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Ronald A, Gui A. The potential and translational application of infant genetic research. Nat Genet 2024; 56:1346-1354. [PMID: 38977854 DOI: 10.1038/s41588-024-01822-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 05/10/2024] [Indexed: 07/10/2024]
Abstract
In the current genomic revolution, the infancy life stage is the most neglected. Although clinical genetics recognizes the value of early identification in infancy of rare genetic causes of disorders and delay, common genetic variation is almost completely ignored in research on infant behavioral and neurodevelopmental traits. In this Perspective, we argue for a much-needed surge in research on common genetic variation influencing infant neurodevelopment and behavior, findings that would be relevant for all children. We now see convincing evidence from different research designs to suggest that developmental milestones, skills and behaviors of infants are heritable and thus are suitable candidates for gene-discovery research. We highlight the resources available to the field, including genotyped infant cohorts, and we outline, with recommendations, special considerations needed for infant data. Therefore, infant genetic research has the potential to impact basic science and to affect educational policy, public health and clinical practice.
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Affiliation(s)
- Angelica Ronald
- School of Psychology, Faculty of Health and Medical Sciences, University of Surrey, Surrey, UK.
| | - Anna Gui
- Department of Psychology, University of Essex, Essex, UK
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2
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Verhoef E, Allegrini AG, Jansen PR, Lange K, Wang CA, Morgan AT, Ahluwalia TS, Symeonides C, Eising E, Franken MC, Hypponen E, Mansell T, Olislagers M, Omerovic E, Rimfeld K, Schlag F, Selzam S, Shapland CY, Tiemeier H, Whitehouse AJO, Saffery R, Bønnelykke K, Reilly S, Pennell CE, Wake M, Cecil CAM, Plomin R, Fisher SE, St Pourcain B. Genome-Wide Analyses of Vocabulary Size in Infancy and Toddlerhood: Associations With Attention-Deficit/Hyperactivity Disorder, Literacy, and Cognition-Related Traits. Biol Psychiatry 2024; 95:859-869. [PMID: 38070845 DOI: 10.1016/j.biopsych.2023.11.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 11/26/2023] [Accepted: 11/29/2023] [Indexed: 02/17/2024]
Abstract
BACKGROUND The number of words children produce (expressive vocabulary) and understand (receptive vocabulary) changes rapidly during early development, partially due to genetic factors. Here, we performed a meta-genome-wide association study of vocabulary acquisition and investigated polygenic overlap with literacy, cognition, developmental phenotypes, and neurodevelopmental conditions, including attention-deficit/hyperactivity disorder (ADHD). METHODS We studied 37,913 parent-reported vocabulary size measures (English, Dutch, Danish) for 17,298 children of European descent. Meta-analyses were performed for early-phase expressive (infancy, 15-18 months), late-phase expressive (toddlerhood, 24-38 months), and late-phase receptive (toddlerhood, 24-38 months) vocabulary. Subsequently, we estimated single nucleotide polymorphism-based heritability (SNP-h2) and genetic correlations (rg) and modeled underlying factor structures with multivariate models. RESULTS Early-life vocabulary size was modestly heritable (SNP-h2 = 0.08-0.24). Genetic overlap between infant expressive and toddler receptive vocabulary was negligible (rg = 0.07), although each measure was moderately related to toddler expressive vocabulary (rg = 0.69 and rg = 0.67, respectively), suggesting a multifactorial genetic architecture. Both infant and toddler expressive vocabulary were genetically linked to literacy (e.g., spelling: rg = 0.58 and rg = 0.79, respectively), underlining genetic similarity. However, a genetic association of early-life vocabulary with educational attainment and intelligence emerged only during toddlerhood (e.g., receptive vocabulary and intelligence: rg = 0.36). Increased ADHD risk was genetically associated with larger infant expressive vocabulary (rg = 0.23). Multivariate genetic models in the ALSPAC (Avon Longitudinal Study of Parents and Children) cohort confirmed this finding for ADHD symptoms (e.g., at age 13; rg = 0.54) but showed that the association effect reversed for toddler receptive vocabulary (rg = -0.74), highlighting developmental heterogeneity. CONCLUSIONS The genetic architecture of early-life vocabulary changes during development, shaping polygenic association patterns with later-life ADHD, literacy, and cognition-related traits.
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Affiliation(s)
- Ellen Verhoef
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands.
| | - Andrea G Allegrini
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Philip R Jansen
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center, Rotterdam, the Netherlands; Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit, Amsterdam, the Netherlands; Section Clinical Genetics, Department Human Genetics, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Katherine Lange
- Murdoch Children's Research Institute, Parkville, Victoria, Australia; Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Carol A Wang
- School of Medicine and Public Health, The University of Newcastle, Newcastle, New South Wales, Australia; Mothers and Babies Research Program, Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - Angela T Morgan
- Murdoch Children's Research Institute, Parkville, Victoria, Australia; Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Department of Audiology and Speech Pathology, University of Melbourne, Parkville, Victoria, Australia; Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Tarunveer S Ahluwalia
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark; Steno Diabetes Center Copenhagen, Herlev, Denmark; Bioinformatics Center, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Christos Symeonides
- Murdoch Children's Research Institute, Parkville, Victoria, Australia; Royal Children's Hospital, Melbourne, Victoria, Australia; Minderoo Foundation, Perth, Western Australia, Australia
| | - Else Eising
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
| | - Marie-Christine Franken
- Erasmus University Medical Center, Sophia Children's Hospital, Department of Otorhinolaryngology and Head and Neck Surgery, Rotterdam, the Netherlands
| | - Elina Hypponen
- Australian Centre for Precision Health, Unit of Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia; South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Toby Mansell
- Murdoch Children's Research Institute, Parkville, Victoria, Australia; Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Mitchell Olislagers
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands; Department of Urology, Erasmus University Medical Center, Erasmus University Medical Center Cancer Institute, Rotterdam, the Netherlands
| | - Emina Omerovic
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Kaili Rimfeld
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK; Department of Psychology, Royal Holloway University of London, London, UK
| | - Fenja Schlag
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
| | - Saskia Selzam
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Chin Yang Shapland
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK; Population Health Sciences, University of Bristol, Bristol, UK
| | - Henning Tiemeier
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center, Rotterdam, the Netherlands; Harvard, T.H. Chan School of Public Health, Boston, Massachusetts
| | - Andrew J O Whitehouse
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia, Australia
| | - Richard Saffery
- Murdoch Children's Research Institute, Parkville, Victoria, Australia; Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Chongqing Medical University, Chongqing, China
| | - Klaus Bønnelykke
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Sheena Reilly
- Murdoch Children's Research Institute, Parkville, Victoria, Australia; Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Menzies Health Institute Queensland, Griffith University, Brisbane, Queensland, Australia
| | - Craig E Pennell
- School of Medicine and Public Health, The University of Newcastle, Newcastle, New South Wales, Australia; Mothers and Babies Research Program, Hunter Medical Research Institute, Newcastle, New South Wales, Australia; Maternity and Gynaecology John Hunter Hospital, Newcastle, New South Wales, Australia
| | - Melissa Wake
- Murdoch Children's Research Institute, Parkville, Victoria, Australia; Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Liggins Institute, The University of Auckland, Grafton, New Zealand
| | - Charlotte A M Cecil
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center, Rotterdam, the Netherlands; Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands; Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Robert Plomin
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - 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 Netherlands
| | - Beate St Pourcain
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands; Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK; Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands.
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3
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Wirthlin ME, Schmid TA, Elie JE, Zhang X, Kowalczyk A, Redlich R, Shvareva VA, Rakuljic A, Ji MB, Bhat NS, Kaplow IM, Schäffer DE, Lawler AJ, Wang AZ, Phan BN, Annaldasula S, Brown AR, Lu T, Lim BK, Azim E, Clark NL, Meyer WK, Pond SLK, Chikina M, Yartsev MM, Pfenning AR. Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements. Science 2024; 383:eabn3263. [PMID: 38422184 PMCID: PMC11313673 DOI: 10.1126/science.abn3263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/20/2024] [Indexed: 03/02/2024]
Abstract
Vocal production learning ("vocal learning") is a convergently evolved trait in vertebrates. To identify brain genomic elements associated with mammalian vocal learning, we integrated genomic, anatomical, and neurophysiological data from the Egyptian fruit bat (Rousettus aegyptiacus) with analyses of the genomes of 215 placental mammals. First, we identified a set of proteins evolving more slowly in vocal learners. Then, we discovered a vocal motor cortical region in the Egyptian fruit bat, an emergent vocal learner, and leveraged that knowledge to identify active cis-regulatory elements in the motor cortex of vocal learners. Machine learning methods applied to motor cortex open chromatin revealed 50 enhancers robustly associated with vocal learning whose activity tended to be lower in vocal learners. Our research implicates convergent losses of motor cortex regulatory elements in mammalian vocal learning evolution.
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Affiliation(s)
- Morgan E. Wirthlin
- Department of Computational Biology, Carnegie Mellon University; Pittsburgh, PA 15213, USA
- Present address: Department of Biomedical Engineering, Duke University; Durham, NC 27705
| | - Tobias A. Schmid
- Helen Wills Neuroscience Institute, University of California, Berkeley; Berkeley, CA 94708, USA
| | - Julie E. Elie
- Helen Wills Neuroscience Institute, University of California, Berkeley; Berkeley, CA 94708, USA
- Department of Bioengineering, University of California, Berkeley; Berkeley, CA 94708, USA
| | - Xiaomeng Zhang
- Department of Computational Biology, Carnegie Mellon University; Pittsburgh, PA 15213, USA
| | - Amanda Kowalczyk
- Department of Computational Biology, Carnegie Mellon University; Pittsburgh, PA 15213, USA
- Present address: Department of Biomedical Engineering, Duke University; Durham, NC 27705
| | - Ruby Redlich
- Department of Computational Biology, Carnegie Mellon University; Pittsburgh, PA 15213, USA
| | - Varvara A. Shvareva
- Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA 94708, USA
| | - Ashley Rakuljic
- Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA 94708, USA
| | - Maria B. Ji
- Department of Psychology, University of California, Berkeley; Berkeley, CA 94708, USA
| | - Ninad S. Bhat
- Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA 94708, USA
| | - Irene M. Kaplow
- Department of Computational Biology, Carnegie Mellon University; Pittsburgh, PA 15213, USA
- Present address: Department of Biomedical Engineering, Duke University; Durham, NC 27705
| | - Daniel E. Schäffer
- Department of Computational Biology, Carnegie Mellon University; Pittsburgh, PA 15213, USA
| | - Alyssa J. Lawler
- Present address: Department of Biomedical Engineering, Duke University; Durham, NC 27705
- Department of Biological Sciences, Carnegie Mellon University; Pittsburgh, PA 15213, USA
| | - Andrew Z. Wang
- Department of Computational Biology, Carnegie Mellon University; Pittsburgh, PA 15213, USA
| | - BaDoi N. Phan
- Department of Computational Biology, Carnegie Mellon University; Pittsburgh, PA 15213, USA
- Present address: Department of Biomedical Engineering, Duke University; Durham, NC 27705
| | - Siddharth Annaldasula
- Department of Computational Biology, Carnegie Mellon University; Pittsburgh, PA 15213, USA
| | - Ashley R. Brown
- Department of Computational Biology, Carnegie Mellon University; Pittsburgh, PA 15213, USA
- Present address: Department of Biomedical Engineering, Duke University; Durham, NC 27705
| | - Tianyu Lu
- Department of Computational Biology, Carnegie Mellon University; Pittsburgh, PA 15213, USA
| | - Byung Kook Lim
- Neurobiology section, Division of Biological Science, University of California, San Diego; La Jolla, CA 92093, USA
| | - Eiman Azim
- Molecular Neurobiology Laboratory, Salk Institute for Biological Studies; La Jolla, CA 92037, USA
| | - Nathan L. Clark
- Department of Biological Sciences, University of Pittsburgh; Pittsburgh, PA 15213, USA
| | - Wynn K. Meyer
- Department of Biological Sciences, Lehigh University; Bethlehem, PA 18015, USA
| | | | - Maria Chikina
- Department of Computational and Systems Biology, University of Pittsburgh; Pittsburgh, PA 15213, USA
| | - Michael M. Yartsev
- Helen Wills Neuroscience Institute, University of California, Berkeley; Berkeley, CA 94708, USA
- Department of Bioengineering, University of California, Berkeley; Berkeley, CA 94708, USA
| | - Andreas R. Pfenning
- Department of Computational Biology, Carnegie Mellon University; Pittsburgh, PA 15213, USA
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Bonaglia MC, Salvo E, Sironi M, Bertuzzo S, Errichiello E, Mattina T, Zuffardi O. Case Report: Decrypting an interchromosomal insertion associated with Marfan's syndrome: how optical genome mapping emphasizes the morbid burden of copy-neutral variants. Front Genet 2023; 14:1244983. [PMID: 37811140 PMCID: PMC10551147 DOI: 10.3389/fgene.2023.1244983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/01/2023] [Indexed: 10/10/2023] Open
Abstract
Optical genome mapping (OGM), which allows analysis of ultra-high molecular weight (UHMW) DNA molecules, represents a response to the restriction created by short-read next-generation-sequencing, even in cases where the causative variant is a neutral copy-number-variant insensitive to quantitative investigations. This study aimed to provide a molecular diagnosis to a boy with Marfan syndrome (MFS) and intellectual disability (ID) carrying a de novo translocation involving chromosomes 3, 4, and 13 and a 1.7 Mb deletion at the breakpoint of chromosome 3. No FBN1 alteration explaining his Marfan phenotype was highlighted. UHMW gDNA was isolated from both the patient and his parents and processed using OGM. Genome assembly was followed by variant calling and annotation. Multiple strategies confirmed the results. The 3p deletion, which disrupted ROBO2, (MIM*602431) included three copy-neutral insertions. Two came from chromosome 13; the third contained 15q21.1, including the FBN1 from intron-45 onwards, thus explaining the MFS phenotype. We could not attribute the ID to a specific gene variant nor to the reshuffling of topologically associating domains (TADs). Our patient did not have vesicular reflux-2, as reported by missense alterations of ROBO2 (VUR2, MIM#610878), implying that reduced expression of all or some isoforms has a different effect than some of the point mutations. Indeed, the ROBO2 expression pattern and its role as an axon-guide suggests that its partial deletion is responsible for the patient's neurological phenotype. Conclusion: OGM testing 1) highlights copy-neutral variants that could remain invisible if no loss of heterozygosity is observed and 2) is mandatory before other molecular studies in the presence of any chromosomal rearrangement for an accurate genotype-phenotype relationship.
