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Niazi Y, Thomsen H, Smolkova B, Vodickova L, Vodenkova S, Kroupa M, Vymetalkova V, Kazimirova A, Barancokova M, Volkovova K, Staruchova M, Hoffmann P, Nöthen MM, Dušinská M, Musak L, Vodicka P, Hemminki K, Försti A. Genetic variation associated with chromosomal aberration frequency: A genome-wide association study. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2019; 60:17-28. [PMID: 30368896 DOI: 10.1002/em.22236] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/18/2018] [Accepted: 07/03/2018] [Indexed: 02/05/2023]
Abstract
Chromosomal aberrations (CAs) in human peripheral blood lymphocytes (PBL) measured with the conventional cytogenetic assay have been used for human biomonitoring of genotoxic exposure for decades. CA frequency in peripheral blood is a marker of cancer susceptibility. Previous studies have shown associations between genetic variants in metabolic pathway, DNA repair and major mitotic checkpoint genes and CAs. We conducted a genome-wide association study on 576 individuals from the Czech Republic and Slovakia followed by a replication in two different sample sets of 482 (replication 1) and 1288 (replication 2) samples. To have a broad look at the genetic susceptibility associated with CA frequency, the sample sets composed of individuals either differentially exposed to smoking, occupational/environmental hazards, or they were untreated cancer patients. Phenotypes were divided into chromosome- and chromatid-type aberrations (CSAs and CTAs, respectively) and total chromosomal aberrations (CAtot). The arbitrary cutoff point between individuals with high and low CA frequency was 2% for CAtot and 1% for CSA and CTA. The data were analyzed using age, sex, occupation/cancer and smoking history as covariates. Altogether 11 loci reached the P-value of 10-5 in the GWAS. Replication 1 supported the association of rs1383997 (8q13.3) and rs2824215 (21q21.1) in CAtot and rs983889 (5p15.1) in CTA analysis. These loci were found to be associated with genes involved in mitosis, response to environmental and chemical factors and genes involved in syndromes linked to chromosomal abnormalities. Identification of new genetic variants for the frequency of CAs offers prediction tools for cancer risk in future. Environ. Mol. Mutagen. 60:17-28, 2019. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Yasmeen Niazi
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
- Medizinische Fakultät, Universität Heidelberg, Im Neuenheimer Feld 672, 69120, Heidelberg
| | - Hauke Thomsen
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Bozena Smolkova
- Department of Molecular Oncology, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 84505, Bratislava, Slovakia
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, The Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00, Prague, Czech Republic
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University in Prague, Pilsen, Czech Republic
| | - Sona Vodenkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, The Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00, Prague, Czech Republic
- Department of Medical Genetics, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Michal Kroupa
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, The Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University in Prague, Pilsen, Czech Republic
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, The Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00, Prague, Czech Republic
| | - Alena Kazimirova
- Department of Biology, Faculty of Medicine, Slovak Medical University, Limbova 12, 833 03, Bratislava, Slovakia
| | - Magdalena Barancokova
- Department of Biology, Faculty of Medicine, Slovak Medical University, Limbova 12, 833 03, Bratislava, Slovakia
| | - Katarina Volkovova
- Department of Biology, Faculty of Medicine, Slovak Medical University, Limbova 12, 833 03, Bratislava, Slovakia
| | - Marta Staruchova
- Department of Biology, Faculty of Medicine, Slovak Medical University, Limbova 12, 833 03, Bratislava, Slovakia
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, D-53127, Bonn, Germany
- Division of Medical Genetics, Department of Biomedicine, University of Basel, 4003, Basel, Switzerland
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, D-53127, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, D-53127, Bonn, Germany
| | - Maria Dušinská
- Health Effects Laboratory, Department of Environmental Chemistry, NILU-Norwegian Institute for Air Research, Instituttveien 18, 2007, Kjeller, Norway
| | - Ludovit Musak
- Clinic of Occupational Medicine and Toxicology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava and University Hospital Martin, Kollarova 2, 03601, Martin, Slovakia
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, The Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00, Prague, Czech Republic
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University in Prague, Pilsen, Czech Republic
| | - Kari Hemminki
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
