51
|
Adams AK, Smith SD, Truong DT, Willcutt EG, Olson RK, DeFries JC, Pennington BF, Gruen JR. Enrichment of putatively damaging rare variants in the DYX2 locus and the reading-related genes CCDC136 and FLNC. Hum Genet 2017; 136:1395-1405. [PMID: 28866788 PMCID: PMC5702371 DOI: 10.1007/s00439-017-1838-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/24/2017] [Indexed: 12/19/2022]
Abstract
Eleven loci with prior evidence for association with reading and language phenotypes were sequenced in 96 unrelated subjects with significant impairment in reading performance drawn from the Colorado Learning Disability Research Center collection. Out of 148 total individual missense variants identified, the chromosome 7 genes CCDC136 and FLNC contained 19. In addition, a region corresponding to the well-known DYX2 locus for RD contained 74 missense variants. Both allele sets were filtered for a minor allele frequency ≤0.01 and high Polyphen-2 scores. To determine if observations of these alleles are occurring more frequently in our cases than expected by chance in aggregate, counts from our sample were compared to the number of observations in the European subset of the 1000 Genomes Project using Fisher's exact test. Significant P values were achieved for both CCDC136/FLNC (P = 0.0098) and the DYX2 locus (P = 0.012). Taken together, this evidence further supports the influence of these regions on reading performance. These results also support the influence of rare variants in reading disability.
Collapse
Affiliation(s)
- Andrew K Adams
- Department of Genetics, Yale University, New Haven, CT, USA
| | - Shelley D Smith
- Munroe Meyer Institute, University of Nebraska Medical Center, Omaha, NE, USA
| | | | - Erik G Willcutt
- Institute for Behavioral Genetics, University of Colorado, Boulder, CO, USA
- Department of Psychology and Neuroscience, University of Colorado, Boulder, CO, USA
| | - Richard K Olson
- Institute for Behavioral Genetics, University of Colorado, Boulder, CO, USA
- Department of Psychology and Neuroscience, University of Colorado, Boulder, CO, USA
| | - John C DeFries
- Institute for Behavioral Genetics, University of Colorado, Boulder, CO, USA
- Department of Psychology and Neuroscience, University of Colorado, Boulder, CO, USA
| | | | - Jeffrey R Gruen
- Department of Genetics, Yale University, New Haven, CT, USA.
- Department of Pediatrics and the Investigative Medicine Program, Yale University, New Haven, CT, USA.
| |
Collapse
|
52
|
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.
Collapse
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
| |
Collapse
|
53
|
Gialluisi A, Guadalupe T, Francks C, Fisher SE. Neuroimaging genetic analyses of novel candidate genes associated with reading and language. BRAIN AND LANGUAGE 2017; 172:9-15. [PMID: 27476042 DOI: 10.1016/j.bandl.2016.07.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 07/07/2016] [Indexed: 05/23/2023]
Abstract
Neuroimaging measures provide useful endophenotypes for tracing genetic effects on reading and language. A recent Genome-Wide Association Scan Meta-Analysis (GWASMA) of reading and language skills (N=1862) identified strongest associations with the genes CCDC136/FLNC and RBFOX2. Here, we follow up the top findings from this GWASMA, through neuroimaging genetics in an independent sample of 1275 healthy adults. To minimize multiple-testing, we used a multivariate approach, focusing on cortical regions consistently implicated in prior literature on developmental dyslexia and language impairment. Specifically, we investigated grey matter surface area and thickness of five regions selected a priori: middle temporal gyrus (MTG); pars opercularis and pars triangularis in the inferior frontal gyrus (IFG-PO and IFG-PT); postcentral parietal gyrus (PPG) and superior temporal gyrus (STG). First, we analysed the top associated polymorphisms from the reading/language GWASMA: rs59197085 (CCDC136/FLNC) and rs5995177 (RBFOX2). There was significant multivariate association of rs5995177 with cortical thickness, driven by effects on left PPG, right MTG, right IFG (both PO and PT), and STG bilaterally. The minor allele, previously associated with reduced reading-language performance, showed negative effects on grey matter thickness. Next, we performed exploratory gene-wide analysis of CCDC136/FLNC and RBFOX2; no other associations surpassed significance thresholds. RBFOX2 encodes an important neuronal regulator of alternative splicing. Thus, the prior reported association of rs5995177 with reading/language performance could potentially be mediated by reduced thickness in associated cortical regions. In future, this hypothesis could be tested using sufficiently large samples containing both neuroimaging data and quantitative reading/language scores from the same individuals.
Collapse
Affiliation(s)
- Alessandro Gialluisi
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands; Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Tulio Guadalupe
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
| | - Clyde Francks
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Netherlands
| | - 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.
| |
Collapse
|
54
|
Zubicaray GD, Fisher SE. Genes, Brain, and Language: A brief introduction to the Special Issue. BRAIN AND LANGUAGE 2017; 172:1-2. [PMID: 28867043 DOI: 10.1016/j.bandl.2017.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Affiliation(s)
- Greig de Zubicaray
- Queensland University of Technology (QUT), Faculty of Health and Institute of Health and Biomedical Innovation, Brisbane, Queensland, 4059, Australia.
| | - Simon E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherland.
