Refinement and discovery of new hotspots of copy number variation associated with autism spectrum disorder

Rare DNA copy-number variation (CNV) plays an important role in the underlying genetic etiology of autism and intellectual disability. Although large numbers of copy-number variants (CNVs) have been recently implicated in autism, most are large affecting many genes and specificity of these lesions with respect to classically defined autism as opposed to more broadly defined developmental delay is unclear. We exploited the repeat architecture of the genome to target smaller regions (n=1340 hotspots, median size 15 kbp) flanked by repetitive sequence among 2,240 autism simplex patients and a subset of unaffected parents. 3,088 test samples and 2 references (NA12878 and NA18507) and an additional 1,214 test samples and 2 references (NA12878 and NA18507)