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Yang Q, Cheng C, Wang Z, Zhang X, Zhao J. Interaction between Risk Single-Nucleotide Polymorphisms of Developmental Dyslexia and Parental Education on Reading Ability: Evidence for Differential Susceptibility Theory. Behav Sci (Basel) 2024; 14:507. [PMID: 38920839 PMCID: PMC11201191 DOI: 10.3390/bs14060507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 06/11/2024] [Accepted: 06/13/2024] [Indexed: 06/27/2024] Open
Abstract
While genetic and environmental factors have been shown as predictors of children's reading ability, the interaction effects of identified genetic risk susceptibility and the specified environment for reading ability have rarely been investigated. The current study assessed potential gene-environment (G×E) interactions on reading ability in 1477 school-aged children. The gene-environment interactions on character recognition were investigated by an exploratory analysis between the risk single-nucleotide polymorphisms (SNPs), which were discovered by previous genome-wide association studies of developmental dyslexia (DD), and parental education (PE). The re-parameterized regression analysis suggested that this G×E interaction conformed to the strong differential susceptibility model. The results showed that rs281238 exhibits a significant interaction with PE on character recognition. Children with the "T" genotype profited from high PE, whereas they performed worse in low PE environments, but "CC" genotype children were not malleable in different PE environments. This study provided initial evidence for how the significant SNPs in developmental dyslexia GWA studies affect children's reading performance by interacting with the environmental factor of parental education.
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Affiliation(s)
| | | | | | | | - Jingjing Zhao
- School of Psychology, Shaanxi Normal University, 199 South Chang’an Road, Xi’an 710062, China; (Q.Y.); (C.C.); (Z.W.); (X.Z.)
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2
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Church JA, Grigorenko EL, Fletcher JM. The Role of Neural and Genetic Processes in Learning to Read and Specific Reading Disabilities: Implications for Instruction. READING RESEARCH QUARTERLY 2023; 58:203-219. [PMID: 37456924 PMCID: PMC10348696 DOI: 10.1002/rrq.439] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 06/29/2021] [Indexed: 07/18/2023]
Abstract
To learn to read, the brain must repurpose neural systems for oral language and visual processing to mediate written language. We begin with a description of computational models for how alphabetic written language is processed. Next, we explain the roles of a dorsal sublexical system in the brain that relates print and speech, a ventral lexical system that develops the visual expertise for rapid orthographic processing at the word level, and the role of cognitive control networks that regulate attentional processes as children read. We then use studies of children, adult illiterates learning to read, and studies of poor readers involved in intervention, to demonstrate the plasticity of these neural networks in development and in relation to instruction. We provide a brief overview of the rapid increase in the field's understanding and technology for assessing genetic influence on reading. Family studies of twins have shown that reading skills are heritable, and molecular genetic studies have identified numerous regions of the genome that may harbor candidate genes for the heritability of reading. In selected families, reading impairment has been associated with major genetic effects, despite individual gene contributions across the broader population that appear to be small. Neural and genetic studies do not prescribe how children should be taught to read, but these studies have underscored the critical role of early intervention and ongoing support. These studies also have highlighted how structured instruction that facilitates access to the sublexical components of words is a critical part of training the brain to read.
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Affiliation(s)
| | - Elena L Grigorenko
- University of Houston, Texas, USA; Baylor College of Medicine, Houston, Texas, USA; and St. Petersburg State University, Russia
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3
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Wang Z, Zhao S, Zhang L, Yang Q, Cheng C, Ding N, Zhu Z, Shu H, Liu C, Zhao J. A genome-wide association study identifies a new variant associated with word reading fluency in Chinese children. GENES, BRAIN, AND BEHAVIOR 2023; 22:e12833. [PMID: 36514817 PMCID: PMC9994172 DOI: 10.1111/gbb.12833] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 11/20/2022] [Accepted: 11/29/2022] [Indexed: 12/15/2022]
Abstract
Reading disability exhibited defects in different cognitive domains, including word reading fluency, word reading accuracy, phonological awareness, rapid automatized naming and morphological awareness. To identify the genetic basis of Chinese reading disability, we conducted a genome-wide association study (GWAS) of the cognitive traits related to Chinese reading disability in 2284 unrelated Chinese children. Among the traits analyzed in the present GWAS, we detected one genome-wide significant association (p < 5 × 10-8 ) on word reading fluency for one SNP on 4p16.2, within EVC genes (rs6446395, p = 7.33 × 10-10 ). Rs6446395 also showed significant association with Chinese character reading accuracy (p = 2.95 × 10-4 ), phonological awareness (p = 7.11 × 10-3 ) and rapid automatized naming (p = 4.71 × 10-3 ), implying multiple effects of this variant. The eQTL data showed that rs6446395 affected EVC expression in the cerebellum. Gene-based analyses identified a gene (PRDM10) to be associated with word reading fluency at the genome-wide level. Our study discovered a new candidate susceptibility variant for reading ability and provided new insights into the genetics of developmental dyslexia in Chinese children.
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Affiliation(s)
- Zhengjun Wang
- School of Psychology, Shaanxi Normal University and Shaanxi Provincial Key Research Center of Child Mental and Behavioral Health, Xi'an, China
| | - Shunan Zhao
- School of Psychology, Shaanxi Normal University and Shaanxi Provincial Key Research Center of Child Mental and Behavioral Health, Xi'an, China
| | - Liming Zhang
- School of Psychology, Shaanxi Normal University and Shaanxi Provincial Key Research Center of Child Mental and Behavioral Health, Xi'an, China
| | - Qing Yang
- School of Psychology, Shaanxi Normal University and Shaanxi Provincial Key Research Center of Child Mental and Behavioral Health, Xi'an, China
| | - Chen Cheng
- School of Psychology, Shaanxi Normal University and Shaanxi Provincial Key Research Center of Child Mental and Behavioral Health, Xi'an, China
| | - Ning Ding
- School of Psychology, Shaanxi Normal University and Shaanxi Provincial Key Research Center of Child Mental and Behavioral Health, Xi'an, China
| | - Zijian Zhu
- School of Psychology, Shaanxi Normal University and Shaanxi Provincial Key Research Center of Child Mental and Behavioral Health, Xi'an, China
| | - Hua Shu
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
| | - Chunyu Liu
- School of Psychology, Shaanxi Normal University and Shaanxi Provincial Key Research Center of Child Mental and Behavioral Health, Xi'an, China.,The School of Life Sciences, Central South University, Changsha, China.,Department of Psychiatry, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Jingjing Zhao
- School of Psychology, Shaanxi Normal University and Shaanxi Provincial Key Research Center of Child Mental and Behavioral Health, Xi'an, China
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4
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Erbeli F, Rice M, Paracchini S. Insights into Dyslexia Genetics Research from the Last Two Decades. Brain Sci 2021; 12:27. [PMID: 35053771 PMCID: PMC8773624 DOI: 10.3390/brainsci12010027] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/21/2021] [Accepted: 12/23/2021] [Indexed: 12/14/2022] Open
Abstract
Dyslexia, a specific reading disability, is a common (up to 10% of children) and highly heritable (~70%) neurodevelopmental disorder. Behavioral and molecular genetic approaches are aimed towards dissecting its significant genetic component. In the proposed review, we will summarize advances in twin and molecular genetic research from the past 20 years. First, we will briefly outline the clinical and educational presentation and epidemiology of dyslexia. Next, we will summarize results from twin studies, followed by molecular genetic research (e.g., genome-wide association studies (GWASs)). In particular, we will highlight converging key insights from genetic research. (1) Dyslexia is a highly polygenic neurodevelopmental disorder with a complex genetic architecture. (2) Dyslexia categories share a large proportion of genetics with continuously distributed measures of reading skills, with shared genetic risks also seen across development. (3) Dyslexia genetic risks are shared with those implicated in many other neurodevelopmental disorders (e.g., developmental language disorder and dyscalculia). Finally, we will discuss the implications and future directions. As the diversity of genetic studies continues to increase through international collaborate efforts, we will highlight the challenges in advances of genetics discoveries in this field.
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Affiliation(s)
- Florina Erbeli
- Department of Educational Psychology, Texas A&M University, College Station, TX 77843, USA;
| | - Marianne Rice
- Department of Educational Psychology, Texas A&M University, College Station, TX 77843, USA;
| | - Silvia Paracchini
- School of Medicine, University of St Andrews, St Andrews KY16 9AJ, UK;
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5
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The Polygenic Nature and Complex Genetic Architecture of Specific Learning Disorder. Brain Sci 2021; 11:brainsci11050631. [PMID: 34068951 PMCID: PMC8156942 DOI: 10.3390/brainsci11050631] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 12/16/2022] Open
Abstract
Specific Learning Disorder (SLD) is a multifactorial, neurodevelopmental disorder which may involve persistent difficulties in reading (dyslexia), written expression and/or mathematics. Dyslexia is characterized by difficulties with speed and accuracy of word reading, deficient decoding abilities, and poor spelling. Several studies from different, but complementary, scientific disciplines have investigated possible causal/risk factors for SLD. Biological, neurological, hereditary, cognitive, linguistic-phonological, developmental and environmental factors have been incriminated. Despite worldwide agreement that SLD is highly heritable, its exact biological basis remains elusive. We herein present: (a) an update of studies that have shaped our current knowledge on the disorder’s genetic architecture; (b) a discussion on whether this genetic architecture is ‘unique’ to SLD or, alternatively, whether there is an underlying common genetic background with other neurodevelopmental disorders; and, (c) a brief discussion on whether we are at a position of generating meaningful correlations between genetic findings and anatomical data from neuroimaging studies or specific molecular/cellular pathways. We conclude with open research questions that could drive future research directions.
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Donati G, Dumontheil I, Pain O, Asbury K, Meaburn EL. Evidence for specificity of polygenic contributions to attainment in English, maths and science during adolescence. Sci Rep 2021; 11:3851. [PMID: 33594131 PMCID: PMC7887196 DOI: 10.1038/s41598-021-82877-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 01/19/2021] [Indexed: 01/31/2023] Open
Abstract
How well one does at school is predictive of a wide range of important cognitive, socioeconomic, and health outcomes. The last few years have shown marked advancement in our understanding of the genetic contributions to, and correlations with, academic attainment. However, there exists a gap in our understanding of the specificity of genetic associations with performance in academic subjects during adolescence, a critical developmental period. To address this, the Avon Longitudinal Study of Parents and Children was used to conduct genome-wide association studies of standardised national English (N = 5983), maths (N = 6017) and science (N = 6089) tests. High SNP-based heritabilities (h2SNP) for all subjects were found (41-53%). Further, h2SNP for maths and science remained after removing shared variance between subjects or IQ (N = 3197-5895). One genome-wide significant single nucleotide polymorphism (rs952964, p = 4.86 × 10-8) and four gene-level associations with science attainment (MEF2C, BRINP1, S100A1 and S100A13) were identified. Rs952964 remained significant after removing the variance shared between academic subjects. The findings highlight the benefits of using environmentally homogeneous samples for genetic analyses and indicate that finer-grained phenotyping will help build more specific biological models of variance in learning processes and abilities.
