To explore the contribution of CNV to ASD, we expanded our previous study (stage 1)6 with an additional 1,604 families (stage 2), bringing the total to 9,050 individuals from 2,845 ASD-affected families. We used an analytical pipeline of Illumina 1M arrays6,30 to detect rare CNV in families and applied a series of QC filters, including validation of all de novo events by at least one method (Tables S1A–S1C). In total, 1,359 stage 2 families passed QC, and 2,446 families were used in the combined analyses of both stages (Tables S2A and S2B). Of these, 2,147 families were European, and 299 were of other ancestries.21 We used the same pipeline to analyze 2,640 control individuals of European ancestry26,27,29 who were genotyped with the same array platforms. Ancestry was inferred by analysis of SNP genotype data (Table S1B). The rate, size, and number of genes affected by rare (<1% frequency) CNVs were assessed. Consistent with our previous data, we observed that compared to control subjects, affected subjects had an increased burden in the number of genes affected by rare CNVs (1.41-fold increase, empirical p = 1 × 10−5; Table 1). This enrichment was apparent for both deletions and duplications and remained after we controlled for potential case-control differences (Table 1). Similar findings were obtained when each stage was considered separately (Tables S3A–S3C).