference, CGH arrays use a single sample reference. The CGH arrays therefore have greater sensitivity to detect small differences in copy number (e.g., four versus five copies).
