At the conclusion of our study, we were able to evaluate this threshold further via a comparison of confirmed de novo CNVs identified here with those reported in 1,340 overlapping offspring (probands or siblings) using the Nimblegen 2.1M array, as described by Levy and colleagues in this issue (Levy et al., 2011). At a threshold defined by the presence of ≥20 Illumina probes within a genomic interval, a combined total of 58 rare de novo CNVs were identified across both studies, with each array type identifying 95% (n=55) of the total events. This suggests that both arrays have high sensitivity for such events at or above this threshold, and that the combined results are very likely to represent the complete set of large de novo CNVs present in the SSC. This situation is reversed below 20 probes: a total of 31 small rare de novo CNVs were identified between the two groups with approximately twice as many found using the 2.1M Nimblegen array vs. the IM Illumina array (23 CNVs vs. 12 CNVs respectively) as would be expected for the
