The Co-existence of ADHD With Autism in Saudi Children: An Analysis Using Next-Generation DNA Sequencing

Bogari, Neda Mostafa; Al‐Allaf, Faisal A.; Aljohani, Ashwag; Taher, Mohiuddin M.; Qutub, Nermeen; Alhelfawi, Suhair; Alobaidi, Amal; Alqudah, Derar; Banni, Hussain; Dairi, Ghida; Amin, Amr

doi:10.3389/fgene.2020.548559

Cited by 4 publications

(4 citation statements)

References 64 publications

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“…Increased expression of IL16 is found in patients with spinal cord injury and Alzheimer’s disease (Di Rosa et al , 2006; Bank et al , 2015). Rare and novel variants of IL16 are identified in Saudi Arabian patients with attention-deficit/hyperactivity disorder (Bogari et al , 2020). It is noted that singleton novel rare loss copy number variation in IL16 is associated with ASD (Prasad et al , 2012).…”

Section: Discussionmentioning

confidence: 99%

Genome-wide DNA methylation profiles of autism spectrum disorder

Sun

Wang

Wang³

et al. 2022

Psychiatric Genetics

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ObjectivesWe aimed to identify differentially methylated genes and related signaling pathways in autism spectrum disorder (ASD).Methods First, the DNA methylation profile in the brain samples (GSE131706 and GSE80017) and peripheral blood samples (GSE109905) was downloaded from the Gene Expression Omnibus database (GEO) dataset, followed by identification of differentially methylated genes and functional analysis. Second, the GSE109905 data set was used to further validate the methylation state and test the ability to diagnose disease of identified differentially methylated genes. Third, expression measurement of selected differentially methylated genes was performed in whole blood from an independent sample. Finally, protein-protein interaction (PPI) network of core differentially methylated genes was constructed.Results Totally, 74 differentially methylated genes were identified in ASD, including 38 hypermethylated genes and 36 hypomethylated genes. 15 differentially methylated genes were further identified after validation in the GSE109905 data set. Among these, major histocompatibility complex (HLA)-DQA1 was involved in the molecular function of myosin heavy chain class II receptor activity; HLA-DRB5 was involved in the signaling pathways of cell adhesion molecules, Epstein-Barr virus infection and antigen processing and presentation. In the PPI analysis, the interaction pairs of HLA-DQA1 and HLA-DRB5, FMN2 and ACTR3, and CALCOCO2 and BAZ2B were identified. Interestingly, FMN2, BAZ2B, HLA-DRB5, CALCOCO2 and DUSP22 had a potential diagnostic value for patients with ASD. The expression result of four differentially methylated genes (HLA-DRB5, NTM, IL16 and COL5A3) in the independent sample was consistent with the integrated analysis.Conclusions Identified differentially methylated genes and enriched signaling pathway could be associated with ASD.

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Section: Discussionmentioning

confidence: 99%

Genome-wide DNA methylation profiles of autism spectrum disorder

Sun

Wang

Wang³

et al. 2022

Psychiatric Genetics

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“…Third, the 64 bp deletion overlaps with the NCK (non-catalytic region of tyrosine kinase adaptor) associated protein 5 ( NCKAP5 ). This protein-coding gene is uncharacterized but associated with attention deficit-hyperactivity disorder [ 46 ] and drug-induced lupus erythematosus in humans [ 47 ]. Last, mutation cluster 2 overlaps with the solute carrier family member 2 ( SLC14A2 ).…”

Section: Discussionmentioning

confidence: 99%

Identification and characterisation of de novo germline structural variants in two commercial pig lines using trio-based whole genome sequencing

