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Eising E, Mirza-Schreiber N, de Zeeuw EL, Wang CA, Truong DT, Allegrini AG, Shapland CY, Zhu G, Wigg KG, Gerritse ML, Molz B, Alagöz G, Gialluisi A, Abbondanza F, Rimfeld K, van Donkelaar M, Liao Z, Jansen PR, Andlauer TFM, Bates TC, Bernard M, Blokland K, Bonte M, Børglum AD, Bourgeron T, Brandeis D, Ceroni F, Csépe V, Dale PS, de Jong PF, DeFries JC, Démonet JF, Demontis D, Feng Y, Gordon SD, Guger SL, Hayiou-Thomas ME, Hernández-Cabrera JA, Hottenga JJ, Hulme C, Kere J, Kerr EN, Koomar T, Landerl K, Leonard GT, Lovett MW, Lyytinen H, Martin NG, Martinelli A, Maurer U, Michaelson JJ, Moll K, Monaco AP, Morgan AT, Nöthen MM, Pausova Z, Pennell CE, Pennington BF, Price KM, Rajagopal VM, Ramus F, Richer L, Simpson NH, Smith SD, Snowling MJ, Stein J, Strug LJ, Talcott JB, Tiemeier H, van der Schroeff MP, Verhoef E, Watkins KE, Wilkinson M, Wright MJ, Barr CL, Boomsma DI, Carreiras M, Franken MCJ, Gruen JR, Luciano M, Müller-Myhsok B, Newbury DF, Olson RK, Paracchini S, Paus T, Plomin R, Reilly S, Schulte-Körne G, Tomblin JB, van Bergen E, Whitehouse AJO, Willcutt EG, St Pourcain B, Francks C, Fisher SE. Genome-wide analyses of individual differences in quantitatively assessed reading- and language-related skills in up to 34,000 people. Proc Natl Acad Sci U S A 2022; 119:e2202764119. [PMID: 35998220 PMCID: PMC9436320 DOI: 10.1073/pnas.2202764119] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/31/2022] [Indexed: 12/14/2022] Open
Abstract
The use of spoken and written language is a fundamental human capacity. Individual differences in reading- and language-related skills are influenced by genetic variation, with twin-based heritability estimates of 30 to 80% depending on the trait. The genetic architecture is complex, heterogeneous, and multifactorial, but investigations of contributions of single-nucleotide polymorphisms (SNPs) were thus far underpowered. We present a multicohort genome-wide association study (GWAS) of five traits assessed individually using psychometric measures (word reading, nonword reading, spelling, phoneme awareness, and nonword repetition) in samples of 13,633 to 33,959 participants aged 5 to 26 y. We identified genome-wide significant association with word reading (rs11208009, P = 1.098 × 10-8) at a locus that has not been associated with intelligence or educational attainment. All five reading-/language-related traits showed robust SNP heritability, accounting for 13 to 26% of trait variability. Genomic structural equation modeling revealed a shared genetic factor explaining most of the variation in word/nonword reading, spelling, and phoneme awareness, which only partially overlapped with genetic variation contributing to nonword repetition, intelligence, and educational attainment. A multivariate GWAS of word/nonword reading, spelling, and phoneme awareness maximized power for follow-up investigation. Genetic correlation analysis with neuroimaging traits identified an association with the surface area of the banks of the left superior temporal sulcus, a brain region linked to the processing of spoken and written language. Heritability was enriched for genomic elements regulating gene expression in the fetal brain and in chromosomal regions that are depleted of Neanderthal variants. Together, these results provide avenues for deciphering the biological underpinnings of uniquely human traits.
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Affiliation(s)
- Else Eising
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, the Netherlands
| | | | - Eveline L. de Zeeuw
- Department of Biological Psychology, Vrije Universiteit Amsterdam, 1081 BT Amsterdam, the Netherlands
| | - Carol A. Wang
- School of Medicine and Public Health, The University of Newcastle, Newcastle, NSW 2308, Australia
- Mothers and Babies Research Program, Hunter Medical Research Institute, Newcastle, NSW 2305, Australia
| | - Dongnhu T. Truong
- Department of Pediatrics and Genetics, Yale Medical School, New Haven, CT 06510
| | - Andrea G. Allegrini
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, United Kingdom
| | - Chin Yang Shapland
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol BS8 2BN, United Kingdom
- Population Health Sciences, University of Bristol, Bristol BS8 2PS, United Kingdom
| | - Gu Zhu
- Genetic Epidemiology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Karen G. Wigg
- Division of Experimental and Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Margot L. Gerritse
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, the Netherlands
| | - Barbara Molz
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, the Netherlands
| | - Gökberk Alagöz
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, the Netherlands
| | - Alessandro Gialluisi
- Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
- Department of Epidemiology and Prevention, IRCCS Istituto Neurologico Mediterraneo Neuromed, 86077 Pozzilli, Italy
- Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy
| | - Filippo Abbondanza
- School of Medicine, University of St Andrews, KY16 9TF, St. Andrews, Scotland
| | - Kaili Rimfeld
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, United Kingdom
- Department of Psychology, Royal Holloway, University of London, Egham TW20 0EY, United Kingdom
| | - Marjolein van Donkelaar
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, the Netherlands
| | - Zhijie Liao
- Department of Psychology, University of Toronto, Toronto, ON M5S 3G3,Canada
| | - Philip R. Jansen
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center, 3000 CB Rotterdam, the Netherlands
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, 1081 HV the Netherlands
- Department of Human Genetics, VU Medical Center, Amsterdam University Medical Center, 1081 BT Amsterdam, the Netherlands
| | - Till F. M. Andlauer
- Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
- Department of Neurology, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Timothy C. Bates
- Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, United Kingdom
| | - Manon Bernard
- Department of Physiology and Nutritional Sciences, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Kirsten Blokland
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, M5G 1X8 ON, Canada
| | - Milene Bonte
- Department of Cognitive Neuroscience and Maastricht Brain Imaging Center, Faculty of Psychology and Neuroscience, Maastricht University, 6229 ER Maastricht, the Netherlands
| | - Anders D. Børglum
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210 Aarhus, Denmark
- Center for Genomics and Personalized Medicine (CGPM), 8000 Aarhus, Denmark
| | - Thomas Bourgeron
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 Centre national de la recherche scientifique (CNRS), Université Paris Cité, Paris, 75015, France
| | - Daniel Brandeis
- Department of Child and Adolescent Psychiatry and Psychotherapy, Psychiatric Hospital, University of Zurich, 8032 Zurich, Switzerland
- Zurich Center for Integrative Human Physiology, University of Zurich and ETH Zurich, 8057 Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich and ETH Zurich, 8057 Zurich, Switzerland
- Department of Child and Adolescent Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159 Mannheim, Germany
| | - Fabiola Ceroni
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
- Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, United Kingdom