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Affiliation(s)
- Georgina Donati
- Centre for Brain and Cognitive Development, Department of Psychological Sciences, Birkbeck, University of London, London, UK
- Centre for Educational Neuroscience, University of London, London, UK
| | - Iroise Dumontheil
- Centre for Brain and Cognitive Development, Department of Psychological Sciences, Birkbeck, University of London, London, UK
- Centre for Educational Neuroscience, University of London, London, UK
| | - Oliver Pain
- Social Genetic and Developmental Psychology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | | | - Emma L Meaburn
- Centre for Brain and Cognitive Development, Department of Psychological Sciences, Birkbeck, University of London, London, UK.
- Centre for Educational Neuroscience, University of London, London, UK.
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7
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Genome-wide association study reveals new insights into the heritability and genetic correlates of developmental dyslexia. Mol Psychiatry 2021; 26:3004-3017. [PMID: 33057169 PMCID: PMC8505236 DOI: 10.1038/s41380-020-00898-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 07/26/2020] [Accepted: 09/18/2020] [Indexed: 02/06/2023]
Abstract
Developmental dyslexia (DD) is a learning disorder affecting the ability to read, with a heritability of 40-60%. A notable part of this heritability remains unexplained, and large genetic studies are warranted to identify new susceptibility genes and clarify the genetic bases of dyslexia. We carried out a genome-wide association study (GWAS) on 2274 dyslexia cases and 6272 controls, testing associations at the single variant, gene, and pathway level, and estimating heritability using single-nucleotide polymorphism (SNP) data. We also calculated polygenic scores (PGSs) based on large-scale GWAS data for different neuropsychiatric disorders and cortical brain measures, educational attainment, and fluid intelligence, testing them for association with dyslexia status in our sample. We observed statistically significant (p < 2.8 × 10-6) enrichment of associations at the gene level, for LOC388780 (20p13; uncharacterized gene), and for VEPH1 (3q25), a gene implicated in brain development. We estimated an SNP-based heritability of 20-25% for DD, and observed significant associations of dyslexia risk with PGSs for attention deficit hyperactivity disorder (at pT = 0.05 in the training GWAS: OR = 1.23[1.16; 1.30] per standard deviation increase; p = 8 × 10-13), bipolar disorder (1.53[1.44; 1.63]; p = 1 × 10-43), schizophrenia (1.36[1.28; 1.45]; p = 4 × 10-22), psychiatric cross-disorder susceptibility (1.23[1.16; 1.30]; p = 3 × 10-12), cortical thickness of the transverse temporal gyrus (0.90[0.86; 0.96]; p = 5 × 10-4), educational attainment (0.86[0.82; 0.91]; p = 2 × 10-7), and intelligence (0.72[0.68; 0.76]; p = 9 × 10-29). This study suggests an important contribution of common genetic variants to dyslexia risk, and novel genomic overlaps with psychiatric conditions like bipolar disorder, schizophrenia, and cross-disorder susceptibility. Moreover, it revealed the presence of shared genetic foundations with a neural correlate previously implicated in dyslexia by neuroimaging evidence.
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8
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Price KM, Wigg KG, Feng Y, Blokland K, Wilkinson M, He G, Kerr EN, Carter TC, Guger SL, Lovett MW, Strug LJ, Barr CL. Genome-wide association study of word reading: Overlap with risk genes for neurodevelopmental disorders. GENES BRAIN AND BEHAVIOR 2020; 19:e12648. [PMID: 32108986 DOI: 10.1111/gbb.12648] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 01/28/2020] [Accepted: 02/24/2020] [Indexed: 12/12/2022]
Abstract
Reading disabilities (RD) are the most common neurocognitive disorder, affecting 5% to 17% of children in North America. These children often have comorbid neurodevelopmental/psychiatric disorders, such as attention deficit/hyperactivity disorder (ADHD). The genetics of RD and their overlap with other disorders is incompletely understood. To contribute to this, we performed a genome-wide association study (GWAS) for word reading. Then, using summary statistics from neurodevelopmental/psychiatric disorders, we computed polygenic risk scores (PRS) and used them to predict reading ability in our samples. This enabled us to test the shared aetiology between RD and other disorders. The GWAS consisted of 5.3 million single nucleotide polymorphisms (SNPs) and two samples; a family-based sample recruited for reading difficulties in Toronto (n = 624) and a population-based sample recruited in Philadelphia [Philadelphia Neurodevelopmental Cohort (PNC)] (n = 4430). The Toronto sample SNP-based analysis identified suggestive SNPs (P ~ 5 × 10-7 ) in the ARHGAP23 gene, which is implicated in neuronal migration/axon pathfinding. The PNC gene-based analysis identified significant associations (P < 2.72 × 10-6 ) for LINC00935 and CCNT1, located in the region of the KANSL2/CCNT1/LINC00935/SNORA2B/SNORA34/MIR4701/ADCY6 genes on chromosome 12q, with near significant SNP-based analysis. PRS identified significant overlap between word reading and intelligence (R2 = 0.18, P = 7.25 × 10-181 ), word reading and educational attainment (R2 = 0.07, P = 4.91 × 10-48 ) and word reading and ADHD (R2 = 0.02, P = 8.70 × 10-6 ; threshold for significance = 7.14 × 10-3 ). Overlap was also found between RD and autism spectrum disorder (ASD) as top-ranked genes were previously implicated in autism by rare and copy number variant analyses. These findings support shared risk between word reading, cognitive measures, educational outcomes and neurodevelopmental disorders, including ASD.
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Affiliation(s)
- Kaitlyn M Price
- Genetics and Development Division, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada.,Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Karen G Wigg
- Genetics and Development Division, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Yu Feng
- Genetics and Development Division, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Kirsten Blokland
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Margaret Wilkinson
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Gengming He
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Elizabeth N Kerr
- Department of Psychology, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Tasha-Cate Carter
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada.,Holland Bloorview Rehabilitation Hospital, Toronto, Ontario, Canada
| | - Sharon L Guger
- Department of Psychology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Maureen W Lovett
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Lisa J Strug
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada.,Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Cathy L Barr
- Genetics and Development Division, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada.,Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Physiology, University of Toronto, Toronto, Ontario, Canada
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9
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Gialluisi A, Andlauer TFM, Mirza-Schreiber N, Moll K, Becker J, Hoffmann P, Ludwig KU, Czamara D, St Pourcain B, Brandler W, Honbolygó F, Tóth D, Csépe V, Huguet G, Morris AP, Hulslander J, Willcutt EG, DeFries JC, Olson RK, Smith SD, Pennington BF, Vaessen A, Maurer U, Lyytinen H, Peyrard-Janvid M, Leppänen PHT, Brandeis D, Bonte M, Stein JF, Talcott JB, Fauchereau F, Wilcke A, Francks C, Bourgeron T, Monaco AP, Ramus F, Landerl K, Kere J, Scerri TS, Paracchini S, Fisher SE, Schumacher J, Nöthen MM, Müller-Myhsok B, Schulte-Körne G. Genome-wide association scan identifies new variants associated with a cognitive predictor of dyslexia. Transl Psychiatry 2019; 9:77. [PMID: 30741946 PMCID: PMC6370792 DOI: 10.1038/s41398-019-0402-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 01/02/2019] [Indexed: 12/12/2022] Open
Abstract
Developmental dyslexia (DD) is one of the most prevalent learning disorders, with high impact on school and psychosocial development and high comorbidity with conditions like attention-deficit hyperactivity disorder (ADHD), depression, and anxiety. DD is characterized by deficits in different cognitive skills, including word reading, spelling, rapid naming, and phonology. To investigate the genetic basis of DD, we conducted a genome-wide association study (GWAS) of these skills within one of the largest studies available, including nine cohorts of reading-impaired and typically developing children of European ancestry (N = 2562-3468). We observed a genome-wide significant effect (p < 1 × 10-8) on rapid automatized naming of letters (RANlet) for variants on 18q12.2, within MIR924HG (micro-RNA 924 host gene; rs17663182 p = 4.73 × 10-9), and a suggestive association on 8q12.3 within NKAIN3 (encoding a cation transporter; rs16928927, p = 2.25 × 10-8). rs17663182 (18q12.2) also showed genome-wide significant multivariate associations with RAN measures (p = 1.15 × 10-8) and with all the cognitive traits tested (p = 3.07 × 10-8), suggesting (relational) pleiotropic effects of this variant. A polygenic risk score (PRS) analysis revealed significant genetic overlaps of some of the DD-related traits with educational attainment (EDUyears) and ADHD. Reading and spelling abilities were positively associated with EDUyears (p ~ [10-5-10-7]) and negatively associated with ADHD PRS (p ~ [10-8-10-17]). This corroborates a long-standing hypothesis on the partly shared genetic etiology of DD and ADHD, at the genome-wide level. Our findings suggest new candidate DD susceptibility genes and provide new insights into the genetics of dyslexia and its comorbities.
