We found the relative contribution of NAHR and VNTR-mediated CNV formation to be largely dependent on CNV size. NAHR was estimated to be 7 times more likely than VNTR to be the underlying mechanism for CNVs in the largest size decile, whereas VNTR were 3.5 times more frequent in the bottom decile. Overall, NAHR and VNTR contribute similarly (13.5% and 11.2% of validated CNVs, respectively; Supplementary Fig. 1.4). Owing to the challenges of designing validation and genotyping assays for VNTR, these loci are probably underrepresented in our genotyping data (5.6% of genotyped CNVs), although we have PCR-validated 11 out of 12 randomly selected VNTR to demonstrate that this class of loci is genuinely polymorphic (Supplementary Table 1.4 and Supplementary Fig. 1.5).
