Supplemental Data Document S1. Figures S1–S18, Tables S1–S7, S9–S11, S13, and S16, and Supplemental Acknowledgments Table S8. Phenotypes in ASD Subjects with Pathogenic CNVs or with Selected CNVs of Uncertain Significance This file also contains information on CNV validation and segregation in siblings, when available. Tables S12A–S12D. GO Terms, Pathways, and MPO Enrichment of Affected versus Control Subjects Tables S14A–S14E. Characterization of Genes Selected by NETBAG Table S15. Functional-Group Enrichment for DAPPLE Results Table S17A. Listing of CNV Calls in Affected Subjects Table S17B. Chromosome Abnormalities in Parents and Control Subjects Chromosome abnormalities in probands are listed in Table S1C. Table S17C. Experimentally Validated CNVs Document S2. Article plus Supplemental Data