| |
Collapse
|
55
|
Deters KD, Nho K, Risacher SL, Kim S, Ramanan VK, Crane PK, Apostolova LG, Saykin AJ. Genome-wide association study of language performance in Alzheimer's disease. BRAIN AND LANGUAGE 2017; 172:22-29. [PMID: 28577822 PMCID: PMC5583024 DOI: 10.1016/j.bandl.2017.04.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 04/25/2017] [Accepted: 04/27/2017] [Indexed: 05/04/2023]
Abstract
Language impairment is common in prodromal stages of Alzheimer's disease (AD) and progresses over time. However, the genetic architecture underlying language performance is poorly understood. To identify novel genetic variants associated with language performance, we analyzed brain MRI and performed a genome-wide association study (GWAS) using a composite measure of language performance from the Alzheimer's Disease Neuroimaging Initiative (ADNI; n=1560). The language composite score was associated with brain atrophy on MRI in language and semantic areas. GWAS identified GLI3 (GLI family zinc finger 3) as significantly associated with language performance (p<5×10-8). Enrichment of GWAS association was identified in pathways related to nervous system development and glutamate receptor function and trafficking. Our results, which warrant further investigation in independent and larger cohorts, implicate GLI3, a developmental transcription factor involved in patterning brain structures, as a putative gene associated with language dysfunction in AD.
Collapse
Affiliation(s)
- Kacie D Deters
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA; Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA; Program in Medical Neuroscience, Paul and Carole Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kwangsik Nho
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA; Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Shannon L Risacher
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA; Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Sungeun Kim
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA; Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Vijay K Ramanan
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA; Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Paul K Crane
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Liana G Apostolova
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA; Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Medicine, University of Washington, Seattle, WA, USA; Department of Neurology, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Andrew J Saykin
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA; Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Medicine, University of Washington, Seattle, WA, USA; Department of Neurology, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA.
| |
Collapse
|
56
|
Deriziotis P, Fisher SE. Speech and Language: Translating the Genome. Trends Genet 2017; 33:642-656. [DOI: 10.1016/j.tig.2017.07.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 07/11/2017] [Accepted: 07/12/2017] [Indexed: 01/30/2023]
|
57
|
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.
Collapse
|
58
|
Abstract
Human genetic studies have been the driving force in bringing to light the underlying biology of psychiatric conditions. As these studies fill in the gaps in our knowledge of the mechanisms at play, we will be better equipped to design therapies in rational and targeted ways, or repurpose existing therapies in previously unanticipated ways. This review is intended for those unfamiliar with psychiatric genetics as a field and provides a primer on different modes of genetic variation, the technologies currently used to probe them, and concepts that provide context for interpreting the gene-phenotype relationship. Like other subfields in human genetics, psychiatric genetics is moving from microarray technology to sequencing-based approaches as barriers of cost and expertise are removed, and the ramifications of this transition are discussed here. A summary is then given of recent genetic discoveries in a number of neuropsychiatric conditions, with particular emphasis on neurodevelopmental conditions. The general impact of genetics on drug development has been to underscore the extensive etiological heterogeneity in seemingly cohesive diagnostic categories. Consequently, the path forward is not in therapies hoping to reach large swaths of patients sharing a clinically defined diagnosis, but rather in targeting patients belonging to specific "biotypes" defined through a combination of objective, quantifiable data, including genotype.
Collapse
Affiliation(s)
- Jacob J Michaelson
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA.
- Department of Biomedical Engineering, University of Iowa College of Engineering, Iowa City, IA, USA.
- Department of Communication Sciences and Disorders, University of Iowa College of Liberal Arts and Sciences, Iowa City, IA, USA.
- Iowa Institute of Human Genetics, University of Iowa, Iowa City, IA, USA.
- Genetics Cluster Initiative, University of Iowa, Iowa City, IA, USA.
- The DeLTA Center, University of Iowa, Iowa City, IA, USA.
- University of Iowa Informatics Initiative, University of Iowa, Iowa City, IA, USA.
| |
Collapse
|
59
|
Carrion-Castillo A, van Bergen E, Vino A, van Zuijen T, de Jong PF, Francks C, Fisher SE. Evaluation of results from genome-wide studies of language and reading in a novel independent dataset. GENES BRAIN AND BEHAVIOR 2017; 15:531-41. [PMID: 27198479 DOI: 10.1111/gbb.12299] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 05/17/2016] [Accepted: 05/17/2016] [Indexed: 01/05/2023]
Abstract
Recent genome-wide association scans (GWAS) for reading and language abilities have pin-pointed promising new candidate loci. However, the potential contributions of these loci remain to be validated. In this study, we tested 17 of the most significantly associated single nucleotide polymorphisms (SNPs) from these GWAS studies (P < 10(-6) in the original studies) in a new independent population dataset from the Netherlands: known as Familial Influences on Literacy Abilities. This dataset comprised 483 children from 307 nuclear families and 505 adults (including parents of participating children), and provided adequate statistical power to detect the effects that were previously reported. The following measures of reading and language performance were collected: word reading fluency, nonword reading fluency, phonological awareness and rapid automatized naming. Two SNPs (rs12636438 and rs7187223) were associated with performance in multivariate and univariate testing, but these did not remain significant after correction for multiple testing. Another SNP (rs482700) was only nominally associated in the multivariate test. For the rest of the SNPs, we did not find supportive evidence of association. The findings may reflect differences between our study and the previous investigations with respect to the language of testing, the exact tests used and the recruitment criteria. Alternatively, most of the prior reported associations may have been false positives. A larger scale GWAS meta-analysis than those previously performed will likely be required to obtain robust insights into the genomic architecture underlying reading and language.