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Affiliation(s)
| | - Eliana Salvo
- Cytogenetics Laboratory, Scientific Institute, IRCCS E. Medea, Lecco, Italy
| | - Manuela Sironi
- Bioinformatics, Scientific Institute, IRCCS E. Medea, Lecco, Italy
| | - Sara Bertuzzo
- Cytogenetics Laboratory, Scientific Institute, IRCCS E. Medea, Lecco, Italy
| | - Edoardo Errichiello
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Neurogenetics Research Center, IRCCS Mondino Foundation, Pavia, Italy
| | - Teresa Mattina
- Medical Genetics Unit, University of Catania, Catania, Italy
- Clinic G.B. Morgagni, Catania, Italy
| | - Orsetta Zuffardi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
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5
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Morozova EA, Belousova MV, Morozov DV, Gabelko DI, Bogolyubova VV. [Genetic aspects of speech disorders in children]. Zh Nevrol Psikhiatr Im S S Korsakova 2023; 123:87-91. [PMID: 37942978 DOI: 10.17116/jnevro202312309287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
Speech disorders still remains one of the cornerstones of pediatric neurology. Against the backdrop of gene diagnostic development, there are a huge amount of information about the role of genetic and chromosomal abnormalities in pathogenesis of speech disorders. In present article authors presenting an actual data on genetic basis of different types of speech disorders. Moreover, authors describing a clinical case of a patient with genetically determined developmental disorder, caused by KMT5B mutation validated by Sanger method.
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Affiliation(s)
- E A Morozova
- Kazan State Medical Academy - Russian Medical Academy of Continuous Professional Education, Kazan, Russia
| | - M V Belousova
- Kazan State Medical Academy - Russian Medical Academy of Continuous Professional Education, Kazan, Russia
| | - D V Morozov
- Kazan State Medical Academy - Russian Medical Academy of Continuous Professional Education, Kazan, Russia
| | - D I Gabelko
- Kazan State Medical Academy - Russian Medical Academy of Continuous Professional Education, Kazan, Russia
| | - V V Bogolyubova
- Kazan State Medical Academy - Russian Medical Academy of Continuous Professional Education, Kazan, Russia
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6
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Chang X, Zhao W, Kang J, Xiang S, Xie C, Corona-Hernández H, Palaniyappan L, Feng J. Language abnormalities in schizophrenia: binding core symptoms through contemporary empirical evidence. SCHIZOPHRENIA (HEIDELBERG, GERMANY) 2022; 8:95. [PMID: 36371445 PMCID: PMC9653408 DOI: 10.1038/s41537-022-00308-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 10/26/2022] [Indexed: 06/16/2023]
Abstract
Both the ability to speak and to infer complex linguistic messages from sounds have been claimed as uniquely human phenomena. In schizophrenia, formal thought disorder (FTD) and auditory verbal hallucinations (AVHs) are manifestations respectively relating to concrete disruptions of those abilities. From an evolutionary perspective, Crow (1997) proposed that "schizophrenia is the price that Homo sapiens pays for the faculty of language". Epidemiological and experimental evidence points to an overlap between FTD and AVHs, yet a thorough investigation examining their shared neural mechanism in schizophrenia is lacking. In this review, we synthesize observations from three key domains. First, neuroanatomical evidence indicates substantial shared abnormalities in language-processing regions between FTD and AVHs, even in the early phases of schizophrenia. Second, neurochemical studies point to a glutamate-related dysfunction in these language-processing brain regions, contributing to verbal production deficits. Third, genetic findings further show how genes that overlap between schizophrenia and language disorders influence neurodevelopment and neurotransmission. We argue that these observations converge into the possibility that a glutamatergic dysfunction in language-processing brain regions might be a shared neural basis of both FTD and AVHs. Investigations of language pathology in schizophrenia could facilitate the development of diagnostic tools and treatments, so we call for multilevel confirmatory analyses focused on modulations of the language network as a therapeutic goal in schizophrenia.
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Affiliation(s)
- Xiao Chang
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Fudan University, Ministry of Education, Shanghai, China
- MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
- Zhangjiang Fudan International Innovation Center, Shanghai, China
| | - Wei Zhao
- MOE-LCSM, School of Mathematics and Statistics, Hunan Normal University, Changsha, PR China
| | - Jujiao Kang
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Fudan University, Ministry of Education, Shanghai, China
- Shanghai Center for Mathematical Sciences, Shanghai, China
| | - Shitong Xiang
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Fudan University, Ministry of Education, Shanghai, China
| | - Chao Xie
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Fudan University, Ministry of Education, Shanghai, China
| | - Hugo Corona-Hernández
- Department of Biomedical Sciences of Cells & Systems, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Lena Palaniyappan
- Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, Quebec, Canada.
- Robarts Research Institute, University of Western Ontario, London, Ontario, Canada.
- Lawson Health Research Institute, London, Ontario, Canada.
| | - Jianfeng Feng
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China.
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Fudan University, Ministry of Education, Shanghai, China.
- MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China.
- Zhangjiang Fudan International Innovation Center, Shanghai, China.
- Shanghai Center for Mathematical Sciences, Shanghai, China.
- Department of Computer Science, University of Warwick, Coventry, UK.
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7
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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: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [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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8
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Buisan R, Moriano J, Andirkó A, Boeckx C. A Brain Region-Specific Expression Profile for Genes Within Large Introgression Deserts and Under Positive Selection in Homo sapiens. Front Cell Dev Biol 2022; 10:824740. [PMID: 35557944 PMCID: PMC9086289 DOI: 10.3389/fcell.2022.824740] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
Analyses of ancient DNA from extinct hominins have provided unique insights into the complex evolutionary history of Homo sapiens, intricately related to that of the Neanderthals and the Denisovans as revealed by several instances of admixture events. These analyses have also allowed the identification of introgression deserts: genomic regions in our species that are depleted of “archaic” haplotypes. The presence of genes like FOXP2 in these deserts has been taken to be suggestive of brain-related functional differences between Homo species. Here, we seek a deeper characterization of these regions and the specific expression trajectories of genes within them, taking into account signals of positive selection in our lineage. Analyzing publicly available transcriptomic data from the human brain at different developmental stages, we found that structures outside the cerebral neocortex, in particular the cerebellum, the striatum and the mediodorsal nucleus of the thalamus show the most divergent transcriptomic profiles when considering genes within large introgression deserts and under positive selection.
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Affiliation(s)
| | - Juan Moriano
- Universitat de Barcelona, Barcelona, Spain
- Universitat de Barcelona Institute of Complex Systems, Barcelona, Spain
| | - Alejandro Andirkó
- Universitat de Barcelona, Barcelona, Spain
- Universitat de Barcelona Institute of Complex Systems, Barcelona, Spain
| | - Cedric Boeckx
- Universitat de Barcelona, Barcelona, Spain
- Universitat de Barcelona Institute of Complex Systems, Barcelona, Spain
- Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain
- *Correspondence: Cedric Boeckx,
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9
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Mountford HS, Braden R, Newbury DF, Morgan AT. The Genetic and Molecular Basis of Developmental Language Disorder: A Review. CHILDREN (BASEL, SWITZERLAND) 2022; 9:children9050586. [PMID: 35626763 PMCID: PMC9139417 DOI: 10.3390/children9050586] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/28/2022] [Accepted: 04/12/2022] [Indexed: 01/05/2023]
Abstract
Language disorders are highly heritable and are influenced by complex interactions between genetic and environmental factors. Despite more than twenty years of research, we still lack critical understanding of the biological underpinnings of language. This review provides an overview of the genetic landscape of developmental language disorders (DLD), with an emphasis on the importance of defining the specific features (the phenotype) of DLD to inform gene discovery. We review the specific phenotype of DLD in the genetic literature, and the influence of historic variation in diagnostic inclusion criteria on researchers' ability to compare and replicate genotype-phenotype studies. This review provides an overview of the recently identified gene pathways in populations with DLD and explores current state-of-the-art approaches to genetic analysis based on the hypothesised architecture of DLD. We will show how recent global efforts to unify diagnostic criteria have vastly increased sample size and allow for large multi-cohort metanalyses, leading the identification of a growing number of contributory loci. We emphasise the important role of estimating the genetic architecture of DLD to decipher underlying genetic associations. Finally, we explore the potential for epigenetics and environmental interactions to further unravel the biological basis of language disorders.
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Affiliation(s)
- Hayley S. Mountford
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK; (H.S.M.); (D.F.N.)
| | - Ruth Braden
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne 3052, Australia;
| | - Dianne F. Newbury
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK; (H.S.M.); (D.F.N.)
| | - Angela T. Morgan
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne 3052, Australia;
- Correspondence:
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10
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Benchek P, Igo RP, Voss-Hoynes H, Wren Y, Miller G, Truitt B, Zhang W, Osterman M, Freebairn L, Tag J, Taylor HG, Chan ER, Roussos P, Lewis B, Stein CM, Iyengar SK. Association between genes regulating neural pathways for quantitative traits of speech and language disorders. NPJ Genom Med 2021; 6:64. [PMID: 34315907 PMCID: PMC8316336 DOI: 10.1038/s41525-021-00225-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 06/22/2021] [Indexed: 02/06/2023] Open
Abstract
Speech sound disorders (SSD) manifest as difficulties in phonological memory and awareness, oral motor function, language, vocabulary, reading, and spelling. Families enriched for SSD are rare, and typically display a cluster of deficits. We conducted a genome-wide association study (GWAS) in 435 children from 148 families in the Cleveland Family Speech and Reading study (CFSRS), examining 16 variables representing 6 domains. Replication was conducted using the Avon Longitudinal Study of Parents and Children (ALSPAC). We identified 18 significant loci (combined p < 10-8) that we pursued bioinformatically. We prioritized 5 novel gene regions with likely functional repercussions on neural pathways, including those which colocalized with differentially methylated regions in our sample. Polygenic risk scores for receptive language, expressive vocabulary, phonological awareness, phonological memory, spelling, and reading decoding associated with increasing clinical severity. In summary, neural-genetic influence on SSD is primarily multigenic and acts on genomic regulatory elements, similar to other neurodevelopmental disorders.