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Affiliation(s)
- Alessandro Gialluisi
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
- Munich Cluster for Systems Neurology (Sypartially), Munich, Germany
- Department of Epidemiology and Prevention, IRCCS Istituto Neurologico Mediterraneo Neuromed, Pozzilli, Italy
| | - Till F M Andlauer
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
- Munich Cluster for Systems Neurology (Sypartially), Munich, Germany
| | - Nazanin Mirza-Schreiber
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Kristina Moll
- Department of Child and Adolescent Psychiatry, Psychosomatic, and Psychotherapy, Ludwig-Maximilians University, Munich, Germany
| | - Jessica Becker
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Kerstin U Ludwig
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Darina Czamara
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Beate St Pourcain
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, Netherlands
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - William Brandler
- University of California San Diego, Department of Psychiatry, San Diego, CA, USA
| | - Ferenc Honbolygó
- Brain Imaging Centre, Research Centre of Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| | - Dénes Tóth
- Brain Imaging Centre, Research Centre of Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| | - Valéria Csépe
- Brain Imaging Centre, Research Centre of Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| | - Guillaume Huguet
- Human Genetics and Cognitive Functions Unit, Institut Pasteur, Paris, France
- University Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Andrew P Morris
- Department of Biostatistics, Universiy of Liverpool, Liverpool, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Jacqueline Hulslander
- Institute for Behavioral Genetics and Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA
| | - Erik G Willcutt
- Institute for Behavioral Genetics and Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA
| | - John C DeFries
- Institute for Behavioral Genetics and Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA
| | - Richard K Olson
- Institute for Behavioral Genetics and Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA
| | - Shelley D Smith
- Developmental Neuroscience Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, NE, USA
| | - Bruce F Pennington
- Developmental Neuropsychology Lab & Clinic, Department of Psychology, University of Denver, Denver, CO, USA
| | - Anniek Vaessen
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience & Maastricht Brain Imaging Center (M-BIC), Maastricht University, Maastricht, Netherlands
| | - Urs Maurer
- Department of Psychology, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong
| | - Heikki Lyytinen
- Centre for Research on Learning and Teaching, Department of Psychology, University of Jyväskylä, Jyväskylä, Finland
| | | | - Paavo H T Leppänen
- Centre for Research on Learning and Teaching, Department of Psychology, University of Jyväskylä, Jyväskylä, Finland
| | - Daniel Brandeis
- Department of Child and Adolescent Psychiatry and Psychotherapy, Psychiatric Hospital, University of Zurich, Zurich, Switzerland
- Zurich Center for Integrative Human Physiology (ZIHP), Zurich, Switzerland
- Department of Child and Adolescent Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany
- Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Milene Bonte
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience & Maastricht Brain Imaging Center (M-BIC), Maastricht University, Maastricht, Netherlands
| | - John F Stein
- Department of Physiology, University of Oxford, Oxford, UK
| | - Joel B Talcott
- School of Life and Health Sciences, Aston University, Birmingham, UK
| | - Fabien Fauchereau
- Human Genetics and Cognitive Functions Unit, Institut Pasteur, Paris, France
- University Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Arndt Wilcke
- Cognitive Genetics Unit, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Clyde Francks
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, Netherlands
| | - Thomas Bourgeron
- Human Genetics and Cognitive Functions Unit, Institut Pasteur, Paris, France
- University Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Anthony P Monaco
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Tufts University, Medford, MA, USA
| | - Franck Ramus
- Laboratoire de Sciences Cognitives et Psycholinguistique, Ecole Normale Supérieure, CNRS, EHESS, PSL Research University, Paris, France
| | - Karin Landerl
- Institute of Psychology, University of Graz, Graz, Austria and BioTechMed, Graz, Austria
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Molecular Medicine Program, Biomedicum, University of Helsinki, and Folkhälsan Institute of Genetics, Helsinki, Finland
- School of Basic and Medical Biosciences, King's College London, London, UK
| | - Thomas S Scerri
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- The Walter and Eliza Hall Institute of Medical Research & Melbourne University, Melbourne, Australia
| | | | - Simon E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, Netherlands
| | - Johannes Schumacher
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Bertram Müller-Myhsok
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany.
- Munich Cluster for Systems Neurology (Sypartially), Munich, Germany.
- Institute of Translational Medicine, University of Liverpool, Liverpool, UK.
| | - Gerd Schulte-Körne
- Department of Child and Adolescent Psychiatry, Psychosomatic, and Psychotherapy, Ludwig-Maximilians University, Munich, Germany.
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Abstract
Developmental dyslexia (DD) is a neurobiological disorder featured by reading disabilities. In recent years, genome-wide approaches provided new perspectives to discover novel candidate genes of DD. In a previous study, rs9313548 located downstream of FGF18 showed borderline genome-wide significant association with DD. Herein, we selected rs9313548 and 11 independent tag single nucleotide polymorphisms covering gene region of FGF18 to perform association analysis with DD among 978 Chinese dyslexic cases and 998 controls recruited from elementary schools. However, we did not observe any single nucleotide polymorphism exceeding significant threshold. Our preliminary results suggested that FGF18 might not be a susceptibility gene for DD in Chinese population.
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11
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Chiba H, Kakuta Y, Kinouchi Y, Kawai Y, Watanabe K, Nagao M, Naito T, Onodera M, Moroi R, Kuroha M, Kanazawa Y, Kimura T, Shiga H, Endo K, Negoro K, Nagasaki M, Unno M, Shimosegawa T. Allele-specific DNA methylation of disease susceptibility genes in Japanese patients with inflammatory bowel disease. PLoS One 2018; 13:e0194036. [PMID: 29547621 PMCID: PMC5856270 DOI: 10.1371/journal.pone.0194036] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 02/25/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Inflammatory bowel disease (IBD) has an unknown etiology; however, accumulating evidence suggests that IBD is a multifactorial disease influenced by a combination of genetic and environmental factors. The influence of genetic variants on DNA methylation in cis and cis effects on expression have been demonstrated. We hypothesized that IBD susceptibility single-nucleotide polymorphisms (SNPs) regulate susceptibility gene expressions in cis by regulating DNA methylation around SNPs. For this, we determined cis-regulated allele-specific DNA methylation (ASM) around IBD susceptibility genes in CD4+ effector/memory T cells (Tem) in lamina propria mononuclear cells (LPMCs) in patients with IBD and examined the association between the ASM SNP genotype and neighboring susceptibility gene expressions. METHODS CD4+ effector/memory T cells (Tem) were isolated from LPMCs in 15 Japanese IBD patients (ten Crohn's disease [CD] and five ulcerative colitis [UC] patients). ASM analysis was performed by methylation-sensitive SNP array analysis. We defined ASM as a changing average relative allele score ([Formula: see text]) >0.1 after digestion by methylation-sensitive restriction enzymes. Among SNPs showing [Formula: see text] >0.1, we extracted the probes located on tag-SNPs of 200 IBD susceptibility loci and around IBD susceptibility genes as candidate ASM SNPs. To validate ASM, bisulfite-pyrosequencing was performed. Transcriptome analysis was examined in 11 IBD patients (seven CD and four UC patients). The relation between rs36221701 genotype and neighboring gene expressions were analyzed. RESULTS We extracted six candidate ASM SNPs around IBD susceptibility genes. The top of [Formula: see text] (0.23) was rs1130368 located on HLA-DQB1. ASM around rs36221701 ([Formula: see text] = 0.14) located near SMAD3 was validated using bisulfite pyrosequencing. The SMAD3 expression was significantly associated with the rs36221701 genotype (p = 0.016). CONCLUSIONS We confirmed the existence of cis-regulated ASM around IBD susceptibility genes and the association between ASM SNP (rs36221701) genotype and SMAD3 expression, a susceptibility gene for IBD. These results give us supporting evidence that DNA methylation mediates genetic effects on disease susceptibility.
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Affiliation(s)
- Hirofumi Chiba
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoichi Kakuta
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoshitaka Kinouchi
- Institute for Excellence in Higher Education, Tohoku University, Sendai, Japan
| | - Yosuke Kawai
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kazuhiro Watanabe
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Munenori Nagao
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takeo Naito
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Motoyuki Onodera
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Rintaro Moroi
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Masatake Kuroha
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoshitake Kanazawa
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tomoya Kimura
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hisashi Shiga
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Katsuya Endo
- Division of Gastroenterology, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Kenichi Negoro
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Masao Nagasaki
- Institute for Excellence in Higher Education, Tohoku University, Sendai, Japan
| | - Michiaki Unno
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tooru Shimosegawa
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
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12
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Luciano M, Hagenaars SP, Cox SR, Hill WD, Davies G, Harris SE, Deary IJ, Evans DM, Martin NG, Wright MJ, Bates TC. Single Nucleotide Polymorphisms Associated with Reading Ability Show Connection to Socio-Economic Outcomes. Behav Genet 2017; 47:469-479. [PMID: 28711986 PMCID: PMC5574963 DOI: 10.1007/s10519-017-9859-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 06/24/2017] [Indexed: 01/15/2023]
Abstract
Impairments in reading and in language have negative consequences on life outcomes, but it is not known to what extent genetic effects influence this association. We constructed polygenic scores for difficulties with language and learning to read from genome-wide data in ~6,600 children, adolescents and young adults, and tested their association with health, socioeconomic outcomes and brain structure measures collected in adults (maximal N = 111,749). Polygenic risk of reading difficulties was associated with reduced income, educational attainment, self-rated health and verbal-numerical reasoning (p < 0.00055). Polygenic risk of language difficulties predicted income (p = 0.0005). The small effect sizes ranged 0.01-0.03 of a standard deviation, but these will increase as genetic studies for reading ability get larger. Polygenic scores for childhood cognitive ability and educational attainment were correlated with polygenic scores of reading and language (up to 0.09 and 0.05, respectively). But when they were included in the prediction models, the observed associations between polygenic reading and adult outcomes mostly remained. This suggests that the pathway from reading ability to social outcomes is not only via associated polygenic loads for general cognitive function and educational attainment. The presence of non-overlapping genetic effect is indicated by the genetic correlations of around 0.40 (childhood intelligence) and 0.70 (educational attainment) with reading ability. Mendelian randomization approaches will be important to dissociate any causal and moderating effects of reading and related traits on social outcomes.