Collapse
Affiliation(s)
- A Carrion-Castillo
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
| | - E van Bergen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands.,Department of Experimental Psychology, University of Oxford, Oxford, UK
| | - A Vino
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
| | - T van Zuijen
- Research Institute of Child Development and Education, University of Amsterdam, Amsterdam, the Netherlands
| | - P F de Jong
- Research Institute of Child Development and Education, University of Amsterdam, Amsterdam, the Netherlands
| | - C Francks
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands
| | - S E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands
| |
Collapse
|
60
|
Chen XS, Reader RH, Hoischen A, Veltman JA, Simpson NH, Francks C, Newbury DF, Fisher SE. Next-generation DNA sequencing identifies novel gene variants and pathways involved in specific language impairment. Sci Rep 2017; 7:46105. [PMID: 28440294 PMCID: PMC5404330 DOI: 10.1038/srep46105] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 03/08/2017] [Indexed: 12/22/2022] Open
Abstract
A significant proportion of children have unexplained problems acquiring proficient linguistic skills despite adequate intelligence and opportunity. Developmental language disorders are highly heritable with substantial societal impact. Molecular studies have begun to identify candidate loci, but much of the underlying genetic architecture remains undetermined. We performed whole-exome sequencing of 43 unrelated probands affected by severe specific language impairment, followed by independent validations with Sanger sequencing, and analyses of segregation patterns in parents and siblings, to shed new light on aetiology. By first focusing on a pre-defined set of known candidates from the literature, we identified potentially pathogenic variants in genes already implicated in diverse language-related syndromes, including ERC1, GRIN2A, and SRPX2. Complementary analyses suggested novel putative candidates carrying validated variants which were predicted to have functional effects, such as OXR1, SCN9A and KMT2D. We also searched for potential “multiple-hit” cases; one proband carried a rare AUTS2 variant in combination with a rare inherited haplotype affecting STARD9, while another carried a novel nonsynonymous variant in SEMA6D together with a rare stop-gain in SYNPR. On broadening scope to all rare and novel variants throughout the exomes, we identified biological themes that were enriched for such variants, including microtubule transport and cytoskeletal regulation.
Collapse
Affiliation(s)
- Xiaowei Sylvia Chen
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Rose H Reader
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Joris A Veltman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Clinical Genetics, University of Maastricht, Maastricht, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Nuala H Simpson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Clyde Francks
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Dianne F Newbury
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.,Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Simon E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| |
Collapse
|
61
|
Neurogenetics of developmental dyslexia: from genes to behavior through brain neuroimaging and cognitive and sensorial mechanisms. Transl Psychiatry 2017; 7:e987. [PMID: 28045463 PMCID: PMC5545717 DOI: 10.1038/tp.2016.240] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 10/15/2016] [Indexed: 01/18/2023] Open
Abstract
Developmental dyslexia (DD) is a complex neurodevelopmental deficit characterized by impaired reading acquisition, in spite of adequate neurological and sensorial conditions, educational opportunities and normal intelligence. Despite the successful characterization of DD-susceptibility genes, we are far from understanding the molecular etiological pathways underlying the development of reading (dis)ability. By focusing mainly on clinical phenotypes, the molecular genetics approach has yielded mixed results. More optimally reduced measures of functioning, that is, intermediate phenotypes (IPs), represent a target for researching disease-associated genetic variants and for elucidating the underlying mechanisms. Imaging data provide a viable IP for complex neurobehavioral disorders and have been extensively used to investigate both morphological, structural and functional brain abnormalities in DD. Performing joint genetic and neuroimaging studies in humans is an emerging strategy to link DD-candidate genes to the brain structure and function. A limited number of studies has already pursued the imaging-genetics integration in DD. However, the results are still not sufficient to unravel the complexity of the reading circuit due to heterogeneous study design and data processing. Here, we propose an interdisciplinary, multilevel, imaging-genetic approach to disentangle the pathways from genes to behavior. As the presence of putative functional genetic variants has been provided and as genetic associations with specific cognitive/sensorial mechanisms have been reported, new hypothesis-driven imaging-genetic studies must gain momentum. This approach would lead to the optimization of diagnostic criteria and to the early identification of 'biologically at-risk' children, supporting the definition of adequate and well-timed prevention strategies and the implementation of novel, specific remediation approach.
Collapse
|
62
|
Pettigrew KA, Frinton E, Nudel R, Chan MTM, Thompson P, Hayiou-Thomas ME, Talcott JB, Stein J, Monaco AP, Hulme C, Snowling MJ, Newbury DF, Paracchini S. Further evidence for a parent-of-origin effect at the NOP9 locus on language-related phenotypes. J Neurodev Disord 2016; 8:24. [PMID: 27307794 PMCID: PMC4908686 DOI: 10.1186/s11689-016-9157-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 06/03/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Specific language impairment (SLI) is a common neurodevelopmental disorder, observed in 5-10 % of children. Family and twin studies suggest a strong genetic component, but relatively few candidate genes have been reported to date. A recent genome-wide association study (GWAS) described the first statistically significant association specifically for a SLI cohort between a missense variant (rs4280164) in the NOP9 gene and language-related phenotypes under a parent-of-origin model. Replications of these findings are particularly challenging because the availability of parental DNA is required. METHODS We used two independent family-based cohorts characterised with reading- and language-related traits: a longitudinal cohort (n = 106 informative families) including children with language and reading difficulties and a nuclear family cohort (n = 264 families) selected for dyslexia. RESULTS We observed association with language-related measures when modelling for parent-of-origin effects at the NOP9 locus in both cohorts: minimum P = 0.001 for phonological awareness with a paternal effect in the first cohort and minimum P = 0.0004 for irregular word reading with a maternal effect in the second cohort. Allelic and parental trends were not consistent when compared to the original study. CONCLUSIONS A parent-of-origin effect at this locus was detected in both cohorts, albeit with different trends. These findings contribute in interpreting the original GWAS report and support further investigations of the NOP9 locus and its role in language-related traits. A systematic evaluation of parent-of-origin effects in genetic association studies has the potential to reveal novel mechanisms underlying complex traits.