| | - Valéria Csépe
- Brain Imaging Centre, Research Centre for Natural Sciences, Budapest, 1117 Hungary
- Multilingualism Doctoral School, Faculty of Modern Philology and Social Sciences, University of Pannonia, Veszprém, 8200 Hungary
| | - Philip S. Dale
- Department of Speech & Hearing Sciences, University of New Mexico, Albuquerque, NM 87131
| | - Peter F. de Jong
- Department of Child Development and Education, University of Amsterdam, 1012 WX Amsterdam, the Netherlands
| | - John C. DeFries
- Institute for Behavioral Genetics, University of Colorado, Boulder, CO 80309-0447
- Department of Psychology and Neuroscience, University of Colorado, Boulder, CO 80309-0447
| | - Jean-François Démonet
- Leenaards Memory Centre, Department of Clinical Neurosciences, Lausanne University Hospital (CHUV), University of Lausanne, CH-1011 Lausanne, Switzerland
| | - Ditte Demontis
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210 Aarhus, Denmark
| | - Yu Feng
- Division of Experimental and Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Scott D. Gordon
- Genetic Epidemiology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Sharon L. Guger
- Department of Psychology, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | | | - Juan A. Hernández-Cabrera
- Departamento de Psicología, Clínica Psicobiología y Metodología, 38200, La Laguna, Santa Cruz de Tenerife, Spain
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit Amsterdam, 1081 BT Amsterdam, the Netherlands
| | - Charles Hulme
- Department of Education, University of Oxford, Oxford, Oxfordshire OX2 6PY, United Kingdom
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, 171 77 Stockholm, Sweden
- Stem Cells and Metabolism Research Program, University of Helsinki and Folkhälsan Research Center, 00014 Helsinki, Finland
| | - Elizabeth N. Kerr
- Department of Psychology, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Department of Neurology, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Department of Paediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Tanner Koomar
- Department of Psychiatry, University of Iowa, Iowa City, IA 52242
| | - Karin Landerl
- Institute of Psychology, University of Graz, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
| | - Gabriel T. Leonard
- Cognitive Neuroscience Neurology and Neurosurgery, McGill University, Montreal, QC H3A 1G1, Canada
| | - Maureen W. Lovett
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, M5G 1X8 ON, Canada
- Department of Paediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Heikki Lyytinen
- Department of Psychology, University of Jyväskylä, 40014 Jyväskylä, Finland
| | - Nicholas G. Martin
- Genetic Epidemiology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Angela Martinelli
- School of Medicine, University of St Andrews, KY16 9TF, St. Andrews, Scotland
| | - Urs Maurer
- Department of Psychology, The Chinese University of Hong Kong, Hong Kong, China
| | | | - Kristina Moll
- Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, Ludwig-Maximilians-University Hospital Munich, Munich, 80336 Germany
| | | | - Angela T. Morgan
- Speech and Language, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
- Department of Audiology and Speech Pathology, University of Melbourne, Melbourne, VIC 3052, Australia
- Speech Pathology Department, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Markus M. Nöthen
- Institute of Human Genetics, University Hospital of Bonn, 53127 Bonn, Germany
| | - Zdenka Pausova
- Department of Physiology and Nutritional Sciences, University of Toronto, Toronto, ON M5S 1A1, Canada
- Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Craig E. Pennell
- School of Medicine and Public Health, The University of Newcastle, Newcastle, NSW 2308, Australia
- Mothers and Babies Research Program, Hunter Medical Research Institute, Newcastle, NSW 2305, Australia
- Maternity and Gynaecology, John Hunter Hospital, Newcastle, NSW 2305, Australia
| | | | - Kaitlyn M. Price
- Division of Experimental and Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, M5G 1X8 ON, Canada
- Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Veera M. Rajagopal
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210 Aarhus, Denmark
| | - Franck Ramus
- Laboratoire de Sciences Cognitives et Psycholinguistique, Ecole Normale Supérieure, Paris Sciences & Lettres University, École des Hautes Études en Sciences Sociales (EHESS), Centre National de la Recherche Scientifique (CNRS), Paris, 75005 France
| | - Louis Richer
- Department of Health Sciences, Université du Québec à Chicoutimi, Chicoutimi, QC G7H 2B1, Canada
| | - Nuala H. Simpson
- Department of Experimental Psychology, University of Oxford, Oxford OX2 6GG, United Kingdom
| | - Shelley D. Smith
- Department of Neurological Sciences, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198
| | - Margaret J. Snowling
- Department of Experimental Psychology, University of Oxford, Oxford OX2 6GG, United Kingdom
- St. John’s College, University of Oxford, Oxford OX1 3JP, United Kingdom
| | - John Stein
- Department of Physiology, Anatomy and Genetics, Oxford University, Oxford OX1 3PT, United Kingdom
| | - Lisa J. Strug
- Department of Statistical Sciences and Computer Science and Division of Biostatistics, University of Toronto, Toronto, ON M5S 3G3, Canada
- Program in Genetics and Genome Biology and the Centre for Applied Genomics, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Joel B. Talcott
- Institute for Health and Neurodevelopment, Aston University, Birmingham B4 7ET, United Kingdom
| | - Henning Tiemeier
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center, 3000 CB Rotterdam, the Netherlands
- T. H. Chan School of Public Health, Harvard, Boston, MA 02115
| | - Marc P. van der Schroeff
- Department of Otolaryngology, Head and Neck Surgery, Erasmus University Medical Center, 3015 GD Rotterdam, the Netherlands
- Generation R Study Group, Erasmus University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Ellen Verhoef
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, the Netherlands
| | - Kate E. Watkins
- Department of Experimental Psychology, University of Oxford, Oxford OX2 6GG, United Kingdom
| | - Margaret Wilkinson
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, M5G 1X8 ON, Canada
| | - Margaret J. Wright
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Cathy L. Barr
- Division of Experimental and Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, M5G 1X8 ON, Canada
- Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Dorret I. Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, 1081 BT Amsterdam, the Netherlands
- Netherlands Twin Register, 1081 BT Amsterdam, the Netherlands
- Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, 1105 AZ Amsterdam, the Netherlands
| | - Manuel Carreiras
- Basque Center on Cognition, Brain and Language, Donostia-San Sebastian, 20009 Gipuzkoa, Spain
- Ikerbasque, Basque Foundation for Science, 48009 Bilbao, Vizcaya, Spain
- Lengua Vasca y Comunicación, University of the Basque Country, 48940 Bilbao, Vizcaya, Spain
| | - Marie-Christine J. Franken
- Department of Otolaryngology, Head and Neck Surgery, Erasmus University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Jeffrey R. Gruen
- Department of Pediatrics and Genetics, Yale Medical School, New Haven, CT 06510
| | - Michelle Luciano
- Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, United Kingdom
| | - Bertram Müller-Myhsok
- Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
- Department of Health Science, University of Liverpool, Liverpool L69 7ZX, United Kingdom
| | - Dianne F. Newbury
- Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, United Kingdom
| | - Richard K. Olson
- Institute for Behavioral Genetics, University of Colorado, Boulder, CO 80309-0447
| | - Silvia Paracchini
- School of Medicine, University of St Andrews, KY16 9TF, St. Andrews, Scotland
| | - Tomáš Paus
- Department of Psychiatry and Neuroscience and Centre Hospitalier Universitaire Sainte Justine, University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Robert Plomin
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, United Kingdom
| | - Sheena Reilly
- Speech and Language, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
- Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD 4222, Australia
| | - Gerd Schulte-Körne
- Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, Ludwig-Maximilians-University Hospital Munich, Munich, 80336 Germany
| | - J. Bruce Tomblin
- Communication Sciences and Disorders, University of Iowa, Iowa City, IA 52242
| | - Elsje van Bergen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, 1081 BT Amsterdam, the Netherlands
- Netherlands Twin Register, 1081 BT Amsterdam, the Netherlands
- Research Institute LEARN!, Vrije Universiteit Amsterdam, 1081 BT Amsterdam, the Netherlands
| | | | - Erik G. Willcutt
- Department of Psychology and Neuroscience, University of Colorado, Boulder, CO 80309-0447
| | - Beate St Pourcain
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, the Netherlands
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol BS8 2BN, United Kingdom
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6525 EN Nijmegen, the Netherlands
| | - Clyde Francks
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6525 EN Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Center, 6525 GA 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 Behaviour, Radboud University, 6525 EN Nijmegen, the Netherlands
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Newbury DF, Simpson NH, Thompson PA, Bishop DVM. Stage 2 Registered Report: Variation in neurodevelopmental outcomes in children with sex chromosome trisomies: testing the double hit hypothesis. Wellcome Open Res 2021; 3:85. [PMID: 30271887 PMCID: PMC6134338 DOI: 10.12688/wellcomeopenres.14677.4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2021] [Indexed: 12/15/2022] Open
Abstract
Background: The presence of an extra sex chromosome is associated with an increased rate of neurodevelopmental difficulties involving language. The 'double hit' hypothesis proposes that the adverse impact of the extra sex chromosome is amplified when genes that are expressed from the sex chromosomes interact with autosomal variants that usually have only mild effects. We predicted that the impact of an additional sex chromosome on neurodevelopment would depend on common autosomal variants involved in synaptic functions. Methods: We analysed data from 130 children with sex chromosome trisomies (SCTs: 42 girls with trisomy X, 43 boys with Klinefelter syndrome, and 45 boys with XYY). Two comparison groups were formed from 370 children from a twin study. Three indicators of phenotype were: (i) Standard score on a test of nonword repetition; (ii). A language factor score derived from a test battery; (iii) A general scale of neurodevelopmental challenges based on all available information. Preselected regions of two genes, CNTNAP2 and NRXN1, were tested for association with neurodevelopmental outcomes using Generalised Structural Component Analysis. Results: There was wide phenotypic variation in the SCT group, as well as overall impairment on all three phenotypic measures. There was no association of phenotype with CNTNAP2 or NRXN1 variants in either the SCT group or the comparison groups. Supplementary analyses found no indication of any impact of trisomy type on the results, and exploratory analyses of individual SNPs confirmed the lack of association. Conclusions: We cannot rule out that a double hit may be implicated in the phenotypic variability in children with SCTs, but our analysis does not find any support for the idea that common variants in CNTNAP2 or NRXN1 are associated with the severity of language and neurodevelopmental impairments that often accompany an extra X or Y chromosome. Stage 1 report: http://dx.doi.org/10.12688/wellcomeopenres.13828.2.
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Affiliation(s)
- Dianne F. Newbury
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Nuala H. Simpson
- Department of Experimental Psychology, University of Oxford, Oxford, OX2 6GG, UK
| | - Paul A. Thompson
- Department of Experimental Psychology, University of Oxford, Oxford, OX2 6GG, UK
| | - Dorothy V. M. Bishop
- Department of Experimental Psychology, University of Oxford, Oxford, OX2 6GG, UK
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Newbury DF, Simpson NH, Thompson PA, Bishop DVM. Stage 2 Registered Report: Variation in neurodevelopmental outcomes in children with sex chromosome trisomies: testing the double hit hypothesis. Wellcome Open Res 2020; 3:85. [PMID: 30271887 PMCID: PMC6134338 DOI: 10.12688/wellcomeopenres.14677.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/18/2020] [Indexed: 04/03/2024] Open
Abstract
Background: The presence of an extra sex chromosome is associated with an increased rate of neurodevelopmental difficulties involving language. The 'double hit' hypothesis proposes that the adverse impact of the extra sex chromosome is amplified when genes that are expressed from the sex chromosomes interact with autosomal variants that usually have only mild effects. We predicted that the impact of an additional sex chromosome on neurodevelopment would depend on common autosomal variants involved in synaptic functions. Methods: We analysed data from 130 children with sex chromosome trisomies (SCTs: 42 girls with trisomy X, 43 boys with Klinefelter syndrome, and 45 boys with XYY). Two comparison groups were formed from 370 children from a twin study. Three indicators of phenotype were: (i) Standard score on a test of nonword repetition; (ii). A language factor score derived from a test battery; (iii) A general scale of neurodevelopmental challenges based on all available information. Preselected regions of two genes, CNTNAP2 and NRXN1, were tested for association with neurodevelopmental outcomes using Generalised Structural Component Analysis. Results: There was wide phenotypic variation in the SCT group, as well as overall impairment on all three phenotypic measures. There was no association of phenotype with CNTNAP2 or NRXN1 variants in either the SCT group or the comparison groups. Supplementary analyses found no indication of any impact of trisomy type on the results, and exploratory analyses of individual SNPs confirmed the lack of association. Conclusions: We cannot rule out that a double hit may be implicated in the phenotypic variability in children with SCTs, but our analysis does not find any support for the idea that common variants in CNTNAP2 or NRXN1 are associated with the severity of language and neurodevelopmental impairments that often accompany an extra X or Y chromosome. Stage 1 report: http://dx.doi.org/10.12688/wellcomeopenres.13828.2.
