We undertook several analytic and validation measures to ensure that the results were not affected by variation in the performance of the two SNP arrays, including cross-platform analysis of CNV calls in 45 samples for which data were available for both BeadChips. We limited CNV analysis to 561 113 autosomal SNPs common to both SNP arrays. CNVs were defined by PennCNV (2009Aug27version).23 Called CNVs were required to span at least 15 consecutive informative SNPs; those with copy number calls lower than two were classed as deletions, and greater than two as duplications. As is customary for this type of analysis,10,11 samples for which high-quality data could not be obtained were excluded on the basis of either a high SD in their genome-wide log R ratio (>0·30) or because they carried more than 30 apparent CNVs larger than 100 kb. These exclusions left 366 patients with ADHD and 1047 controls for full analyses. These samples had minimum difference in the distribution of the mean SNP call rate (cases=0·999, SD=0·001; controls=0·992, SD=0·005) or the mean SD of the genome-wide log R ratio (cases=0·19, SD=0·03; controls=0·21, SD=0·03).
