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Warrier V, Chakrabarti B, Murphy L, Chan A, Craig I, Mallya U, Lakatošová S, Rehnstrom K, Peltonen L, Wheelwright S, Allison C, Fisher SE, Baron-Cohen S. A Pooled Genome-Wide Association Study of Asperger Syndrome. PLoS One 2015; 10:e0131202. [PMID: 26176695 PMCID: PMC4503355 DOI: 10.1371/journal.pone.0131202] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 05/30/2015] [Indexed: 12/27/2022] Open
Abstract
Asperger Syndrome (AS) is a neurodevelopmental condition characterized by impairments in social interaction and communication, alongside the presence of unusually repetitive, restricted interests and stereotyped behaviour. Individuals with AS have no delay in cognitive and language development. It is a subset of Autism Spectrum Conditions (ASC), which are highly heritable and has a population prevalence of approximately 1%. Few studies have investigated the genetic basis of AS. To address this gap in the literature, we performed a genome-wide pooled DNA association study to identify candidate loci in 612 individuals (294 cases and 318 controls) of Caucasian ancestry, using the Affymetrix GeneChip Human Mapping version 6.0 array. We identified 11 SNPs that had a p-value below 1x10-5. These SNPs were independently genotyped in the same sample. Three of the SNPs (rs1268055, rs7785891 and rs2782448) were nominally significant, though none remained significant after Bonferroni correction. Two of our top three SNPs (rs7785891 and rs2782448) lie in loci previously implicated in ASC. However, investigation of the three SNPs in the ASC genome-wide association dataset from the Psychiatric Genomics Consortium indicated that these three SNPs were not significantly associated with ASC. The effect sizes of the variants were modest, indicating that our study was not sufficiently powered to identify causal variants with precision.
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Affiliation(s)
- Varun Warrier
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (VW); (SB-C)
| | - Bhismadev Chakrabarti
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
- School of Psychology and Clinical Language Sciences, Centre for Integrative Neuroscience and Neurodynamics, University of Reading, Reading, United Kingdom
| | - Laura Murphy
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
| | - Allen Chan
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
| | - Ian Craig
- MRC Centre for Social, Genetic and Developmental Psychiatry, King’s College London, Institute of Psychiatry, London, United Kingdom
| | - Uma Mallya
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
| | - Silvia Lakatošová
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
| | - Karola Rehnstrom
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Leena Peltonen
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Sally Wheelwright
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
| | - Carrie Allison
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
| | - Simon E. Fisher
- Max Planck Institute for Psycholinguistics, 6500 AH, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Simon Baron-Cohen
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
- CLASS Clinic, Cambridgeshire and Peterborough NHS Foundation Trust (CPFT), Cambridge, United Kingdom
- * E-mail: (VW); (SB-C)
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Di Napoli A, Warrier V, Baron-Cohen S, Chakrabarti B. Genetic variant rs17225178 in the ARNT2 gene is associated with Asperger Syndrome. Mol Autism 2015; 6:9. [PMID: 25745553 PMCID: PMC4350913 DOI: 10.1186/s13229-015-0009-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 02/12/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Autism Spectrum Conditions (ASC) are neurodevelopmental conditions characterized by difficulties in communication and social interaction, alongside unusually repetitive behaviours and narrow interests. Asperger Syndrome (AS) is one subgroup of ASC and differs from classic autism in that in AS there is no language or general cognitive delay. Genetic, epigenetic and environmental factors are implicated in ASC and genes involved in neural connectivity and neurodevelopment are good candidates for studying the susceptibility to ASC. The aryl-hydrocarbon receptor nuclear translocator 2 (ARNT2) gene encodes a transcription factor involved in neurodevelopmental processes, neuronal connectivity and cellular responses to hypoxia. A mutation in this gene has been identified in individuals with ASC and single nucleotide polymorphisms (SNPs) have been nominally associated with AS and autistic traits in previous studies. METHODS In this study, we tested 34 SNPs in ARNT2 for association with AS in 118 cases and 412 controls of Caucasian origin. P values were adjusted for multiple comparisons, and linkage disequilibrium (LD) among the SNPs analysed was calculated in our sample. Finally, SNP annotation allowed functional and structural analyses of the genetic variants in ARNT2. We tested the replicability of our result using the genome-wide association studies (GWAS) database of the Psychiatric Genomics Consortium (PGC). RESULTS We report statistically significant association of rs17225178 with AS. This SNP modifies transcription factor binding sites and regions that regulate the chromatin state in neural cell lines. It is also included in a LD block in our sample, alongside other genetic variants that alter chromatin regulatory regions in neural cells. CONCLUSIONS These findings demonstrate that rs17225178 in the ARNT2 gene is associated with AS and support previous studies that pointed out an involvement of this gene in the predisposition to ASC.
