Microarray platform heterogeneity may yield false CNV enrichments signals as a function of differential detection power related to probe density, data quality, analysis methods, etc. We made a number of efforts to control for such potential effects and believe our study design is robust to this source of error for a number of reasons. First, the control data for this study were generated on higher resolution platforms (317,000 to 1,200,000 probe Illumina SNP arrays, with 88% of controls being profiled on 550,000 probe or higher density platforms) compared to the case data (median array is ~97,000 probes, highest density is ~130,000). As a result, our CNV detection power is substantially higher for cases than controls; notably, such differences will tend to manifest as false positive enrichments for CNVs in controls while we are focused exclusively on enrichments within cases. Second, we rigorously eliminated potential sources of errors in the case CNV data with a combination of both manual and automated filters, including calls with low probe counts, high degrees of overlap with segmental duplications in the reference assembly, and likely
