Encouraged by the additional refinement provided by atypical deletion events, we performed a gene-based analysis on the complete ID/DD dataset, as well as on patient subsets partitioned by additional phenotypic data. We identified 615 genes as significantly deleted in any phenotype (Benjamini-Hochberg corrected p < 0.05; Supplementary Table 12), the vast majority of which associated with known pathogenic loci or subtelomeric alterations. An Ingenuity Pathways Analysis (IPA) (www.ingenuity.com) showed significant enrichment in expected functional categories (e.g. cardiovascular disease, developmental, endocrine system and developmental disorders).
