In order to exclude the possibility that the increased de novo rate seen in cases reflected the different platforms28 used in our cases and the control studies, we undertook sensitivity analyses. If the elevation in de novos in cases is an artefact of greater call sensitivity in the present study, the enrichment we observed should be biased towards smaller CNVs, larger CNVs being called reliably after exclusion of CNVs spanning complex repeat regions (as we have done).28 However, relative enrichment for de novos among cases was similar for large de novos >500 kb (2.1% vs 0.8%, P=0.0014) as it was for small de novos <200 kb (2.3% vs 0.9%, P=0.0035), and the overall size distribution of case de novos was not shifted towards smaller CNVs (Figure 2 and Supplementary Table S3) compared with the control de novos. In general, duplications are less easily detected by microarrays than deletions. To exclude the possibility that the excess of de novos in cases reflects a lower sensitivity of the control platforms to detect duplications, we also examined the duplication/deletion ratios in the data
