These findings stood in contrast to a recent rigorous large-scale CNV study undertaken by the Autism Genome Project (AGP) (Pinto et al., 2010). Their sample included both simplex and multiplex families and identified a significantly higher burden of genic and ASD-related CNVs in cases versus unrelated controls. Notably they did not differentiate between transmitted and de novo events in this analysis. We reanalyzed our data using the identical criteria detailed in their manuscript and found similar results (Table S6). However, when we again restricted the analysis of our sample to rare transmitted CNVs, by removing confirmed rare de novo events; there was no significant difference found between proband and siblings, suggesting that the excess burden in the SSC sample was entirely driven by rare de novo events.