et al. 2023

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Background De novo mutations arising in the germline are a source of genetic variation and their discovery broadens our understanding of genetic disorders and evolutionary patterns. Although the number of de novo single nucleotide variants (dnSNVs) has been studied in a number of species, relatively little is known about the occurrence of de novo structural variants (dnSVs). In this study, we investigated 37 deeply sequenced pig trios from two commercial lines to identify dnSVs present in the offspring. The identified dnSVs were characterised by identifying their parent of origin, their functional annotations and characterizing sequence homology at the breakpoints. Results We identified four swine germline dnSVs, all located in intronic regions of protein-coding genes. Our conservative, first estimate of the swine germline dnSV rate is 0.108 (95% CI 0.038–0.255) per generation (one dnSV per nine offspring), detected using short-read sequencing. Two detected dnSVs are clusters of mutations. Mutation cluster 1 contains a de novo duplication, a dnSNV and a de novo deletion. Mutation cluster 2 contains a de novo deletion and three de novo duplications, of which one is inverted. Mutation cluster 2 is 25 kb in size, whereas mutation cluster 1 (197 bp) and the other two individual dnSVs (64 and 573 bp) are smaller. Only mutation cluster 2 could be phased and is located on the paternal haplotype. Mutation cluster 2 originates from both micro-homology as well as non-homology mutation mechanisms, where mutation cluster 1 and the other two dnSVs are caused by mutation mechanisms lacking sequence homology. The 64 bp deletion and mutation cluster 1 were validated through PCR. Lastly, the 64 bp deletion and the 573 bp duplication were validated in sequenced offspring of probands with three generations of sequence data. Conclusions Our estimate of 0.108 dnSVs per generation in the swine germline is conservative, due to our small sample size and restricted possibilities of dnSV detection from short-read sequencing. The current study highlights the complexity of dnSVs and shows the potential of breeding programs for pigs and livestock species in general, to provide a suitable population structure for identification and characterisation of dnSVs.

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“…In a different study, intronic SNV rs4675502 of PARD3b was found to be associated with autism spectrum disorder (Anney et al, 2010(Anney et al, , 2012. In another study, missense SNV rs80119103, which causes a Pro1145His mutation in PARD3b at the C-terminus that is not conserved with PARD3, was found in 1 of 8 Saudi children with attention-deficit/hyperactivity disorder (Bogari et al, 2020).…”

Section: Neuropsychiatric Disorders Pard3 and Pard3bmentioning

confidence: 95%

The Roles of Par3, Par6, and aPKC Polarity Proteins in Normal Neurodevelopment and in Neurodegenerative and Neuropsychiatric Disorders

Zhang

Wei

2022

J. Neurosci.

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Normal neural circuits and functions depend on proper neuronal differentiation, migration, synaptic plasticity, and maintenance. Abnormalities in these processes underlie various neurodevelopmental, neuropsychiatric, and neurodegenerative disorders. Neural development and maintenance are regulated by many proteins. Among them are Par3, Par6 (partitioning defective 3 and 6), and aPKC (atypical protein kinase C) families of evolutionarily conserved polarity proteins. These proteins perform versatile functions by forming tripartite or other combinations of protein complexes, which hereafter are collectively referred to as "Par complexes." In this review, we summarize the major findings on their biophysical and biochemical properties in cell polarization and signaling pathways. We next summarize their expression and localization in the nervous system as well as their versatile functions in various aspects of neurodevelopment, including neuroepithelial polarity, neurogenesis, neuronal migration, neurite differentiation, synaptic plasticity, and memory. These versatile functions rely on the fundamental roles of Par complexes in cell polarity in distinct cellular contexts. We also discuss how cell polarization may correlate with subcellular polarization in neurons. Finally, we review the involvement of Par complexes in neuropsychiatric and neurodegenerative disorders, such as schizophrenia and Alzheimer's disease. While emerging evidence indicates that Par complexes are essential for proper neural development and maintenance, many questions on their in vivo functions have yet to be answered. Thus, Par3, Par6, and aPKC continue to be important research topics to advance neuroscience.

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The Co-existence of ADHD With Autism in Saudi Children: An Analysis Using Next-Generation DNA Sequencing

Cited by 4 publications

References 64 publications

Genome-wide DNA methylation profiles of autism spectrum disorder

Genome-wide DNA methylation profiles of autism spectrum disorder

Identification and characterisation of de novo germline structural variants in two commercial pig lines using trio-based whole genome sequencing

The Roles of Par3, Par6, and aPKC Polarity Proteins in Normal Neurodevelopment and in Neurodegenerative and Neuropsychiatric Disorders

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