Collapse
Affiliation(s)
| | - Emily Frinton
- />School of Medicine, University of St Andrews, St Andrews, KY16 9TF UK
| | - Ron Nudel
- />Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN UK
| | - May T. M. Chan
- />Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN UK
- />Worcester College, University of Oxford, Oxford, OX1 2HB UK
| | - Paul Thompson
- />Department of Experimental Psychology, University of Oxford, South Parks Road, Oxford, OX1 3PT UK
| | | | - Joel B. Talcott
- />School of Life and Health Sciences, Aston University, Birmingham, B4 7ET UK
| | - John Stein
- />Department of Physiology, University of Oxford, Parks Road, Oxford, OX1 3PT UK
| | - Anthony P. Monaco
- />Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN UK
| | - Charles Hulme
- />Division of Psychology and Language Sciences, University College London, London, WC1 3PG UK
| | - Margaret J. Snowling
- />Department of Experimental Psychology, University of Oxford, South Parks Road, Oxford, OX1 3PT UK
- />St John’s College, University of Oxford, Oxford, OX1 3JP UK
| | - Dianne F. Newbury
- />Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN UK
| | - Silvia Paracchini
- />School of Medicine, University of St Andrews, St Andrews, KY16 9TF UK
| |
Collapse
|
63
|
Gialluisi A, Visconti A, Willcutt EG, Smith SD, Pennington BF, Falchi M, DeFries JC, Olson RK, Francks C, Fisher SE. Investigating the effects of copy number variants on reading and language performance. J Neurodev Disord 2016; 8:17. [PMID: 27186239 PMCID: PMC4868026 DOI: 10.1186/s11689-016-9147-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 03/31/2016] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Reading and language skills have overlapping genetic bases, most of which are still unknown. Part of the missing heritability may be caused by copy number variants (CNVs). METHODS In a dataset of children recruited for a history of reading disability (RD, also known as dyslexia) or attention deficit hyperactivity disorder (ADHD) and their siblings, we investigated the effects of CNVs on reading and language performance. First, we called CNVs with PennCNV using signal intensity data from Illumina OmniExpress arrays (~723,000 probes). Then, we computed the correlation between measures of CNV genomic burden and the first principal component (PC) score derived from several continuous reading and language traits, both before and after adjustment for performance IQ. Finally, we screened the genome, probe-by-probe, for association with the PC scores, through two complementary analyses: we tested a binary CNV state assigned for the location of each probe (i.e., CNV+ or CNV-), and we analyzed continuous probe intensity data using FamCNV. RESULTS No significant correlation was found between measures of CNV burden and PC scores, and no genome-wide significant associations were detected in probe-by-probe screening. Nominally significant associations were detected (p~10(-2)-10(-3)) within CNTN4 (contactin 4) and CTNNA3 (catenin alpha 3). These genes encode cell adhesion molecules with a likely role in neuronal development, and they have been previously implicated in autism and other neurodevelopmental disorders. A further, targeted assessment of candidate CNV regions revealed associations with the PC score (p~0.026-0.045) within CHRNA7 (cholinergic nicotinic receptor alpha 7), which encodes a ligand-gated ion channel and has also been implicated in neurodevelopmental conditions and language impairment. FamCNV analysis detected a region of association (p~10(-2)-10(-4)) within a frequent deletion ~6 kb downstream of ZNF737 (zinc finger protein 737, uncharacterized protein), which was also observed in the association analysis using CNV calls. CONCLUSIONS These data suggest that CNVs do not underlie a substantial proportion of variance in reading and language skills. Analysis of additional, larger datasets is warranted to further assess the potential effects that we found and to increase the power to detect CNV effects on reading and language.
