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Variant detection and the Autism sequencing project

Orion Buske, Misko Dzamba, Justin Foong, Lynette Lau, Marc Fiume, Christian Marshall, Susan Walker, Aparna Prasad, Michael Brudno
2011 BMC Bioinformatics  
Background Early detection of autism can improve the quality of life of affected individuals [1] .  ...  tools we have developed for color-space-aware alignment, variant detection, and visualization of next-generation sequencing data.  ... 
doi:10.1186/1471-2105-12-s11-a4 pmcid:PMC3277254 fatcat:lrt6r4h7brekxg2bha6rejbrle

Sequencing ASMT Identifies Rare Mutations in Chinese Han Patients with Autism

Lifang Wang, Jun Li, Yanyan Ruan, Tianlan Lu, Chenxing Liu, Meixiang Jia, Weihua Yue, Jing Liu, Thomas Bourgeron, Dai Zhang, Michael Edward Zwick
2013 PLoS ONE  
To investigate the association between ASMT and autism, we sequenced all ASMT exons and its neighboring region in 398 Chinese Han individuals with autism and 437 healthy controls.  ...  Among these rare variants, 4 were exclusively detected in patients with autism including a stop mutation (p.R115W, p.V166I, p.V179G, and p.W257X).  ...  Acknowledgments We would like to thank all subjects who participated in this study and our colleagues for their assistance in recruiting patients for inclusion in the study. Author Contributions  ... 
doi:10.1371/journal.pone.0053727 pmid:23349736 pmcid:PMC3547942 fatcat:uws2mlgofbcivjxbopl6v7o6bi

A Strategy to Identify de Novo Mutations in Common Disorders such as Autism and Schizophrenia

Gauthier Julie, Fadi F. Hamdan, Guy A. Rouleau
2011 Journal of Visualized Experiments  
Such is the case for diseases such as autism and schizophrenia.  ...  to multiple family members, and therefore will not be detected by linkage gene mapping or association studies.  ...  ' (S2D) project.  ... 
doi:10.3791/2534 pmid:21712793 pmcid:PMC3197027 fatcat:mgugj4wzcbcnrpgfnrkax2zh54

Excess variants in AFF2 detected by massively parallel sequencing of males with autism spectrum disorder

K. Mondal, D. Ramachandran, V. C. Patel, K. R. Hagen, P. Bose, D. J. Cutler, M. E. Zwick
2012 Human Molecular Genetics  
We hypothesized that other rare X-linked sequence variants at the AFF2 locus might contribute to ASD.  ...  We sequenced the AFF2 genomic region in 202 male ASD probands and found that 2.5% of males sequenced had missense mutations at highly conserved evolutionary sites.  ...  The authors would like to thank the NHLBI GO Exome Sequencing Project and its ongoing studies, which produced and provided exome variant calls for comparison: the Lung GO Sequencing Project (HL-102923)  ... 
doi:10.1093/hmg/dds267 pmid:22773736 pmcid:PMC3441129 fatcat:gsqwcyqdjjegjbmvdxxpmd7t6e

Mutation screening of the UBE3A gene in Chinese Han population with autism

Xue Zhao, Ran Zhang, Shunying Yu
2020 BMC Psychiatry  
288 bp of the CDS2 of UBE3A gene were detected using Sanger sequencing method.  ...  We further increased sample size to validate the detected variants using HRM and conducted association analysis between case and control groups.  ...  The found variants were further detected in the expanded samples using the HRM method and performed followup analyses.  ... 
doi:10.1186/s12888-020-03000-5 pmid:33308194 pmcid:PMC7733270 fatcat:dqanu2ugf5d7paqcssf62ggaiy

Next Generation Sequencing in Autism Spectrum Disorder

Jiani Yin, David Oleson, Christian P. Schaaf
2018 OBM Genetics  
Autism displays significant genetic heterogeneity. In the past one and a half decades, next generation sequencing has enabled identification of many variants that predispose to autism.  ...  In this review article, we will address how development of next generation sequencing has helped answer the following questions: 1. What are the modes of transmission/inheritance of autism? 2.  ...  Christian Schaaf is the Joan and Stanford Alexander Chair for Neuropsychiatric Genetics at Texas Children's Hospital.  ... 
doi:10.21926/obm.genet.1801014 fatcat:hf3zqvnrjjg2ziklxkonxsiys4