- Center of Primary Health Care Research, Clinical Research Center, Lund University, 20502, Malmö, Sweden
| | - Asta Försti
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
- Center of Primary Health Care Research, Clinical Research Center, Lund University, 20502, Malmö, Sweden
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Clinical and molecular characterization of three genomic rearrangements at chromosome 22q13.3 associated with autism spectrum disorder. Psychiatr Genet 2017; 27:23-33. [PMID: 27846046 DOI: 10.1097/ypg.0000000000000151] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVES Chromosome 22q13 is a hot region of genomic rearrangements that may result in deletion, duplication, and translocation, and that may lead to neurodevelopmental disorders in affected patients. MATERIALS AND METHODS We carried out an array-based comparative genomic hybridization analysis to detect copy number variations (CNVs) of genomic DNA in patients with autism spectrum disorders (ASD) who were consecutively recruited into our molecular genetic study of ASD. Karyotyping, fluorescent in-situ hybridization analysis, and real time-quantitative PCR were used for validation tests. RESULTS We completed a genome-wide CNV analysis of 335 patients with ASD from Taiwan. Three unrelated male patients were found to carry three different CNVs at 22q13.3, respectively, including a de novo terminal deletion of ∼106 kb at 22q13.33, a de novo interstitial duplication of ∼1.8 Mb at 22q13.32-q13.33, and a microdeletion of ∼147 kb at 22q13.33. These three CNVs all involved the dosage change of the SHANK3 gene. The last patient also carried a genomic duplication of ∼3.86 Mb at 19q13.42-q13.4 in addition to a microdeletion of ∼147 kb at 22q13.33. His younger sister also carried these two CNVs, but she had developmental delay and other neurological deficits without ASD. These two CNVs were transmitted from their unaffected father, who carried a balanced translocation between chromosome 22q and 19q. CONCLUSION Our data support that recurrent genomic rearrangements at 22q13.3 are part of the genetic landscape of ASD in our patients and changes in SHANK3 dosage are associated with neurodevelopmental disorders. However, the clinical symptoms of patients with 22q13.3 rearrangements can vary depending on other genetic and nongenetic factors, not limited to genes involved in CNVs in this region.
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Chen CH, Chen HI, Chien WH, Li LH, Wu YY, Chiu YN, Tsai WC, Gau SSF. High resolution analysis of rare copy number variants in patients with autism spectrum disorder from Taiwan. Sci Rep 2017; 7:11919. [PMID: 28931914 PMCID: PMC5607249 DOI: 10.1038/s41598-017-12081-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 09/04/2017] [Indexed: 12/27/2022] Open
Abstract
Rare genomic copy number variations (CNVs) (frequency <1%) contribute a part to the genetic underpinnings of autism spectrum disorders (ASD). The study aimed to understand the scope of rare CNV in Taiwanese patients with ASD. We conducted a genome-wide CNV screening of 335 ASD patients (299 males, 36 females) from Taiwan using Affymetrix Genome-Wide Human SNP Array 6.0 and compared the incidence of rare CNV with that of 1093 control subjects (525 males, 568 females). We found a significantly increased global burden of rare CNVs in the ASD group compared to the controls as a whole or when the rare CNVs were classified by the size and types of CNV. Further analysis confirmed the presence of several rare CNVs at regions strongly associated with ASD as reported in the literature in our sample. Additionally, we detected several new private pathogenic CNVs in our samples and five patients carrying two pathogenic CNVs. Our data indicate that rare genomic CNVs contribute a part to the genetic landscape of our ASD patients. These CNVs are highly heterogeneous, and the clinical interpretation of the pathogenic CNVs of ASD is not straightforward in consideration of the incomplete penetrance, varied expressivity, and individual genetic background.
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Affiliation(s)
- Chia-Hsiang Chen
- Department of Psychiatry, Chang Gung Memorial Hospital-Linkou, Taoyuan, Taiwan.,Department and Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - Hsin-I Chen
- Department of Psychiatry, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
| | - Wei-Hsien Chien
- Department of Occupational Therapy, College of Medicine, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Ling-Hui Li
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Yu-Yu Wu
- Department of Psychiatry, Chang Gung Memorial Hospital-Linkou, Taoyuan, Taiwan
| | - Yen-Nan Chiu
- Department of Psychiatry, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
| | - Wen-Che Tsai
- Department of Psychiatry, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
| | - Susan Shur-Fen Gau
- Department of Psychiatry, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan. .,Graduate Institute of Brain and Mind Sciences, National Taiwan University, Taipei, Taiwan. .,Graduate Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan.