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Affiliation(s)
- Penelope Benchek
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Robert P Igo
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Heather Voss-Hoynes
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Yvonne Wren
- Bristol Dental School, Faculty of Health Sciences, University of Bristol, and Bristol Speech and Language Therapy Research Unit, North Bristol NHS Trust, Bristol, UK
| | - Gabrielle Miller
- Department of Psychological Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Barbara Truitt
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Wen Zhang
- Department of Psychiatry, Friedman Brain Institute, and Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Osterman
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Lisa Freebairn
- Department of Psychological Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Jessica Tag
- Department of Psychological Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - H Gerry Taylor
- Department of Pediatrics, Case Western Reserve University, and Rainbow Babies & Children's Hospital, University Hospital Case Medical Center, Cleveland, OH, USA
- Nationwide Children's Hospital Research Institute and Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - E Ricky Chan
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Panos Roussos
- Department of Psychiatry, Friedman Brain Institute, and Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mental Illness Research, Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, NY, USA
| | - Barbara Lewis
- Department of Psychological Sciences, Case Western Reserve University, Cleveland, OH, USA
- Cleveland Hearing and Speech Center, Cleveland, OH, USA
| | - Catherine M Stein
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA.
| | - Sudha K Iyengar
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA.
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11
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Martinelli A, Rice ML, Talcott JB, Diaz R, Smith S, Raza MH, Snowling MJ, Hulme C, Stein J, Hayiou-Thomas ME, Hawi Z, Kent L, Pitt SJ, Newbury DF, Paracchini S. A rare missense variant in the ATP2C2 gene is associated with language impairment and related measures. Hum Mol Genet 2021; 30:1160-1171. [PMID: 33864365 PMCID: PMC8188402 DOI: 10.1093/hmg/ddab111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 04/09/2021] [Accepted: 04/12/2021] [Indexed: 01/02/2023] Open
Abstract
At least 5% of children present unexpected difficulties in expressing and understanding spoken language. This condition is highly heritable and often co-occurs with other neurodevelopmental disorders such as dyslexia and ADHD. Through an exome sequencing analysis, we identified a rare missense variant (chr16:84405221, GRCh38.p12) in the ATP2C2 gene. ATP2C2 was implicated in language disorders by linkage and association studies, and exactly the same variant was reported previously in a different exome sequencing study for language impairment (LI). We followed up this finding by genotyping the mutation in cohorts selected for LI and comorbid disorders. We found that the variant had a higher frequency in LI cases (1.8%, N = 360) compared with cohorts selected for dyslexia (0.8%, N = 520) and ADHD (0.7%, N = 150), which presented frequencies comparable to reference databases (0.9%, N = 24 046 gnomAD controls). Additionally, we observed that carriers of the rare variant identified from a general population cohort (N = 42, ALSPAC cohort) presented, as a group, lower scores on a range of reading and language-related measures compared to controls (N = 1825; minimum P = 0.002 for non-word reading). ATP2C2 encodes for an ATPase (SPCA2) that transports calcium and manganese ions into the Golgi lumen. Our functional characterization suggested that the rare variant influences the ATPase activity of SPCA2. Thus, our results further support the role of ATP2C2 locus in language-related phenotypes and pinpoint the possible effects of a specific rare variant at molecular level.
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Affiliation(s)
| | - Mabel L Rice
- Child Language Doctoral Program, University of Kansas, Lawrence, KS, USA
| | - Joel B Talcott
- Aston Brain Centre, School of Life and Health Sciences, Aston University, Birmingham, UK
| | - Rebeca Diaz
- School of Medicine, University of St Andrews, St Andrews, UK
| | - Shelley Smith
- Department of Neurological Sciences, University of Nebraska Medical Center, Lincoln, NE, USA
| | | | - Margaret J Snowling
- Department of Experimental Psychology and St John's College, University of Oxford, Oxford, UK
| | - Charles Hulme
- Department of Education, University of Oxford, Oxford, UK
| | - John Stein
- Department of Physiology, University of Oxford, Oxford, UK
| | | | - Ziarih Hawi
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Clayton, VIC, Australia
| | - Lindsey Kent
- School of Medicine, University of St Andrews, St Andrews, UK
| | - Samantha J Pitt
- School of Medicine, University of St Andrews, St Andrews, UK
| | - Dianne F Newbury
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
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12
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Mountford HS, Hill A, Barnett AL, Newbury DF. Genome-Wide Association Study of Motor Coordination. Front Hum Neurosci 2021; 15:669902. [PMID: 34177493 PMCID: PMC8219980 DOI: 10.3389/fnhum.2021.669902] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/10/2021] [Indexed: 11/13/2022] Open
Abstract
The ability to finely control our movement is key to achieving many of the educational milestones and life-skills we develop throughout our lives. Despite the centrality of coordination to early development, there is a vast gap in our understanding of the underlying biology. Like most complex traits, both genetics and environment influence motor coordination, however, the specific genes, early environmental risk factors and molecular pathways are unknown. Previous studies have shown that about 5% of school-age children experience unexplained difficulties with motor coordination. These children are said to have Developmental Coordination Disorder (DCD). For children with DCD, these motor coordination difficulties significantly impact their everyday life and learning. DCD is associated with poorer academic achievement, reduced quality of life, it can constrain career opportunities and increase the risk of mental health issues in adulthood. Despite the high prevalence of coordination difficulties, many children remain undiagnosed by healthcare professionals. Compounding under-diagnosis in the clinic, research into the etiology of DCD is severely underrepresented in the literature. Here we present the first genome-wide association study to examine the genetic basis of early motor coordination in the context of motor difficulties. Using data from the Avon Longitudinal Study of Parents and Children we generate a derived measure of motor coordination from four components of the Movement Assessment Battery for Children, providing an overall measure of coordination across the full range of ability. We perform the first genome-wide association analysis focused on motor coordination (N = 4542). No single nucleotide polymorphisms (SNPs) met the threshold for genome-wide significance, however, 59 SNPs showed suggestive associations. Three regions contained multiple suggestively associated SNPs, within five preliminary candidate genes: IQSEC1, LRCC1, SYNJ2B2, ADAM20, and ADAM21. Association to the gene IQSEC1 suggests a potential link to axon guidance and dendritic projection processes as a potential underlying mechanism of motor coordination difficulties. This represents an interesting potential mechanism, and whilst further validation is essential, it generates a direct window into the biology of motor coordination difficulties. This research has identified potential biological drivers of DCD, a first step towards understanding this common, yet neglected neurodevelopmental disorder.
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Affiliation(s)
- Hayley S. Mountford
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Amanda Hill
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Anna L. Barnett
- Centre for Psychological Research, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Dianne F. Newbury
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, United Kingdom
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13
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Verhoef E, Shapland CY, Fisher SE, Dale PS, St Pourcain B. The developmental origins of genetic factors influencing language and literacy: Associations with early-childhood vocabulary. J Child Psychol Psychiatry 2021; 62:728-738. [PMID: 32924135 DOI: 10.1111/jcpp.13327] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/11/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND The heritability of language and literacy skills increases from early-childhood to adolescence. The underlying mechanisms are little understood and may involve (a) the amplification of genetic influences contributing to early language abilities, and/or (b) the emergence of novel genetic factors (innovation). Here, we investigate the developmental origins of genetic factors influencing mid-childhood/early-adolescent language and literacy. We evaluate evidence for the amplification of early-childhood genetic factors for vocabulary, in addition to genetic innovation processes. METHODS Expressive and receptive vocabulary scores at 38 months, thirteen language- and literacy-related abilities and nonverbal cognition (7-13 years) were assessed in unrelated children from the Avon Longitudinal Study of Parents and Children (ALSPAC, Nindividuals ≤ 6,092). We investigated the multivariate genetic architecture underlying early-childhood expressive and receptive vocabulary, and each of 14 mid-childhood/early-adolescent language, literacy or cognitive skills with trivariate structural equation (Cholesky) models as captured by genome-wide genetic relationship matrices. The individual path coefficients of the resulting structural models were finally meta-analysed to evaluate evidence for overarching patterns. RESULTS We observed little support for the emergence of novel genetic sources for language, literacy or cognitive abilities during mid-childhood or early adolescence. Instead, genetic factors of early-childhood vocabulary, especially those unique to receptive skills, were amplified and represented the majority of genetic variance underlying many of these later complex skills (≤99%). The most predictive early genetic factor accounted for 29.4%(SE = 12.9%) to 45.1%(SE = 7.6%) of the phenotypic variation in verbal intelligence and literacy skills, but also for 25.7%(SE = 6.4%) in performance intelligence, while explaining only a fraction of the phenotypic variation in receptive vocabulary (3.9%(SE = 1.8%)). CONCLUSIONS Genetic factors contributing to many complex skills during mid-childhood and early adolescence, including literacy, verbal cognition and nonverbal cognition, originate developmentally in early-childhood and are captured by receptive vocabulary. This suggests developmental genetic stability and overarching aetiological mechanisms.
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Affiliation(s)
- Ellen Verhoef
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands.,International Max Planck Research School for Language Sciences, Nijmegen, The Netherlands
| | - Chin Yang Shapland
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands.,MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,Population Health Sciences, University of Bristol, Bristol, UK
| | - 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 Netherlands
| | - Philip S Dale
- Speech and Hearing Sciences, University of New Mexico, Albuquerque, NM, USA
| | - Beate St Pourcain
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands.,MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
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14
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Verhoef E, Shapland CY, Fisher SE, Dale PS, St Pourcain B. The developmental genetic architecture of vocabulary skills during the first three years of life: Capturing emerging associations with later-life reading and cognition. PLoS Genet 2021; 17:e1009144. [PMID: 33577555 PMCID: PMC7880480 DOI: 10.1371/journal.pgen.1009144] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/22/2020] [Indexed: 11/18/2022] Open
Abstract
Individual differences in early-life vocabulary measures are heritable and associated with subsequent reading and cognitive abilities, although the underlying mechanisms are little understood. Here, we (i) investigate the developmental genetic architecture of expressive and receptive vocabulary in early-life and (ii) assess timing of emerging genetic associations with mid-childhood verbal and non-verbal skills. We studied longitudinally assessed early-life vocabulary measures (15–38 months) and later-life verbal and non-verbal skills (7–8 years) in up to 6,524 unrelated children from the population-based Avon Longitudinal Study of Parents and Children (ALSPAC) cohort. We dissected the phenotypic variance of rank-transformed scores into genetic and residual components by fitting multivariate structural equation models to genome-wide genetic-relationship matrices. Our findings show that the genetic architecture of early-life vocabulary involves multiple distinct genetic factors. Two of these genetic factors are developmentally stable and also contribute to genetic variation in mid-childhood skills: One genetic factor emerging with expressive vocabulary at 24 months (path coefficient: 0.32(SE = 0.06)) was also related to later-life reading (path coefficient: 0.25(SE = 0.12)) and verbal intelligence (path coefficient: 0.42(SE = 0.13)), explaining up to 17.9% of the phenotypic variation. A second, independent genetic factor emerging with receptive vocabulary at 38 months (path coefficient: 0.15(SE = 0.07)), was more generally linked to verbal and non-verbal cognitive abilities in mid-childhood (reading path coefficient: 0.57(SE = 0.07); verbal intelligence path coefficient: 0.60(0.10); performance intelligence path coefficient: 0.50(SE = 0.08)), accounting for up to 36.1% of the phenotypic variation and the majority of genetic variance in these later-life traits (≥66.4%). Thus, the genetic foundations of mid-childhood reading and cognitive abilities are diverse. They involve at least two independent genetic factors that emerge at different developmental stages during early language development and may implicate differences in cognitive processes that are already detectable during toddlerhood. Differences in the number of words young children produce (expressive vocabulary) and understand (receptive vocabulary) can be partially explained by common genetic variation, and are related to reading and cognitive abilities later in life. Here, we studied genetic influences underlying expressive and receptive vocabulary during early development (15–38 months) and their genetic relationship with mid-childhood reading and cognitive skills (7–8 years), based on longitudinal phenotype measures and genome-wide genetic data from up to 6,524 unrelated children. We showed that early-life vocabulary skills are influenced by multiple independent genetic factors, of which two also relate to mid-childhood skills, suggesting developmental stability. One genetic factor emerging with expressive vocabulary at 24 months was linked to subsequent verbal abilities, including vocabulary measures at 38 months, as well as mid-childhood reading and verbal intelligence performance. A second, independent genetic factor related to receptive vocabulary at 38 months contributed more generally to variation in mid-childhood reading, verbal and non-verbal intelligence. Thus, the genetic foundations of mid-childhood reading and cognitive abilities involve at least two independent genetic factors that emerge during early-life language development and may implicate differences in overarching cognitive mechanisms.