Online Resources for Genomic Structural Variation [chapter]

Tam P. Sneddon, Deanna M. Church
2011 Msphere  
These variants can occur in coding or non-coding DNA, they can be inherited or arise sporadically in the germline or somatic cells.  ...  Many of these events are segregating in the population and can be considered common alleles while others are new alleles and thus rare events.  ...  Acknowledgments This research was supported [in part] by the Intramural Research Program of the NIH, National Library of Medicine.  ... 
doi:10.1007/978-1-61779-507-7_13 pmid:22228017 pmcid:PMC3804003 fatcat:7wzdh7fknfa4jm5c6in326gbee

High-Throughput Sequencing of mGluR Signaling Pathway Genes Reveals Enrichment of Rare Variants in Autism

Raymond J. Kelleher III, Ute Geigenmüller, Hayk Hovhannisyan, Edwin Trautman, Robert Pinard, Barbara Rathmell, Randall Carpenter, David Margulies, Francisco José Esteban
2012 PLoS ONE  
Rare, potentially deleterious HOMER1 variants identified uniquely in the autism population affected functionally important protein regions or regulatory sequences and co-segregated closely with autism  ...  Single-nucleotide variants in genes encoding components of the mGluR signaling pathway were identified by high-throughput multiplex sequencing of pooled samples from 290 non-syndromic autism cases and  ...  Mark Bear for his role in conceiving this study and for valuable advice and guidance in all aspects of the project.  ... 
doi:10.1371/journal.pone.0035003 pmid:22558107 pmcid:PMC3338748 fatcat:h6ckgfyuwfca5lsq45wzrptzj4

Whole Exome Sequencing Revealed Clinical Relevant Variants in A Family Affected with Autism Spectrum Disorder

2016 Journal of Psychiatry and Brain Science  
The authors would like to thank the groups that generated Whole Exome Sequencing data from Joint lab between Children's Hospital of Fudan University and Wuxi NextCODE Co., Ltd.  ...  ACKNOWLEDGEMENTS We are sincerely grateful to the family members for their participation and cooperation in the study.  ...  Sanger Sequencing Validation We used Sanger sequencing to confirm the variants in the trio and other members that did not undergone the WES.  ... 
doi:10.20900/jpbs.20160017 fatcat:34puwhnluzb53gyajxzggsz5pa

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

Chuphong Thongnak, Areerat Hnoonual, Duangkamol Tangviriyapaiboon, Suchaya Silvilairat, Apichaya Puangpetch, Ekawat Pasomsub, Wasun Chantratita, Pornprot Limprasert, Chonlaphat Sukasem
2018 International Journal of Genomics  
Candidate variants were validated, and the segregation study with other family members was performed using Sanger sequencing.  ...  Autism spectrum disorder (ASD) has a strong genetic basis, although the genetics of autism is complex and it is unclear.  ...  Acknowledgments This study was supported by grants from the (1)  ... 
doi:10.1155/2018/8231547 pmid:29888248 pmcid:PMC5985066 fatcat:qz4cmgva4vfildu2jakk22c4lu

Impact of Next-Generation Sequencing (NGS) technology on cardiovascular disease research

Fengping Xu, Qin Wang, Fangfang Zhang, Yinling Zhu, Qingquan Gu, Liping Wu, Lin Yang, Xu Yang
2012 Cardiovascular Diagnosis and Therapy  
Due to the increasing efficiency and decreasing cost of NGS, rapid progresses anticipated in the field of CVD research.  ...  In recent years, hundreds of gene loci associated with multiple cardiovascular pathologies and traits have been identified through high-throughput Next-Generation Sequencing (NGS) technology.  ...  Acknowledgements Disclosure: The authors declare no conflict of interest.  ... 
doi:10.3978/j.issn.2223-3652.2012.06.01 pmid:24282707 pmcid:PMC3839151 fatcat:mjjd3sv4ibfybjsr4jv54jn46u