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Affiliation(s)
- Dianne F. Newbury
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Nuala H. Simpson
- Department of Experimental Psychology, University of Oxford, Oxford, OX2 6GG, UK
| | - Paul A. Thompson
- Department of Experimental Psychology, University of Oxford, Oxford, OX2 6GG, UK
| | - Dorothy V. M. Bishop
- Department of Experimental Psychology, University of Oxford, Oxford, OX2 6GG, UK
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Mountford HS, Bishop DVM, Thompson PA, Simpson NH, Newbury DF. Copy number variation burden does not predict severity of neurodevelopmental phenotype in children with a sex chromosome trisomy. Am J Med Genet C Semin Med Genet 2020; 184:256-266. [PMID: 32452638 DOI: 10.1002/ajmg.c.31791] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 12/14/2022]
Abstract
Sex chromosome trisomies (SCTs) (XXX, XXY, and XYY karyotypes) are associated with an elevated risk of neurodevelopmental disorders. The range of severity of the phenotype is substantial. We considered whether this variable outcome was related to the presence of copy number variants (CNVs)-stretches of duplicated or deleted DNA. A sample of 125 children with an SCT were compared with 181 children of normal karyotype who had been given the same assessments. First, we compared the groups on measures of overall CNV burden: number of CNVs, total span of CNVs, and likely functional impact (probability of loss-of-function intolerance, pLI, summed over CNVs). Differences between groups were small relative to within-group variance and not statistically significant on overall test. Next, we considered whether a measure of general neurodevelopmental impairment was predicted by pLI summed score, SCT versus comparison group, or the interaction between them. There was a substantial effect of SCT/comparison status but the pLI score was not predictive of outcomes in either group. We conclude that variable presence of CNVs is not a likely explanation for the wide phenotypic variation in children with SCTs. We discuss methodological challenges of testing whether CNVs are implicated in causing neurodevelopmental problems.
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Affiliation(s)
- Hayley S Mountford
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, Oxfordshire, UK
| | - Dorothy V M Bishop
- Department of Experimental Psychology, University of Oxford, Oxford, Oxfordshire, UK
| | - Paul A Thompson
- Department of Experimental Psychology, University of Oxford, Oxford, Oxfordshire, UK
| | - Nuala H Simpson
- Department of Experimental Psychology, University of Oxford, Oxford, Oxfordshire, UK
| | - Dianne F Newbury
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, Oxfordshire, UK
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Newbury DF, Simpson NH, Thompson PA, Bishop DVM. Stage 2 Registered Report: Variation in neurodevelopmental outcomes in children with sex chromosome trisomies: testing the double hit hypothesis. Wellcome Open Res 2018; 3:85. [PMID: 30271887 PMCID: PMC6134338 DOI: 10.12688/wellcomeopenres.14677.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/02/2018] [Indexed: 01/26/2024] Open
Abstract
Background: The presence of an extra sex chromosome is associated with an increased rate of neurodevelopmental difficulties involving language. The 'double hit' hypothesis proposes that the adverse impact of the extra sex chromosome is amplified when genes that are expressed from the sex chromosomes interact with autosomal variants that usually have only mild effects. We predicted that the impact of an additional sex chromosome on neurodevelopment would depend on common autosomal variants involved in synaptic functions. Methods: We analysed data from 130 children with sex chromosome trisomies (SCTs: 42 girls with trisomy X, 43 boys with Klinefelter syndrome, and 45 boys with XYY). Two comparison groups were formed from 370 children from a twin study. Three indicators of phenotype were: (i) Standard score on a test of nonword repetition; (ii). A language factor score derived from a test battery; (iii) A general scale of neurodevelopmental challenges based on all available information. Preselected regions of two genes, CNTNAP2 and NRXN1, were tested for association with neurodevelopmental outcomes using Generalised Structural Component Analysis. Results: There was wide phenotypic variation in the SCT group, as well as overall impairment on all three phenotypic measures. There was no association of phenotype with CNTNAP2 or NRXN1 variants in either the SCT group or the comparison groups. Supplementary analyses found no indication of any impact of trisomy type on the results, and exploratory analyses of individual SNPs confirmed the lack of association. Conclusions: We cannot rule out that a double hit may be implicated in the phenotypic variability in children with SCTs, but our analysis does not find any support for the idea that common variants in CNTNAP2 or NRXN1 are associated with the severity of language and neurodevelopmental impairments that often accompany an extra X or Y chromosome. Stage 1 report: http://dx.doi.org/10.12688/wellcomeopenres.13828.2.
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Affiliation(s)
- Dianne F. Newbury
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Nuala H. Simpson
- Department of Experimental Psychology, University of Oxford, Oxford, OX2 6GG, UK
| | - Paul A. Thompson
- Department of Experimental Psychology, University of Oxford, Oxford, OX2 6GG, UK
| | - Dorothy V. M. Bishop
- Department of Experimental Psychology, University of Oxford, Oxford, OX2 6GG, UK
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6
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Newbury DF, Simpson NH, Thompson PA, Bishop DVM. Stage 2 Registered Report: Variation in neurodevelopmental outcomes in children with sex chromosome trisomies: testing the double hit hypothesis. Wellcome Open Res 2018; 3:85. [PMID: 30271887 PMCID: PMC6134338 DOI: 10.12688/wellcomeopenres.14677.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2018] [Indexed: 12/26/2022] Open
Abstract
Background: The presence of an extra sex chromosome is associated with an increased rate of neurodevelopmental difficulties involving language. The 'double hit' hypothesis proposes that the adverse impact of the extra sex chromosome is amplified when genes that are expressed from the sex chromosomes interact with autosomal variants that usually have only mild effects. We predicted that the impact of an additional sex chromosome on neurodevelopment would depend on common autosomal variants involved in synaptic functions. Methods: We analysed data from 130 children with sex chromosome trisomies (SCTs: 42 girls with trisomy X, 43 boys with Klinefelter syndrome, and 45 boys with XYY). Two comparison groups were formed from 370 children from a twin study. Three indicators of phenotype were: (i) Standard score on a test of nonword repetition; (ii). A language factor score derived from a test battery; (iii) A general scale of neurodevelopmental challenges based on all available information. Preselected regions of two genes, CNTNAP2 and NRXN1, were tested for association with neurodevelopmental outcomes using Generalised Structural Component Analysis. Results: There was wide phenotypic variation in the SCT group, as well as overall impairment on all three phenotypic measures. There was no association of phenotype with CNTNAP2 or NRXN1 variants in either the SCT group or the comparison groups. Supplementary analyses found no indication of any impact of trisomy type on the results, and exploratory analyses of individual SNPs confirmed the lack of association. Conclusions: We cannot rule out that a double hit may be implicated in the phenotypic variability in children with SCTs, but our analysis does not find any support for the idea that common variants in CNTNAP2 or NRXN1 are associated with the severity of language and neurodevelopmental impairments that often accompany an extra X or Y chromosome. Stage 1 report: http://dx.doi.org/10.12688/wellcomeopenres.13828.2.