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Affiliation(s)
- Ellen Verhoef
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- International Max Planck Research School for Language Sciences, Nijmegen, The Netherlands
- * E-mail: (EV); (BSTP)
| | - Chin Yang Shapland
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- Population Health Sciences, University of Bristol, Bristol, United Kingdom
| | - 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 Netherlands
| | - Philip S. Dale
- Speech & Hearing Sciences, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Beate St Pourcain
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
- * E-mail: (EV); (BSTP)
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15
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Tsetsos F, Yu D, Sul JH, Huang AY, Illmann C, Osiecki L, Darrow SM, Hirschtritt ME, Greenberg E, Muller-Vahl KR, Stuhrmann M, Dion Y, Rouleau GA, Aschauer H, Stamenkovic M, Schlögelhofer M, Sandor P, Barr CL, Grados MA, Singer HS, Nöthen MM, Hebebrand J, Hinney A, King RA, Fernandez TV, Barta C, Tarnok Z, Nagy P, Depienne C, Worbe Y, Hartmann A, Budman CL, Rizzo R, Lyon GJ, McMahon WM, Batterson JR, Cath DC, Malaty IA, Okun MS, Berlin C, Woods DW, Lee PC, Jankovic J, Robertson MM, Gilbert DL, Brown LW, Coffey BJ, Dietrich A, Hoekstra PJ, Kuperman S, Zinner SH, Wagner M, Knowles JA, Jeremy Willsey A, Tischfield JA, Heiman GA, Cox NJ, Freimer NB, Neale BM, Davis LK, Coppola G, Mathews CA, Scharf JM, Paschou P, Barr CL, Batterson JR, Berlin C, Budman CL, Cath DC, Coppola G, Cox NJ, Darrow S, Davis LK, Dion Y, Freimer NB, Grados MA, Greenberg E, Hirschtritt ME, Huang AY, Illmann C, King RA, Kurlan R, Leckman JF, Lyon GJ, Malaty IA, Mathews CA, McMahon WM, Neale BM, Okun MS, Osiecki L, Robertson MM, Rouleau GA, Sandor P, Scharf JM, Singer HS, Smit JH, Sul JH, Yu D, Aschauer HAH, Barta C, Budman CL, Cath DC, Depienne C, Hartmann A, Hebebrand J, Konstantinidis A, Mathews CA, Müller-Vahl K, Nagy P, Nöthen MM, Paschou P, Rizzo R, Rouleau GA, Sandor P, Scharf JM, Schlögelhofer M, Stamenkovic M, Stuhrmann M, Tsetsos F, Tarnok Z, Wolanczyk T, Worbe Y, Brown L, Cheon KA, Coffey BJ, Dietrich A, Fernandez TV, Garcia-Delgar B, Gilbert D, Grice DE, Hagstrøm J, Hedderly T, Heiman GA, Heyman I, Hoekstra PJ, Huyser C, Kim YK, Kim YS, King RA, Koh YJ, Kook S, Kuperman S, Leventhal BL, Madruga-Garrido M, Mir P, Morer A, Münchau A, Plessen KJ, Roessner V, Shin EY, Song DH, Song J, Tischfield JA, Willsey AJ, Zinner S, Aschauer H, Barr CL, Barta C, Batterson JR, Berlin C, Brown L, Budman CL, Cath DC, Coffey BJ, Coppola G, Cox NJ, Darrow S, Davis LK, Depienne C, Dietrich A, Dion Y, Fernandez T, Freimer NB, Gilbert D, Grados MA, Greenberg E, Hartmann A, Hebebrand J, Heiman G, Hirschtritt ME, Hoekstra P, Huang AY, Illmann C, Jankovic J, King RA, Kuperman S, Lee PC, Lyon GJ, Malaty IA, Mathews CA, McMahon WM, Müller-Vahl K, Nagy P, Neale BM, Nöthen MM, Okun MS, Osiecki L, Paschou P, Rizzo R, Robertson MM, Rouleau GA, Sandor P, Scharf JM, Schlögelhofer M, Singer HS, Stamenkovic M, Stuhrmann M, Sul JH, Tarnok Z, Tischfield J, Tsetsos F, Willsey AJ, Woods D, Worbe Y, Yu D, Zinner S. Synaptic processes and immune-related pathways implicated in Tourette syndrome. Transl Psychiatry 2021; 11:56. [PMID: 33462189 PMCID: PMC7814139 DOI: 10.1038/s41398-020-01082-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 09/18/2020] [Accepted: 10/21/2020] [Indexed: 12/23/2022] Open
Abstract
Tourette syndrome (TS) is a neuropsychiatric disorder of complex genetic architecture involving multiple interacting genes. Here, we sought to elucidate the pathways that underlie the neurobiology of the disorder through genome-wide analysis. We analyzed genome-wide genotypic data of 3581 individuals with TS and 7682 ancestry-matched controls and investigated associations of TS with sets of genes that are expressed in particular cell types and operate in specific neuronal and glial functions. We employed a self-contained, set-based association method (SBA) as well as a competitive gene set method (MAGMA) using individual-level genotype data to perform a comprehensive investigation of the biological background of TS. Our SBA analysis identified three significant gene sets after Bonferroni correction, implicating ligand-gated ion channel signaling, lymphocytic, and cell adhesion and transsynaptic signaling processes. MAGMA analysis further supported the involvement of the cell adhesion and trans-synaptic signaling gene set. The lymphocytic gene set was driven by variants in FLT3, raising an intriguing hypothesis for the involvement of a neuroinflammatory element in TS pathogenesis. The indications of involvement of ligand-gated ion channel signaling reinforce the role of GABA in TS, while the association of cell adhesion and trans-synaptic signaling gene set provides additional support for the role of adhesion molecules in neuropsychiatric disorders. This study reinforces previous findings but also provides new insights into the neurobiology of TS.
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Grants
- R01 NS102371 NINDS NIH HHS
- R01 NS096207 NINDS NIH HHS
- R01 NS096008 NINDS NIH HHS
- R01 MH115958 NIMH NIH HHS
- K08 MH099424 NIMH NIH HHS
- U24 NS095914 NINDS NIH HHS
- K02 NS085048 NINDS NIH HHS
- R01 MH115963 NIMH NIH HHS
- U01 HG009086 NHGRI NIH HHS
- R56 MH120736 NIMH NIH HHS
- U54 MD010722 NIMHD NIH HHS
- UL1 TR001863 NCATS NIH HHS
- R01 DC016977 NIDCD NIH HHS
- R01 NS105746 NINDS NIH HHS
- R01 MH118233 NIMH NIH HHS
- DP2 HD098859 NICHD NIH HHS
- R01 MH115961 NIMH NIH HHS
- U24 MH068457 NIMH NIH HHS
- R25 NS108939 NINDS NIH HHS
- R01 MH114927 NIMH NIH HHS
- R01 NR014852 NINR NIH HHS
- R21 HG010652 NHGRI NIH HHS
- R01 MH113362 NIMH NIH HHS
- RM1 HG009034 NHGRI NIH HHS
- FT is co-financed by Greece and the European Union (European Social Fund- ESF) through the Operational Programme «Human Resources Development, Education and Lifelong Learning» in the context of the project “Reinforcement of Postdoctoral Researchers - 2nd Cycle” (MIS-5033021), implemented by the State Scholarships Foundation (IKY)
- KMV has received financial or material research support from the EU (FP7-HEALTH-2011 No. 278367, FP7-PEOPLE-2012-ITN No. 316978), the German Research Foundation (DFG: GZ MU 1527/3-1), the German Ministry of Education and Research (BMBF: 01KG1421), the National Institute of Mental Health (NIMH), the Tourette Gesellschaft Deutschland e.V., the Else-Kroner-Fresenius-Stiftung, and GW, Almirall, Abide Therapeutics, and Therapix Biosiences and has received consultant’s honoraria from Abide Therapeutics, Tilray, Resalo Vertrieb GmbH, and Wayland Group, speaker’s fees from Tilray and Cogitando GmbH, and royalties from Medizinisch Wissenschaftliche Verlagsgesellschaft Berlin, Elsevier, and Kohlhammer; and is a consultant for Nuvelution TS Pharma Inc., Zynerba Pharmaceuticals, Resalo Vertrieb GmbH, CannaXan GmbH, Therapix Biosiences, Syqe, Nomovo Pharma, and Columbia Care.
- MMN has received fees for memberships in Scientific Advisory Boards from the Lundbeck Foundation and the Robert-Bosch-Stiftung, and for membership in the Medical-Scientific Editorial Office of the Deutsches Ärzteblatt. MMN was reimbursed travel expenses for a conference participation by Shire Deutschland GmbH. MMN receives salary payments from Life & Brain GmbH and holds shares in Life & Brain GmbH. All this concerned activities outside the submitted work.
- IM has participated in research funded by the Parkinson Foundation, Tourette Association, Dystonia Coalition, AbbVie, Biogen, Boston Scientific, Eli Lilly, Impax, Neuroderm, Prilenia, Revance, Teva but has no owner interest in any pharmaceutical company. She has received travel compensation or honoraria from the Tourette Association of America, Parkinson Foundation, International Association of Parkinsonism and Related Disorders, Medscape, and Cleveland Clinic, and royalties for writing a book with Robert rose publishers.
- MSO serves as a consultant for the Parkinson’s Foundation, and has received research grants from NIH, Parkinson’s Foundation, the Michael J. Fox Foundation, the Parkinson Alliance, Smallwood Foundation, the Bachmann-Strauss Foundation, the Tourette Syndrome Association, and the UF Foundation. MSO’s DBS research is supported by: NIH R01 NR014852 and R01NS096008. MSO is PI of the NIH R25NS108939 Training Grant. MSO has received royalties for publications with Demos, Manson, Amazon, Smashwords, Books4Patients, Perseus, Robert Rose, Oxford and Cambridge (movement disorders books). MSO is an associate editor for New England Journal of Medicine Journal Watch Neurology. MSO has participated in CME and educational activities on movement disorders sponsored by the Academy for Healthcare Learning, PeerView, Prime, QuantiaMD, WebMD/Medscape, Medicus, MedNet, Einstein, MedNet, Henry Stewart, American Academy of Neurology, Movement Disorders Society and by Vanderbilt University. The institution and not MSO receives grants from Medtronic, Abbvie, Boston Scientific, Abbott and Allergan and the PI has no financial interest in these grants. MSO has participated as a site PI and/or co-I for several NIH, foundation, and industry sponsored trials over the years but has not received honoraria. Research projects at the University of Florida receive device and drug donations.
- DW receives royalties for books on Tourette Syndrome with Guilford Press, Oxford University Press, and Springer Press.
- BMN is a member of the scientific advisory board at Deep Genomics and consultant for Camp4 Therapeutics, Takeda Pharmaceutical and Biogen.
