Genetic landscape of autism spectrum disorder in Vietnamese children

Abstract

Autism spectrum disorder (ASD) is a complex disorder with an unclear aetiology and an estimated global prevalence of 1%. However, studies of ASD in the Vietnamese population are limited. Here, we first conducted whole exome sequencing (WES) of 100 children with ASD and their unaffected parents. Our stringent analysis pipeline was able to detect 18 unique variants (8 de novo and 10 ×-linked, all validated), including 12 newly discovered variants. Interestingly, a notable number of X-linked variants were detected (56%), and all of them were found in affected males but not in affected females. We uncovered 17 genes from our ASD cohort in which CHD8, DYRK1A, GRIN2B, SCN2A, OFD1 and MDB5 have been previously identified as ASD risk genes, suggesting the universal aetiology of ASD for these genes. In addition, we identified six genes that have not been previously reported in any autism database: CHM, ENPP1, IGF1, LAS1L, SYP and TBX22. Gene ontology and phenotype-genotype analysis suggested that variants in IGF1, SYP and LAS1L could plausibly confer risk for ASD. Taken together, this study adds to the genetic heterogeneity of ASD and is the first report elucidating the genetic landscape of ASD in Vietnamese children.Autism spectrum disorder (ASD) is a group of neurodevelopmental disorders that includes autism, Asperger's syndrome and pervasive developmental disorder not otherwise specified and is characterized by restricted repetitive behaviour, delays in language development and lack of reciprocal social communication and interaction 1 . The common psychiatric and cognitive comorbidities with ASD include intellectual disability (ID) 2-4 , sleep deprivation 5,6 and epilepsy (EP) 3,7 .Recent studies have gradually emphasized the role of genetics in ASD, with up to 25% of ASD cases having genetically identifiable causes 8 . Males have a 4-fold higher incidence of ASD than females 9 , suggesting the involvement of genetics in the aetiology of ASD. Previous studies have shown that 5% to 15% of patients with ASD have inherited copy number variations (CNVs) or de novo CNVs in some affected genes with synaptic function 10 . Genome-wide association studies have indicated that common variations are risk factors for ASD 11,12 . Meanwhile, de novo CNV and loss of function (LoF) mutations merely explain 2.6% of the variance in liability 12 . Other studies have revealed that non-coding de novo mutations in the promoter regions also affect ASD 13,14 . Recent genomic studies with large samples have explored new genes linked to ASD 15,16 . To date, over 100 genes have been identified as strongly linked to the risk of ASD 17,18 and enriched in the following three main pathways: chromatin remodelling, transcription and splicing, and synaptic function [18][19][20] . In fact, ASD is highly genetically heterogeneous due to multiple familial inheritance patterns and the occurrence of a large number of de novo variations. It is estimated that up to 1000 genes are potentially implicated ASD 21,22 , making it one of the most complex disorders. G...

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