scholarly journals Whole-Exome Sequencing Identifies One De Novo Variant in the FGD6 Gene in a Thai Family with Autism Spectrum Disorder

2018 ◽  
Vol 2018 ◽  
pp. 1-7 ◽  
Author(s):  
Chuphong Thongnak ◽  
Areerat Hnoonual ◽  
Duangkamol Tangviriyapaiboon ◽  
Suchaya Silvilairat ◽  
Apichaya Puangpetch ◽  
...  
Keyword(s):  
Autism Spectrum Disorder ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
De Novo ◽  
Autism Spectrum ◽  
Spectrum Disorder ◽  
Bioinformatics Pipeline ◽  
Whole Exome ◽  
De Novo Variant ◽  
Genetic Analyzer

Autism spectrum disorder (ASD) has a strong genetic basis, although the genetics of autism is complex and it is unclear. Genetic testing such as microarray or sequencing was widely used to identify autism markers, but they are unsuccessful in several cases. The objective of this study is to identify causative variants of autism in two Thai families by using whole-exome sequencing technique. Whole-exome sequencing was performed with autism-affected children from two unrelated families. Each sample was sequenced on SOLiD 5500xl Genetic Analyzer system followed by combined bioinformatics pipeline including annotation and filtering process to identify candidate variants. Candidate variants were validated, and the segregation study with other family members was performed using Sanger sequencing. This study identified a possible causative variant for ASD, c.2951G>A, in the FGD6 gene. We demonstrated the potential for ASD genetic variants associated with ASD using whole-exome sequencing and a bioinformatics filtering procedure. These techniques could be useful in identifying possible causative ASD variants, especially in cases in which variants cannot be identified by other techniques.

scholarly journals Whole exome sequencing reveals inherited and de novo variants in autism spectrum disorder: a trio study from Saudi families

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Bashayer Al-Mubarak ◽  
Mohamed Abouelhoda ◽  
Aisha Omar ◽  
Hesham AlDhalaan ◽  
Mohammed Aldosari ◽  
...  
Keyword(s):  
Autism Spectrum Disorder ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
De Novo ◽  
Autism Spectrum ◽  
Spectrum Disorder ◽  
Whole Exome

Family-based Whole Exome Sequencing of Autism Spectrum Disorder Reveals Novel De Novo Variants in Korean Population

2017 ◽  
Vol 41 (S1) ◽  
pp. S309-S309 ◽  
Author(s):  
H. Yoo ◽  
S.A. Kim ◽  
M. Park ◽  
J. Kim ◽  
W.J. Lim ◽  
...  
Keyword(s):  
Autism Spectrum Disorder ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
De Novo ◽  
Autism Spectrum ◽  
Spectrum Disorder ◽  
Korean Population ◽  
De Novo Mutation ◽  
Whole Exome ◽  
Family Based

ObjectivesThe objective of this family-based whole exome sequencing (WES) is to examine genetic variants of autism spectrum disorder (ASD) in Korean population.MethodsThe probands with ASD and their biological parents were recruited in this study. We ascertained diagnosis based on DSM-5™ criteria, using Autism Diagnostic Observation Schedule and Autism Diagnostic Interview–Revised. We selected probands with typical phenotypes of ASD both in social interaction/communication and repetitive behaviour/limited interest domains, with intellectual disability (IQ < 70), for attaining homogeneity of the phenotypes. First, we performed WES minimum 50× for 13 probands and high-coverage pooled sequencing for their parents. We performed additional WES for 38 trio families, at least 100× depth. De novo mutations were confirmed by Sanger sequencing. All the sequence reads were mapped onto the human reference genome (hg19 without Y chromosome). Bioinformatics analyses were performed by BWA-MEM, Picard, GATK, and snpEff for variant annotation. We selected de novo mutation candidates from probands, which are neither detected in two pooled samples nor both parents.ResultsFifty-one subjects with ASD (5 females, 40∼175 months, mean IQ 42) and their families were included in this study. We discovered 109 de novo variants from 46 families. Twenty-nine variants are expected to be amino acid changing, potentially causing deleterious effects. We assume CELSR3, MYH1, ATXN1, IDUA, NFKB1, and C4A/C4B may have adverse effect on central nerve system.ConclusionsWe observed novel de novo variants which are assumed to contribute to development of ASD with typical phenotypes and low intelligence in WES study.Disclosure of interestThis work has been supported by Healthcare Technology R&D project (No: A120029) by Ministry of Health and Welfare, Republic of Korea.

scholarly journals Identification of De Novo JAK2 and MAPK7 Mutations Related to Autism Spectrum Disorder Using Whole-Exome Sequencing in a Chinese Child and Adolescent Trio-Based Sample