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Affiliation(s)
- Dianne F. Newbury
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Nuala H. Simpson
- Department of Experimental Psychology, University of Oxford, Oxford, OX2 6GG, UK
| | - Paul A. Thompson
- Department of Experimental Psychology, University of Oxford, Oxford, OX2 6GG, UK
| | - Dorothy V. M. Bishop
- Department of Experimental Psychology, University of Oxford, Oxford, OX2 6GG, UK
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7
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Newbury DF, Simpson NH, Thompson PA, Bishop DVM. Stage 1 Registered Report: Variation in neurodevelopmental outcomes in children with sex chromosome trisomies: protocol for a test of the double hit hypothesis. Wellcome Open Res 2018; 3:10. [PMID: 29744390 PMCID: PMC5904730 DOI: 10.12688/wellcomeopenres.13828.2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2018] [Indexed: 12/20/2022] Open
Abstract
Background: The presence of an extra sex chromosome is associated with an increased rate of neurodevelopmental difficulties involving language. Group averages, however, obscure a wide range of outcomes. Hypothesis: The 'double hit' hypothesis proposes that the adverse impact of the extra sex chromosome is amplified when genes that are expressed from the sex chromosomes interact with autosomal variants that usually have only mild effects.
Neuroligin-4 genes are expressed from X and Y chromosomes; they play an important role in synaptic development and have been implicated in neurodevelopment. We predict that the impact of an additional sex chromosome on neurodevelopment will be correlated with common autosomal variants involved in related synaptic functions. We describe here an analysis plan for testing this hypothesis using existing data. The analysis of genotype-phenotype associations will be conducted after this plan is published and peer-reviewed Methods: Neurodevelopmental data and DNA are available for 130 children with sex chromosome trisomies (SCTs: 42 girls with trisomy X, 43 boys with Klinefelter syndrome, and 45 boys with XYY). Children from a twin study using the same phenotype measures will form two comparison groups (Ns = 184 and 186). Three indicators of a neurodevelopment disorder phenotype will be used: (i) Standard score on a test of nonword repetition; (ii). A language factor score derived from a test battery; (iii) A general scale of neurodevelopmental challenges based on all available information. Autosomal genes were identified by literature search on the basis of prior association with (a) speech/language/reading phenotypes and (b) synaptic function. Preselected regions of two genes scoring high on both criteria,
CNTNAP2 and
NRXN1, will be tested for association with neurodevelopmental outcomes using Generalised Structural Component Analysis. We predict the association with one or both genes will be detectable in children with SCTs and stronger than in the comparison samples.
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Affiliation(s)
- Dianne F Newbury
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, Oxfordshire, OX3 0BP, UK
| | - Nuala H Simpson
- Department of Experimental Psychology, University of Oxford, Oxford, Oxfordshire, OX1 3UD, UK
| | - Paul A Thompson
- Department of Experimental Psychology, University of Oxford, Oxford, Oxfordshire, OX1 3UD, UK
| | - Dorothy V M Bishop
- Department of Experimental Psychology, University of Oxford, Oxford, Oxfordshire, OX1 3UD, UK
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8
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Newbury DF, Simpson NH, Thompson PA, Bishop DVM. Stage 1 Registered Report: Variation in neurodevelopmental outcomes in children with sex chromosome trisomies: protocol for a test of the double hit hypothesis. Wellcome Open Res 2018. [DOI: 10.12688/wellcomeopenres.13828.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: The presence of an extra sex chromosome is associated with an increased rate of neurodevelopmental difficulties involving language. Group averages, however, obscure a wide range of outcomes. Hypothesis: The 'double hit' hypothesis proposes that the adverse impact of the extra sex chromosome is amplified when genes that are expressed from the sex chromosomes interact with autosomal variants that usually have only mild effects. Neuroligin-4 genes are expressed from X and Y chromosomes; they play an important role in synaptic development and have been implicated in neurodevelopment. We predict that the impact of an additional sex chromosome on neurodevelopment will be correlated with common autosomal variants involved in related synaptic functions. We describe here an analysis plan for testing this hypothesis using existing data. The analysis of genotype-phenotype associations will be conducted after this plan is published and peer-reviewed Methods: Neurodevelopmental data and DNA are available for 130 children with sex chromosome trisomies (SCTs: 42 girls with trisomy X, 43 boys with Klinefelter syndrome, and 45 boys with XYY). Children from a twin study using the same phenotype measures will form two comparison groups (Ns = 184 and 186). Three indicators of a neurodevelopment disorder phenotype will be used: (i) Standard score on a test of nonword repetition; (ii). A language factor score derived from a test battery; (iii) A general scale of neurodevelopmental challenges based on all available information. Autosomal genes were identified by literature search on the basis of prior association with (a) speech/language/reading phenotypes and (b) synaptic function. Preselected regions of two genes scoring high on both criteria, CNTNAP2 and NRXN1, will be tested for association with neurodevelopmental outcomes using Generalised Structural Component Analysis. We predict the association with one or both genes will be detectable in children with SCTs and stronger than in the comparison samples.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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10
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Pettigrew KA, Fajutrao Valles SF, Moll K, Northstone K, Ring S, Pennell C, Wang C, Leavett R, Hayiou-Thomas ME, Thompson P, Simpson NH, Fisher SE, Whitehouse AJO, Snowling MJ, Newbury DF, Paracchini S. Lack of replication for the myosin-18B association with mathematical ability in independent cohorts. Genes Brain Behav 2015; 14:369-76. [PMID: 25778778 PMCID: PMC4672701 DOI: 10.1111/gbb.12213] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 03/12/2015] [Accepted: 03/12/2015] [Indexed: 12/20/2022]
Abstract
Twin studies indicate that dyscalculia (or mathematical disability) is caused partly by a genetic component, which is yet to be understood at the molecular level. Recently, a coding variant (rs133885) in the myosin-18B gene was shown to be associated with mathematical abilities with a specific effect among children with dyslexia. This association represents one of the most significant genetic associations reported to date for mathematical abilities and the only one reaching genome-wide statistical significance. We conducted a replication study in different cohorts to assess the effect of rs133885 maths-related measures. The study was conducted primarily using the Avon Longitudinal Study of Parents and Children (ALSPAC), (N = 3819). We tested additional cohorts including the York Cohort, the Specific Language Impairment Consortium (SLIC) cohort and the Raine Cohort, and stratified them for a definition of dyslexia whenever possible. We did not observe any associations between rs133885 in myosin-18B and mathematical abilities among individuals with dyslexia or in the general population. Our results suggest that the myosin-18B variant is unlikely to be a main factor contributing to mathematical abilities.
