that spanned BP2 through BP542 were counted in the BP2-BP3 frequency and not the BP4-BP5 frequency. Both the smaller and larger rearrangements (~1.5 and ~3.0 Mb) for 16p13.1128 and 22q1143 were included in their respective CNV categories. For this study, we excluded recurrent CNVs involving 17p12 (HNPP/CMT1A) since these CNVs are either not associated with cognitive defects or are late-onset in nature (and therefore not expected to be enriched in our mostly pediatric patient population) and 15q11 (BP1-2) which were not consistently reported by the contributing laboratories. CNV data from 10,118 individuals from control populations was obtained from several recent reports.44–47 Processed CNV data were used directly from three of the previous control studies.44–46 For the data from the Shi et al. paper,47 we performed CNV analysis of the raw data for regions of interest using the Affymetrix Power Tools software (Affymetrix, Santa Clara, CA). Log2 ratio data were extracted and analyzed using the BEAST algorithm (Satten et al., submitted). All p-values and odds ratios for case-control analyses were calculated using Fisher’s exact test.