Whole-Exome Sequencing and Homozygosity Analysis Implicate Depolarization-Regulated Neuronal Genes in Autism

Maria H. Chahrour, Timothy W. Yu, Elaine T. Lim, Bulent Ataman, Michael E. Coulter, R. Sean Hill, Christine R. Stevens, Christian R. Schubert, Michael E. Greenberg, Stacey B. Gabriel, Christopher A. Walsh, Daniel H. Geschwind
2012 PLoS Genetics  
We would like to acknowledge the ARRA Autism Sequencing Consortium (AASC) principle investigators (PIs) for the use of the autism case-control datasets: Eric Boerwinkle, Joseph D. Buxbaum, Edwin H.  ...  Schellenberg, and James S. Sutcliffe. We thank Thomas Lehner (NIMH), Adam Felsenfeld (NHGRI), and Patrick Bender (NIMH) for their support and contribution to the AASC project. Author Contributions  ...  Results from variant validation and homozygosity analysis were combined with neuronal activity data to identify candidate autism genes from whole exome sequence. 1000G: 1000 Genomes Project, GMCC: genomic  ... 
doi:10.1371/journal.pgen.1002635 pmid:22511880 pmcid:PMC3325173 fatcat:3ceidxnh45gdrd6vxa6yn3etoe

Towards a molecular characterization of autism spectrum disorders: an exome sequencing and systems approach

J Y An, A S Cristino, Q Zhao, J Edson, S M Williams, D Ravine, J Wray, V M Marshall, A Hunt, A J O Whitehouse, C Claudianos
2014 Translational Psychiatry  
Inherited variants from parents with a broader autism phenotype and de novo variants were found to be significantly associated with ASD.  ...  deficit and hyperactivity disorder and schizophrenia was used in this current study to analyze whole exome sequencing data from an Australian ASD cohort.  ...  Circle plots show the type and localization of filtered DNA variants detected by exome sequence analysis.  ... 
doi:10.1038/tp.2014.38 pmid:24893065 pmcid:PMC4080319 fatcat:tyoihdbmwrfe7klxxmz7vu5dym

Both rare and common genetic variants contribute to autism in the Faroe Islands

Claire S Leblond, Freddy Cliquet, Coralie Carton, Guillaume Huguet, Alexandre Mathieu, Thomas Kergrohen, Julien Buratti, Nathalie Lemière, Laurence Cuisset, Thierry Bienvenu, Anne Boland, Jean-François Deleuze (+7 others)
2019 npj Genomic Medicine  
Data from SNP array and whole exome sequencing revealed that individuals with autism had a higher burden of rare exonic copy-number variants altering autism associated genes (deletions (p = 0.0352) or  ...  In summary, our analysis provides a better understanding of the genetic architecture of autism in isolated populations by highlighting the role of both common and rare gene variants and pointing at new  ...  ), Fabrice de Chaumont for his help with python and Thomas Rolland for his feedback on the revised manuscript.  ... 
doi:10.1038/s41525-018-0075-2 pmid:30675382 pmcid:PMC6341098 fatcat:tnzalhaa5nh3tawkctpxtm3aam

Genome-wide variant analysis of simplex autism families with an integrative clinical-bioinformatics pipeline

Laura T. Jiménez-Barrón, Jason A. O'Rawe, Yiyang Wu, Margaret Yoon, Han Fang, Ivan Iossifov, Gholson J. Lyon
2015 Molecular Case Studies  
Genotyping arrays and whole-genome sequencing were performed on each member, and the resulting sequencing data were analyzed using a variety of available bioinformatics tools.  ...  Our study focuses on the analysis of three simplex autism families consisting of one affected child, unaffected parents, and one unaffected sibling.  ...  The authors would like to thank the Exome Aggregation Consortium and the groups that provided exome variant data for comparison.  ... 
doi:10.1101/mcs.a000422 pmid:27148569 pmcid:PMC4850892 fatcat:gce36ebpwfbxvlvdhpxi7e7jda
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