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Affiliation(s)
- Fotis Tsetsos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Dongmei Yu
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jae Hoon Sul
- Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA
| | - Alden Y Huang
- Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
| | - Cornelia Illmann
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Lisa Osiecki
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Sabrina M Darrow
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Matthew E Hirschtritt
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Erica Greenberg
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Kirsten R Muller-Vahl
- Clinic of Psychiatry, Social Psychiatry, and Psychotherapy, Hannover Medical School, Hannover, Germany
| | - Manfred Stuhrmann
- Institute of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Yves Dion
- McGill University Health Center, University of Montreal, McGill University Health Centre, Montreal, Canada
| | - Guy A Rouleau
- Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, Canada
| | - Harald Aschauer
- Department of Psychiatry and Psychotherapy, Medical University Vienna, Vienna, Austria
- Biopsychosocial Corporation, Vienna, Austria
| | - Mara Stamenkovic
- Department of Psychiatry and Psychotherapy, Medical University Vienna, Vienna, Austria
| | | | - Paul Sandor
- University Health Network, Youthdale Treatment Centres, and University of Toronto, Toronto, Canada
| | - Cathy L Barr
- Krembil Research Institute, University Health Network, Hospital for Sick Children, and University of Toronto, Toronto, Canada
| | - Marco A Grados
- Johns Hopkins University School of Medicine and the Kennedy Krieger Institute, Baltimore, MD, USA
| | - Harvey S Singer
- Johns Hopkins University School of Medicine and the Kennedy Krieger Institute, Baltimore, MD, USA
| | - Markus M Nöthen
- Institute of Human Genetics, University Hospital Bonn, University of Bonn Medical School, Bonn, Germany
| | - Johannes Hebebrand
- Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Anke Hinney
- Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Robert A King
- Yale Child Study Center and the Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Thomas V Fernandez
- Yale Child Study Center and the Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Csaba Barta
- Institute of Medical Chemistry, Molecular Biology, and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Zsanett Tarnok
- Vadaskert Child and Adolescent Psychiatric Hospital, Budapest, Hungary
| | - Peter Nagy
- Vadaskert Child and Adolescent Psychiatric Hospital, Budapest, Hungary
| | - Christel Depienne
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
- Sorbonne Universités, UPMC Université Paris 06, UMR S 1127, CNRS UMR 7225, ICM, Paris, France
| | - Yulia Worbe
- Sorbonne Universités, UPMC Université Paris 06, UMR S 1127, CNRS UMR 7225, ICM, Paris, France
- French Reference Centre for Gilles de la Tourette Syndrome, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
- Assistance Publique-Hôpitaux de Paris, Department of Neurology, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
- Assistance Publique Hôpitaux de Paris, Hopital Saint Antoine, Paris, France
| | - Andreas Hartmann
- Sorbonne Universités, UPMC Université Paris 06, UMR S 1127, CNRS UMR 7225, ICM, Paris, France
- French Reference Centre for Gilles de la Tourette Syndrome, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
- Assistance Publique-Hôpitaux de Paris, Department of Neurology, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Cathy L Budman
- Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
| | - Renata Rizzo
- Child Neuropsychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Gholson J Lyon
- Jervis Clinic, NYS Institute for Basic Research in Developmental Disabilities (IBR), Staten Island, NY, USA
| | - William M McMahon
- Department of Psychiatry, University of Utah, Salt Lake City, UT, USA
| | | | - Danielle C Cath
- Department of Psychiatry, University Medical Center Groningen and Rijksuniversity Groningen, and Drenthe Mental Health Center, Groningen, the Netherlands
| | - Irene A Malaty
- Department of Neurology, Norman Fixel Institute for Neurological Diseases, University of Florida Health, Gainesville, FL, USA
| | - Michael S Okun
- Department of Neurology, Norman Fixel Institute for Neurological Diseases, University of Florida Health, Gainesville, FL, USA
| | - Cheston Berlin
- Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Douglas W Woods
- Marquette University and University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Paul C Lee
- Tripler Army Medical Center and University of Hawaii John A. Burns School of Medicine, Honolulu, HI, USA
| | - Joseph Jankovic
- Parkinson's Disease Center and Movement Disorders Clinic, Department of Neurology, Baylor College of Medicine, Houston, TX, USA
| | - Mary M Robertson
- Division of Psychiatry, Department of Neuropsychiatry, University College London, London, UK
| | - Donald L Gilbert
- Division of Pediatric Neurology, Cincinnati Children's Hospital Medical Center; Department of Pediatrics, University of Cincinnati, Cincinnati, USA
| | | | - Barbara J Coffey
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Andrea Dietrich
- Department of Child and Adolescent Psychiatry, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Pieter J Hoekstra
- Department of Child and Adolescent Psychiatry, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Samuel Kuperman
- University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Samuel H Zinner
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Michael Wagner
- Department of Psychiatry and Psychotherapy, University Hospital Bonn, Bonn, Germany
| | | | - A Jeremy Willsey
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Jay A Tischfield
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Gary A Heiman
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Nancy J Cox
- Division of Genetic Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nelson B Freimer
- Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA
| | - Benjamin M Neale
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Lea K Davis
- Division of Genetic Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Giovanni Coppola
- Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA
| | - Carol A Mathews
- Department of Psychiatry, Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Jeremiah M Scharf
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Brigham and Women's Hospital, and the Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Peristera Paschou
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
| | - Cathy L Barr
- Krembil Research Institute, University Health Network, Hospital for Sick Children, and University of Toronto, Toronto, Canada
| | | | - Cheston Berlin
- Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Cathy L Budman
- Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
| | - Danielle C Cath
- Department of Psychiatry, University Medical Center Groningen and Rijksuniversity Groningen, and Drenthe Mental Health Center, Groningen, the Netherlands
| | - Giovanni Coppola
- Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA
| | - Nancy J Cox
- Division of Genetic Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sabrina Darrow
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Lea K Davis
- Division of Genetic Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yves Dion
- McGill University Health Center, University of Montreal, McGill University Health Centre, Montreal, Canada
| | - Nelson B Freimer
- Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA
| | - Marco A Grados
- Johns Hopkins University School of Medicine and the Kennedy Krieger Institute, Baltimore, MD, USA
| | - Erica Greenberg
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Matthew E Hirschtritt
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Alden Y Huang
- Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
| | - Cornelia Illmann
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Robert A King
- Yale Child Study Center and the Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Roger Kurlan
- Atlantic Neuroscience Institute, Overlook Hospital, Summit, NJ, USA
| | - James F Leckman
- Yale Child Study Center, Yale University School of Medicine, New Haven, CT, USA
| | - Gholson J Lyon
- Jervis Clinic, NYS Institute for Basic Research in Developmental Disabilities (IBR), Staten Island, NY, USA
| | - Irene A Malaty
- Department of Neurology, Norman Fixel Institute for Neurological Diseases, University of Florida Health, Gainesville, FL, USA
| | - Carol A Mathews
- Department of Psychiatry, Genetics Institute, University of Florida, Gainesville, FL, USA
| | - William M McMahon
- Department of Psychiatry, University of Utah, Salt Lake City, UT, USA
| | - Benjamin M Neale
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Michael S Okun
- Department of Neurology, Norman Fixel Institute for Neurological Diseases, University of Florida Health, Gainesville, FL, USA
| | - Lisa Osiecki
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Mary M Robertson
- Division of Psychiatry, Department of Neuropsychiatry, University College London, London, UK
| | - Guy A Rouleau
- Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, Canada
| | - Paul Sandor
- University Health Network, Youthdale Treatment Centres, and University of Toronto, Toronto, Canada
| | - Jeremiah M Scharf
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Brigham and Women's Hospital, and the Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Harvey S Singer
- Johns Hopkins University School of Medicine and the Kennedy Krieger Institute, Baltimore, MD, USA
| | - Jan H Smit
- Department of Psychiatry, VU UniversityMedical Center, Amsterdam, The Netherlands
| | - Jae Hoon Sul
- Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA
| | - Dongmei Yu
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Harald Aschauer Harald Aschauer
- Department of Psychiatry and Psychotherapy, Medical University Vienna, Vienna, Austria
- Biopsychosocial Corporation, Vienna, Austria
| | - Csaba Barta
- Institute of Medical Chemistry, Molecular Biology, and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Cathy L Budman
- Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
| | - Danielle C Cath
- Department of Psychiatry, University Medical Center Groningen and Rijksuniversity Groningen, and Drenthe Mental Health Center, Groningen, the Netherlands
| | - Christel Depienne
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
- Sorbonne Universités, UPMC Université Paris 06, UMR S 1127, CNRS UMR 7225, ICM, Paris, France
| | - Andreas Hartmann
- Sorbonne Universités, UPMC Université Paris 06, UMR S 1127, CNRS UMR 7225, ICM, Paris, France
- French Reference Centre for Gilles de la Tourette Syndrome, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
- Assistance Publique-Hôpitaux de Paris, Department of Neurology, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Johannes Hebebrand
- Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Anastasios Konstantinidis
- Department of Psychiatry and Psychotherapy, Medical University Vienna, Vienna, Austria
- Center for Mental Health Muldenstrasse, BBRZMed, Linz, Austria
| | - Carol A Mathews
- Department of Psychiatry, Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Kirsten Müller-Vahl
- Clinic of Psychiatry, Social Psychiatry, and Psychotherapy, Hannover Medical School, Hannover, Germany
| | - Peter Nagy
- Vadaskert Child and Adolescent Psychiatric Hospital, Budapest, Hungary
| | - Markus M Nöthen
- Institute of Human Genetics, University Hospital Bonn, University of Bonn Medical School, Bonn, Germany
| | - Peristera Paschou
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Renata Rizzo
- Child Neuropsychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Guy A Rouleau
- Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, Canada
| | - Paul Sandor
- University Health Network, Youthdale Treatment Centres, and University of Toronto, Toronto, Canada
| | - Jeremiah M Scharf
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Brigham and Women's Hospital, and the Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | | | - Mara Stamenkovic
- Department of Psychiatry and Psychotherapy, Medical University Vienna, Vienna, Austria
| | - Manfred Stuhrmann
- Institute of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Fotis Tsetsos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Zsanett Tarnok
- Vadaskert Child and Adolescent Psychiatric Hospital, Budapest, Hungary
| | - Tomasz Wolanczyk
- Department of Child Psychiatry, Medical University of Warsaw, 00-001, Warsaw, Poland
| | - Yulia Worbe
- Sorbonne Universités, UPMC Université Paris 06, UMR S 1127, CNRS UMR 7225, ICM, Paris, France
- French Reference Centre for Gilles de la Tourette Syndrome, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
- Assistance Publique-Hôpitaux de Paris, Department of Neurology, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
- Assistance Publique Hôpitaux de Paris, Hopital Saint Antoine, Paris, France
| | - Lawrence Brown
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Keun-Ah Cheon
- Yonsei University College of Medicine, Yonsei Yoo & Kim Mental Health Clinic, Seoul, South Korea
| | - Barbara J Coffey
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Andrea Dietrich
- Department of Child and Adolescent Psychiatry, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Thomas V Fernandez
- Yale Child Study Center and the Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Blanca Garcia-Delgar
- Department of Child and Adolescent Psychiatry and Psychology, Institute of Neurosciences, Hospital Clinic Universitari, Barcelona, Spain
| | - Donald Gilbert
- Division of Pediatric Neurology, Cincinnati Children's Hospital Medical Center; Department of Pediatrics, University of Cincinnati, Cincinnati, USA
| | - Dorothy E Grice
- Department of Psychiatry, Friedman Brain Institute, Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Julie Hagstrøm
- Child and Adolescent Mental Health Center, Mental Health Services, Capital Region of Denmark and University of Copenhagen, Copenhagen, Denmark
| | - Tammy Hedderly
- Tic and Neurodevelopmental Movements Service (TANDeM), Evelina Children's Hospital, Guys and St Thomas' NHS Foundation Trust, London, UK
- Paediatric Neurosciences, Kings College London, London, UK
| | - Gary A Heiman
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Isobel Heyman
- UCL Great Ormond Street Institute of Child Health, University College London, London, UK
- Psychological and Mental Health Services, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Pieter J Hoekstra
- Department of Child and Adolescent Psychiatry, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Chaim Huyser
- De Bascule, Academic Centre for Child and Adolescent Psychiatry, Amsterdam, The Netherlands
| | | | - Young-Shin Kim
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA
| | - Robert A King
- Yale Child Study Center and the Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Yun-Joo Koh
- The Korea Institute for Children's Social Development, Rudolph Child Research Center, Seoul, South Korea
| | - Sodahm Kook
- Kangbuk Samsung Hospital, Seoul, South Korea
| | - Samuel Kuperman
- University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Bennett L Leventhal
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA
| | - Marcos Madruga-Garrido
- Sección de Neuropediatría, Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
| | - Pablo Mir
- Hospital Universitario Virgen del Rocío, Sevilla, Spain
- Centro de Investigación en Red-Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Astrid Morer
- Department of Child and Adolescent Psychiatry and Psychology, Institute of Neurosciences, Hospital Clínic Universitari, Barcelona, Spain
- Department of Medicine, University of Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en red de Salud Mental (CIBERSAM), Barcelona, Spain
| | - Alexander Münchau
- Institute of Systems Motor Science, University of Lübeck, Lübeck, Germany
| | - Kerstin J Plessen
- Child and Adolescent Mental Health Centre, Mental Health Services, Capital Region of Denmark, Copenhagen, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Service of Child and Adolescent Psychiatry, Department of Psychiatry, University Medical Center, University of Lausanne, Lausanne, Switzerland
| | - Veit Roessner
- Department of Child and Adolescent Psychiatry, Faculty of Medicine, University Hospital Carl Gustav CarusTU Dresden, Dresden, Germany
| | - Eun-Young Shin
- Yonsei University College of Medicine, Yonsei Yoo & Kim Mental Health Clinic, Seoul, South Korea
| | - Dong-Ho Song
- Yonsei University College of Medicine, Yonsei Yoo & Kim Mental Health Clinic, Seoul, South Korea
| | - Jungeun Song
- National Health Insurance Service Ilsan Hospital, Goyang-Si, South Korea
| | - Jay A Tischfield
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - A Jeremy Willsey
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Samuel Zinner
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Harald Aschauer
- Department of Psychiatry and Psychotherapy, Medical University Vienna, Vienna, Austria
- Biopsychosocial Corporation, Vienna, Austria
| | - Cathy L Barr
- Krembil Research Institute, University Health Network, Hospital for Sick Children, and University of Toronto, Toronto, Canada
| | - Csaba Barta
- Institute of Medical Chemistry, Molecular Biology, and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | | | - Cheston Berlin
- Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Lawrence Brown
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Cathy L Budman
- Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
| | - Danielle C Cath
- Department of Psychiatry, University Medical Center Groningen and Rijksuniversity Groningen, and Drenthe Mental Health Center, Groningen, the Netherlands
| | - Barbara J Coffey
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Giovanni Coppola
- Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA
| | - Nancy J Cox
- Division of Genetic Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sabrina Darrow
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Lea K Davis
- Division of Genetic Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Christel Depienne
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
- Sorbonne Universités, UPMC Université Paris 06, UMR S 1127, CNRS UMR 7225, ICM, Paris, France
| | - Andrea Dietrich
- Department of Child and Adolescent Psychiatry, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Yves Dion
- McGill University Health Center, University of Montreal, McGill University Health Centre, Montreal, Canada
| | - Thomas Fernandez
- Yale Child Study Center and the Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Nelson B Freimer
- Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA
| | - Donald Gilbert
- Division of Pediatric Neurology, Cincinnati Children's Hospital Medical Center; Department of Pediatrics, University of Cincinnati, Cincinnati, USA
| | - Marco A Grados
- Johns Hopkins University School of Medicine and the Kennedy Krieger Institute, Baltimore, MD, USA
| | - Erica Greenberg
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Andreas Hartmann
- Sorbonne Universités, UPMC Université Paris 06, UMR S 1127, CNRS UMR 7225, ICM, Paris, France
- French Reference Centre for Gilles de la Tourette Syndrome, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
- Assistance Publique-Hôpitaux de Paris, Department of Neurology, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Johannes Hebebrand
- Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Gary Heiman
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Matthew E Hirschtritt
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Pieter Hoekstra
- Department of Child and Adolescent Psychiatry, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Alden Y Huang
- Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
| | - Cornelia Illmann
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Joseph Jankovic
- Parkinson's Disease Center and Movement Disorders Clinic, Department of Neurology, Baylor College of Medicine, Houston, TX, USA
| | - Robert A King
- Yale Child Study Center and the Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Samuel Kuperman
- University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Paul C Lee
- Tripler Army Medical Center and University of Hawaii John A. Burns School of Medicine, Honolulu, HI, USA
| | - Gholson J Lyon
- Jervis Clinic, NYS Institute for Basic Research in Developmental Disabilities (IBR), Staten Island, NY, USA
| | - Irene A Malaty
- Department of Neurology, Norman Fixel Institute for Neurological Diseases, University of Florida Health, Gainesville, FL, USA
| | - Carol A Mathews
- Department of Psychiatry, Genetics Institute, University of Florida, Gainesville, FL, USA
| | - William M McMahon
- Department of Psychiatry, University of Utah, Salt Lake City, UT, USA
| | - Kirsten Müller-Vahl
- Clinic of Psychiatry, Social Psychiatry, and Psychotherapy, Hannover Medical School, Hannover, Germany
| | - Peter Nagy
- Vadaskert Child and Adolescent Psychiatric Hospital, Budapest, Hungary
| | - Benjamin M Neale
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Markus M Nöthen
- Institute of Human Genetics, University Hospital Bonn, University of Bonn Medical School, Bonn, Germany
| | - Michael S Okun
- Department of Neurology, Norman Fixel Institute for Neurological Diseases, University of Florida Health, Gainesville, FL, USA
| | - Lisa Osiecki
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Peristera Paschou
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Renata Rizzo
- Child Neuropsychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Mary M Robertson
- Division of Psychiatry, Department of Neuropsychiatry, University College London, London, UK
| | - Guy A Rouleau
- Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, Canada
| | - Paul Sandor
- University Health Network, Youthdale Treatment Centres, and University of Toronto, Toronto, Canada
| | - Jeremiah M Scharf
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Brigham and Women's Hospital, and the Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | | | - Harvey S Singer
- Johns Hopkins University School of Medicine and the Kennedy Krieger Institute, Baltimore, MD, USA
| | - Mara Stamenkovic
- Department of Psychiatry and Psychotherapy, Medical University Vienna, Vienna, Austria
| | - Manfred Stuhrmann
- Institute of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Jae Hoon Sul
- Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA
| | - Zsanett Tarnok
- Vadaskert Child and Adolescent Psychiatric Hospital, Budapest, Hungary
| | - Jay Tischfield
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Fotis Tsetsos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - A Jeremy Willsey
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Douglas Woods
- Marquette University and University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Yulia Worbe
- Sorbonne Universités, UPMC Université Paris 06, UMR S 1127, CNRS UMR 7225, ICM, Paris, France
- French Reference Centre for Gilles de la Tourette Syndrome, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
- Assistance Publique-Hôpitaux de Paris, Department of Neurology, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
- Assistance Publique Hôpitaux de Paris, Hopital Saint Antoine, Paris, France
| | - Dongmei Yu
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Samuel Zinner
- Department of Pediatrics, University of Washington, Seattle, WA, USA
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16
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Nudel R, Christiani CAJ, Ohland J, Uddin MJ, Hemager N, Ellersgaard D, Spang KS, Burton BK, Greve AN, Gantriis DL, Bybjerg-Grauholm J, Jepsen JRM, Thorup AAE, Mors O, Werge T, Nordentoft M. Quantitative genome-wide association analyses of receptive language in the Danish High Risk and Resilience Study. BMC Neurosci 2020; 21:30. [PMID: 32635940 PMCID: PMC7341668 DOI: 10.1186/s12868-020-00581-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/28/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND One of the most basic human traits is language. Linguistic ability, and disability, have been shown to have a strong genetic component in family and twin studies, but molecular genetic studies of language phenotypes are scarce, relative to studies of other cognitive traits and neurodevelopmental phenotypes. Moreover, most genetic studies examining such phenotypes do not incorporate parent-of-origin effects, which could account for some of the heritability of the investigated trait. We performed a genome-wide association study of receptive language, examining both child genetic effects and parent-of-origin effects. RESULTS Using a family-based cohort with 400 children with receptive language scores, we found a genome-wide significant paternal parent-of-origin effect with a SNP, rs11787922, on chromosome 9q21.31, whereby the T allele reduced the mean receptive language score by ~ 23, constituting a reduction of more than 1.5 times the population SD (P = 1.04 × 10-8). We further confirmed that this association was not driven by broader neurodevelopmental diagnoses in the child or a family history of psychiatric diagnoses by incorporating covariates for the above and repeating the analysis. CONCLUSIONS Our study reports a genome-wide significant association for receptive language skills; to our knowledge, this is the first documented genome-wide significant association for this phenotype. Furthermore, our study illustrates the importance of considering parent-of-origin effects in association studies, particularly in the case of cognitive or neurodevelopmental traits, in which parental genetic data are not always incorporated.
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Affiliation(s)
- Ron Nudel
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
| | - Camilla A J Christiani
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark
| | - Jessica Ohland
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark
| | - Md Jamal Uddin
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark
- Section for Biostatistics, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Nicoline Hemager
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark
| | - Ditte Ellersgaard
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark
| | - Katrine S Spang
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Mental Health Centre for Child and Adolescent Psychiatry-Research unit, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark
| | - Birgitte K Burton
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Mental Health Centre for Child and Adolescent Psychiatry-Research unit, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark
| | - Aja N Greve
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Psychosis Research Unit, Aarhus University Hospital-Psychiatry, Aarhus, Denmark
| | - Ditte L Gantriis
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Psychosis Research Unit, Aarhus University Hospital-Psychiatry, Aarhus, Denmark
| | - Jonas Bybjerg-Grauholm
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Jens Richardt M Jepsen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark
- Mental Health Centre for Child and Adolescent Psychiatry-Research unit, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark
- Center for Neuropsychiatric Schizophrenia Research and Center for Clinical Intervention and Neuropsychiatric Schizophrenia Research, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark
| | - Anne A E Thorup
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Mental Health Centre for Child and Adolescent Psychiatry-Research unit, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark
| | - Ole Mors
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Psychosis Research Unit, Aarhus University Hospital-Psychiatry, Aarhus, Denmark
| | - Thomas Werge
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark.
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark.
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Merete Nordentoft
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark.
- Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark.
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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17
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Price KM, Wigg KG, Feng Y, Blokland K, Wilkinson M, He G, Kerr EN, Carter TC, Guger SL, Lovett MW, Strug LJ, Barr CL. Genome-wide association study of word reading: Overlap with risk genes for neurodevelopmental disorders. GENES BRAIN AND BEHAVIOR 2020; 19:e12648. [PMID: 32108986 DOI: 10.1111/gbb.12648] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 01/28/2020] [Accepted: 02/24/2020] [Indexed: 12/12/2022]
Abstract
Reading disabilities (RD) are the most common neurocognitive disorder, affecting 5% to 17% of children in North America. These children often have comorbid neurodevelopmental/psychiatric disorders, such as attention deficit/hyperactivity disorder (ADHD). The genetics of RD and their overlap with other disorders is incompletely understood. To contribute to this, we performed a genome-wide association study (GWAS) for word reading. Then, using summary statistics from neurodevelopmental/psychiatric disorders, we computed polygenic risk scores (PRS) and used them to predict reading ability in our samples. This enabled us to test the shared aetiology between RD and other disorders. The GWAS consisted of 5.3 million single nucleotide polymorphisms (SNPs) and two samples; a family-based sample recruited for reading difficulties in Toronto (n = 624) and a population-based sample recruited in Philadelphia [Philadelphia Neurodevelopmental Cohort (PNC)] (n = 4430). The Toronto sample SNP-based analysis identified suggestive SNPs (P ~ 5 × 10-7 ) in the ARHGAP23 gene, which is implicated in neuronal migration/axon pathfinding. The PNC gene-based analysis identified significant associations (P < 2.72 × 10-6 ) for LINC00935 and CCNT1, located in the region of the KANSL2/CCNT1/LINC00935/SNORA2B/SNORA34/MIR4701/ADCY6 genes on chromosome 12q, with near significant SNP-based analysis. PRS identified significant overlap between word reading and intelligence (R2 = 0.18, P = 7.25 × 10-181 ), word reading and educational attainment (R2 = 0.07, P = 4.91 × 10-48 ) and word reading and ADHD (R2 = 0.02, P = 8.70 × 10-6 ; threshold for significance = 7.14 × 10-3 ). Overlap was also found between RD and autism spectrum disorder (ASD) as top-ranked genes were previously implicated in autism by rare and copy number variant analyses. These findings support shared risk between word reading, cognitive measures, educational outcomes and neurodevelopmental disorders, including ASD.
