To assess whether the CNVs identified in our ADHD cohort were significantly enriched for loci previously implicated in autism and schizophrenia, we first defined the genomic coordinates for a list of 14 loci enriched for CNVs associated with autism7,26–30 and six for schizophrenia.9,10,22,31 Apart from 16p11, all autism and schizophrenia loci were independent. After counting the number of CNVs larger than 500 kb in the patients and controls (conservatively, we did not stratify by CNV type) that overlapped with any of these test regions, we performed locus-specific tests of association using PLINK (10 000 permutations, one-sided). We also tested the overall significance of case-control comparisons for the total burden of CNVs at these loci using logistic regression analysis. To allow for the possibility that any significant overlap was caused by differences in the size of CNVs in the ADHD and control groups, we included CNV size as an independent variable.