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Affiliation(s)
- Agnese Di Napoli
- Department of Psychiatry, Autism Research Centre, University of Cambridge, Douglas House, 18B Trumpington Road, Cambridge, CB2 8AH UK
| | - Varun Warrier
- Department of Psychiatry, Autism Research Centre, University of Cambridge, Douglas House, 18B Trumpington Road, Cambridge, CB2 8AH UK
| | - Simon Baron-Cohen
- Department of Psychiatry, Autism Research Centre, University of Cambridge, Douglas House, 18B Trumpington Road, Cambridge, CB2 8AH UK ; Cambridgeshire and Peterborough NHS Foundation Trust, CLASS Clinic, Cambridge, UK
| | - Bhismadev Chakrabarti
- Centre for Integrative Neuroscience and Neurodynamics, School of Psychology and Clinical Language Sciences, University of Reading, Reading, UK
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Di Napoli A, Warrier V, Baron-Cohen S, Chakrabarti B. Genetic variation in the oxytocin receptor (OXTR) gene is associated with Asperger Syndrome. Mol Autism 2014; 5:48. [PMID: 25264479 PMCID: PMC4175274 DOI: 10.1186/2040-2392-5-48] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 08/27/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Autism Spectrum Conditions (ASC) are a group of neurodevelopmental conditions characterized by impairments in communication and social interaction, alongside unusually repetitive behaviors and narrow interests. ASC are highly heritable and have complex patterns of inheritance where multiple genes are involved, alongside environmental and epigenetic factors. Asperger Syndrome (AS) is a subgroup of these conditions, where there is no history of language or cognitive delay. Animal models suggest a role for oxytocin (OXT) and oxytocin receptor (OXTR) genes in social-emotional behaviors, and several studies indicate that the oxytocin/oxytocin receptor system is altered in individuals with ASC. Previous studies have reported associations between genetic variations in the OXTR gene and ASC. METHODS The present study tested for an association between nine single nucleotide polymorphisms (SNPs) in the OXTR gene and AS in 530 individuals of Caucasian origin, using SNP association test and haplotype analysis. RESULTS There was a significant association between rs2268493 in OXTR and AS. Multiple haplotypes that include this SNP (rs2268493-rs2254298, rs2268490-rs2268493-rs2254298, rs2268493-rs2254298-rs53576, rs237885-rs2268490-rs2268493-rs2254298, rs2268490-rs2268493-rs2254298-rs53576) were also associated with AS. rs2268493 has been previously associated with ASC and putatively alters several transcription factor-binding sites and regulates chromatin states, either directly or through other variants in linkage disequilibrium (LD). CONCLUSIONS This study reports a significant association of the sequence variant rs2268493 in the OXTR gene and associated haplotypes with AS.