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Affiliation(s)
- Michelle Luciano
- Department of Psychology, School of Philosophy, Psychology and Language Sciences, Centre for Cognitive Ageing and Cognitive Epidemiology, The University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK.
| | - Saskia P Hagenaars
- Department of Psychology, School of Philosophy, Psychology and Language Sciences, Centre for Cognitive Ageing and Cognitive Epidemiology, The University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
- Division of Psychiatry, University of Edinburgh, Edinburgh, EH10 5HF, UK
| | - Simon R Cox
- Department of Psychology, School of Philosophy, Psychology and Language Sciences, Centre for Cognitive Ageing and Cognitive Epidemiology, The University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - William David Hill
- Department of Psychology, School of Philosophy, Psychology and Language Sciences, Centre for Cognitive Ageing and Cognitive Epidemiology, The University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - Gail Davies
- Department of Psychology, School of Philosophy, Psychology and Language Sciences, Centre for Cognitive Ageing and Cognitive Epidemiology, The University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - Sarah E Harris
- Department of Psychology, School of Philosophy, Psychology and Language Sciences, Centre for Cognitive Ageing and Cognitive Epidemiology, The University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
- Medical Genetics Section, University of Edinburgh Centre for Genomic and Experimental Medicine and MRC Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Ian J Deary
- Department of Psychology, School of Philosophy, Psychology and Language Sciences, Centre for Cognitive Ageing and Cognitive Epidemiology, The University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - David M Evans
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, QLD, Australia
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Nicholas G Martin
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Margaret J Wright
- Queensland Brain Institute, University of Queensland, Brisbane, Australia
| | - Timothy C Bates
- Department of Psychology, School of Philosophy, Psychology and Language Sciences, Centre for Cognitive Ageing and Cognitive Epidemiology, The University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
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13
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Selzam S, Dale PS, Wagner RK, DeFries JC, Cederlöf M, O’Reilly PF, Krapohl E, Plomin R. Genome-Wide Polygenic Scores Predict Reading Performance Throughout the School Years. SCIENTIFIC STUDIES OF READING : THE OFFICIAL JOURNAL OF THE SOCIETY FOR THE SCIENTIFIC STUDY OF READING 2017; 21:334-349. [PMID: 28706435 PMCID: PMC5490720 DOI: 10.1080/10888438.2017.1299152] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
It is now possible to create individual-specific genetic scores, called genome-wide polygenic scores (GPS). We used a GPS for years of education (EduYears) to predict reading performance assessed at UK National Curriculum Key Stages 1 (age 7), 2 (age 12) and 3 (age 14) and on reading tests administered at ages 7 and 12 in a UK sample of 5,825 unrelated individuals. EduYears GPS accounts for up to 5% of the variance in reading performance at age 14. GPS predictions remained significant after accounting for general cognitive ability and family socioeconomic status. Reading performance of children in the lowest and highest 12.5% of the EduYears GPS distribution differed by a mean growth in reading ability of approximately two school years. It seems certain that polygenic scores will be used to predict strengths and weaknesses in education.
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14
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Kong R, Shao S, Wang J, Zhang X, Guo S, Zou L, Zhong R, Lou J, Zhou J, Zhang J, Song R. Genetic variant in DIP2A gene is associated with developmental dyslexia in Chinese population. Am J Med Genet B Neuropsychiatr Genet 2016; 171B:203-8. [PMID: 26452339 DOI: 10.1002/ajmg.b.32392] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/02/2015] [Indexed: 11/07/2022]
Abstract
Increasing evidence suggests that there is a substantial heritable component including several risk loci and candidate genes for developmental dyslexia (DD). DIP2A has been identified to be partially deleted on chromosome region 21q22.3, which cosegregates with DD. And it fits into a theoretical molecular network of DD implicated in the development of DD. Compared with some DD candidate genes that have been extensively studied (e.g., DYX1C1, DCDC2, KIAA0319, and ROBO1), very little is known about the association between candidate gene DIP2A and DD susceptibility. And given the linguistic and genetic differences between Chinese and other Western populations, it is worthwhile validating the association of DIP2A in Chinese dyslexic children. Here, we investigated two genetic variants, selected by bioinformatics analysis, in DIP2A in a Chinese population with 409 dyslexic cases and 410 healthy controls. We observed a significantly increased DD risk associated with rs2255526 G allele (OR = 1.297, 95% CI = 1.036-1.623, Padjusted = 0.023) and GG genotypes (OR = 1.833, 95% CI = 1.043-3.223, Padjusted = 0.035), compared with their wild-type counterparts. In addition, it was marginally significantly associated with DD under the recessive model (OR = 1.677, 95% CI = 0.967-2.908, Padjusted = 0.066) and the dominant model (OR = 1.314, 95% CI = 0.992-1.741, Padjusted = 0.057). However, we found no evidence of an association of SNP rs16979358 with DD. In conclusion, this study showed that a genetic variant in the DIP2A gene was associated with increased DD risk in China.
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Affiliation(s)
- Rui Kong
- Department of Maternal and Child Health and MOE (Ministry of Education) Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shanshan Shao
- Department of Maternal and Child Health and MOE (Ministry of Education) Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jia Wang
- Department of Maternal and Child Health and MOE (Ministry of Education) Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaohui Zhang
- Department of Maternal and Child Health and MOE (Ministry of Education) Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shengnan Guo
- Department of Maternal and Child Health and MOE (Ministry of Education) Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Li Zou
- Department of Health Care, Baoan Maternal and Child Health Hospital, Shenzhen, China
| | - Rong Zhong
- Department of Maternal and Child Health and MOE (Ministry of Education) Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiao Lou
- Department of Maternal and Child Health and MOE (Ministry of Education) Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jie Zhou
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, District of Columbia
| | - Jiajia Zhang
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, District of Columbia
| | - Ranran Song
- Department of Maternal and Child Health and MOE (Ministry of Education) Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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15
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Paracchini S, Diaz R, Stein J. Advances in Dyslexia Genetics—New Insights Into the Role of Brain Asymmetries. ADVANCES IN GENETICS 2016; 96:53-97. [DOI: 10.1016/bs.adgen.2016.08.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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16
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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] [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
| | - 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
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17
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Yokoyama JS, Bonham LW, Sears RL, Klein E, Karydas A, Kramer JH, Miller BL, Coppola G. Decision tree analysis of genetic risk for clinically heterogeneous Alzheimer's disease. BMC Neurol 2015; 15:47. [PMID: 25880661 PMCID: PMC4459447 DOI: 10.1186/s12883-015-0304-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 03/12/2015] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Heritability of Alzheimer's disease (AD) is estimated at 74% and genetic contributors have been widely sought. The ε4 allele of apolipoprotein E (APOE) remains the strongest common risk factor for AD, with numerous other common variants contributing only modest risk for disease. Variability in clinical presentation of AD, which is typically amnestic (AmnAD) but can less commonly involve visuospatial, language and/or dysexecutive syndromes (atypical or AtAD), further complicates genetic analyses. Taking a multi-locus approach may increase the ability to identify individuals at highest risk for any AD syndrome. In this study, we sought to develop and investigate the utility of a multi-variant genetic risk assessment on a cohort of phenotypically heterogeneous patients with sporadic AD clinical diagnoses. METHODS We genotyped 75 variants in our cohort and, using a two-staged study design, we developed a 17-marker AD risk score in a Discovery cohort (n = 59 cases, n = 133 controls) then assessed its utility in a second Validation cohort (n = 126 cases, n = 150 controls). We also performed a data-driven decision tree analysis to identify genetic and/or demographic criteria that are most useful for accurately differentiating all AD cases from controls. RESULTS We confirmed APOE ε4 as a strong risk factor for AD. A 17-marker risk panel predicted AD significantly better than APOE genotype alone (P < 0.00001) in the Discovery cohort, but not in the Validation cohort. In decision tree analyses, we found that APOE best differentiated cases from controls only in AmnAD but not AtAD. In AtAD, HFE SNP rs1799945 was the strongest predictor of disease; variation in HFE has previously been implicated in AD risk in non-ε4 carriers. CONCLUSIONS Our study suggests that APOE ε4 remains the best predictor of broad AD risk when compared to multiple other genetic factors with modest effects, that phenotypic heterogeneity in broad AD can complicate simple polygenic risk modeling, and supports the association between HFE and AD risk in individuals without APOE ε4.
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Affiliation(s)
- Jennifer S Yokoyama
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, CA, 94158, USA.
| | - Luke W Bonham
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, CA, 94158, USA.
| | - Renee L Sears
- Semel Institute for Neuroscience and Human Behavior, Departments of Neurology and Psychiatry, The David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA, 90095, USA.
| | - Eric Klein
- Semel Institute for Neuroscience and Human Behavior, Departments of Neurology and Psychiatry, The David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA, 90095, USA.
| | - Anna Karydas
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, CA, 94158, USA.
| | - Joel H Kramer
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, CA, 94158, USA.
| | - Bruce L Miller
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, CA, 94158, USA.
| | - Giovanni Coppola
- Semel Institute for Neuroscience and Human Behavior, Departments of Neurology and Psychiatry, The David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA, 90095, USA.
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18
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Affiliation(s)
- Robin L. Peterson
- Department of Rehabilitation Medicine, Children's Hospital Colorado, Aurora, Colorado 80045;
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19
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Gialluisi A, Newbury DF, Wilcutt EG, Olson RK, DeFries JC, Brandler WM, Pennington BF, Smith SD, Scerri TS, Simpson NH, Luciano M, Evans DM, Bates TC, Stein JF, Talcott JB, Monaco AP, Paracchini S, Francks C, Fisher SE. Genome-wide screening for DNA variants associated with reading and language traits. GENES BRAIN AND BEHAVIOR 2014; 13:686-701. [PMID: 25065397 PMCID: PMC4165772 DOI: 10.1111/gbb.12158] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 07/20/2014] [Accepted: 07/24/2014] [Indexed: 01/04/2023]
Abstract
Reading and language abilities are heritable traits that are likely to share some genetic influences with each other. To identify pleiotropic genetic variants affecting these traits, we first performed a genome-wide association scan (GWAS) meta-analysis using three richly characterized datasets comprising individuals with histories of reading or language problems, and their siblings. GWAS was performed in a total of 1862 participants using the first principal component computed from several quantitative measures of reading- and language-related abilities, both before and after adjustment for performance IQ. We identified novel suggestive associations at the SNPs rs59197085 and rs5995177 (uncorrected P ≈ 10–7 for each SNP), located respectively at the CCDC136/FLNC and RBFOX2 genes. Each of these SNPs then showed evidence for effects across multiple reading and language traits in univariate association testing against the individual traits. FLNC encodes a structural protein involved in cytoskeleton remodelling, while RBFOX2 is an important regulator of alternative splicing in neurons. The CCDC136/FLNC locus showed association with a comparable reading/language measure in an independent sample of 6434 participants from the general population, although involving distinct alleles of the associated SNP. Our datasets will form an important part of on-going international efforts to identify genes contributing to reading and language skills.
