Several limitations of our study deserve mention. First, the size of our patient cohort was relatively small, particularly with regard to the detection and analysis de novo CNVs. This issue was exacerbated by the removal of 185 probands during quality control steps, including matching for ancestry. On balance, though, the aforementioned findings with regard to the FHIT locus underscore the importance of rigorous control for population stratification. In addition, the reliance on differing arrays resulted in a smaller sample and lower resolution of CNV detection in order to avoid the significant confound of batch effects. In light of the fact that an increased burden of de novo CNVs in ASD and SCZ was initially identified using arrays with less than half the probe number present in the consensus set used in the current study (28, 35), it is unlikely that the failure to detect a statistically significant difference, if it is a false negative finding, was the result of insufficient resolution, but more likely the limitations imposed by sample size. Finally, our use of a subgroup of controls related to