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Affiliation(s)
- Kaitlyn M Price
- Genetics and Development Division, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada.,Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Karen G Wigg
- Genetics and Development Division, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Yu Feng
- Genetics and Development Division, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Kirsten Blokland
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Margaret Wilkinson
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Gengming He
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Elizabeth N Kerr
- Department of Psychology, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Tasha-Cate Carter
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada.,Holland Bloorview Rehabilitation Hospital, Toronto, Ontario, Canada
| | - Sharon L Guger
- Department of Psychology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Maureen W Lovett
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Lisa J Strug
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada.,Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Cathy L Barr
- Genetics and Development Division, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada.,Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Physiology, University of Toronto, Toronto, Ontario, Canada
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18
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Abstract
PURPOSE OF REVIEW To better understand the shared basis of language and mental health, this review examines the behavioral and neurobiological features of aberrant language in five major neuropsychiatric conditions. Special attention is paid to genes implicated in both language and neuropsychiatric disorders, as they reveal biological domains likely to underpin the processes controlling both. RECENT FINDINGS Abnormal language and communication are common manifestations of neuropsychiatric conditions, and children with impaired language are more likely to develop psychiatric disorders than their peers. Major themes in the genetics of both language and psychiatry include master transcriptional regulators, like FOXP2; key developmental regulators, like AUTS2; and mediators of neurotransmission, like GRIN2A and CACNA1C.
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19
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Kong XZ, Tzourio-Mazoyer N, Joliot M, Fedorenko E, Liu J, Fisher SE, Francks C. Gene Expression Correlates of the Cortical Network Underlying Sentence Processing. NEUROBIOLOGY OF LANGUAGE (CAMBRIDGE, MASS.) 2020; 1:77-103. [PMID: 36794006 PMCID: PMC9923707 DOI: 10.1162/nol_a_00004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 12/19/2019] [Indexed: 04/16/2023]
Abstract
A pivotal question in modern neuroscience is which genes regulate brain circuits that underlie cognitive functions. However, the field is still in its infancy. Here we report an integrated investigation of the high-level language network (i.e., sentence-processing network) in the human cerebral cortex, combining regional gene expression profiles, task fMRI, large-scale neuroimaging meta-analysis, and resting-state functional network approaches. We revealed reliable gene expression-functional network correlations using three different network definition strategies, and identified a consensus set of genes related to connectivity within the sentence-processing network. The genes involved showed enrichment for neural development and actin-related functions, as well as association signals with autism, which can involve disrupted language functioning. Our findings help elucidate the molecular basis of the brain's infrastructure for language. The integrative approach described here will be useful for studying other complex cognitive traits.
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Affiliation(s)
| | - Nathalie Tzourio-Mazoyer
- University of Bordeaux, GIN, IMN, UMR 5293, Bordeaux, France
- CNRS, GIN, IMN, UMR 5293, Bordeaux, France
- CEA, GIN, IMN, UMR 5293, Bordeaux, France
| | - Marc Joliot
- University of Bordeaux, GIN, IMN, UMR 5293, Bordeaux, France
- CNRS, GIN, IMN, UMR 5293, Bordeaux, France
- CEA, GIN, IMN, UMR 5293, Bordeaux, France
| | - Evelina Fedorenko
- Department of Brain and Cognitive Sciences and McGovern Institute for Brain Research, MIT, Cambridge, MA, 02139, USA
| | - Jia Liu
- Faculty of Psychology, Beijing Normal University, Beijing 100875, China
| | - 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 Netherlands
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20
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Rakhlin N, Landi N, Lee M, Magnuson JS, Naumova OY, Ovchinnikova IV, Grigorenko EL. Cohesion of Cortical Language Networks During Word Processing Is Predicted by a Common Polymorphism in the
SETBP1
Gene. New Dir Child Adolesc Dev 2020; 2020:131-155. [DOI: 10.1002/cad.20331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | | | | | | | | | | | - Elena L. Grigorenko
- Haskins Laboratories
- Yale University
- University of Houston
- Saint-Petersburg State University
- Moscow State University for Psychology and Education
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21
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Warrington NM, Freathy RM, Neale MC, Evans DM. Using structural equation modelling to jointly estimate maternal and fetal effects on birthweight in the UK Biobank. Int J Epidemiol 2019; 47:1229-1241. [PMID: 29447406 PMCID: PMC6124616 DOI: 10.1093/ije/dyy015] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/25/2018] [Indexed: 02/07/2023] Open
Abstract
Background To date, 60 genetic variants have been robustly associated with birthweight. It is unclear whether these associations represent the effect of an individual's own genotype on their birthweight, their mother's genotype, or both. Methods We demonstrate how structural equation modelling (SEM) can be used to estimate both maternal and fetal effects when phenotype information is present for individuals in two generations and genotype information is available on the older individual. We conduct an extensive simulation study to assess the bias, power and type 1 error rates of the SEM and also apply the SEM to birthweight data in the UK Biobank study. Results Unlike simple regression models, our approach is unbiased when there is both a maternal and a fetal effect. The method can be used when either the individual's own phenotype or the phenotype of their offspring is not available, and allows the inclusion of summary statistics from additional cohorts where raw data cannot be shared. We show that the type 1 error rate of the method is appropriate, and that there is substantial statistical power to detect a genetic variant that has a moderate effect on the phenotype and reasonable power to detect whether it is a fetal and/or a maternal effect. We also identify a subset of birthweight-associated single nucleotide polymorphisms (SNPs) that have opposing maternal and fetal effects in the UK Biobank. Conclusions Our results show that SEM can be used to estimate parameters that would be difficult to quantify using simple statistical methods alone.
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Affiliation(s)
- Nicole M Warrington
- University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
| | - Rachel M Freathy
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Royal Devon and Exeter Hospital, Exeter, UK.,Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Michael C Neale
- Virginia Institute for Psychiatric and Behavioral Genetics, Departments of Psychiatry and Human & Molecular Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - David M Evans
- University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD, Australia.,Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,School of Social and Community Medicine, University of Bristol, Bristol, UK
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22
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Middeldorp CM, Felix JF, Mahajan A, McCarthy MI. The Early Growth Genetics (EGG) and EArly Genetics and Lifecourse Epidemiology (EAGLE) consortia: design, results and future prospects. Eur J Epidemiol 2019; 34:279-300. [PMID: 30887376 PMCID: PMC6447695 DOI: 10.1007/s10654-019-00502-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 01/25/2019] [Indexed: 11/14/2022]
Abstract
The impact of many unfavorable childhood traits or diseases, such as low birth weight and mental disorders, is not limited to childhood and adolescence, as they are also associated with poor outcomes in adulthood, such as cardiovascular disease. Insight into the genetic etiology of childhood and adolescent traits and disorders may therefore provide new perspectives, not only on how to improve wellbeing during childhood, but also how to prevent later adverse outcomes. To achieve the sample sizes required for genetic research, the Early Growth Genetics (EGG) and EArly Genetics and Lifecourse Epidemiology (EAGLE) consortia were established. The majority of the participating cohorts are longitudinal population-based samples, but other cohorts with data on early childhood phenotypes are also involved. Cohorts often have a broad focus and collect(ed) data on various somatic and psychiatric traits as well as environmental factors. Genetic variants have been successfully identified for multiple traits, for example, birth weight, atopic dermatitis, childhood BMI, allergic sensitization, and pubertal growth. Furthermore, the results have shown that genetic factors also partly underlie the association with adult traits. As sample sizes are still increasing, it is expected that future analyses will identify additional variants. This, in combination with the development of innovative statistical methods, will provide detailed insight on the mechanisms underlying the transition from childhood to adult disorders. Both consortia welcome new collaborations. Policies and contact details are available from the corresponding authors of this manuscript and/or the consortium websites.
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Affiliation(s)
- Christel M Middeldorp
- Child Health Research Centre, University of Queensland, Brisbane, QLD, Australia.
- Child and Youth Mental Health Service, Children's Health Queensland Hospital and Health Service, Brisbane, QLD, Australia.
- Department of Biological Psychology, Vrije Universiteit Amsterdam, 1081 BT, Amsterdam, The Netherlands.
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, 3015 CE, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, 3015 CE, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, 3015 CE, Rotterdam, The Netherlands
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, OX3 7LE, UK
| | - Mark I McCarthy
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, OX3 7LE, UK
- Oxford National Institute for Health Research (NIHR) Biomedical Research Centre, Churchill Hospital, Oxford, OX3 7LE, UK
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23
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Onnis L, Truzzi A, Ma X. Language development and disorders: Possible genes and environment interactions. RESEARCH IN DEVELOPMENTAL DISABILITIES 2018; 82:132-146. [PMID: 30077386 DOI: 10.1016/j.ridd.2018.06.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 06/22/2018] [Accepted: 06/23/2018] [Indexed: 06/08/2023]
Abstract
Language development requires both basic cognitive mechanisms for learning language and a rich social context from which learning takes off. Disruptions in learning mechanisms, processing abilities, and/or social interactions increase the risks associated with social exclusion or developmental delays. Given the complexity of language processes, a multilevel approach is proposed where both cognitive mechanisms, genetic and environmental factors need to be probed together with their possible interactions. Here we review and discuss such interplay between environment and genetic predispositions in understanding language disorders, with a particular focus on a possible endophenotype, the ability for statistical sequential learning.
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Affiliation(s)
- Luca Onnis
- Nanyang Technological University, Singapore.
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24
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Bitarello BD, de Filippo C, Teixeira JC, Schmidt JM, Kleinert P, Meyer D, Andrés AM. Signatures of Long-Term Balancing Selection in Human Genomes. Genome Biol Evol 2018; 10:939-955. [PMID: 29608730 PMCID: PMC5952967 DOI: 10.1093/gbe/evy054] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2018] [Indexed: 12/15/2022] Open
Abstract
Balancing selection maintains advantageous diversity in populations through various mechanisms. Although extensively explored from a theoretical perspective, an empirical understanding of its prevalence and targets lags behind our knowledge of positive selection. Here, we describe the Non-central Deviation (NCD), a simple yet powerful statistic to detect long-term balancing selection (LTBS) that quantifies how close frequencies are to expectations under LTBS, and provides the basis for a neutrality test. NCD can be applied to a single locus or genomic data, and can be implemented considering only polymorphisms (NCD1) or also considering fixed differences with respect to an outgroup (NCD2) species. Incorporating fixed differences improves power, and NCD2 has higher power to detect LTBS in humans under different frequencies of the balanced allele(s) than other available methods. Applied to genome-wide data from African and European human populations, in both cases using chimpanzee as an outgroup, NCD2 shows that, albeit not prevalent, LTBS affects a sizable portion of the genome: ∼0.6% of analyzed genomic windows and 0.8% of analyzed positions. Significant windows (P < 0.0001) contain 1.6% of SNPs in the genome, which disproportionally fall within exons and change protein sequence, but are not enriched in putatively regulatory sites. These windows overlap ∼8% of the protein-coding genes, and these have larger number of transcripts than expected by chance even after controlling for gene length. Our catalog includes known targets of LTBS but a majority of them (90%) are novel. As expected, immune-related genes are among those with the strongest signatures, although most candidates are involved in other biological functions, suggesting that LTBS potentially influences diverse human phenotypes.