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Affiliation(s)
- A Gialluisi
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
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20
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The correlation between reading and mathematics ability at age twelve has a substantial genetic component. Nat Commun 2014; 5:4204. [PMID: 25003214 PMCID: PMC4102107 DOI: 10.1038/ncomms5204] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 05/23/2014] [Indexed: 01/23/2023] Open
Abstract
Dissecting how genetic and environmental influences impact on learning is helpful for maximizing numeracy and literacy. Here we show, using twin and genome-wide analysis, that there is a substantial genetic component to children’s ability in reading and mathematics, and estimate that around one half of the observed correlation in these traits is due to shared genetic effects (so-called Generalist Genes). Thus, our results highlight the potential role of the learning environment in contributing to differences in a child’s cognitive abilities at age twelve. Understanding the genetic basis of cognitive traits could aid the development of numeracy and literacy skills in children. Here the authors show that reading and mathematics have a large overlapping genetic component and suggest that a child's learning environment has a key role in creating differences between them.
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21
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Harlaar N, Trzaskowski M, Dale PS, Plomin R. Word reading fluency: role of genome-wide single-nucleotide polymorphisms in developmental stability and correlations with print exposure. Child Dev 2014; 85:1190-1205. [PMID: 24392801 PMCID: PMC4064251 DOI: 10.1111/cdev.12207] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The genetic effects on individual differences in reading development were examined using genome-wide complex trait analysis (GCTA) in a twin sample. In unrelated individuals (one twin per pair, n = 2,942), the GCTA-based heritability of reading fluency was ~20%-29% at ages 7 and 12. GCTA bivariate results showed that the phenotypic stability of reading fluency from 7 to 12 years (r = 0.69) is largely driven by genetic stability (genetic r = 0.69). Genetic effects on print exposure at age 12 were moderate (~26%) and correlated with those influencing reading fluency at 12 (genetic r = 0.89), indicative of a gene-environment correlation. These findings were largely consistent with quantitative genetic twin analyses that used both twins in each pair (n = 1,066-1,409).
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Reading and language disorders: the importance of both quantity and quality. Genes (Basel) 2014; 5:285-309. [PMID: 24705331 PMCID: PMC4094934 DOI: 10.3390/genes5020285] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 03/11/2014] [Accepted: 03/12/2014] [Indexed: 01/25/2023] Open
Abstract
Reading and language disorders are common childhood conditions that often co-occur with each other and with other neurodevelopmental impairments. There is strong evidence that disorders, such as dyslexia and Specific Language Impairment (SLI), have a genetic basis, but we expect the contributing genetic factors to be complex in nature. To date, only a few genes have been implicated in these traits. Their functional characterization has provided novel insight into the biology of neurodevelopmental disorders. However, the lack of biological markers and clear diagnostic criteria have prevented the collection of the large sample sizes required for well-powered genome-wide screens. One of the main challenges of the field will be to combine careful clinical assessment with high throughput genetic technologies within multidisciplinary collaborations.
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Nudel R, Simpson NH, Baird G, O'Hare A, Conti-Ramsden G, Bolton PF, Hennessy ER, Ring SM, Davey Smith G, Francks C, Paracchini S, Monaco AP, Fisher SE, Newbury DF. Genome-wide association analyses of child genotype effects and parent-of-origin effects in specific language impairment. GENES BRAIN AND BEHAVIOR 2014; 13:418-29. [PMID: 24571439 PMCID: PMC4114547 DOI: 10.1111/gbb.12127] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 01/30/2014] [Accepted: 02/22/2014] [Indexed: 12/19/2022]
Abstract
Specific language impairment (SLI) is a neurodevelopmental disorder that affects linguistic abilities when development is otherwise normal. We report the results of a genome-wide association study of SLI which included parent-of-origin effects and child genotype effects and used 278 families of language-impaired children. The child genotype effects analysis did not identify significant associations. We found genome-wide significant paternal parent-of-origin effects on chromosome 14q12 (P = 3.74 × 10−8) and suggestive maternal parent-of-origin effects on chromosome 5p13 (P = 1.16 × 10−7). A subsequent targeted association of six single-nucleotide-polymorphisms (SNPs) on chromosome 5 in 313 language-impaired individuals and their mothers from the ALSPAC cohort replicated the maternal effects, albeit in the opposite direction (P = 0.001); as fathers’ genotypes were not available in the ALSPAC study, the replication analysis did not include paternal parent-of-origin effects. The paternally-associated SNP on chromosome 14 yields a non-synonymous coding change within the NOP9 gene. This gene encodes an RNA-binding protein that has been reported to be significantly dysregulated in individuals with schizophrenia. The region of maternal association on chromosome 5 falls between the PTGER4 and DAB2 genes, in a region previously implicated in autism and ADHD. The top SNP in this association locus is a potential expression QTL of ARHGEF19 (also called WGEF) on chromosome 1. Members of this protein family have been implicated in intellectual disability. In summary, this study implicates parent-of-origin effects in language impairment, and adds an interesting new dimension to the emerging picture of shared genetic etiology across various neurodevelopmental disorders.
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Affiliation(s)
- R Nudel
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
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Harlaar N, Meaburn EL, Hayiou-Thomas ME, Davis OSP, Docherty S, Hanscombe KB, Haworth CMA, Price TS, Trzaskowski M, Dale PS, Plomin R. Genome-wide association study of receptive language ability of 12-year-olds. JOURNAL OF SPEECH, LANGUAGE, AND HEARING RESEARCH : JSLHR 2014; 57:96-105. [PMID: 24687471 PMCID: PMC3974169 DOI: 10.1044/1092-4388(2013/12-0303)] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
PURPOSE Researchers have previously shown that individual differences in measures of receptive language ability at age 12 are highly heritable. In the current study, the authors attempted to identify some of the genes responsible for the heritability of receptive language ability using a genome-wide association approach. METHOD The authors administered 4 Internet-based measures of receptive language (vocabulary, semantics, syntax, and pragmatics) to a sample of 2,329 twelve-year-olds for whom DNA and genome-wide genotyping were available. Nearly 700,000 single-nucleotide polymorphisms (SNPs) and 1 million imputed SNPs were included in a genome-wide association analysis of receptive language composite scores. RESULTS No SNP associations met the demanding criterion of genome-wide significance that corrects for multiple testing across the genome ( p < 5 × 10 -8). The strongest SNP association did not replicate in an additional sample of 2,639 twelve-year-olds. CONCLUSIONS These results indicate that individual differences in receptive language ability in the general population do not reflect common genetic variants that account for more than 3% of the phenotypic variance. The search for genetic variants associated with language skill will require larger samples and additional methods to identify and functionally characterize the full spectrum of risk variants.
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Luciano M, Evans DM, Hansell NK, Medland SE, Montgomery GW, Martin NG, Wright MJ, Bates TC. A genome-wide association study for reading and language abilities in two population cohorts. GENES BRAIN AND BEHAVIOR 2013; 12:645-52. [PMID: 23738518 PMCID: PMC3908370 DOI: 10.1111/gbb.12053] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 03/04/2013] [Accepted: 05/24/2013] [Indexed: 01/21/2023]
Abstract
Candidate genes have been identified for both reading and language, but most of the heritable variance in these traits remains unexplained. Here, we report a genome-wide association meta-analysis of two large cohorts: population samples of Australian twins and siblings aged 12–25 years (n = 1177 from 538 families), and a younger cohort of children of the UK Avon Longitudinal Study of Parents and their Children (aged 8 and 9 years; maximum n = 5472). Suggestive association was indicated for reading measures and non-word repetition (NWR), with the greatest support found for single nucleotide polymorphisms (SNPs) in the pseudogene, ABCC13 (P = 7.34 × 10−8), and the gene, DAZAP1 (P = 1.32 × 10−6). Gene-based analyses showed significant association (P < 2.8 × 10−6) for reading and spelling with genes CD2L1, CDC2L2 and RCAN3 in two loci on chromosome 1. Some support was found for the same SNPs having effects on both reading skill and NWR, which is compatible with behavior genetic evidence for influences of reading acquisition on phonological-task performance. The results implicate novel candidates for study in additional cohorts for reading and language abilities.
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Affiliation(s)
- M Luciano
- Centre for Cognitive Aging and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, UK.
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26
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Trzaskowski M, Eley TC, Davis OSP, Doherty SJ, Hanscombe KB, Meaburn EL, Haworth CMA, Price T, Plomin R. First genome-wide association study on anxiety-related behaviours in childhood. PLoS One 2013; 8:e58676. [PMID: 23565138 PMCID: PMC3614558 DOI: 10.1371/journal.pone.0058676] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 02/05/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Twin studies have shown that anxiety in a general population sample of children involves both domain-general and trait-specific genetic effects. For this reason, in an attempt to identify genes responsible for these effects, we investigated domain-general and trait-specific genetic associations in the first genome-wide association (GWA) study on anxiety-related behaviours (ARBs) in childhood. METHODS The sample included 2810 7-year-olds drawn from the Twins Early Development Study (TEDS) with data available for parent-rated anxiety and genome-wide DNA markers. The measure was the Anxiety-Related Behaviours Questionnaire (ARBQ), which assesses four anxiety traits and also yields a general anxiety composite. Affymetrix GeneChip 6.0 DNA arrays were used to genotype nearly 700,000 single-nucleotide polymorphisms (SNPs), and IMPUTE v2 was used to impute more than 1 million SNPs. Several GWA associations from this discovery sample were followed up in another TEDS sample of 4804 children. In addition, Genome-wide Complex Trait Analysis (GCTA) was used on the discovery sample, to estimate the total amount of variance in ARBs that can be accounted for by SNPs on the array. RESULTS No SNP associations met the demanding criterion of genome-wide significance that corrects for multiple testing across the genome (p<5×10(-8)). Attempts to replicate the top associations did not yield significant results. In contrast to the substantial twin study estimates of heritability which ranged from 0.50 (0.03) to 0.61 (0.01), the GCTA estimates of phenotypic variance accounted for by the SNPs were much lower 0.01 (0.11) to 0.19 (0.12). CONCLUSIONS Taken together, these GWAS and GCTA results suggest that anxiety--similar to height, weight and intelligence--is affected by many genetic variants of small effect, but unlike these other prototypical polygenic traits, genetic influence on anxiety is not well tagged by common SNPs.
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Affiliation(s)
- Maciej Trzaskowski
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, De Crespigny Park, London, United Kingdom.