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Affiliation(s)
- Agnese Di Napoli
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Douglas House, 18B Trumpington Road, Cambridge, CB2 8AH UK
| | - Varun Warrier
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Douglas House, 18B Trumpington Road, Cambridge, CB2 8AH UK
| | - Simon Baron-Cohen
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Douglas House, 18B Trumpington Road, Cambridge, CB2 8AH UK ; Cambridgeshire and Peterborough NHS Foundation Trust, CLASS Clinic, Cambridge, Elizabeth House, Fulbourn Hospital, Cambridge, CB21 5EF UK
| | - Bhismadev Chakrabarti
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Douglas House, 18B Trumpington Road, Cambridge, CB2 8AH UK ; Centre for Integrative Neurosciences and Neurodynamics, School of Psychology and Clinical Language Sciences, University of Reading, Reading, RG6 6AL UK
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Baron-Cohen S, Murphy L, Chakrabarti B, Craig I, Mallya U, Lakatošová S, Rehnstrom K, Peltonen L, Wheelwright S, Allison C, Fisher SE, Warrier V. A genome wide association study of mathematical ability reveals an association at chromosome 3q29, a locus associated with autism and learning difficulties: a preliminary study. PLoS One 2014; 9:e96374. [PMID: 24801482 PMCID: PMC4011843 DOI: 10.1371/journal.pone.0096374] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Accepted: 04/04/2014] [Indexed: 12/14/2022] Open
Abstract
Mathematical ability is heritable, but few studies have directly investigated its molecular genetic basis. Here we aimed to identify specific genetic contributions to variation in mathematical ability. We carried out a genome wide association scan using pooled DNA in two groups of U.K. samples, based on end of secondary/high school national academic exam achievement: high (n = 419) versus low (n = 183) mathematical ability while controlling for their verbal ability. Significant differences in allele frequencies between these groups were searched for in 906,600 SNPs using the Affymetrix GeneChip Human Mapping version 6.0 array. After meeting a threshold of p<1.5×10−5, 12 SNPs from the pooled association analysis were individually genotyped in 542 of the participants and analyzed to validate the initial associations (lowest p-value 1.14 ×10−6). In this analysis, one of the SNPs (rs789859) showed significant association after Bonferroni correction, and four (rs10873824, rs4144887, rs12130910 rs2809115) were nominally significant (lowest p-value 3.278 × 10−4). Three of the SNPs of interest are located within, or near to, known genes (FAM43A, SFT2D1, C14orf64). The SNP that showed the strongest association, rs789859, is located in a region on chromosome 3q29 that has been previously linked to learning difficulties and autism. rs789859 lies 1.3 kbp downstream of LSG1, and 700 bp upstream of FAM43A, mapping within the potential promoter/regulatory region of the latter. To our knowledge, this is only the second study to investigate the association of genetic variants with mathematical ability, and it highlights a number of interesting markers for future study.
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Affiliation(s)
- Simon Baron-Cohen
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridgeshire, United Kingdom
- CLASS Clinic, Cambridgeshire and Peterborough NHS Foundation Trust (CPFT), Cambridgeshire, United Kingdom
- * E-mail: (VW); (SBC)
| | - Laura Murphy
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridgeshire, United Kingdom
| | - Bhismadev Chakrabarti
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridgeshire, United Kingdom
- School of Psychology and Clinical Language Sciences, Centre for Integrative Neuroscience and Neurodynamics, University of Reading, Reading, United Kingdom
| | - Ian Craig
- MRC Centre for Social, Genetic and Developmental Psychiatry, King's College London, Institute of Psychiatry, London, United Kingdom
| | - Uma Mallya
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridgeshire, United Kingdom
| | - Silvia Lakatošová
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridgeshire, United Kingdom
| | - Karola Rehnstrom
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Leena Peltonen
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Sally Wheelwright
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridgeshire, United Kingdom
| | - Carrie Allison
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridgeshire, United Kingdom
| | - Simon E. Fisher
- Max Planck Institute for Psycholinguistics, 6500 AH Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Varun Warrier