Collapse
Affiliation(s)
- Alessandro Gialluisi
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Wundtlaan 1, 6525 XD Nijmegen, The Netherlands ; Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Alessia Visconti
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Erik G Willcutt
- Institute for Behavioral Genetics, University of Colorado, Boulder, CO USA ; Department of Psychology and Neuroscience, University of Colorado, Boulder, CO USA
| | - Shelley D Smith
- Munroe Meyer Institute, University of Nebraska Medical Center, Omaha, NE USA
| | | | - Mario Falchi
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - John C DeFries
- Institute for Behavioral Genetics, University of Colorado, Boulder, CO USA ; Department of Psychology and Neuroscience, University of Colorado, Boulder, CO USA
| | - Richard K Olson
- Institute for Behavioral Genetics, University of Colorado, Boulder, CO USA ; Department of Psychology and Neuroscience, University of Colorado, Boulder, CO USA
| | - Clyde Francks
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Wundtlaan 1, 6525 XD Nijmegen, The Netherlands ; Donders Institute for Brain Cognition and Behaviour, Nijmegen, The Netherlands
| | - Simon E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Wundtlaan 1, 6525 XD Nijmegen, The Netherlands ; Donders Institute for Brain Cognition and Behaviour, Nijmegen, The Netherlands
| |
Collapse
|
64
|
Mueller KL, Murray JC, Michaelson JJ, Christiansen MH, Reilly S, Tomblin JB. Common Genetic Variants in FOXP2 Are Not Associated with Individual Differences in Language Development. PLoS One 2016; 11:e0152576. [PMID: 27064276 PMCID: PMC4827837 DOI: 10.1371/journal.pone.0152576] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 03/16/2016] [Indexed: 02/07/2023] Open
Abstract
Much of our current knowledge regarding the association of FOXP2 with speech and language development comes from singleton and small family studies where a small number of rare variants have been identified. However, neither genome-wide nor gene-specific studies have provided evidence that common polymorphisms in the gene contribute to individual differences in language development in the general population. One explanation for this inconsistency is that previous studies have been limited to relatively small samples of individuals with low language abilities, using low density gene coverage. The current study examined the association between common variants in FOXP2 and a quantitative measure of language ability in a population-based cohort of European decent (n = 812). No significant associations were found for a panel of 13 SNPs that covered the coding region of FOXP2 and extended into the promoter region. Power analyses indicated we should have been able to detect a QTL variance of 0.02 for an associated allele with MAF of 0.2 or greater with 80% power. This suggests that, if a common variant associated with language ability in this gene does exist, it is likely of small effect. Our findings lead us to conclude that while genetic variants in FOXP2 may be significant for rare forms of language impairment, they do not contribute appreciably to individual variation in the normal range as found in the general population.
Collapse
Affiliation(s)
- Kathryn L. Mueller
- Hearing, Language and Literacy, Murdoch Childrens Institute, Melbourne, Australia
- Dept. of Communication Sciences and Disorders, The University of Iowa, Iowa City, United States of America
- * E-mail:
| | - Jeffrey C. Murray
- Dept. of Pediatrics, The University of Iowa, Iowa City, United States of America
| | - Jacob J. Michaelson
- Dept. of Psychiatry, The University of Iowa, Iowa City, United States of America
| | | | | | - J. Bruce Tomblin
- Dept. of Communication Sciences and Disorders, The University of Iowa, Iowa City, United States of America
| |
Collapse
|
65
|
Kornilov SA, Rakhlin N, Koposov R, Lee M, Yrigollen C, Caglayan AO, Magnuson JS, Mane S, Chang JT, Grigorenko EL. Genome-Wide Association and Exome Sequencing Study of Language Disorder in an Isolated Population. Pediatrics 2016; 137:peds.2015-2469. [PMID: 27016271 PMCID: PMC4811310 DOI: 10.1542/peds.2015-2469] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/26/2016] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND AND OBJECTIVE Developmental language disorder (DLD) is a highly prevalent neurodevelopmental disorder associated with negative outcomes in different domains; the etiology of DLD is unknown. To investigate the genetic underpinnings of DLD, we performed genome-wide association and whole exome sequencing studies in a geographically isolated population with a substantially elevated prevalence of the disorder (ie, the AZ sample). METHODS DNA samples were collected from 359 individuals for the genome-wide association study and from 12 severely affected individuals for whole exome sequencing. Multifaceted phenotypes, representing major domains of expressive language functioning, were derived from collected speech samples. RESULTS Gene-based analyses revealed a significant association between SETBP1 and complexity of linguistic output (P = 5.47 × 10(-7)). The analysis of exome variants revealed coding sequence variants in 14 genes, most of which play a role in neural development. Targeted enrichment analysis implicated myocyte enhancer factor-2 (MEF2)-regulated genes in DLD in the AZ population. The main findings were successfully replicated in an independent cohort of children at risk for related disorders (n = 372). CONCLUSIONS MEF2-regulated pathways were identified as potential candidate pathways in the etiology of DLD. Several genes (including the candidate SETBP1 and other MEF2-related genes) seem to jointly influence certain, but not all, facets of the DLD phenotype. Even when genetic and environmental diversity is reduced, DLD is best conceptualized as etiologically complex. Future research should establish whether the signals detected in the AZ population can be replicated in other samples and languages and provide further characterization of the identified pathway.
