We performed high-resolution genome-wide copy-number scans, using the NimbleGen HD2 array comparative genomic hybridization (CGH) platform, on all subjects and their biological parents. Data processing and CNV detection were performed as described in Experimental Procedures. CNV call sets were filtered based on probe ratio (≤0.8 and ≥ 1.2), number of probes (≥10), frequency (<1%), and confidence score (Supplemental Experimental Procedures, Tables S1 and S2, and Figures S1 and S2). Rare CNVs that were present in subjects and not in their parents were subsequently validated and fine mapped using a custom tiling-resolution CGH array (Oxford Gene Technology) (Table S3. Custom Tiling array CGH Validation of Putative De Novo CNVs and Document S1. Figures S1–S3; Tables S1, S2, S4–S8, and S10; and Supplemental Experimental Procedures). Results for the genome-wide scans, tiling array validations, and breakpoint sequencing are illustrated by four examples: a deletion involving CMIP and PLCG2 genes (Figure 1I) and an exonic deletion of LINGO2 gene (Figure 1II) detected in subjects with a diagnosis of BD, and an intronic deletion of CSMD3 gene (Figure 2I) and a deletion adjacent to UGT8 gene (Figure 2II) detected in subjects with a diagnosis of SCZ.