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Stenberg A. Interpreting estimates of heritability--a note on the twin decomposition. ECONOMICS AND HUMAN BIOLOGY 2013; 11:201-205. [PMID: 22676967 DOI: 10.1016/j.ehb.2012.05.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 03/31/2012] [Accepted: 05/11/2012] [Indexed: 06/01/2023]
Abstract
While most outcomes may in part be genetically mediated, quantifying genetic heritability is a different matter. To explore data on twins and decompose the variation is a classical method to determine whether variation in outcomes, e.g. IQ or schooling, originate from genetic endowments or environmental factors. Despite some criticism, the model is still widely used. The critique is generally related to how estimates of heritability may encompass environmental mediation. This aspect is sometimes left implicit by authors even though its relevance for the interpretation is potentially profound. This short note is an appeal for clarity from authors when interpreting the magnitude of heritability estimates. It is demonstrated how disregarding existing theoretical contributions can easily lead to unnecessary misinterpretations and/or controversies. The key arguments are relevant also for estimates based on data of adopted children or from modern molecular genetics research.
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Affiliation(s)
- Anders Stenberg
- Stockholm University, Institute for Social Research, Stockholm, Sweden.
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28
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Tran C, Gagnon F, Wigg K, Feng Y, Gomez L, Cate-Carter T, Kerr E, Field L, Kaplan B, Lovett M, Barr C. A family-based association analysis and meta-analysis of the reading disabilities candidate gene DYX1C1. Am J Med Genet B Neuropsychiatr Genet 2013; 162B:146-56. [PMID: 23341075 PMCID: PMC5381964 DOI: 10.1002/ajmg.b.32123] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 11/07/2012] [Indexed: 11/11/2022]
Abstract
Reading disabilities (RD) have a significant genetic basis and have shown linkage to multiple regions including chromosome 15q. Dyslexia susceptibility 1 candidate gene 1 (DYX1C1) on chromosome 15q21 was originally proposed as a candidate gene with two potentially functional polymorphisms at the -3G/A and 1249G/T positions showing association with RD. However, subsequent studies have yielded mixed results. We performed a literature review and meta-analysis of the -3G/A and 1249G/T polymorphisms, including new unpublished data from two family-based samples. Ten markers in DYX1C1 were genotyped in the two independently ascertained samples. Single marker and -3G/A:1249G/T haplotype analyses were performed for RD in both samples, and quantitative trait analyses using standardized reading-related measures was performed in one of the samples. For the meta-analysis, we used a random-effects model to summarize studies that tested for association between -3G/A or 1249G/T and RD. No significant association was found between the DYX1C1 SNPs and RD or any of the reading-related measures tested after correction for the number of tests performed. The previously reported risk haplotype (-3A:1249T) was not biased in transmission. A total of 9 and 10 study samples were included in the meta-analysis of the -3G/A and 1249G/T polymorphisms, respectively. Neither polymorphism reached statistical significance, but the heterogeneity for the 1249G/T polymorphism was high. The results of this study do not provide evidence for association between the putatively functional SNPs -3G/A and 1249G/T and RD.
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Affiliation(s)
- C. Tran
- Genetics and Development Division, Toronto Western Research Institute, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
| | - F. Gagnon
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - K.G. Wigg
- Genetics and Development Division, Toronto Western Research Institute, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
| | - Y. Feng
- Genetics and Development Division, Toronto Western Research Institute, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
| | - L. Gomez
- Genetics and Development Division, Toronto Western Research Institute, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
| | - T.D. Cate-Carter
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - E.N. Kerr
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - L.L. Field
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - B.J. Kaplan
- Alberta Children’s Hospital and Department of Paediatrics, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - M.W. Lovett
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - C.L. Barr
- Genetics and Development Division, Toronto Western Research Institute, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada,Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, Ontario, Canada,Correspondence to: Dr. C.L. Barr, Genetics and Development Division, The Toronto Western Hospital, 399 Bathurst St., Room MP14-302, Toronto, ON, Canada M5T 2S8.
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Centanni TM, Booker AB, Sloan AM, Chen F, Maher BJ, Carraway RS, Khodaparast N, Rennaker R, LoTurco JJ, Kilgard MP. Knockdown of the dyslexia-associated gene Kiaa0319 impairs temporal responses to speech stimuli in rat primary auditory cortex. Cereb Cortex 2013; 24:1753-66. [PMID: 23395846 DOI: 10.1093/cercor/bht028] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
One in 15 school age children have dyslexia, which is characterized by phoneme-processing problems and difficulty learning to read. Dyslexia is associated with mutations in the gene KIAA0319. It is not known whether reduced expression of KIAA0319 can degrade the brain's ability to process phonemes. In the current study, we used RNA interference (RNAi) to reduce expression of Kiaa0319 (the rat homolog of the human gene KIAA0319) and evaluate the effect in a rat model of phoneme discrimination. Speech discrimination thresholds in normal rats are nearly identical to human thresholds. We recorded multiunit neural responses to isolated speech sounds in primary auditory cortex (A1) of rats that received in utero RNAi of Kiaa0319. Reduced expression of Kiaa0319 increased the trial-by-trial variability of speech responses and reduced the neural discrimination ability of speech sounds. Intracellular recordings from affected neurons revealed that reduced expression of Kiaa0319 increased neural excitability and input resistance. These results provide the first evidence that decreased expression of the dyslexia-associated gene Kiaa0319 can alter cortical responses and impair phoneme processing in auditory cortex.
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Affiliation(s)
- T M Centanni
- School of Behavioral and Brain Sciences, University of Texas at Dallas
| | | | - A M Sloan
- School of Behavioral and Brain Sciences, University of Texas at Dallas
| | - F Chen
- University of Connecticut
| | | | - R S Carraway
- School of Behavioral and Brain Sciences, University of Texas at Dallas
| | - N Khodaparast
- School of Behavioral and Brain Sciences, University of Texas at Dallas
| | - R Rennaker
- School of Behavioral and Brain Sciences, University of Texas at Dallas
| | | | - M P Kilgard
- School of Behavioral and Brain Sciences, University of Texas at Dallas
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Haworth CMA, Davis OSP, Plomin R. Twins Early Development Study (TEDS): a genetically sensitive investigation of cognitive and behavioral development from childhood to young adulthood. Twin Res Hum Genet 2013; 16:117-25. [PMID: 23110994 PMCID: PMC3817931 DOI: 10.1017/thg.2012.91] [Citation(s) in RCA: 213] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The Twins Early Development Study (TEDS) is a large longitudinal sample of twins born in England and Wales between 1994 and 1996. The focus of TEDS has been on cognitive and behavioral development, including difficulties in the context of normal development. TEDS began when multiple births were identified from birth records and the families were invited to take part in the study; 16,810 pairs of twins were originally enrolled in TEDS. More than 10,000 of these twin pairs remain enrolled in the study to date. DNA has been collected for more than 7,000 pairs, and genome-wide genotyping data for two million DNA markers are available for 3,500 individuals. The TEDS families have taken part in studies when the twins were aged 2, 3, 4, 7, 8, 9, 10, 12, 14, and 16 years of age. Data collection is currently underway to assess the adult destinations of the twins as they move from school to university and the workplace. Between January 2012 and December 2014, all of the TEDS twins will turn 18, and the study will transition to an adult sample. TEDS represents an outstanding resource for investigating the developmental effects of genes and environments on complex quantitative traits from childhood to young adulthood and beyond.
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Raskind WH, Peter B, Richards T, Eckert MM, Berninger VW. The genetics of reading disabilities: from phenotypes to candidate genes. Front Psychol 2013; 3:601. [PMID: 23308072 PMCID: PMC3538356 DOI: 10.3389/fpsyg.2012.00601] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 12/18/2012] [Indexed: 12/19/2022] Open
Abstract
This article provides an overview of (a) issues in definition and diagnosis of specific reading disabilities at the behavioral level that may occur in different constellations of developmental and phenotypic profiles (patterns); (b) rapidly expanding research on genetic heterogeneity and gene candidates for dyslexia and other reading disabilities; (c) emerging research on gene-brain relationships; and (d) current understanding of epigenetic mechanisms whereby environmental events may alter behavioral expression of genetic variations. A glossary of genetic terms (denoted by bold font) is provided for readers not familiar with the technical terms.
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Affiliation(s)
- Wendy H Raskind
- Department of Medicine, University of Washington Seattle, WA, USA ; Department of Psychiatry and Behavioral Sciences, University of Washington Seattle, WA, USA
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Field LL, Shumansky K, Ryan J, Truong D, Swiergala E, Kaplan BJ. Dense-map genome scan for dyslexia supports loci at 4q13, 16p12, 17q22; suggests novel locus at 7q36. GENES BRAIN AND BEHAVIOR 2012. [PMID: 23190410 DOI: 10.1111/gbb.12003] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Analysis of genetic linkage to dyslexia was performed using 133,165 array-based SNPs genotyped in 718 persons from 101 dyslexia-affected families. Results showed five linkage peaks with lod scores >2.3 (4q13.1, 7q36.1-q36.2, 7q36.3, 16p12.1, and 17q22). Of these five regions, three have been previously implicated in dyslexia (4q13.1, 16p12.1, and 17q22), three have been implicated in attention-deficit hyperactivity disorder (ADHD, which highly co-occurs with dyslexia; 4q13.1, 7q36.3, 16p12.1) and four have been implicated in autism (a condition characterized by language deficits; 7q36.1-q36.2, 7q36.3, 16p12.1, and 17q22). These results highlight the reproducibility of dyslexia linkage signals, even without formally significant lod scores, and suggest dyslexia predisposing genes with relatively major effects and locus heterogeneity. The largest lod score (2.80) occurred at 17q22 within the MSI2 gene, involved in neuronal stem cell lineage proliferation. Interestingly, the 4q13.1 linkage peak (lod 2.34) occurred immediately upstream of the LPHN3 gene, recently reported both linked and associated with ADHD. Separate analyses of larger pedigrees revealed lods >2.3 at 1-3 regions per family; one family showed strong linkage (lod 2.9) to a known dyslexia locus (18p11) not detected in our overall data, demonstrating the value of analyzing single large pedigrees. Association analysis identified no SNPs with genome-wide significance, although a borderline significant SNP (P = 6 × 10(-7)) occurred at 5q35.1 near FGF18, involved in laminar positioning of cortical neurons during development. We conclude that dyslexia genes with relatively major effects exist, are detectable by linkage analysis despite genetic heterogeneity, and show substantial overlapping predisposition with ADHD and autism.
