For this study, we have combined these two approaches by exploiting a large CNV dataset derived from a consortium of clinical laboratories to explore the frequency and functional significance of rare CNVs. Our analysis of the first 15,749 ISCA cases, one of the largest CNV studies to date, has confirmed the power of this approach. We have defined the frequency (17.1%) of pathogenic CNVs in a cohort of individuals with intellectual and developmental disabilities and performed formal case-control studies of selected recurrent genomic regions whose frequency was sufficient for statistical analysis.