We evaluated the performance of our de novo CNV calling method by: i) analyzing a small set of 45 ASD trios included in our previous CNV study (Sebat et al., 2007) and, ii) by comparing results on validated control de novo CNVs identified by our group with results from a recent study(Levy et al., 2011) by Mike Wigler's group. In 45 ASD trios we detected and validated all 3 de novo CNVs that were identified in our previous study and in addition, we identified one novel de novo CNV 38 kb in size (Table S8). We compared our list of validated control de novo CNVs with de novo CNVs reported by (Levy et al., 2011) in the same 426 control trios using an entirely different informatics approach to identify de novo CNVs. Both groups identified four validated de novo CNVs in controls and therefore observed an identical rate (0.9%) of de novo CNVs in 426 controls. Three out of four de novo events overlapped between two groups. One de novo event that was unique to each group was < 20
