We then tested whether any of the more common CNVs were significantly different in frequency between cases and controls, using Fisher's exact test. This has not been investigated in any of these samples previously. In this case common is a relative term rather than defined by a particular frequency cut-off, since a common CNV was defined as one that was present in three or more individuals in any particular cohort. We did not attempt to classify different CNVs as identical or different, as use of the different BeadChips can make the beginning and endpoints of the CNVs unclear. Additionally, the actual length of the CNV may be unimportant if it covers the same critical region as a shorter or longer CNV. We therefore performed this analysis by determining copy number for each SNP on the Beadchip, and performing Fisher's Exact test for each SNP included in a CNV. Low confidence CNVs, those in some telomeric and centromeric regions and those coding for immunoglobulin genes were removed (see Methods) before beginning the analysis, since these are particularly susceptible to false positive calls.
