To evaluate the possible use of the current Infinium®-based assays for copy number variation detection and the possible effect of CNV on our own analysis, we mapped the SNPs present in the Human-1 and/or the HumanHap300 to known copy number variants from the database of genomic variants (http://projects.tcag.ca/variation/—12th October 2006 Release). To further evaluate the assays we also mapped the SNP content for the HumanHap550, which is the combination of the HumanHap240S and HumanHap300. As expected, known copy number variation regions are underrepresented in these arrays, this is possibly due to the SNP selection process that is in favour of polymorphisms showing clear Mendelian inheritance and thus will tend to exclude SNP's mapping to CNP regions. Overall 46.47% of unique copy number variation loci (excluding inversions) do not have any SNP mapping to them in the combined data (55.65% Human-1; 47.86% HumanHap300). In the combined data from both arrays, 39.79% of the copy number variants are covered by at least five SNP on the array (25.63% Human-1; 37.34% HumanHap300) and thus it should be possible to detect them using QuantiSNP
