Autism Spectrum Disorder and other Neurodevelopmental Disorders: cytogenetic and genomic approaches

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Introduction: Neurodevelopmental disorders (NDDs) are a heterogeneous class of conditions involving the brain, including intellectual disability (ID) and autism spectrum disorder (ASD), that affect about 1%-3% of children (Miller et al., 2010). The genetics of NDDs is complex and include copy number variations (CNVs), pathogenetic mutations in single genes. To date, more than 1000 genes have been implicated in the etiopathogenesis of NNDs. Preliminary investigations have suggested that the majority of Developmental Disorders, in particular ASD, are actually polygenic; in addition, the genetic and environmental interplay in defining the phenotype clearly classifies NDDs such as ID and ASD as complex disorders. In this dissertation, I sought to explore the contribution of rare de novo and inherited coding variation in neurodevelopmental disorders and use these genetic variations to identify neurodevelopmental disorder associated genes and new/unknown oligogenic mechanisms. Methods: In a retrospective review of data, we re-evaluated all the results of diagnostic array-CGH tests on 700 cases with NDDs, focusing on variants previously interpreted as VOUS. Furthermore a series of 68 patients with autism spectrum disorder were recruited to perform whole exome sequencing and eventual whole genome sequencing. A deep analysis of VOUS, mainly consisting in a revision of gene expression/function annotation, and chromatine organization data, was performed. New candidate genes were analysed by GeneCodis4 to evidence enrichment for known NDD-associated GeneOntology terms and pathways. Whole exome sequencing was performed and potentially deleterious variants prioritized by custom filtering strategies including the use of ORVAL (Oligogenic Resource for Variant Analysis Platform) and enrichment analysis of candidate genes with GeneCodis4. Results: In about 42% of cases pathogenic CNVs were found, while in 58% identified CNVs remained initially VOUS. New potential genes and mechanisms such as double-hit mechanisms were found in our patients. In our 34 analysed ASD patients 11 cases showed possible deleterious rare variants, in different and, in the majority of cases, in multiple genes. The role of X chromosome and neurotransmitter pathways appears important. Conclusion: In our cohort of NDDs patients CNV-mediated double-hit mechanisms seem to play a relevant role in elucidate complex phenotypes. About 10% of patients from our ASD cohort also showed rare deleterious variants in multiple genes that seem to fully explain their complex phenotype.

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