DNA samples obtained from whole blood were analyzed by customized array comparative genomic hybridization (CGH) at an average probe density of ~97,000 oligonucleotides, sufficient for reliable genome-wide detection of CNVs >300 kbp and for targeted detection of events >40 kbp for approximately one-fourth of the genome13. After filtering, a total of 16,526 rare (< 1% population frequency) autosomal CNV calls were made with an average of 1.05 CNV events per individual (median size 213 kbp). Using a customized higher density microarray and fluorescent in situ hybridization, we validated 402/425 CNVs (precision of 0.945) greater than 150 kbp (Supplementary Note, and Supplementary Table 3). Similarly, manual inspection of calls with low log ratios or z-scores (absolute values of <0.25 and <1.5, respectively) suggests a false discovery rate of 0.0138. For comparison, we identified CNVs from a control set of 8,329 adult samples assayed using multiple Illumina genome-wide single-nucleotide polymorphism (SNP) microarrays. These samples were studied as part of genome-wide association studies (dbGaP) for phenotypes unrelated to neurological disease (e.g. lipid concentration levels, blood pressure, asthma, etc.) (Supplementary Table 4). CNVs were
