Novel Copy Number Variants in Children with Autism and Additional Developmental Anomalies

Background: The etiology of autism appears to be primarily genetic, with karyotypically detectable chromosomal abnormalities accounting for ~5-7% of autism spectrum disorder cases. The emergence of DNA microarray technology has enabled detection of submicroscopic deletions and duplications that are referred to as copy number variants (CNVs) and are operationally defined as insertions or deletions larger than 1 kb. Recent studies have suggested a role for CNVs, both de novo and inherited, in the etiology of autism. Objectives: We hypothesized that children with autism and additional developmental abnormalities may be more likely to harbor novel CNVs whether de novo or inherited. We used this model for two reasons: 1) children with chromosomal abnormalities often have multiple or syndromic developmental anomalies and 2) we recently reported a pathogenic microdeletion in a child with autism and structural eye abnormalities, stimulating our interest in investigating other individuals with autism and additional developmental disturbances. Methods: We used Affymetrix 250K GeneChip Microarray technology to detect CNVs in a subset of children from the Autism Genetic Resource Exchange (AGRE). We selected children with autism who had additional phenotypic features suggestive of a developmental disturbance (positive criteria filter) but who had normal cytogenetic testing (negative criteria filter). We identified 17 families (typically excluded from genetic studies because of these additional phenotypes) with the following features: two or more children with autism, at least one of whom also had cranio-facial dysmorphology, limb or digit abnormalities, or ocular abnormalities. We also analyzed a group of 19 unrelated children with autism and no additional dysmorphology to compare numbers of novel CNVs between syndromic autism and non-syndromic autism. We also screened a sample of 716 unselected controls from a study of age related eye disorders ongoing at the University of Iowa. To detect changes in copy number we used a publicly available program, Copy Number Analyser for GeneChip® (CNAG) Ver. 2.0. The CNVs of interest were validated using quantitative PCR. Results: A fisher's exact test of the number of novel CNVs out of the total number of CNVs in each group yields a one-tailed p-value of .04, suggesting that there are significantly more novel CNVs in the sample of syndromic autism. However, the number of individual carriers of novel CNVs did not differ significantly between the groups as there were two individuals in the syndromic autism group who each carried two novel CNVs. We identified novel deletions and duplications on chromosomes 1q24.2, 3p26.1, 4q34.2, 6q24.3, 7q35 and 22q11.2. Conclusions: Several of these deletions and duplications include new and compelling candidate genes for autism such as syntaxin binding protein 5 (STXBP5 also known as tomosyn), CNTNAP2 and leucine rich repeat neuronal 1 (LRRN1 also known as NLRR1). The implications of these novel and potentially pathogenic CNVs will be discussed as well as the psychiatric phenotypes found in the transmitting parents. Lastly, our data suggest that rare microdeletions and duplications may have a substantially higher prevalence in children with autism plus additional developmental anomalies.