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Affiliation(s)
- K A Pettigrew
- School of Medicine, University of St Andrews, St Andrews, UK
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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.
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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)
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Simpson NH, Ceroni F, Reader RH, Covill LE, Knight JC, Hennessy ER, Bolton PF, Conti-Ramsden G, O'Hare A, Baird G, Fisher SE, Newbury DF. Genome-wide analysis identifies a role for common copy number variants in specific language impairment. Eur J Hum Genet 2015; 23:1370-7. [PMID: 25585696 PMCID: PMC4592089 DOI: 10.1038/ejhg.2014.296] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 12/08/2014] [Accepted: 12/12/2014] [Indexed: 11/29/2022] Open
Abstract
An exploratory genome-wide copy number variant (CNV) study was performed in 127 independent cases with specific language impairment (SLI), their first-degree relatives (385 individuals) and 269 population controls. Language-impaired cases showed an increased CNV burden in terms of the average number of events (11.28 vs 10.01, empirical P=0.003), the total length of CNVs (717 vs 513 Kb, empirical P=0.0001), the average CNV size (63.75 vs 51.6 Kb, empirical P=0.0005) and the number of genes spanned (14.29 vs 10.34, empirical P=0.0007) when compared with population controls, suggesting that CNVs may contribute to SLI risk. A similar trend was observed in first-degree relatives regardless of affection status. The increased burden found in our study was not driven by large or de novo events, which have been described as causative in other neurodevelopmental disorders. Nevertheless, de novo CNVs might be important on a case-by-case basis, as indicated by identification of events affecting relevant genes, such as ACTR2 and CSNK1A1, and small events within known micro-deletion/-duplication syndrome regions, such as chr8p23.1. Pathway analysis of the genes present within the CNVs of the independent cases identified significant overrepresentation of acetylcholine binding, cyclic-nucleotide phosphodiesterase activity and MHC proteins as compared with controls. Taken together, our data suggest that the majority of the risk conferred by CNVs in SLI is via common, inherited events within a ‘common disorder–common variant' model. Therefore the risk conferred by CNVs will depend upon the combination of events inherited (both CNVs and SNPs), the genetic background of the individual and the environmental factors.
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Affiliation(s)
- Nuala H Simpson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Fabiola Ceroni
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Rose H Reader
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Laura E Covill
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Julian C Knight
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | | | - Patrick F Bolton
- Departments of Child and Adolescent Psychiatry, Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, UK
| | - Gina Conti-Ramsden
- School of Psychological Sciences, University of Manchester, Manchester, UK
| | - Anne O'Hare
- Department of Reproductive and Developmental Sciences, University of Edinburgh, Edinburgh, UK
| | - Gillian Baird
- Children's Neurosciences Department, Evelina Children's Hospital and King's Health Partners, London, UK
| | - 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, UK.,St John's College, University of Oxford, Oxford, UK
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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 Behav 2014; 13:686-701. [PMID: 25065397 PMCID: PMC4165772 DOI: 10.1111/gbb.12158] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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14
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Simpson NH, Addis L, Brandler WM, Slonims V, Clark A, Watson J, Scerri TS, Hennessy ER, Bolton PF, Conti-Ramsden G, Fairfax BP, Knight JC, Stein J, Talcott JB, O'Hare A, Baird G, Paracchini S, Fisher SE, Newbury DF, Consortium SLI. Increased prevalence of sex chromosome aneuploidies in specific language impairment and dyslexia. Dev Med Child Neurol 2014; 56:346-53. [PMID: 24117048 PMCID: PMC4293460 DOI: 10.1111/dmcn.12294] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/09/2013] [Indexed: 12/05/2022]
Abstract
AIM Sex chromosome aneuploidies increase the risk of spoken or written language disorders but individuals with specific language impairment (SLI) or dyslexia do not routinely undergo cytogenetic analysis. We assess the frequency of sex chromosome aneuploidies in individuals with language impairment or dyslexia. METHOD Genome-wide single nucleotide polymorphism genotyping was performed in three sample sets: a clinical cohort of individuals with speech and language deficits (87 probands: 61 males, 26 females; age range 4 to 23 years), a replication cohort of individuals with SLI, from both clinical and epidemiological samples (209 probands: 139 males, 70 females; age range 4 to 17 years), and a set of individuals with dyslexia (314 probands: 224 males, 90 females; age range 7 to 18 years). RESULTS In the clinical language-impaired cohort, three abnormal karyotypic results were identified in probands (proband yield 3.4%). In the SLI replication cohort, six abnormalities were identified providing a consistent proband yield (2.9%). In the sample of individuals with dyslexia, two sex chromosome aneuploidies were found giving a lower proband yield of 0.6%. In total, two XYY, four XXY (Klinefelter syndrome), three XXX, one XO (Turner syndrome), and one unresolved karyotype were identified. INTERPRETATION The frequency of sex chromosome aneuploidies within each of the three cohorts was increased over the expected population frequency (approximately 0.25%) suggesting that genetic testing may prove worthwhile for individuals with language and literacy problems and normal non-verbal IQ. Early detection of these aneuploidies can provide information and direct the appropriate management for individuals.