Collapse
Affiliation(s)
- Sergey A. Kornilov
- Child Study Center, School of Medicine, Yale University, New Haven, Connecticut;,Department of Psychology, University of Connecticut, Storrs, Connecticut;,Haskins Laboratories, New Haven, Connecticut;,Department of Psychology, Moscow State University, Moscow, Russia;,Department of Psychology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Natalia Rakhlin
- Child Study Center, School of Medicine, Yale University, New Haven, Connecticut;,Department of Communication Sciences and Disorders, Wayne State University, Detroit, Michigan
| | - Roman Koposov
- Regional Centre for Child and Youth Mental Health and Child Welfare, UiT The Arctic University of Norway, Tromsø, Norway
| | - Maria Lee
- Child Study Center, School of Medicine, Yale University, New Haven, Connecticut
| | - Carolyn Yrigollen
- The Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ahmet Okay Caglayan
- Child Study Center, School of Medicine, Yale University, New Haven, Connecticut;,Department of Medical Genetics, Istanbul Bilim University, Istanbul, Turkey; and
| | - James S. Magnuson
- Department of Psychology, University of Connecticut, Storrs, Connecticut;,Haskins Laboratories, New Haven, Connecticut
| | - Shrikant Mane
- Child Study Center, School of Medicine, Yale University, New Haven, Connecticut
| | - Joseph T. Chang
- Child Study Center, School of Medicine, Yale University, New Haven, Connecticut
| | - Elena L. Grigorenko
- Child Study Center, School of Medicine, Yale University, New Haven, Connecticut;,Haskins Laboratories, New Haven, Connecticut;,Department of Psychology, Saint Petersburg State University, Saint Petersburg, Russia;,Moscow State University for Psychology and Education, Moscow, Russia
| |
Collapse
|
66
|
Evans PD, Mueller KL, Gamazon ER, Cox NJ, Tomblin JB. A genome-wide sib-pair scan for quantitative language traits reveals linkage to chromosomes 10 and 13. GENES BRAIN AND BEHAVIOR 2016; 14:387-97. [PMID: 25997078 DOI: 10.1111/gbb.12223] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 05/06/2015] [Accepted: 05/06/2015] [Indexed: 02/03/2023]
Abstract
Although there is considerable evidence that individual differences in language development are highly heritable, there have been few genome-wide scans to locate genes associated with the trait. Previous analyses of language impairment have yielded replicable evidence for linkage to regions on chromosomes 16q, 19q, 13q (within lab) and at 13q (between labs). Here we report the first linkage study to screen the continuum of language ability, from normal to disordered, as found in the general population. 383 children from 147 sib-ships (214 sib-pairs) were genotyped on the Illumina(®) Linkage IVb Marker Panel using three composite language-related phenotypes and a measure of phonological memory (PM). Two regions (10q23.33; 13q33.3) yielded genome-wide significant peaks for linkage with PM. A peak suggestive of linkage was also found at 17q12 for the overall language composite. This study presents two novel genetic loci for the study of language development and disorders, but fails to replicate findings by previous groups. Possible reasons for this are discussed.
Collapse
Affiliation(s)
- P D Evans
- Department of Medicine, The University of Chicago, IL, USA
| | - K L Mueller
- Murdoch Childrens Research Institute, Melbourne, Australia.,Department of Communication Sciences and Disorders, The University of Iowa, IA, USA
| | - E R Gamazon
- Department of Medicine, The University of Chicago, IL, USA.,Present address: Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN, USA
| | - N J Cox
- Department of Medicine, The University of Chicago, IL, USA.,Department of Communication Sciences and Disorders, The University of Iowa, IA, USA.,Present address: Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN, USA
| | - J B Tomblin
- Department of Communication Sciences and Disorders, The University of Iowa, IA, USA
| |
Collapse
|
67
|
Massinen S, Wang J, Laivuori K, Bieder A, Tapia Paez I, Jiao H, Kere J. Genomic sequencing of a dyslexia susceptibility haplotype encompassing ROBO1. J Neurodev Disord 2016; 8:4. [PMID: 26877820 PMCID: PMC4751651 DOI: 10.1186/s11689-016-9136-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 01/17/2016] [Indexed: 12/19/2022] Open
Abstract
Background The DYX5 locus for developmental dyslexia was mapped to chromosome 3 by linkage study of a large Finnish family, and later, roundabout guidance receptor 1 (ROBO1) was implicated as a candidate gene at DYX5 with suppressed expression from the segregating rare haplotype. A functional magnetoencephalographic study of several family members revealed abnormal auditory processing of interaural interaction, supporting a defect in midline crossing of auditory pathways. In the current study, we have characterized genetic variation in the broad ROBO1 gene region in the DYX5-linked family, aiming to identify variants that would increase our understanding of the altered expression of ROBO1. Methods We have used a whole genome sequencing strategy on a pooled sample of 19 individuals in combination with two individually sequenced genomes. The discovered genetic variants were annotated and filtered. Subsequently, the most interesting variants were functionally tested using relevant methods, including electrophoretic mobility shift assay (EMSA), luciferase assay, and gene knockdown by lentiviral small hairpin RNA (shRNA) in lymphoblasts. Results We found one novel intronic single nucleotide variant (SNV) and three novel intergenic SNVs in the broad region of ROBO1 that were specific to the dyslexia susceptibility haplotype. Functional testing by EMSA did not support the binding of transcription factors to three of the SNVs, but one of the SNVs was bound by the LIM homeobox 2 (LHX2) protein, with increased binding affinity for the non-reference allele. Knockdown of LHX2 in lymphoblast cell lines extracted from subjects from the DYX5-linked family showed decreasing expression of ROBO1, supporting the idea that LHX2 regulates ROBO1 also in human. Conclusions The discovered variants may explain the segregation of dyslexia in this family, but the effect appears subtle in the experimental settings. Their impact on the developing human brain remains suggestive based on the association and subtle experimental support. Electronic supplementary material The online version of this article (doi:10.1186/s11689-016-9136-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Satu Massinen
- Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland ; Folkhälsan Institute of Genetics, Biomedicum Helsinki, Helsinki, Finland
| | - Jingwen Wang
- Department of Biosciences and Nutrition, and Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Krista Laivuori
- Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland ; Folkhälsan Institute of Genetics, Biomedicum Helsinki, Helsinki, Finland
| | - Andrea Bieder
- Department of Biosciences and Nutrition, and Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Isabel Tapia Paez
- Department of Biosciences and Nutrition, and Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Hong Jiao
- Department of Biosciences and Nutrition, and Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Juha Kere
- Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland ; Folkhälsan Institute of Genetics, Biomedicum Helsinki, Helsinki, Finland ; Department of Biosciences and Nutrition, and Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
68
|
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]
|
69
|
Abstract
Language is a defining characteristic of the human species, but its foundations remain mysterious. Heritable disorders offer a gateway into biological underpinnings, as illustrated by the discovery that FOXP2 disruptions cause a rare form of speech and language impairment. The genetic architecture underlying language-related disorders is complex, and although some progress has been made, it has proved challenging to pinpoint additional relevant genes with confidence. Next-generation sequencing and genome-wide association studies are revolutionizing understanding of the genetic bases of other neurodevelopmental disorders, like autism and schizophrenia, and providing fundamental insights into the molecular networks crucial for typical brain development. We discuss how a similar genomic perspective, brought to the investigation of language-related phenotypes, promises to yield equally informative discoveries. Moreover, we outline how follow-up studies of genetic findings using cellular systems and animal models can help to elucidate the biological mechanisms involved in the development of brain circuits supporting language.
