Following Walsh et al., we defined rare copy number variations as those with at least 100 kb in size, at least 20 SNPs and not previously described the Database of Genomic Variants (DGV, http://projects.tcag.ca/variation/; dgv18v6). Any previously described event that had at least a 60% overlap with a newly discovered event was considered ‘not rare’ and excluded from further evaluation (for details see [21]). We then looked to see if there was an increase in particular types of rare CNVs between cases and controls using a 2-tailed Fisher's Exact test to compare number of cases versus number of controls with and without the event.