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Affiliation(s)
- Nuala H Simpson
- Wellcome Trust Centre for Human Genetics, University of OxfordOxford, UK
| | - Laura Addis
- Department of Clinical Neuroscience, Institute of Psychiatry, King's College LondonLondon, UK
| | - William M Brandler
- MRC Functional Genomics Unit, Department of Physiology, Anatomy & Genetics, University of OxfordOxford, UK
| | - Vicky Slonims
- Newcomen Centre, Evelina Children's HospitalLondon, UK
| | - Ann Clark
- Speech and Hearing Sciences, Queen Margaret UniversityEdinburgh, UK
| | - Jocelynne Watson
- Speech and Hearing Sciences, Queen Margaret UniversityEdinburgh, UK
| | - Thomas S Scerri
- The Walter and Eliza Hall Institute of Medical ResearchMelbourne, Australia
| | | | - Patrick F Bolton
- Departments of Child & Adolescent Psychiatry & Social Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, King's College LondonLondon, UK
| | - Gina Conti-Ramsden
- School of Psychological Sciences, University of ManchesterManchester, UK
| | - Benjamin P Fairfax
- Wellcome Trust Centre for Human Genetics, University of OxfordOxford, UK
| | - Julian C Knight
- Wellcome Trust Centre for Human Genetics, University of OxfordOxford, UK
| | | | | | - Anne O'Hare
- Department of Reproductive and Developmental Sciences, University of EdinburghEdinburgh, UK
| | - Gillian Baird
- Newcomen Centre, Evelina Children's HospitalLondon, UK
| | | | - Simon E Fisher
- Max Planck Institute for PsycholinguisticsNijmegen, the Netherlands,Donders Institute for Brain, Cognition and Behaviour, Radboud UniversityNijmegen, the Netherlands
| | - Dianne F Newbury
- Wellcome Trust Centre for Human Genetics, University of OxfordOxford, UK,Correspondence to Dianne F Newbury, MRC Career Development Fellow, Office 00/008, Lab 1, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Headington, Oxford OX3 7BN, UK. E-mail:
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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 Behav 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Ceroni F, Sagar A, Simpson NH, Gawthrope AJT, Newbury DF, Pinto D, Francis SM, Tessman DC, Cook EH, Monaco AP, Maestrini E, Pagnamenta AT, Jacob S. A deletion involving CD38 and BST1 results in a fusion transcript in a patient with autism and asthma. Autism Res 2014; 7:254-63. [PMID: 24634087 DOI: 10.1002/aur.1365] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 01/18/2014] [Indexed: 11/11/2022]
Abstract
CD38 encodes a ligand in the oxytocin signaling pathway. Some single nucleotide polymorphisms in this gene have been associated with low serum oxytocin levels in autism spectrum disorder (ASD) patients. Oxytocin disruption has been hypothesized to account for features of ASD, including impaired communication and social behavior, based on animal studies. Recent human studies have shown administration of oxytocin improving emotion recognition, promoting social behavior, and improving auditory processing of social stimuli in ASD patients. In addition to its role in oxytocin signaling, CD38 is involved in the regulation of calcium concentration in airway smooth muscle with impairment of CD38 being implicated in airway diseases like asthma. While a number of studies have implicated rare chromosomal deletions and duplications in helping determine genetic risk for autism, there are to our knowledge no reports describing rearrangements involving CD38 or deletions in patients with ASD. Here, we present two sisters diagnosed with autism and with features of regression-previously acquired speech lost in the second year of life. The younger sister, who also had asthma, inherited a maternal deletion of 4p15.32 that results in a BST1-CD38 fusion transcript. Their mother's deletion was mosaic and she was not affected. Although further work is required to assess functional consequences of the fusion transcript, we hypothesize that the proband's deletion may have served as a risk factor for autism that, when combined with other susceptibility variants, resulted in a more severe presentation than her sister.
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Affiliation(s)
- Fabiola Ceroni
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
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Ceroni F, Simpson NH, Francks C, Baird G, Conti-Ramsden G, Clark A, Bolton PF, Hennessy ER, Donnelly P, Bentley DR, Martin H, Parr J, Pagnamenta AT, Maestrini E, Bacchelli E, Fisher SE, Newbury DF. Homozygous microdeletion of exon 5 in ZNF277 in a girl with specific language impairment. Eur J Hum Genet 2014; 22:1165-71. [PMID: 24518835 PMCID: PMC4169542 DOI: 10.1038/ejhg.2014.4] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 10/28/2013] [Accepted: 12/18/2013] [Indexed: 01/22/2023] Open
Abstract
Specific language impairment (SLI), an unexpected failure to develop appropriate language skills despite adequate non-verbal intelligence, is a heterogeneous multifactorial disorder with a complex genetic basis. We identified a homozygous microdeletion of 21,379 bp in the ZNF277 gene (NM_021994.2), encompassing exon 5, in an individual with severe receptive and expressive language impairment. The microdeletion was not found in the proband's affected sister or her brother who had mild language impairment. However, it was inherited from both parents, each of whom carries a heterozygous microdeletion and has a history of language problems. The microdeletion falls within the AUTS1 locus, a region linked to autistic spectrum disorders (ASDs). Moreover, ZNF277 is adjacent to the DOCK4 and IMMP2L genes, which have been implicated in ASD. We screened for the presence of ZNF277 microdeletions in cohorts of children with SLI or ASD and panels of control subjects. ZNF277 microdeletions were at an increased allelic frequency in SLI probands (1.1%) compared with both ASD family members (0.3%) and independent controls (0.4%). We performed quantitative RT-PCR analyses of the expression of IMMP2L, DOCK4 and ZNF277 in individuals carrying either an IMMP2L_DOCK4 microdeletion or a ZNF277 microdeletion. Although ZNF277 microdeletions reduce the expression of ZNF277, they do not alter the levels of DOCK4 or IMMP2L transcripts. Conversely, IMMP2L_DOCK4 microdeletions do not affect the expression levels of ZNF277. We postulate that ZNF277 microdeletions may contribute to the risk of language impairments in a manner that is independent of the autism risk loci previously described in this region.