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Genetic architecture, epigenetic influence and environment exposure in the pathogenesis of Autism. SCIENCE CHINA-LIFE SCIENCES 2016; 58:958-67. [PMID: 26490976 DOI: 10.1007/s11427-015-4941-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Autism spectrum disorder (ASD) is a spectral neurodevelopment disorder affecting approximately 1% of the population. ASD is characterized by impairments in reciprocal social interaction, communication deficits and restricted patterns of behavior. Multiple factors, including genetic/genomic, epigenetic/epigenomic and environmental, are thought to be necessary for autism development. Recent reviews have provided further insight into the genetic/genomic basis of ASD. It has long been suspected that epigenetic mechanisms, including DNA methylation, chromatin structures and long non-coding RNAs may play important roles in the pathology of ASD. In addition to genetic/genomic alterations and epigenetic/epigenomic influences, environmental exposures have been widely accepted as an important role in autism etiology, among which immune dysregulation and gastrointestinal microbiota are two prominent ones.
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What Do Parents Think about Chromosomal Microarray Testing? A Qualitative Report from Parents of Children with Autism Spectrum Disorders. AUTISM RESEARCH AND TREATMENT 2016; 2016:6852539. [PMID: 27413549 PMCID: PMC4931081 DOI: 10.1155/2016/6852539] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 04/28/2016] [Accepted: 05/18/2016] [Indexed: 11/18/2022]
Abstract
Background. Chromosomal Microarray Analysis (CMA) is increasingly utilized to detect copy number variants among children and families affected with autism spectrum disorders (ASD). However, CMA is controversial due to possible ambiguous test findings, uncertain clinical implications, and other social and legal issues related to the test. Methods. Participants were parents of children with ASD residing in the North Eastern region of North Carolina, USA. We conducted individual, face-to-face interviews with 45 parents and inquired about their perceptions of CMA. Results. Three major themes dominated parents' perceptions of CMA. None of the parents had ever heard of the test before and the majority of the parents postulated positive attitudes toward the test. Parents' motivations in undergoing the test were attributed to finding a potential cause of ASD, to being better prepared for having another affected child, and to helping with future reproductive decisions. Perceived barriers included the cost of testing, risk/pain of CMA testing, and fear of test results. Conclusion. This study contributes to the understanding of psychosocial aspects and cultural influences towards adoption of genetic testing for ASD in clinical practice. Genetic education can aid informed decision-making related to CMA genetic testing among parents of children with ASD.
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Chen SF, Chien YL, Wu CT, Shang CY, Wu YY, Gau SS. Deficits in executive functions among youths with autism spectrum disorders: an age-stratified analysis. Psychol Med 2016; 46:1625-1638. [PMID: 26997535 PMCID: PMC4873936 DOI: 10.1017/s0033291715002238] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 09/24/2015] [Accepted: 09/25/2015] [Indexed: 12/27/2022]
Abstract
BACKGROUND Impaired executive function (EF) is suggested to be one of the core features in individuals with autism spectrum disorders (ASD); however, little is known about whether the extent of worse EF in ASD than typically developing (TD) controls is age-dependent. We used age-stratified analysis to reveal this issue. METHOD We assessed 111 youths with ASD (aged 12.5 ± 2.8 years, male 94.6%) and 114 age-, and sex-matched TD controls with Digit Span and four EF tasks of the Cambridge Neuropsychological Test Automated Battery (CANTAB): Spatial Span (SSP), Spatial Working Memory (SWM), Stockings of Cambridge (SOC), and Intradimensional/Extradimensional Shift Test (I/ED). RESULTS Compared to TD controls, youths with ASD performed poorer on the Digit Span, SWM, SOC, and I/ED tasks. The performance of all the tasks improved with age for both groups. Age-stratified analyses were conducted due to significant age × group interactions in visuospatial planning (SOC) and set-shifting (I/ED) and showed that poorer performance on these two tasks in ASD than TD controls was found only in the child (aged 8-12 years) rather than the adolescent (aged 13-18 years) group. By contrast, youths with ASD had impaired working memory, regardless of age. The increased magnitude of group difference in visuospatial planning (SOC) with increased task demands differed between the two age groups but no age moderating effect on spatial working memory. CONCLUSIONS Our findings support deficits in visuospatial working memory and planning in youths with ASD; however, worse performance in set-shifting may only be demonstrated in children with ASD.
