Whole Exome Sequencing Identifies Novel De Novo Variants Interacting with Six Gene Networks in Autism Spectrum Disorder

Abstract

Autism spectrum disorder (ASD) is a highly heritable condition caused by a combination of environmental and genetic factors such as de novo and inherited variants, as well as rare or common variants among hundreds of related genes. Previous genome-wide association studies have identified susceptibility genes; however, most ASD-associated genes remain undiscovered. This study aimed to examine rare de novo variants to identify genetic risk factors of ASD using whole exome sequencing (WES), functional characterization, and genetic network analyses of identified variants using Korean familial dataset. We recruited children with ASD and their biological parents. The clinical best estimate diagnosis of ASD was made according to the Diagnostic and Statistical Manual of Mental Disorders (DSM-5TM), using comprehensive diagnostic instruments. The final analyses included a total of 151 individuals from 51 families. Variants were identified and filtered using the GATK Best Practices for bioinformatics analysis, followed by genome alignments and annotation to the reference genome assembly GRCh37 (liftover to GRCh38), and further annotated using dbSNP 154 build databases. To evaluate allele frequencies of de novo variants, we used the dbSNP, gnomAD exome v2.1.1, and genome v3.0. We used Ingenuity Pathway Analysis (IPA, Qiagen) software to construct networks using all identified de novo variants with known autism-related genes to find probable relationships. We identified 36 de novo variants with potential relations to ASD; 27 missense, two silent, one nonsense, one splice region, one splice site, one 5′ UTR, and one intronic SNV and two frameshift deletions. We identified six networks with functional relationships. Among the interactions between de novo variants, the IPA assay found that the NF-κB signaling pathway and its interacting genes were commonly observed at two networks. The relatively small cohort size may affect the results of novel ASD genes with de novo variants described in our findings. We did not conduct functional experiments in this study. Because of the diversity and heterogeneity of ASD, the primary purpose of this study was to investigate probable causative relationships between novel de novo variants and known autism genes. Additionally, we based functional relationships with known genes on network analysis rather than on statistical analysis. We identified new variants that may underlie genetic factors contributing to ASD in Korean families using WES and genetic network analyses. We observed novel de novo variants that might be functionally linked to ASD, of which the variants interact with six genetic networks.

Molecular Dysregulation in Autism Spectrum Disorder

“…Missense variants in one gene, CEP41 , associated significantly with ASD [ 65 ] and overexpression of CEP41 pathogenic alleles in zebrafish model, showed that variants in embryos induces axonal defects and also affects cranial neural crest (CNC) cell migration and exhibited deficits in social behavior. More recently, Kim and co-workers [ 66 ] performed WES on 51 Korean families (n = 151 individuals) to identify putative causal variants of ASD and identified 36 de novo variants, which were confirmed by Sanger sequencing (27 missense, two silent, one nonsense, one splice region, one splice site, one 5′ UTR, one intronic SNVs, and two frameshift deletions). A retrospective study on 343 ASD patients using different genetic approaches of FMR1 testing, chromosomal microarray (CMA) and/or WES, recommend WES as the first-tier approach in the diagnosis of ASD patients [ 67 ].…”

Duchenne muscular dystrophy cell culture models created by CRISPR/Cas9 gene editing and their application in drug screening

“…More importantly, as well as these preclinical problems others such as possible off-target problems or immunogenicity linked with the use of Cas9 39 may delay their clinical application. However, while gene editing as therapeutic option still needs further development, CRISPR/Cas9 methodology has been applied to provide a large number of new animal models to further understand DMD pathology and perform preclinical studies 40 .…”

Meta-Analysis Identifies BDNF and Novel Common Genes Differently Altered in Cross-Species Models of Rett Syndrome

“…Adenylate Cyclases 7 and 9 ( ADCY7 and ADCY9 ) are membrane-bound enzymes that catalyze the formation of cyclic AMP from ATP and are highly expressed in the brain. De novo mutations in ADCY7 have been reported in autism spectrum disorders (ASD) where the gene has been proposed to be a risk factor [ 39 ]. ASD and RTT share some commonalities with RTT individuals showing some ASD-like behaviors [ 40 , 41 ].…”