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Affiliation(s)
- L L Field
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
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Zou L, Chen W, Shao S, Sun Z, Zhong R, Shi J, Miao X, Song R. Genetic variant in KIAA0319, but not in DYX1C1, is associated with risk of dyslexia: an integrated meta-analysis. Am J Med Genet B Neuropsychiatr Genet 2012; 159B:970-6. [PMID: 23065966 DOI: 10.1002/ajmg.b.32102] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 09/14/2012] [Indexed: 01/13/2023]
Abstract
DYX1C1 and KIAA0319 have been two of the most extensively studied candidate genes for dyslexia given their important roles in the neuronal migration and neurite growth. The -3G > A in DYX1C1 and the 931C > T in KIAA0319 were of special interest for dyslexia but with inconsistent results. We performed a meta-analysis integrating case-control and transmission/disequilibrium test (TDT) studies to clearly discern the effect of these two variants in dyslexia. Data from case-control and TDT studies were analyzed in an allelic model using the Catmap software. In overall meta-analysis, the pooled OR for the -3A allele and the 931T allele was 0.68 (95% CI = 0.25-1.87, P(heterogeneity) = 0.000) and 0.87 (95% CI = 0.78-0.98, P(heterogeneity)= 0.125), respectively. The stratified analysis showed that the between-study heterogeneity regarding the -3G > A polymorphism might be accounted by the publication year. Additionally, the sensitivity analysis of -3G > A polymorphism indicated the stability of the result. In conclusion, our results suggested that the 931C > T variant in KIAA0319, but not the -3G > A in DYX1C1, was significantly associated with the risk of dyslexia.
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Affiliation(s)
- Li Zou
- Department of Maternal and Child Health, School of Public Health, Tongji Medical College, Huangzhong University of Science and Technology, Wuhan, China
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Al-Shidhani TA, Arora V. Understanding Dyslexia in Children through Human Development Theories. Sultan Qaboos Univ Med J 2012; 12:286-94. [PMID: 23269949 DOI: 10.12816/0003141] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Revised: 03/13/2012] [Accepted: 05/14/2012] [Indexed: 11/27/2022] Open
Abstract
Dyslexia is a specific learning disability that is neurological in origin, with an estimated overall worldwide prevalence of 5-10% of the population. It is characterised by difficulties in reading, accuracy, fluency, spelling and decoding abilities. The majority of publications reviewed indicated that screening is performed at the preschool level. Screening can also be conducted at birth or the first year of life. Understanding human development theory, for example, Piaget's human development theory, may help determine at which stage of childhood development dyslexia is more detectable, and therefore guide the management of this disability. The objective of this review is to provide a brief and updated overview of dyslexia and its management in children through human development issues.
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Affiliation(s)
- Thuraya Ahmed Al-Shidhani
- Department of Sports Medicine, McGill University, Montreal, Quebec, Canada; ; Department of Family & Community Medicine, University of Toronto, Ontario, Canada; ; Department of Family Medicine & Public Health, Oman Medical Specialty Board, Muscat, Oman
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35
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Abstract
Dyslexia is a neurodevelopmental disorder that is characterised by slow and inaccurate word recognition. Dyslexia has been reported in every culture studied, and mounting evidence draws attention to cross-linguistic similarity in its neurobiological and neurocognitive bases. Much progress has been made across research specialties spanning the behavioural, neuropsychological, neurobiological, and causal levels of analysis in the past 5 years. From a neuropsychological perspective, the phonological theory remains the most compelling, although phonological problems also interact with other cognitive risk factors. Work confirms that, neurobiologically, dyslexia is characterised by dysfunction of the normal left hemisphere language network and also implicates abnormal white matter development. Studies accounting for reading experience demonstrate that many recorded neural differences show causes rather than effects of dyslexia. Six predisposing candidate genes have been identified, and evidence shows gene by environment interaction.
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Affiliation(s)
- Robin L Peterson
- Department of Psychology, University of Denver, Denver, CO 80208, USA.
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Abstract
Fourteen years ago, the first article on molecular genetics was published in this journal: Child Development, Molecular Genetics, andWhat to Do With Genes Once They Are Found (R. Plomin & M. Rutter, 1998). The goal of the article was to outline what developmentalists can do with genes once they are found. These new directions for developmental research are still relevant today. The problem lies with the phrase “once they are found”: It has been much more difficult than expected to identify genes responsible for the heritability of complex traits and common disorders, the so-called missing heritability problem. The present article considers reasons for the missing heritability problem and possible solutions.
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Luciano M, Montgomery GW, Martin NG, Wright MJ, Bates TC. SNP sets and reading ability: testing confirmation of a 10-SNP set in a population sample. Twin Res Hum Genet 2012; 14:228-32. [PMID: 21623652 DOI: 10.1375/twin.14.3.228] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
A set of 10 SNPs associated with reading ability in 7-year-olds was reported based on initial pooled analyses of 100K SNP chip data, with follow-up testing stages using pooling and individual testing. Here we examine this association in an adolescent population sample of Australian twins and siblings (N = 1177) aged 12 to 25 years. One (rs1842129) of the 10 SNPs approached significance (P = .05) but no support was found for the remaining 9 SNPs or the SNP set itself. Results indicate that these SNPs are not associated with reading ability in an Australian population. The results are interpreted as supporting use of much larger SNP sets in common disorders where effects are small.
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Affiliation(s)
- Michelle Luciano
- Centre for Cognitive Aging and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, United Kingdom.
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38
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Gene-by-environment experiments: a new approach to finding the missing heritability. Nat Rev Genet 2011; 12:881; author reply 881. [PMID: 22094952 DOI: 10.1038/nrg2764-c1] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Poelmans G, Buitelaar JK, Pauls DL, Franke B. A theoretical molecular network for dyslexia: integrating available genetic findings. Mol Psychiatry 2011; 16:365-82. [PMID: 20956978 DOI: 10.1038/mp.2010.105] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Developmental dyslexia is a common specific childhood learning disorder with a strong heritable component. Previous studies using different genetic approaches have identified several genetic loci and candidate genes for dyslexia. In this article, we have integrated the current knowledge on 14 dyslexia candidate genes suggested by cytogenetic findings, linkage and association studies. We found that 10 of the 14 dyslexia candidate genes (ROBO1, KIAA0319, KIAA0319L, S100B, DOCK4, FMR1, DIP2A, GTF2I, DYX1C1 and DCDC2) fit into a theoretical molecular network involved in neuronal migration and neurite outgrowth. Based on this, we also propose three novel dyslexia candidate genes (SLIT2, HMGB1 and VAPA) from known linkage regions, and we discuss the possible involvement of genes emerging from the two reported genome-wide association studies for reading impairment-related phenotypes in the identified network.
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Affiliation(s)
- G Poelmans
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
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The efficacy of detecting variants with small effects on the Affymetrix 6.0 platform using pooled DNA. Hum Genet 2011; 130:607-21. [PMID: 21424828 DOI: 10.1007/s00439-011-0974-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Accepted: 03/06/2011] [Indexed: 01/10/2023]
Abstract
Genome-wide genotyping of a cohort using pools rather than individual samples has long been proposed as a cost-saving alternative for performing genome-wide association (GWA) studies. However, successful disease gene mapping using pooled genotyping has thus far been limited to detecting common variants with large effect sizes, which tend not to exist for many complex common diseases or traits. Therefore, for DNA pooling to be a viable strategy for conducting GWA studies, it is important to determine whether commonly used genome-wide SNP array platforms such as the Affymetrix 6.0 array can reliably detect common variants of small effect sizes using pooled DNA. Taking obesity and age at menarche as examples of human complex traits, we assessed the feasibility of genome-wide genotyping of pooled DNA as a single-stage design for phenotype association. By individually genotyping the top associations identified by pooling, we obtained a 14- to 16-fold enrichment of SNPs nominally associated with the phenotype, but we likely missed the top true associations. In addition, we assessed whether genotyping pooled DNA can serve as an inexpensive screen as the second stage of a multi-stage design with a large number of samples by comparing the most cost-effective 3-stage designs with 80% power to detect common variants with genotypic relative risk of 1.1, with and without pooling. Given the current state of the specific technology we employed and the associated genotyping costs, we showed through simulation that a design involving pooling would be 1.07 times more expensive than a design without pooling. Thus, while a significant amount of information exists within the data from pooled DNA, our analysis does not support genotyping pooled DNA as a means to efficiently identify common variants contributing small effects to phenotypes of interest. While our conclusions were based on the specific technology and study design we employed, the approach presented here will be useful for evaluating the utility of other or future genome-wide genotyping platforms in pooled DNA studies.
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Docherty SJ, Kovas Y, Plomin R. Gene-environment interaction in the etiology of mathematical ability using SNP sets. Behav Genet 2011; 41:141-54. [PMID: 20978832 PMCID: PMC3029801 DOI: 10.1007/s10519-010-9405-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Accepted: 10/06/2010] [Indexed: 11/01/2022]
Abstract
Mathematics ability and disability is as heritable as other cognitive abilities and disabilities, however its genetic etiology has received relatively little attention. In our recent genome-wide association study of mathematical ability in 10-year-old children, 10 SNP associations were nominated from scans of pooled DNA and validated in an individually genotyped sample. In this paper, we use a 'SNP set' composite of these 10 SNPs to investigate gene-environment (GE) interaction, examining whether the association between the 10-SNP set and mathematical ability differs as a function of ten environmental measures in the home and school in a sample of 1888 children with complete data. We found two significant GE interactions for environmental measures in the home and the school both in the direction of the diathesis-stress type of GE interaction: The 10-SNP set was more strongly associated with mathematical ability in chaotic homes and when parents are negative.
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Affiliation(s)
- Sophia J Docherty
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College, London SE5 8AF, UK.
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Skiba T, Landi N, Wagner R, Grigorenko EL. In search of the perfect phenotype: an analysis of linkage and association studies of reading and reading-related processes. Behav Genet 2011; 41:6-30. [PMID: 21243420 PMCID: PMC3056345 DOI: 10.1007/s10519-011-9444-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Accepted: 12/22/2010] [Indexed: 01/15/2023]
Abstract
Reading ability and specific reading disability (SRD) are complex traits involving several cognitive processes and are shaped by a complex interplay of genetic and environmental forces. Linkage studies of these traits have identified several susceptibility loci. Association studies have gone further in detecting candidate genes that might underlie these signals. These results have been obtained in samples of mainly European ancestry, which vary in their languages, inclusion criteria, and phenotype assessments. Such phenotypic heterogeneity across samples makes understanding the relationship between reading (dis)ability and reading-related processes and the genetic factors difficult; in addition, it may negatively influence attempts at replication. In moving forward, the identification of preferable phenotypes for future sample collection may improve the replicability of findings. This review of all published linkage and association results from the past 15 years was conducted to determine if certain phenotypes produce more replicable and consistent results than others.
