scholarly journals Gene expression analysis in lymphoblasts derived from patients with autism spectrum disorder

2011 ◽  
Vol 2 (1) ◽  
pp. 9 ◽  
Author(s):  
Yuka Yasuda ◽  
Ryota Hashimoto ◽  
Hidenaga Yamamori ◽  
Kazutaka Ohi ◽  
Motoyuki Fukumoto ◽  
...  
Keyword(s):  
Gene Expression ◽  
Autism Spectrum Disorder ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Autism Spectrum ◽  
Spectrum Disorder

scholarly journals Noncoding de novo mutations contribute to autism spectrum disorder via chromatin interactions

2019 ◽  
Author(s):  
Il Bin Kim ◽  
Taeyeop Lee ◽  
Junehawk Lee ◽  
Jonghun Kim ◽  
Hyunseong Lee ◽  
...  
Keyword(s):  
Gene Expression ◽  
Autism Spectrum Disorder ◽  
Stem Cells ◽  
Target Genes ◽  
De Novo ◽  
Regulatory Elements ◽  
Autism Spectrum ◽  
Spectrum Disorder ◽  
De Novo Mutations ◽  
Chromatin Interactions

Three-dimensional chromatin structures regulate gene expression across genome. The significance of de novo mutations (DNMs) affecting chromatin interactions in autism spectrum disorder (ASD) remains poorly understood. We generated 931 whole-genome sequences for Korean simplex families to detect DNMs and identified target genes dysregulated by noncoding DNMs via long-range chromatin interactions between regulatory elements. Notably, noncoding DNMs that affect chromatin interactions exhibited transcriptional dysregulation implicated in ASD risks. Correspondingly, target genes were significantly involved in histone modification, prenatal brain development, and pregnancy. Both noncoding and coding DNMs collectively contributed to low IQ in ASD. Indeed, noncoding DNMs resulted in alterations, via chromatin interactions, in target gene expression in primitive neural stem cells derived from human induced pluripotent stem cells from an ASD subject. The emerging neurodevelopmental genes, not previously implicated in ASD, include CTNNA2, GRB10, IKZF1, PDE3B, and BACE1. Our results were reproducible in 517 probands from MSSNG cohort. This work demonstrates that noncoding DNMs contribute to ASD via chromatin interactions.

scholarly journals SFARI Genes and where to find them; classification modelling to identify genes associated with Autism Spectrum Disorder from RNA-seq data

2021 ◽  
Author(s):  
Magdalena Navarro ◽  
T Ian Simpson
Keyword(s):  
Gene Expression ◽  
Autism Spectrum Disorder ◽  
Differential Gene Expression ◽  
Gene Expression Data ◽  
Gene List ◽  
Autism Spectrum ◽  
Spectrum Disorder ◽  
Expression Data ◽  
Link Type ◽  
Differential Gene

AbstractMotivationAutism spectrum disorder (ASD) has a strong, yet heterogeneous, genetic component. Among the various methods that are being developed to help reveal the underlying molecular aetiology of the disease, one that is gaining popularity is the combination of gene expression and clinical genetic data. For ASD, the SFARI-gene database comprises lists of curated genes in which presumed causative mutations have been identified in patients. In order to predict novel candidate SFARI-genes we built classification models combining differential gene expression data for ASD patients and unaffected individuals with a gene’s status in the SFARI-gene list.ResultsSFARI-genes were not found to be significantly associated with differential gene expression patterns, nor were they enriched in gene co-expression network modules that had a strong correlation with ASD diagnosis. However, network analysis and machine learning models that incorporate information from the whole gene co-expression network were able to predict novel candidate genes that share features of existing SFARI genes and have support for roles in ASD in the literature. We found a statistically significant bias related to the absolute level of gene expression for existing SFARI genes and their scores. It is essential that this bias be taken into account when studies interpret ASD gene expression data at gene, module and whole-network levels.AvailabilitySource code is available from GitHub (https://doi.org/10.5281/zenodo.4463693) and the accompanying data from The University of Edinburgh DataStore (https://doi.org/10.7488/ds/2980)[email protected]

scholarly journals Blood-Based Gene Expression in children with Autism spectrum disorder

Biodiscovery ◽  
2015 ◽  
pp. 2 ◽  
Author(s):  
Hristo Ivanov ◽  
◽  
Vili Stoyanova ◽  
Nikolay Popov ◽  
M Bosheva ◽  
...  
Keyword(s):  
Gene Expression ◽  
Autism Spectrum Disorder ◽  
Children With Autism ◽  
Autism Spectrum ◽  
Spectrum Disorder

scholarly journals Neuroinflammatory Gene Expression Alterations in Anterior Cingulate Cortical White and Gray Matter of Males With Autism Spectrum Disorder

2020 ◽  
Vol 13 (6) ◽  
pp. 870-884
Author(s):  
Aubrey N. Sciara ◽  
Brooke Beasley ◽  
Jessica D. Crawford ◽  
Emma P. Anderson ◽  
Tiffani Carrasco ◽  
...  
Keyword(s):  
Gene Expression ◽  
Autism Spectrum Disorder ◽  
Gray Matter ◽  
Autism Spectrum ◽  
Spectrum Disorder ◽  
Anterior Cingulate ◽  
Gene Expression Alterations

scholarly journals Biological Understanding of Neurodevelopmental Disorders Based on Epigenetics, a New Genetic Concept in Education

2021 ◽  
Author(s):  
Takeo Kubota
Keyword(s):  
Gene Expression ◽  
Autism Spectrum Disorder ◽  
Environmental Factors ◽  
Attention Deficit ◽  
Neurodevelopmental Disorders ◽  
Autism Spectrum ◽  
Spectrum Disorder ◽  
Chemical Modifications ◽  
Attention Deficit Hyperactive Disorder ◽  
Modifications In The Brain

Neurodevelopmental disorders, such as autism spectrum disorder, attention deficit hyperactive disorder, and learning disabilities, are heterogeneous conditions that are thought to have a multifactorial etiology including congenital genetic abnormalities and acquired environmental factors. Epigenetics is a biological mechanism that controls gene expression based on chemical modifications of DNA and chromosomal histone proteins. Environmental factors, such as severe mental stress, have been demonstrated to alter gene expression by changing epigenetic chemical modifications in the brain. Therefore, epigenetics is not only involved in congenital autism spectrum disorder-like conditions (e.g., Prader-Willi syndrome and Rett syndrome) but may also be involved in acquired attention deficit hyperactive disorder-like conditions (e.g., via child abuse and neglect). In this chapter, we introduce the basis of the epigenetic mechanism and the recent biological understanding of neurodevelopmental disorders based on epigenetics, which is a new genetic concept not only in medicine but also in education, which bridges internal brain mechanisms and external environmental factors.

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