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Affiliation(s)
- Fabiola Ceroni
- Dipartimento di Farmacia e Biotecnologie, University of Bologna, Bologna, Italy
| | - Nuala H Simpson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Clyde Francks
- 1] Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands [2] Donders Institute for Brain, Cognition & Behaviour, Nijmegen, Netherlands
| | - Gillian Baird
- Guy's & St Thomas NHS Foundation Trust, Newcomen Children's Neurosciences Centre, St Thomas' Hospital, London, UK
| | - Gina Conti-Ramsden
- School of Psychological Sciences, The University of Manchester, Manchester, UK
| | - Ann Clark
- Speech and Hearing Sciences, Queen Margaret University, Edinburgh, UK
| | - Patrick F Bolton
- Departments of Child & Adolescent Psychiatry & Social Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Kings College London, London, UK
| | | | - Peter Donnelly
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - David R Bentley
- Illumina Cambridge Ltd., Chesterford Research Park, Little Chesterford, Essex, UK
| | - Hilary Martin
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | | | | | - Jeremy Parr
- Institute of Neuroscience and Health and Society, Newcastle University, Newcastle, UK
| | - Alistair T Pagnamenta
- 1] Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK [2] NIHR Biomedical Research Centre, Oxford and Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Elena Maestrini
- Dipartimento di Farmacia e Biotecnologie, University of Bologna, Bologna, Italy
| | - Elena Bacchelli
- Dipartimento di Farmacia e Biotecnologie, University of Bologna, Bologna, Italy
| | - Simon E Fisher
- 1] Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands [2] Donders Institute for Brain, Cognition & Behaviour, Nijmegen, Netherlands
| | - Dianne F Newbury
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
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Nudel R, Simpson NH, Baird G, O'Hare A, Conti-Ramsden G, Bolton PF, Hennessy ER, Monaco AP, Knight JC, Winney B, Fisher SE, Newbury DF. Associations of HLA alleles with specific language impairment. J Neurodev Disord 2014; 6:1. [PMID: 24433325 PMCID: PMC3906746 DOI: 10.1186/1866-1955-6-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 01/02/2014] [Indexed: 01/28/2023] Open
Abstract
Background Human leukocyte antigen (HLA) loci have been implicated in several neurodevelopmental disorders in which language is affected. However, to date, no studies have investigated the possible involvement of HLA loci in specific language impairment (SLI), a disorder that is defined primarily upon unexpected language impairment. We report association analyses of single-nucleotide polymorphisms (SNPs) and HLA types in a cohort of individuals affected by language impairment. Methods We perform quantitative association analyses of three linguistic measures and case-control association analyses using both SNP data and imputed HLA types. Results Quantitative association analyses of imputed HLA types suggested a role for the HLA-A locus in susceptibility to SLI. HLA-A A1 was associated with a measure of short-term memory (P = 0.004) and A3 with expressive language ability (P = 0.006). Parent-of-origin effects were found between HLA-B B8 and HLA-DQA1*0501 and receptive language. These alleles have a negative correlation with receptive language ability when inherited from the mother (P = 0.021, P = 0.034, respectively) but are positively correlated with the same trait when paternally inherited (P = 0.013, P = 0.029, respectively). Finally, case control analyses using imputed HLA types indicated that the DR10 allele of HLA-DRB1 was more frequent in individuals with SLI than population controls (P = 0.004, relative risk = 2.575), as has been reported for individuals with attention deficit hyperactivity disorder (ADHD). Conclusion These preliminary data provide an intriguing link to those described by previous studies of other neurodevelopmental disorders and suggest a possible role for HLA loci in language disorders.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Dianne F Newbury
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
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Abstract
Recent studies have suggested that Bcl-2 can affect cell cycle re-entry by inhibiting the transition from G0/G1 to S phase. In this study, we have taken a novel route to the study of the relationship between Bcl-2 expression and cell cycle progression. Continuous cultures of pEF (control) and Bcl-2 transfected murine hybridoma cells were operated at a range of dilution rates from 0.8 day-1 down to 0.2 day-1. The specific growth rate of the pEF cell line was the same as the dilution rate down to a value of 0.6 day-1. However, as the dilution rate was reduced stepwise to 0.2 day-1, the growth rate levelled-off at approximately 0.55 day-1 and this coincided with a fall in culture viability. By contrast, the specific growth rate of the Bcl-2 transfected cell line followed the dilution rate down to a value of 0.3 day-1 with high levels of cell survival. At high dilution rates, the cell cycle distributions were very similar for both cell lines. However, the distributions diverged as the dilution rate was reduced and, at a rate of 0.2 day-1, the percentage of G1 cells in the Bcl-2 culture was 80%, compared to only 56% in the pEF cell population. This corresponded with a greater extension in the duration of the G1 phase in the Bcl-2 cells, which was 1.7 days at the lowest dilution rate tested, compared to only 0.6 day for the pEF cell line. The durations of the G2/M and S phases remained constant throughout the culture. The maximum doubling time was 1.2 days in the pEF culture compared to 2.3 days in the Bcl-2 culture. Analysis of amino acids, ammonia and lactate concentrations indicated that the observed effects on cell cycle dynamics were probably not due to differences in the culture environment. It is suggested that the expression of Bcl-2 can effect G1 to S phase transition in continuously cycling cells, but this is only apparent at suboptimal growth rates.
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Affiliation(s)
- N H Simpson
- Animal Cell Technology Group, School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
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Simpson NH, Singh RP, Perani A, Goldenzon C, Al-Rubeai M. In hybridoma cultures, deprivation of any single amino acid leads to apoptotic death, which is suppressed by the expression of the bcl-2 gene. Biotechnol Bioeng 1998; 59:90-8. [PMID: 10099318 DOI: 10.1002/(sici)1097-0290(19980705)59:1<90::aid-bit12>3.0.co;2-6] [Citation(s) in RCA: 109] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The transfection of murine hybridomas with the apoptosis suppressor gene bcl-2 has been reported to result in the extension of batch culture duration, leading to significant improvements in culture productivity. In the present study, the effect of deprivation, individually, of each amino acid found in culture medium was examined to characterize the chemical environment of the culture in terms of its propensity to induce apoptosis. When cells were deprived of each amino acid, individually for 48 h, the majority of cell deaths in each case occurred by apoptosis, with essential amino acids being clearly most effective. For nearly all the amino acids, the viability of the bcl-2 cell line cultures was greater than 70% after 48 h, representing a substantial improvement in viability over control cell line cultures. Time course studies revealed that the induction of death could be divided into two phases. Initially, following the deprivation of a single essential amino acid, there was a period of time during which all the control cell line cultures retained high viability. The duration of this phase varied from 15 h in the case of lysine deprivation, through to 40 h in the case methionine deprivation. In the second phase of deprivation, the cultures exhibited an abrupt and rapid collapse in viability. The time taken for the viability to fall to 50% was similar for each amino acid. In every case, the duration of both phases of the bcl-2 cultures was considerably extended. Specific utilization rates were increased during the control cultures relative to the bcl-2 cultures for both the growth phase (ranging between 2% and 57% higher than the bcl-2 cultures) and the death phase (ranging between 172% to 1900% higher than the bcl-2 culture).
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Affiliation(s)
- N H Simpson
- Centre for Bioprocess Engineering, School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
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Abstract
There are many potential causes for malpractice actions in outpatient psychotherapy. Pertinent cases are reviewed, their implications discussed, and means by which practitioners can avert malpractice are described.
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