Three CNV categories were defined: A, B, and C (Figure S2, available online). Category A consists of stereotyped, recurrent CNVs whereby multiple cases of a particular CNV encompassed the same region. Category A CNVs are widely known to be generated in stereotyped fashion due to flanking segmental duplications and non-allelic homologous recombination (such as 16p11.2 deletions/duplications). Category B consists of CNVs that may be variable but hit a singular, common gene (such as NRXN1 deletions/duplications). Category C consists of non-stereotyped, recurrent CNVs that overlap with a common region, which contains many genes (for example, 1p36 deletions/duplications). To determine CNV category, we reviewed Decipher CNV cases (when possible) and entered CNV coordinates into the UCSC Genome Browser database searching for “segmental dups” (http://www.genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=263029387&c=chr2&g=genomicSuperDups). If a CNV was positive for flanking segmental duplications, then it provided further evidence for Category A inclusion.