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridgeshire, United Kingdom
- * E-mail: (VW); (SBC)
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Durdiaková J, Warrier V, Baron-Cohen S, Chakrabarti B. Single nucleotide polymorphism rs6716901 in SLC25A12 gene is associated with Asperger syndrome. Mol Autism 2014; 5:25. [PMID: 24679184 PMCID: PMC3973607 DOI: 10.1186/2040-2392-5-25] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 03/20/2014] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Autism Spectrum Conditions (ASC) are a group of developmental conditions which affect communication, social interactions and behaviour. Mitochondrial oxidative dysfunction has been suggested as a mechanism of autism based on the results of multiple genetic association and expression studies. SLC25A12 is a gene encoding a calcium-binding carrier protein that localizes to the mitochondria and is involved in the exchange of aspartate for glutamate in the inner membrane of the mitochondria regulating the cytosolic redox state. rs2056202 SNP in this gene has previously been associated with ASC. SNPs rs6716901 and rs3765166 analysed in this study have not been previously explored in association with AS. METHODS We genotyped three SNPs (rs2056202, rs3765166, and rs6716901) in SLC25A12 in n?=?117 individuals with Asperger syndrome (AS) and n?=?426 controls, all of Caucasian ancestry. RESULTS rs6716901 showed significant association with AS (P?=?0.008) after correcting for multiple testing. We did not replicate the previously identified association between rs2056202 and AS in our sample. Similarly, rs3765166 (P?=?0.11) showed no significant association with AS. CONCLUSION The present study, in combination with previous studies, provides evidence for SLC25A12 as involved in the etiology of AS. Further cellular and molecular studies are required to elucidate the role of this gene in ASC.
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Affiliation(s)
| | | | - Simon Baron-Cohen
- Autism Research Centre, Department of Psychiatry, University of Cambridge, 18b Trumpington Road, Cambridge CB2 8AH, UK.
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Warrier V, Baron-Cohen S, Chakrabarti B. Genetic variation in GABRB3 is associated with Asperger syndrome and multiple endophenotypes relevant to autism. Mol Autism 2013; 4:48. [PMID: 24321478 PMCID: PMC3903107 DOI: 10.1186/2040-2392-4-48] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 10/31/2013] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Autism spectrum conditions (ASC) are associated with deficits in social interaction and communication, alongside repetitive, restricted, and stereotyped behavior. ASC is highly heritable. The gamma-aminobutyric acid (GABA)-ergic system has been associated consistently with atypicalities in autism, in both genetic association and expression studies. A key component of the GABA-ergic system is encoded by the GABRB3 gene, which has been previously implicated both in ASC and in individual differences in empathy. METHODS In this study, 45 genotyped single nucleotide polymorphisms (SNPs) within GABRB3 were tested for association with Asperger syndrome (AS), and related quantitative traits measured through the following tests: the Empathy Quotient (EQ), the Autism Spectrum Quotient (AQ), the Systemizing Quotient-Revised (SQ-R), the Embedded Figures Test (EFT), the Reading the Mind in the Eyes Test (RMET), and the Mental Rotation Test (MRT). Two-loci, three-loci, four-loci haplotype analyses, and one seven-loci haplotype analysis were also performed in the AS case-control sample. RESULTS Three SNPs (rs7180158, rs7165604, rs12593579) were significantly associated with AS, and two SNPs (rs9806546, rs11636966) were significantly associated with EQ. Two SNP-SNP pairs, rs12438141-rs1035751 and rs12438141-rs7179514, showed significant association with variation in the EFT scores. One SNP-SNP pair, rs7174437-rs1863455, was significantly associated with variation in the MRT scores. Additionally, a few haplotypes, including a 19 kb genomic region that formed a linkage disequilibrium (LD) block in our sample and contained several nominally significant SNPs, were found to be significantly associated with AS. CONCLUSION The current study confirms the role of GABRB3 as an important candidate gene in both ASC and normative variation in related endophenotypes.
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Affiliation(s)
- Varun Warrier
- Department of Psychiatry, Autism Research Centre, University of Cambridge, Cambridgeshire, UK.
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