Unraveling genetic mechanisms in autism spectrum disorders

Autism Spectrum Disorders (ASDs) are a group of neurodevelopmental disorders characterized by impairments in socialization and communication accompanied by repetitive and stereotypic behaviors. ASDs are highly heritable and heterogeneous with a complex genetic etiology. Numerous candidate genes have been suggested by linkage, association and candidate gene studies and recurrent submicroscopic deletions and duplications have been identified using array technology. In order to screen for deletions and duplications in ASD candidate genes and regions, we developed a Multiplex Ligation-dependent Probe Amplification (MLPA) assay (paper I). Screening of 26 genes in 148 individuals we found a 15q11-13 interstitial duplication, which had escaped detection by conventional karyotyping, in 1.3% of the patients. Synthetic MLPA showed to be an easy, reliable and cost-effective method for the identification of Copy Number Variants (CNVs) in selected candidate regions. In order to screen the whole genome for CNVs in ASD patients and identify alterations associated with susceptibility for ASDs we used high resolution array-based comparative genomic hybridization (array-CGH). In 4-year-old girl we identified a 7.1 Mb interstitial deletion of chromosome band 6p22.3 (paper II). The patient had cognitive delay, specific language impairments and dysmorphic features. The deletion overlapped with six previously reported cases with a 6p22–24 interstitial deletion. Developmental delay was present in all cases, while heart defects, short neck and/or redundant skin folds, eye abnormalities, and ear anomalies were present in the majority of cases. By our finding we could narrow down the critical region for the 6p22 deletion phenotype to 2.2 Mb comprising twelve genes including the ATXN1 gene previously reported susceptibility gene for learning difficulties. In the whole genome screening of 223 ASD patients by array-CGH (paper III), clinically significant CNVs were identified in 18 individuals (8%) and CNVs of unclear clinical relevance in 20 individuals (9%). Among the latter cases, 13 individuals carried rare inherited CNVs, while parental samples were unavailable in the remaining seven cases. All patients were classified into different phenotype and inheritance subgroups. Rare inherited CNVs were present in a higher proportion of ASD cases having first- or second-degree relatives with an ASD related neuropsychiatric phenotype in comparison with cases without reported heredity (P=0.0096). We concluded that rare CNVs, encompassing potential candidate regions for ASDs, increase the susceptibility for ASDs and related neuropsychiatric disorders. In 514 ASD patients screened by array-CGH (paper IV), an exonic PARK2 deletion was found in three cases (~0.6%). No such deletion was identified in 149 control subjects. In a summary of comparable CNVs reported in the Database of Genomic Variants (DGV), 9/5141 controls had a deletion within the PARK2 gene (~0.2%). Compared with the DGV controls, deletions in the PARK2 gene were significantly more common in our ASD patient cohort (p=0.019). PARK2 deletions have previously been reported in autism and our results further support that PARK2 deletions may be a risk factor for the development of ASDs. PARK2 encodes for the E3 ubiquitin-protein ligase Parkin, which belongs to the Ubiquitin proteasome system (UPS). UPS operate pre- and postsynaptic compartments demonstrating a direct link between these two major systems that may be important in the pathophysiology of autism. The future challenge will be to, in combination with the increased usage of high resolution array-CGH and whole genome sequencing identifying genetic alterations, create useful analysis systems in which the co-occurring pathways and gene-gene interactions in ASDs can be linked together and the different genes involved identified.