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Affiliation(s)
- S.-F. Chen
- Department of Psychiatry,
National Taiwan University Hospital & College of
Medicine, Taipei, Taiwan
- Department of Psychiatry,
Taipei Tzu Chi General Hospital, Buddhist Tzu Chi
Medical Foundation, Taipei, Taiwan
- School of Occupational Therapy,
College of Medicine, National Taiwan
University, Taipei, Taiwan
| | - Y.-L. Chien
- Department of Psychiatry,
National Taiwan University Hospital & College of
Medicine, Taipei, Taiwan
- Graduate Institute of Clinical Medicine,
College of Medicine, National Taiwan
University, Taipei, Taiwan
| | - C.-T. Wu
- Department of Psychiatry,
National Taiwan University Hospital & College of
Medicine, Taipei, Taiwan
- School of Occupational Therapy,
College of Medicine, National Taiwan
University, Taipei, Taiwan
| | - C.-Y. Shang
- Department of Psychiatry,
National Taiwan University Hospital & College of
Medicine, Taipei, Taiwan
| | - Y.-Y. Wu
- Department of Psychiatry,
Chang Gung Memorial Hospital-Linkou,
Taoyuan, Taiwan
| | - S. S. Gau
- Department of Psychiatry,
National Taiwan University Hospital & College of
Medicine, Taipei, Taiwan
- School of Occupational Therapy,
College of Medicine, National Taiwan
University, Taipei, Taiwan
- Graduate Institute of Clinical Medicine,
College of Medicine, National Taiwan
University, Taipei, Taiwan
- Department of Psychology,
Graduate Institute of Brain and Mind Sciences, Graduate
Institute of Epidemiology and Preventive Medicine, National
Taiwan University, Taipei, Taiwan
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Yang L, Faraone SV, Zhang-James Y. Autism spectrum disorder traits in Slc9a9 knock-out mice. Am J Med Genet B Neuropsychiatr Genet 2016; 171B:363-76. [PMID: 26755066 DOI: 10.1002/ajmg.b.32415] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 12/22/2015] [Indexed: 11/09/2022]
Abstract
Autism spectrum disorders (ASDs) are a group of neurodevelopmental disorders which begin in childhood and persist into adulthood. They cause lifelong impairments and are associated with substantial burdens to patients, families, and society. Genetic studies have implicated the sodium/proton exchanger (NHE) nine gene, Slc9a9, to ASDs and attention-deficit/hyperactivity disorder(ADHD). Slc9a9 encodes, NHE9, a membrane protein of the late recycling endosomes. The recycling endosome plays an important role in synapse development and plasticity by regulating the trafficking of membrane neurotransmitter receptors and transporters. Here we tested the hypothesis that Slc9a9 knock-out (KO) mice would show ADHD-like and ASD-like traits. Ultrasonic vocalization (USV) recording showed that Slc9a9 KO mice emitted fewer calls and had shorter call durations, which suggest communication impairment. Slc9a9 KO mice lacked a preference for social novelty, but did not show deficits in social approach; Slc9a9 KO mice spent more time self-grooming, an indicator for restricted and repetitive behavior. We did not observe hyperactivity or other behavior impairments which are commonly comorbid with ASDs in human, such as anxiety-like behavior. Our study is the first animal behavior study that links Slc9a9 to ASDs. By eliminatingNHE9 activity, it provides strong evidence that lack of Slc9a9leads to ASD-like behaviors in mice and provides the field with a new mouse model of ASDs.