Collapse
Affiliation(s)
- Sarah A Graham
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, The Netherlands;
| | - Simon E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, The Netherlands; .,Donders Institute for Brain, Cognition and Behavior, Radboud University, 6525 EN Nijmegen, The Netherlands;
| |
Collapse
|
70
|
Affiliation(s)
- Robin L. Peterson
- Department of Rehabilitation Medicine, Children's Hospital Colorado, Aurora, Colorado 80045;
| | | |
Collapse
|
71
|
Villanueva P, Nudel R, Hoischen A, Fernández MA, Simpson NH, Gilissen C, Reader RH, Jara L, Echeverry MM, Francks C, Baird G, Conti-Ramsden G, O’Hare A, Bolton PF, Hennessy ER, Palomino H, Carvajal-Carmona L, Veltman JA, Cazier JB, De Barbieri Z, Fisher SE, Newbury DF. Exome sequencing in an admixed isolated population indicates NFXL1 variants confer a risk for specific language impairment. PLoS Genet 2015; 11:e1004925. [PMID: 25781923 PMCID: PMC4363375 DOI: 10.1371/journal.pgen.1004925] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 11/25/2014] [Indexed: 11/06/2022] Open
Abstract
Children affected by Specific Language Impairment (SLI) fail to acquire age appropriate language skills despite adequate intelligence and opportunity. SLI is highly heritable, but the understanding of underlying genetic mechanisms has proved challenging. In this study, we use molecular genetic techniques to investigate an admixed isolated founder population from the Robinson Crusoe Island (Chile), who are affected by a high incidence of SLI, increasing the power to discover contributory genetic factors. We utilize exome sequencing in selected individuals from this population to identify eight coding variants that are of putative significance. We then apply association analyses across the wider population to highlight a single rare coding variant (rs144169475, Minor Allele Frequency of 4.1% in admixed South American populations) in the NFXL1 gene that confers a nonsynonymous change (N150K) and is significantly associated with language impairment in the Robinson Crusoe population (p = 2.04 × 10–4, 8 variants tested). Subsequent sequencing of NFXL1 in 117 UK SLI cases identified four individuals with heterozygous variants predicted to be of functional consequence. We conclude that coding variants within NFXL1 confer an increased risk of SLI within a complex genetic model. Children affected by Specific Language Impairment (SLI) have unexpected problems learning to talk and understand language, despite developing normally in all other areas. This disorder runs in families but we do not understand how the genetic contributions work, or which genetic mechanisms might be important. In this paper, we study a Chilean population who are affected by a high incidence of SLI. Such populations may provide increased power to discover contributory genetic factors, under appropriate conditions. We identify a genetic change in the population that causes a change to a protein called NFXL1. This change is usually very rare but is found at a higher frequency than expected in our population, particularly in those people affected by SLI. We then looked at this gene in over 100 individuals from the UK affected by SLI and found four more changes that probably affect the protein. This is a higher number than we would expect by chance. We therefore propose that the NFXL1 gene and the protein it encodes might be important in risk of SLI.
Collapse
Affiliation(s)
- Pía Villanueva
- Human Genetics Program, Institute of Biomedical Sciences (ICBM), Faculty of Medicine, University of Chile, Santiago, Chile
- School of Speech and Hearing Therapy, Faculty of Medicine, University of Chile, Santiago, Chile
- Department of Child and Dental Maxillary Orthopedics, Faculty of Dentistry, University of Chile, Santiago, Chile
- Doctoral Program of Psychology, Graduate School, University of Granada, Granada, Spain
- * E-mail: (PV, linguistic and population queries); (DFN, genetic queries)
| | - Ron Nudel
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Alexander Hoischen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences and Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Nuala H. Simpson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Christian Gilissen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences and Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rose H. Reader
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Lillian Jara
- Human Genetics Program, Institute of Biomedical Sciences (ICBM), Faculty of Medicine, University of Chile, Santiago, Chile
| | - Maria Magdalena Echeverry
- Grupo de Citogenetica, Filogenia y Evolucion de las Poblaciones, Facultades de Ciencias y de Ciencias de la Salud, Universidad del Tolima, Ibague, Colombia
| | - Clyde Francks
- Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands
| | - Gillian Baird
- Newcomen Centre, the Evelina Children’s Hospital, London, United Kingdom
| | - Gina Conti-Ramsden
- School of Psychological Sciences, University of Manchester, Manchester, United Kingdom
| | - Anne O’Hare
- Department of Reproductive and Developmental Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Patrick F. Bolton
- Departments of Child & Adolescent Psychiatry & Social Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, King’s College London, London, United Kingdom
| | | | | | - Hernán Palomino
- Department of Child and Dental Maxillary Orthopedics, Faculty of Dentistry, University of Chile, Santiago, Chile
| | - Luis Carvajal-Carmona
- Grupo de Citogenetica, Filogenia y Evolucion de las Poblaciones, Facultades de Ciencias y de Ciencias de la Salud, Universidad del Tolima, Ibague, Colombia
- UC Davis Genome Center, Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Davis, California, United States of America
| | - Joris A. Veltman
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences and Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jean-Baptiste Cazier
- Department of Oncology, University of Oxford, Oxford, United Kingdom
- Centre for Computational Biology, University of Birmingham, Edgbaston, United Kingdom
| | - Zulema De Barbieri
- School of Speech and Hearing Therapy, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Simon E. Fisher
- Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands
| | - Dianne F. Newbury
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- St Johns College, University of Oxford, Oxford, United Kingdom
- * E-mail: (PV, linguistic and population queries); (DFN, genetic queries)
| |
Collapse
|
72
|
Insights into the genetic foundations of human communication. Neuropsychol Rev 2015; 25:3-26. [PMID: 25597031 DOI: 10.1007/s11065-014-9277-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 12/22/2014] [Indexed: 12/19/2022]
Abstract
The human capacity to acquire sophisticated language is unmatched in the animal kingdom. Despite the discontinuity in communicative abilities between humans and other primates, language is built on ancient genetic foundations, which are being illuminated by comparative genomics. The genetic architecture of the language faculty is also being uncovered by research into neurodevelopmental disorders that disrupt the normally effortless process of language acquisition. In this article, we discuss the strategies that researchers are using to reveal genetic factors contributing to communicative abilities, and review progress in identifying the relevant genes and genetic variants. The first gene directly implicated in a speech and language disorder was FOXP2. Using this gene as a case study, we illustrate how evidence from genetics, molecular cell biology, animal models and human neuroimaging has converged to build a picture of the role of FOXP2 in neurodevelopment, providing a framework for future endeavors to bridge the gaps between genes, brains and behavior.
Collapse
|
73
|
Hofmeister W, Nilsson D, Topa A, Anderlid BM, Darki F, Matsson H, Tapia Páez I, Klingberg T, Samuelsson L, Wirta V, Vezzi F, Kere J, Nordenskjöld M, Syk Lundberg E, Lindstrand A. CTNND2-a candidate gene for reading problems and mild intellectual disability. J Med Genet 2014; 52:111-22. [PMID: 25473103 DOI: 10.1136/jmedgenet-2014-102757] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND Cytogenetically visible chromosomal translocations are highly informative as they can pinpoint strong effect genes even in complex genetic disorders. METHODS AND RESULTS Here, we report a mother and daughter, both with borderline intelligence and learning problems within the dyslexia spectrum, and two apparently balanced reciprocal translocations: t(1;8)(p22;q24) and t(5;18)(p15;q11). By low coverage mate-pair whole-genome sequencing, we were able to pinpoint the genomic breakpoints to 2 kb intervals. By direct sequencing, we then located the chromosome 5p breakpoint to intron 9 of CTNND2. An additional case with a 163 kb microdeletion exclusively involving CTNND2 was identified with genome-wide array comparative genomic hybridisation. This microdeletion at 5p15.2 is also present in mosaic state in the patient's mother but absent from the healthy siblings. We then investigated the effect of CTNND2 polymorphisms on normal variability and identified a polymorphism (rs2561622) with significant effect on phonological ability and white matter volume in the left frontal lobe, close to cortical regions previously associated with phonological processing. Finally, given the potential role of CTNND2 in neuron motility, we used morpholino knockdown in zebrafish embryos to assess its effects on neuronal migration in vivo. Analysis of the zebrafish forebrain revealed a subpopulation of neurons misplaced between the diencephalon and telencephalon. CONCLUSIONS Taken together, our human genetic and in vivo data suggest that defective migration of subpopulations of neuronal cells due to haploinsufficiency of CTNND2 contribute to the cognitive dysfunction in our patients.
Collapse
Affiliation(s)
- Wolfgang Hofmeister
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Daniel Nilsson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden Science for Life Laboratory, Karolinska Institutet Science Park, Solna, Sweden
| | - Alexandra Topa
- Department of Clinical Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Britt-Marie Anderlid
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Fahimeh Darki
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Hans Matsson
- Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Isabel Tapia Páez
- Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Torkel Klingberg
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Lena Samuelsson
- Department of Clinical Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Valtteri Wirta
- SciLifeLab, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Francesco Vezzi
- SciLifeLab, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Juha Kere
- Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden Molecular Neurology Research Program, University of Helsinki, and Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Magnus Nordenskjöld
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Elisabeth Syk Lundberg
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| |
Collapse
|
74
|
Abstract
Specific language impairment (SLI) is a multifactorial neurodevelopmental disorder which occurs unexpectedly and without an obvious cause. Over a decade of research suggests that SLI is highly heritable. Several genes and loci have already been implicated in SLI through linkage and targeted association methods. Recently, genome-wide association studies (GWAS) of SLI and language traits in the general population have been reported and, consequently, new candidate genes have been identified. This review aims to summarise the literature concerning genome-wide studies of SLI. In addition, this review highlights the methodologies that have been used to research the genetics of SLI to date, and also considers the current, and future, contributions that GWAS can offer.
Collapse
Affiliation(s)
- Rose H Reader
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN UK
| | - Laura E Covill
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN UK
| | - Ron Nudel
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN UK
| | - Dianne F Newbury
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN UK ; St John's College, University of Oxford, Oxford, OX1 3JP UK
| |
Collapse
|