CNV formation mediated by recombination between interspersed duplicated sequences by non-allelic homologous recombination (NAHR), or corresponding to tandem arrays of variable numbers of tandem repeats (VNTR), can readily be identified at the resolution afforded in our experiments by analyses of local sequence homology (Supplementary Methods). Although germline mutation processes at VNTR, like NAHR, are primarily driven by meiotic recombination, detailed mutation analyses have shown a major role for complex intra- and inter-allelic exchanges at VNTR that are not a major source of CNV at interspersed duplicated sequences26. Sequence analysis of CNV breakpoints is required to estimate the contribution to CNV formation of other mechanisms including non-homologous end joining and microhomology-mediated break-induced repair.