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Affiliation(s)
- Lina Yang
- Departments of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, New York
| | - Stephen V Faraone
- Departments of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, New York.,Departments of Psychiatry, SUNY Upstate Medical University, Syracuse, New York.,K.G. Jebsen Centre for Research on Neuropsychiatric Disorders, University of Bergen, Bergen, Norway
| | - Yanli Zhang-James
- Departments of Psychiatry, SUNY Upstate Medical University, Syracuse, New York
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Yin CL, Chen HI, Li LH, Chien YL, Liao HM, Chou MC, Chou WJ, Tsai WC, Chiu YN, Wu YY, Lo CZ, Wu JY, Chen YT, Gau SSF. Genome-wide analysis of copy number variations identifies PARK2 as a candidate gene for autism spectrum disorder. Mol Autism 2016; 7:23. [PMID: 27042285 PMCID: PMC4818409 DOI: 10.1186/s13229-016-0087-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 03/22/2016] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Autism spectrum disorder (ASD) is an early-onset neurodevelopmental disorder with complex genetic underpinning in its etiology. Copy number variations (CNVs) as one of the genetic factors associated with ASD have been addressed in recent genome-wide association studies (GWAS). However, the significance of CNV has not been well investigated in non-Caucasian ASD population. METHODS To identify the pathogenic CNVs responsible for ASD in Han Chinese, we performed a segment-based GWAS of CNV in 335 ASD cases and 1093 healthy controls using Affymetrix single nucleotide polymorphism (SNP) array by focusing on case-specific CNVs. PARK2 was one of the important genes with several case-specific regions overlapped on it. The findings were validated in the initial screen sample set and replicated in another sample set by real-time quantitative PCR (qPCR). RESULTS A total of six CNVs at 6q26 that spanned different exons of PARK2 were identified. The PARK2 expression level was down-regulated at exon-dependent manner in cases with either deletion or duplication. The result revealed that the gene function might be disrupted by exonic deletion and duplication. We also observed that the ASD case with exonic duplication demonstrated a more severe interference of PARK2 expression and the clinical feature than the ones with deletion at the exons 2-4 of the PARK2 gene. CONCLUSIONS Our finding provides evidence to support that CNVs affecting PARK2 function might contribute to genetic etiology of a proportion of cases with ASD. The intriguing results of this work warrant further study on characterizing the functional impact of various exonic CNVs on the PARK2 gene. TRIAL REGISTRATION ClinicalTrials.gov NCT00494754.
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Affiliation(s)
- Chia-Lin Yin
- Department of Psychiatry, National Taiwan University Hospital and College of Medicine, No. 7, Chung-Shan South Road, Taipei, 10002 Taiwan.,Graduate Institute of Brain Sciences, National Yang-Ming University, Taipei, 11221 Taiwan
| | - Hsin-I Chen
- Department of Psychiatry, National Taiwan University Hospital and College of Medicine, No. 7, Chung-Shan South Road, Taipei, 10002 Taiwan
| | - Ling-Hui Li
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529 Taiwan
| | - Yi-Ling Chien
- Department of Psychiatry, National Taiwan University Hospital and College of Medicine, No. 7, Chung-Shan South Road, Taipei, 10002 Taiwan
| | - Hsiao-Mei Liao
- Department of Psychiatry, National Taiwan University Hospital and College of Medicine, No. 7, Chung-Shan South Road, Taipei, 10002 Taiwan.,Section on Molecular Neurobiology, National Institute of Mental Health, National Institutes of Health, Bethesda, 20892 USA
| | - Miao Chun Chou
- Department of Child Psychiatry, Chang Gung Memorial Hospital-Kaohsiung Medical Center, Chang Gung University College of Medicine, Kaohsiung, 83301 Taiwan
| | - Wen-Jiun Chou
- Department of Child Psychiatry, Chang Gung Memorial Hospital-Kaohsiung Medical Center, Chang Gung University College of Medicine, Kaohsiung, 83301 Taiwan
| | - Wen-Che Tsai
- Department of Psychiatry, National Taiwan University Hospital and College of Medicine, No. 7, Chung-Shan South Road, Taipei, 10002 Taiwan
| | - Yen-Nan Chiu
- Department of Psychiatry, National Taiwan University Hospital and College of Medicine, No. 7, Chung-Shan South Road, Taipei, 10002 Taiwan
| | - Yu-Yu Wu
- Department of Child Psychiatry, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, 33302 Taiwan
| | - Chen-Zen Lo
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529 Taiwan
| | - Jer-Yuarn Wu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529 Taiwan
| | - Yuan-Tsong Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529 Taiwan
| | - Susan Shur-Fen Gau
- Department of Psychiatry, National Taiwan University Hospital and College of Medicine, No. 7, Chung-Shan South Road, Taipei, 10002 Taiwan
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Vijayakumar NT, Judy MV. Autism spectrum disorders: Integration of the genome, transcriptome and the environment. J Neurol Sci 2016; 364:167-76. [PMID: 27084239 DOI: 10.1016/j.jns.2016.03.026] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 02/18/2016] [Accepted: 03/10/2016] [Indexed: 10/22/2022]
Abstract
Autism spectrum disorders denote a series of lifelong neurodevelopmental conditions characterized by an impaired social communication profile and often repetitive, stereotyped behavior. Recent years have seen the complex genetic architecture of the disease being progressively unraveled with advancements in gene finding technology and next generation sequencing methods. However, a complete elucidation of the molecular mechanisms behind autism is necessary for potential diagnostic and therapeutic applications. A multidisciplinary approach should be adopted where the focus is not only on the 'genetics' of autism but also on the combinational roles of epigenetics, transcriptomics, immune system disruption and environmental factors that could all influence the etiopathogenesis of the disease. ASD is a clinically heterogeneous disorder with great genetic complexity; only through an integrated multidimensional effort can modern autism research progress further.
