A systematic review of CNVs was pursued based on the outline in Figure S1A, available online. CNVs associated with neurodevelopmental disorders were searched in PubMed through June 2012. Specific searches were employed for ASD (“copy number” and “autism”), ID (“copy number”, “intellectual disability”, and “mental retardation”), schizophrenia (“copy number” and “schizophrenia”), and epilepsy (“copy number” and “epilepsy”). Searches were limited to English language, humans, and publications after 2005. CNVs were considered highly recurrent and associated with disease if they were identified in a PubMed publication with the following features: (a) genetically tested in a large disease cohort (N>400); (b) included a comparison control sample; (c) statistically compared the CNV frequencies in cases and controls; (d) and the CNV was significantly enriched in the case sample. CNV significance was based on criteria established by the given publication. In all cases, this represented p<0.05, but the majority of studies used much stricter genome-wide criteria for significance. All CNV coordinates are reported in NCBI build 36, hg18. In general, we were able to consider deletions and duplications as separate CNVs.
