About one-third (8/23) of de novo CNVs in our study were flanked by segmental duplications (SDs) at one (6/23) or at both boundaries (2/23). This class of CNV most likely occurred by nonallelic homologous recombination (NAHR) (Lupski, 1998). By contrast, the majority of de novo CNVs were not flanked by SDs. Breakpoint sequences were obtained for five deletions (Table 1). Junction sequences of three out of five deletions were in short interspersed nuclear element (SINE) repetitive elements and two deletions had unique sequences at their breakpoints. A 1 bp insertion occurred at one of the breakpoints (see underlined base in Figure 2I). Notably, the median size of SD and non-SD-mediated de novo CNVs was 722 kb and 67 kb respectively, consistent with previous studies that have found differences in CNV size related to the underlying mutational mechanism (Itsara et al., 2010 and Stefansson et al., 2008).