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Affiliation(s)
- N Thushara Vijayakumar
- Department of Computer Science & IT., Amrita School of Arts & Sciences, Amrita Vishwa Vidyapeetham, Amrita University, Kochi, India.
| | - M V Judy
- Department of Computer Science & IT., Amrita School of Arts & Sciences, Amrita Vishwa Vidyapeetham, Amrita University, Kochi, India
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Kuo PH, Chuang LC, Su MH, Chen CH, Chen CH, Wu JY, Yen CJ, Wu YY, Liu SK, Chou MC, Chou WJ, Chiu YN, Tsai WC, Gau SSF. Genome-Wide Association Study for Autism Spectrum Disorder in Taiwanese Han Population. PLoS One 2015; 10:e0138695. [PMID: 26398136 PMCID: PMC4580585 DOI: 10.1371/journal.pone.0138695] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 09/02/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Autism spectrum disorder (ASD) is a neurodevelopmental disorder with strong genetic components. Several recent genome-wide association (GWA) studies in Caucasian samples have reported a number of gene regions and loci correlated with the risk of ASD--albeit with very little consensus across studies. METHODS A two-stage GWA study was employed to identify common genetic variants for ASD in the Taiwanese Han population. The discovery stage included 315 patients with ASD and 1,115 healthy controls, using the Affymetrix SNP array 6.0 platform for genotyping. Several gene regions were then selected for fine-mapping and top markers were examined in extended samples. Single marker, haplotype, gene-based, and pathway analyses were conducted for associations. RESULTS Seven SNPs had p-values ranging from 3.4~9.9*10-6, but none reached the genome-wide significant level. Five of them were mapped to three known genes (OR2M4, STYK1, and MNT) with significant empirical gene-based p-values in OR2M4 (p = 3.4*10(-5)) and MNT (p = 0.0008). Results of the fine-mapping study showed single-marker associations in the GLIS1 (rs12082358 and rs12080993) and NAALADL2 (rs3914502 and rs2222447) genes, and gene-based associations for the OR2M3-OR2T5 (olfactory receptor genes, p = 0.02), and GLIPR1/KRR1 gene regions (p = 0.015). Pathway analyses revealed important pathways for ASD, such as olfactory and G protein-coupled receptors signaling pathways. CONCLUSIONS We reported Taiwanese Han specific susceptibility genes and variants for ASD. However, further replication in other Asian populations is warranted to validate our findings. Investigation in the biological functions of our reported genetic variants might also allow for better understanding on the underlying pathogenesis of autism.
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Affiliation(s)
- Po-Hsiu Kuo
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
- Research Center for Genes, Environment and Human Health, National Taiwan University, Taipei, Taiwan
| | - Li-Chung Chuang
- Department of Nursing, Cardinal Tien Junior College of Healthcare & Management, I-Lan, Taiwan
| | - Mei-Hsin Su
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Chia-Hsiang Chen
- Department of Psychiatry, Chang Gung Memorial Hospital-Linkou, Taoyuan, Taiwan
- Department and Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - Chien-Hsiun Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Jer-Yuarn Wu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Chung-Jen Yen
- Department of Internal Medicine, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
| | - Yu-Yu Wu
- Department of Psychiatry, Chang Gung Memorial Hospital-Linkou, Taoyuan, Taiwan
| | - Shih-Kai Liu
- Department of Child and Adolescent Psychiatry, Taoyaun Psychiatric Center, Ministry of Health and Welfare, Taoyuan, Taiwan
| | - Miao-Chun Chou
- Department of Child Psychiatry, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Wen-Jiun Chou
- Department of Child Psychiatry, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Yen-Nan Chiu
- Department of Psychiatry, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
| | - Wen-Che Tsai
- Department of Psychiatry, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
| | - Susan Shur-Fen Gau
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
- Department of Psychiatry, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
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11