2019 ◽  
Vol 70 (2) ◽  
pp. 219-229 ◽  
Author(s):  
Jian Jiao ◽  
Manxue Zhang ◽  
Pingyuan Yang ◽  
Yan Huang ◽  
Xiao Hu ◽  
...  
Keyword(s):  
Autism Spectrum Disorder ◽  
Exome Sequencing ◽  
Candidate Genes ◽  
Whole Exome Sequencing ◽  
De Novo ◽  
Mapk Signaling ◽  
Autism Spectrum ◽  
Spectrum Disorder ◽  
Analysis Tool ◽  
Whole Exome

AbstractAutism spectrum disorder (ASD) is a neurodevelopmental disorder with high phenotypic and genetic heterogeneity. Whole-exome sequencing studies have shown that de novo single-nucleotide variations (SNVs) play an important role in sporadic ASD. The present study aimed to search for de novo SNVs using whole-exome sequencing in 59 unrelated Chinese ASD sporadic trios, and found 24 genes (including five reported ASD candidate genes CACNA1D, ACHE, YY1, TTN, and FBXO11) with de novo harmful SNVs. Five genes (CACNA1D, JAK2, ACHE, MAPK7, and PRKAG2) classified as “medium-confidence” genes were found to be related to ASD using the Phenolyzer gene analysis tool, which predicts the correlation between the candidate genes and the ASD phenotype. De novo SNVs in JAK2, MAPK7, and PRKAG2 were first found in ASD. Both JAK2 and MAPK7 were involved in the regulation of the MAPK signaling pathway. Gene co-expression and inter-gene interaction networks were constructed and gene expression data in different brain regions were further extracted, revealing that JAK2 and MAPK7 genes were associated with certain previously reported ASD genes and played an important role in early brain development. The findings of this study suggest that the aforementioned five reported ASD genes and JAK2 and MAPK7 may be related to ASD susceptibility. Further investigations of expression studies in cellular and animal models are needed to explore the mechanism underlying the involvement of JAK2 and MAPK7 in ASD.

Determination of genetic changes in etiology of autism spectrum disorder in twins by whole-exome sequencing

Gene Reports ◽  
2020 ◽  
Vol 19 ◽  
pp. 100618
Author(s):  
Ceyda Hayretdag ◽  
Pinar Algedik ◽  
Cumhur Gokhan Ekmekci ◽  
Ozlem Bozdagi Gunal ◽  
Umut Agyuz ◽  
...  
Keyword(s):  
Autism Spectrum Disorder ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Autism Spectrum ◽  
Spectrum Disorder ◽  
Genetic Changes ◽  
Whole Exome

Case Report: Whole Exome Sequencing Unveils an Inherited Truncating Variant in CNTN6 (p.Ser189Ter) in a Mexican Child with Autism Spectrum Disorder

2019 ◽  
Vol 50 (6) ◽  
pp. 2247-2251 ◽  
Author(s):  
José E. García-Ortiz ◽  
Ana I. Zarazúa-Niño ◽  
Angélica A. Hernández-Orozco ◽  
Edwin A. Reyes-Oliva ◽  
Carlos E. Pérez-Ávila ◽  
...  
Keyword(s):  
Autism Spectrum Disorder ◽  
Case Report ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Autism Spectrum ◽  
Spectrum Disorder ◽  
Whole Exome ◽  
Mexican Child

scholarly journals Whole exome sequencing in extended families with autism spectrum disorder implicates four candidate genes

2015 ◽  
Vol 134 (10) ◽  
pp. 1055-1068 ◽  
Author(s):  
Nicola H. Chapman ◽  
Alejandro Q. Nato ◽  
Raphael Bernier ◽  
Katy Ankenman ◽  
Harkirat Sohi ◽  
...  
Keyword(s):  
Autism Spectrum Disorder ◽  
Exome Sequencing ◽  
Candidate Genes ◽  
Whole Exome Sequencing ◽  
Autism Spectrum ◽  
Spectrum Disorder ◽  
Extended Families ◽  
Whole Exome

scholarly journals Whole-Exome Sequencing Identifies Three Candidate Homozygous Variants in a Consanguineous Iranian Family with Autism Spectrum Disorder and Skeletal Problems

2020 ◽  
Vol 11 (2) ◽  
pp. 62-72
Author(s):  
Saeed Farajzadeh Valilou ◽  
Afagh Alavi ◽  
Mahdiyeh Pashaei ◽  
Saghar Ghasemi Firouzabadi ◽  
Yousef Shafeghati ◽  
...  
Keyword(s):  
Autism Spectrum Disorder ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Autism Spectrum ◽  
Spectrum Disorder ◽  
Whole Exome ◽  
Iranian Family
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