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Affiliation(s)
| | - Nicole Landi
- Yale University & Haskins Laboratories, New Haven, CT, USA
| | | | - Elena L. Grigorenko
- Yale University, New Heaven, CT, USA
- Moscow State University, Moscow, Russia
- Columbia University, New York, NY, USA
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Lundborg P, Stenberg A. Nature, nurture and socioeconomic policy-what can we learn from molecular genetics? ECONOMICS AND HUMAN BIOLOGY 2010; 8:320-330. [PMID: 20833117 DOI: 10.1016/j.ehb.2010.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2009] [Revised: 08/17/2010] [Accepted: 08/17/2010] [Indexed: 05/29/2023]
Abstract
Many countries use public resources to compensate individuals with genetic disorders, identified by behaviors/symptoms such as chronic diseases and disabilities. This paper draws attention to molecular genetic research which may provide a new dimension to our understanding of how socioeconomic outcomes are generated. We provide an overview of the recently emerging evidence of gene-environment interaction effects. This literature points out specific areas where policies may compensate groups of individuals carrying genetic risks, without the need to identify anyone's genetic endowments. Moreover, epigenetics studies, which concern heritable changes in gene functions that occur independently of the DNA sequence, have shown that environments may affect heritable traits across generations. It means that policies which neutralize adverse environments may also increase intergenerational mobility, given that genetic and/or environmental risk factors are more common in socially disadvantaged groups.
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Affiliation(s)
- Petter Lundborg
- Department of Economics, Lund University and affiliated with VU University Amsterdam, Tinbergen Institute, IZA, Centre for Economic Demography (CED), and the Health Economic Program (HEP Lund), Sweden
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DNA methylation profiling using bisulfite-based epityping of pooled genomic DNA. Methods 2010; 52:255-8. [DOI: 10.1016/j.ymeth.2010.06.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Revised: 06/24/2010] [Accepted: 06/25/2010] [Indexed: 12/16/2022] Open
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Haworth CMA, Plomin R. Quantitative genetics in the era of molecular genetics: learning abilities and disabilities as an example. J Am Acad Child Adolesc Psychiatry 2010; 49:783-93. [PMID: 20643312 PMCID: PMC2908597 DOI: 10.1016/j.jaac.2010.01.026] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2009] [Revised: 12/17/2009] [Accepted: 03/22/2010] [Indexed: 10/18/2022]
Abstract
OBJECTIVE To consider recent findings from quantitative genetic research in the context of molecular genetic research, especially genome-wide association studies. We focus on findings that go beyond merely estimating heritability. We use learning abilities and disabilities as examples. METHOD Recent twin research in the area of learning abilities and disabilities was reviewed. RESULTS Three findings from quantitative genetic research stand out for their far-reaching implications for child and adolescent psychiatry. First, common disorders such as learning difficulties are the quantitative extreme of the same genetic factors responsible for genetic influence throughout the normal distribution (the Common Disorders are Quantitative Traits Hypothesis). Second, the same set of genes is largely responsible for genetic influence across diverse learning and cognitive abilities and disabilities (the Generalist Genes Hypothesis). Third, experiences are just as influenced genetically as are behaviors and genetic factors mediate associations between widely used measures of the environment and behavioural outcomes (the Nature of Nurture Hypothesis). CONCLUSIONS Quantitative genetics can go far beyond the rudimentary "how much" question about nature versus nurture, and can continue to provide important findings in the era of molecular genetics.
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Affiliation(s)
- Claire M A Haworth
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, United Kingdom.
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Genetics of learning abilities and disabilities: recent developments from the UK and possible directions for research in China. 2008. Behav Genet 2010; 40:297-305. [PMID: 20358396 DOI: 10.1007/s10519-010-9355-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Docherty SJ, Kovas Y, Petrill SA, Plomin R. Generalist genes analysis of DNA markers associated with mathematical ability and disability reveals shared influence across ages and abilities. BMC Genet 2010; 11:61. [PMID: 20602751 PMCID: PMC2909150 DOI: 10.1186/1471-2156-11-61] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Accepted: 07/05/2010] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND The Generalist Genes Hypothesis is based upon quantitative genetic findings which indicate that many of the same genes influence diverse cognitive abilities and disabilities across age. In a recent genome-wide association study of mathematical ability in 10-year-old children, 43 SNP associations were nominated from scans of pooled DNA, 10 of which were validated in an individually genotyped sample. The 4927 children in this genotyped sample have also been studied at 7, 9 and 12 years of age on measures of mathematical ability, as well as on other cognitive and learning abilities. RESULTS Using these data we have explored the Generalist Genes Hypothesis by assessing the association of the available measures of ability at age 10 and other ages with two composite 'SNP-set' scores, formed from the full set of 43 nominated SNPs and the sub-set of 10 SNPs that were previously found to be associated with mathematical ability at age 10. Both SNP sets yielded significant associations with mathematical ability at ages 7, 9 and 12, as well as with reading and general cognitive ability at age 10. CONCLUSIONS Although effect sizes are small, our results correspond with those of quantitative genetic research in supporting the Generalist Genes Hypothesis. SNP sets identified on the basis of their associations with mathematical ability at age 10 show associations with mathematical ability at earlier and later ages and show associations of similar magnitude with reading and general cognitive ability. With small effect sizes expected in such complex traits, future studies may be able to capitalise on power by searching for 'generalist genes' using longitudinal and multivariate approaches.
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Affiliation(s)
- Sophia J Docherty
- King's College London, MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, De Crespigny Park, London, SE5 8AF, UK
| | - Yulia Kovas
- King's College London, MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, De Crespigny Park, London, SE5 8AF, UK
- Department of Psychology, Goldsmiths, University of London, New Cross, London, UK
| | - Stephen A Petrill
- Center for Developmental and Health Genetics, The Pennsylvania State University, USA
| | - Robert Plomin
- King's College London, MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, De Crespigny Park, London, SE5 8AF, UK
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Viding E, Hanscombe KB, Curtis CJC, Davis OSP, Meaburn EL, Plomin R. In search of genes associated with risk for psychopathic tendencies in children: a two-stage genome-wide association study of pooled DNA. J Child Psychol Psychiatry 2010; 51:780-8. [PMID: 20345837 DOI: 10.1111/j.1469-7610.2010.02236.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Quantitative genetic data from our group indicates that antisocial behaviour (AB) is strongly heritable when coupled with psychopathic, callous-unemotional (CU) personality traits. We have also demonstrated that the genetic influences for AB and CU overlap considerably. We conducted a genome-wide association scan that capitalises on these findings in an attempt to identify quantitative trait loci (QTLs) that may increase risk for psychopathic tendencies (AB+/CU+). METHODS Teacher ratings at age 7 were used to screen 8374 twins with available DNA samples for individuals that were high vs. low on both AB and CU. In Stage 1, we screened for allele frequency differences in 642,432 autosomal single-nucleotide polymorphisms (SNPs) using the Affymetrix 6.0 GeneChip with pooled DNA for high-scoring (AB+/CU+) versus low-scoring children (N = approximately 300/group). In Stage 2, we tested the 3000 most strongly associated SNPs from Stage 1 for association in the same direction in a second sample of high- versus low-scoring children from the same twin study (18% co-twins). RESULTS Using allele frequencies estimated from pooled DNA, we found suggestive evidence for enrichment of association in the second stage of our two-stage genome-wide association design and focus on reporting the 30 top-ranking SNPs nominally associated with psychopathic tendencies. These SNPs include neurodevelopmental genes such as ROBO2. CONCLUSIONS Although none of the SNPs reached genome-wide statistical significance we have generated a list of SNPs that are potentially associated with psychopathic tendencies, which we believe warrant verification and replication in large independent and clinical samples.
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Affiliation(s)
- Essi Viding
- Division of Psychology and Language Sciences, University College London, UK.
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Docherty SJ, Davis OSP, Kovas Y, Meaburn EL, Dale PS, Petrill SA, Schalkwyk LC, Plomin R. A genome-wide association study identifies multiple loci associated with mathematics ability and disability. GENES, BRAIN, AND BEHAVIOR 2010; 9:234-47. [PMID: 20039944 PMCID: PMC2855870 DOI: 10.1111/j.1601-183x.2009.00553.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Revised: 09/08/2009] [Accepted: 11/02/2009] [Indexed: 12/01/2022]
Abstract
Numeracy is as important as literacy and exhibits a similar frequency of disability. Although its etiology is relatively poorly understood, quantitative genetic research has demonstrated mathematical ability to be moderately heritable. In this first genome-wide association study (GWAS) of mathematical ability and disability, 10 out of 43 single nucleotide polymorphism (SNP) associations nominated from two high- vs. low-ability (n = 600 10-year-olds each) scans of pooled DNA were validated (P < 0.05) in an individually genotyped sample of (*)2356 individuals spanning the entire distribution of mathematical ability, as assessed by teacher reports and online tests. Although the effects are of the modest sizes now expected for complex traits and require further replication, interesting candidate genes are implicated such as NRCAM which encodes a neuronal cell adhesion molecule. When combined into a set, the 10 SNPs account for 2.9% (F = 56.85; df = 1 and 1881; P = 7.277e-14) of the phenotypic variance. The association is linear across the distribution consistent with a quantitative trait locus (QTL) hypothesis; the third of children in our sample who harbour 10 or more of the 20 risk alleles identified are nearly twice as likely (OR = 1.96; df = 1; P = 3.696e-07) to be in the lowest performing 15% of the distribution. Our results correspond with those of quantitative genetic research in indicating that mathematical ability and disability are influenced by many genes generating small effects across the entire spectrum of ability, implying that more highly powered studies will be needed to detect and replicate these QTL associations.
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Affiliation(s)
- S J Docherty
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, UK.
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Abstract
Developmental dyslexia is a highly heritable disorder with a prevalence of at least 5% in school-aged children. Linkage studies have identified numerous loci throughout the genome that are likely to harbour candidate dyslexia susceptibility genes. Association studies and the refinement of chromosomal translocation break points in individuals with dyslexia have resulted in the discovery of candidate genes at some of these loci. A key function of many of these genes is their involvement in neuronal migration. This complements anatomical abnormalities discovered in dyslexic brains, such as ectopias, that may be the result of irregular neuronal migration.
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