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Liu X, Shimada T, Otowa T, Wu YY, Kawamura Y, Tochigi M, Iwata Y, Umekage T, Toyota T, Maekawa M, Iwayama Y, Suzuki K, Kakiuchi C, Kuwabara H, Kano Y, Nishida H, Sugiyama T, Kato N, Chen CH, Mori N, Yamada K, Yoshikawa T, Kasai K, Tokunaga K, Sasaki T, Gau SSF. Genome-wide Association Study of Autism Spectrum Disorder in the East Asian Populations. Autism Res 2015; 9:340-9. [PMID: 26314684 DOI: 10.1002/aur.1536] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 07/07/2015] [Accepted: 07/29/2015] [Indexed: 12/29/2022]
Abstract
Autism spectrum disorder is a heterogeneous neurodevelopmental disorder with strong genetic basis. To identify common genetic variations conferring the risk of ASD, we performed a two-stage genome-wide association study using ASD family and healthy control samples obtained from East Asian populations. A total of 166 ASD families (n = 500) and 642 healthy controls from the Japanese population were used as the discovery cohort. Approximately 900,000 single nucleotide polymorphisms (SNPs) were genotyped using Affymetrix Genome-Wide Human SNP array 6.0 chips. In the replication stage, 205 Japanese ASD cases and 184 healthy controls, as well as 418 Chinese Han trios (n = 1,254), were genotyped by TaqMan platform. Case-control analysis, family based association test, and transmission/disequilibrium test (TDT) were then conducted to test the association. In the discovery stage, significant associations were suggested for 14 loci, including 5 known ASD candidate genes: GPC6, JARID2, YTHDC2, CNTN4, and CSMD1. In addition, significant associations were identified for several novel genes with intriguing functions, such as JPH3, PTPRD, CUX1, and RIT2. After a meta-analysis combining the Japanese replication samples, the strongest signal was found at rs16976358 (P = 6.04 × 10(-7)), which is located near the RIT2 gene. In summary, our results provide independent support to known ASD candidate genes and highlight a number of novel genes warranted to be further investigated in a larger sample set in an effort to improve our understanding of the genetic basis of ASD.
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Affiliation(s)
- Xiaoxi Liu
- Department of Human Genetics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Takafumi Shimada
- Department of Neuropsychiatry, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Takeshi Otowa
- Department of Neuropsychiatry, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Yu-Yu Wu
- Department of Psychiatry, Chang Gung Memorial Hospital-Linkou, Taoyuan, Taiwan
| | - Yoshiya Kawamura
- Department of Psychiatry, Sakae Seijinkai Hospital, Kanagawa, Japan
| | - Mamoru Tochigi
- Department of Neuropsychiatry, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Yasuhide Iwata
- Department of Psychiatry and Neurology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Tadashi Umekage
- Department of Neuropsychiatry, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Tomoko Toyota
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Wako, Saitama, Japan
| | - Motoko Maekawa
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Wako, Saitama, Japan
| | - Yoshimi Iwayama
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Wako, Saitama, Japan
| | - Katsuaki Suzuki
- Department of Psychiatry and Neurology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Chihiro Kakiuchi
- Department of Neuropsychiatry, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Hitoshi Kuwabara
- Department of Child Psychiatry, University of Tokyo Hospital, Tokyo, Japan
| | - Yukiko Kano
- Department of Child Psychiatry, University of Tokyo Hospital, Tokyo, Japan
| | - Hisami Nishida
- Asunaro Hospital for Child and Adolescent Psychiatry, Tsu, Japan
| | - Toshiro Sugiyama
- Department of Child and Adolescent Psychiatry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Nobumasa Kato
- Department of Psychiatry, Graduate School of Medicine, University of Showa, Tokyo, Japan
| | - Chia-Hsiang Chen
- Department of Psychiatry, Chang Gung Memorial Hospital-Linkou, Taoyuan, Taiwan.,Department and Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - Norio Mori
- Department of Child and Adolescent Psychiatry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Kazuo Yamada
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Wako, Saitama, Japan
| | - Takeo Yoshikawa
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Wako, Saitama, Japan
| | - Kiyoto Kasai
- Department of Neuropsychiatry, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Tsukasa Sasaki
- Department of Physical and Health Education, Graduate School of Education, The University of Tokyo, Tokyo, Japan
| | - Susan Shur-Fen Gau
- Department of Psychiatry, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
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