The ADHD sample is an extension of 366 cases previously examined for large, rare CNVs (5). All quality control and CNV detection protocols were identical to those previously described. BeadStudio was used to determine the log R ratio and B allele frequency at each SNP according to standard Illumina protocols. CNVs were defined by PennCNV (24) with loci spanning at least 15 consecutive informative SNPs, with those having copy number calls <2 and >2 being classed as deletions and duplications, respectively. Samples with a high standard deviation in their genome-wide log R ratio (>0.30) and carrying more than 30 apparent CNVs over 100 kb were also excluded. Large (classified as those >500 kb) and rare (<1% frequency) CNVs were used in this analysis because they are called with greater accuracy, have better concordance across different platforms, and show the most robust associations with neurodevelopmental disorders (5).