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Affiliation(s)
- Bárbara D Bitarello
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, Brazil.,Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Cesare de Filippo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - João C Teixeira
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Unit of Human Evolutionary Genetics, Institut Pasteur, Paris, France
| | - Joshua M Schmidt
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Philip Kleinert
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Computational Molecular Biology Department, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Diogo Meyer
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, Brazil
| | - Aida M Andrés
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London, United Kingdom
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25
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Abstract
The post-genomic era is an exciting time for researchers interested in the biology of speech and language. Substantive advances in molecular methodologies have opened up entire vistas of investigation that were not previously possible, or in some cases even imagined. Speculations concerning the origins of human cognitive traits are being transformed into empirically addressable questions, generating specific hypotheses that can be explicitly tested using data collected from both the natural world and experimental settings. In this article, I discuss a number of promising lines of research in this area. For example, the field has begun to identify genes implicated in speech and language skills, including not just disorders but also the normal range of abilities. Such genes provide powerful entry points for gaining insights into neural bases and evolutionary origins, using sophisticated experimental tools from molecular neuroscience and developmental neurobiology. At the same time, sequencing of ancient hominin genomes is giving us an unprecedented view of the molecular genetic changes that have occurred during the evolution of our species. Synthesis of data from these complementary sources offers an opportunity to robustly evaluate alternative accounts of language evolution. Of course, this endeavour remains challenging on many fronts, as I also highlight in the article. Nonetheless, such an integrated approach holds great potential for untangling the complexities of the capacities that make us human.
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26
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Peyrégne S, Boyle MJ, Dannemann M, Prüfer K. Detecting ancient positive selection in humans using extended lineage sorting. Genome Res 2017; 27:1563-1572. [PMID: 28720580 PMCID: PMC5580715 DOI: 10.1101/gr.219493.116] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 07/05/2017] [Indexed: 01/20/2023]
Abstract
Natural selection that affected modern humans early in their evolution has likely shaped some of the traits that set present-day humans apart from their closest extinct and living relatives. The ability to detect ancient natural selection in the human genome could provide insights into the molecular basis for these human-specific traits. Here, we introduce a method for detecting ancient selective sweeps by scanning for extended genomic regions where our closest extinct relatives, Neandertals and Denisovans, fall outside of the present-day human variation. Regions that are unusually long indicate the presence of lineages that reached fixation in the human population faster than expected under neutral evolution. Using simulations, we show that the method is able to detect ancient events of positive selection and that it can differentiate those from background selection. Applying our method to the 1000 Genomes data set, we find evidence for ancient selective sweeps favoring regulatory changes and present a list of genomic regions that are predicted to underlie positively selected human specific traits.
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Affiliation(s)
- Stéphane Peyrégne
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Michael James Boyle
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Michael Dannemann
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Kay Prüfer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
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27
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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]
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28
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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.
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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
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29
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Gore BB, Miller SM, Jo YS, Baird MA, Hoon M, Sanford CA, Hunker A, Lu W, Wong RO, Zweifel LS. Roundabout receptor 2 maintains inhibitory control of the adult midbrain. eLife 2017; 6. [PMID: 28394253 PMCID: PMC5419739 DOI: 10.7554/elife.23858] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 04/09/2017] [Indexed: 12/22/2022] Open
Abstract
The maintenance of excitatory and inhibitory balance in the brain is essential for its function. Here we find that the developmental axon guidance receptor Roundabout 2 (Robo2) is critical for the maintenance of inhibitory synapses in the adult ventral tegmental area (VTA), a brain region important for the production of the neurotransmitter dopamine. Following selective genetic inactivation of Robo2 in the adult VTA of mice, reduced inhibitory control results in altered neural activity patterns, enhanced phasic dopamine release, behavioral hyperactivity, associative learning deficits, and a paradoxical inversion of psychostimulant responses. These behavioral phenotypes could be phenocopied by selective inactivation of synaptic transmission from local GABAergic neurons of the VTA, demonstrating an important function for Robo2 in regulating the excitatory and inhibitory balance of the adult brain. DOI:http://dx.doi.org/10.7554/eLife.23858.001 Although no two people are alike, we all share the same basic brain structure. This similarity arises because the same developmental program takes place in every human embryo. Specific genes are activated in a designated sequence to generate the structure of a typical human brain. But what happens to these genes when development is complete – do they remain active in the adult brain? A gene known as Robo2 encodes a protein that helps neurons find their way through the developing brain. Many of these neurons will ultimately form part of the brain’s reward system. This is a network of brain regions that communicate with one another using a chemical called dopamine. The reward system contributes to motivation, learning and memory, and also underlies drug addiction. In certain mental illnesses such as Parkinson’s disease and schizophrenia, the dopamine-producing neurons in the reward system work incorrectly or die. To find out whether Robo2 is active in the mature nervous system, Gore et al. used genetic techniques to selectively remove the gene from the reward system of adult mice. Doing so reduced the ability of the dopamine neurons within the reward system to inhibit one another, which in turn increased their activity. This changed the behavior of the mice, making them hyperactive and less able to learn and remember. Cocaine makes normal mice more active; however, mice that lacked the Robo2 gene became less active when given cocaine. Overall, the work of Gore et al. suggests that developmental axon guidance genes remain important in the adult brain. Studying developmental genes such as Robo2 may therefore open up new treatment possibilities for a number of mental illnesses and brain disorders. DOI:http://dx.doi.org/10.7554/eLife.23858.002
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Affiliation(s)
- Bryan B Gore
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, United States.,Department of Pharmacology, University of Washington, Seattle, United States
| | - Samara M Miller
- Department of Pharmacology, University of Washington, Seattle, United States
| | - Yong Sang Jo
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, United States.,Department of Pharmacology, University of Washington, Seattle, United States
| | - Madison A Baird
- Department of Pharmacology, University of Washington, Seattle, United States
| | - Mrinalini Hoon
- Department of Biological Structure, University of Washington, Seattle, United States
| | - Christina A Sanford
- Department of Pharmacology, University of Washington, Seattle, United States
| | - Avery Hunker
- Department of Pharmacology, University of Washington, Seattle, United States
| | - Weining Lu
- Department of Medicine, Renal Section, Boston University Medical Center, Boston, United States
| | - Rachel O Wong
- Department of Biological Structure, University of Washington, Seattle, United States
| | - Larry S Zweifel
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, United States.,Department of Pharmacology, University of Washington, Seattle, United States
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30
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Onnis L. Caregiver communication to the child as moderator and mediator of genes for language. Behav Brain Res 2017; 325:197-202. [PMID: 28215549 DOI: 10.1016/j.bbr.2017.02.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 02/01/2017] [Accepted: 02/02/2017] [Indexed: 11/18/2022]
Abstract
Human language appears to be unique among natural communication systems, and such uniqueness impinges on both nature and nurture. Human babies are endowed with cognitive abilities that predispose them to learn language, and this process cannot operate in an impoverished environment. To be effectively complete the acquisition of human language in human children requires highly socialised forms of learning, scaffolded over years of prolonged and intense caretaker-child interactions. How genes and environment operate in shaping language is unknown. These two components have traditionally been considered as independent, and often pitted against each other in terms of the nature versus nurture debate. This perspective article considers how innate abilities and experience might instead work together. In particular, it envisages potential scenarios for research, in which early caregiver verbal and non-verbal attachment practices may mediate or moderate the expression of human genetic systems for language.
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Affiliation(s)
- Luca Onnis
- Division of Linguistics and Multilingual Studies Nanyang Technological University, Singapore
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31
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32
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An JY, Claudianos C. Genetic heterogeneity in autism: From single gene to a pathway perspective. Neurosci Biobehav Rev 2016; 68:442-453. [DOI: 10.1016/j.neubiorev.2016.06.013] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 05/15/2016] [Accepted: 06/14/2016] [Indexed: 12/22/2022]
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33
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Benítez-Burraco A, Lattanzi W, Murphy E. Language Impairments in ASD Resulting from a Failed Domestication of the Human Brain. Front Neurosci 2016; 10:373. [PMID: 27621700 PMCID: PMC5002430 DOI: 10.3389/fnins.2016.00373] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 08/02/2016] [Indexed: 11/16/2022] Open
Abstract
Autism spectrum disorders (ASD) are pervasive neurodevelopmental disorders entailing social and cognitive deficits, including marked problems with language. Numerous genes have been associated with ASD, but it is unclear how language deficits arise from gene mutation or dysregulation. It is also unclear why ASD shows such high prevalence within human populations. Interestingly, the emergence of a modern faculty of language has been hypothesized to be linked to changes in the human brain/skull, but also to the process of self-domestication of the human species. It is our intention to show that people with ASD exhibit less marked domesticated traits at the morphological, physiological, and behavioral levels. We also discuss many ASD candidates represented among the genes known to be involved in the “domestication syndrome” (the constellation of traits exhibited by domesticated mammals, which seemingly results from the hypofunction of the neural crest) and among the set of genes involved in language function closely connected to them. Moreover, many of these genes show altered expression profiles in the brain of autists. In addition, some candidates for domestication and language-readiness show the same expression profile in people with ASD and chimps in different brain areas involved in language processing. Similarities regarding the brain oscillatory behavior of these areas can be expected too. We conclude that ASD may represent an abnormal ontogenetic itinerary for the human faculty of language resulting in part from changes in genes important for the “domestication syndrome” and, ultimately, from the normal functioning of the neural crest.
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Affiliation(s)
| | - Wanda Lattanzi
- Institute of Anatomy and Cell Biology, Università Cattolica del Sacro Cuore Rome, Italy
| | - Elliot Murphy
- Division of Psychology and Language Sciences, University College London London, UK
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Murphy E, Benítez-Burraco A. Language deficits in schizophrenia and autism as related oscillatory connectomopathies: An evolutionary account. Neurosci Biobehav Rev 2016; 83:742-764. [PMID: 27475632 DOI: 10.1016/j.neubiorev.2016.07.029] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 06/23/2016] [Accepted: 07/25/2016] [Indexed: 01/28/2023]
Abstract
Schizophrenia (SZ) and autism spectrum disorders (ASD) are characterised by marked language deficits, but it is not clear how these arise from gene mutations associated with the disorders. Our goal is to narrow the gap between SZ and ASD and, ultimately, give support to the view that they represent abnormal (but related) ontogenetic itineraries for the human faculty of language. We will focus on the distinctive oscillatory profiles of the SZ and ASD brains, in turn using these insights to refine our understanding of how the brain implements linguistic computations by exploring a novel model of linguistic feature-set composition. We will argue that brain rhythms constitute the best route to interpreting language deficits in both conditions and mapping them to neural dysfunction and risk alleles of the genes. Importantly, candidate genes for SZ and ASD are overrepresented among the gene sets believed to be important for language evolution. This translational effort may help develop an understanding of the aetiology of SZ and ASD and their high prevalence among modern populations.
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Affiliation(s)
- Elliot Murphy
- Division of Psychology and Language Sciences, University College London, London, United Kingdom.
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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.
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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
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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.
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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
| | - 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
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Mozzi A, Forni D, Clerici M, Pozzoli U, Mascheretti S, Guerini FR, Riva S, Bresolin N, Cagliani R, Sironi M. The evolutionary history of genes involved in spoken and written language: beyond FOXP2. Sci Rep 2016; 6:22157. [PMID: 26912479 PMCID: PMC4766443 DOI: 10.1038/srep22157] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 02/08/2016] [Indexed: 12/14/2022] Open
Abstract
Humans possess a communication system based on spoken and written language. Other animals can learn vocalization by imitation, but this is not equivalent to human language. Many genes were described to be implicated in language impairment (LI) and developmental dyslexia (DD), but their evolutionary history has not been thoroughly analyzed. Herein we analyzed the evolution of ten genes involved in DD and LI. Results show that the evolutionary history of LI genes for mammals and aves was comparable in vocal-learner species and non-learners. For the human lineage, several sites showing evidence of positive selection were identified in KIAA0319 and were already present in Neanderthals and Denisovans, suggesting that any phenotypic change they entailed was shared with archaic hominins. Conversely, in FOXP2, ROBO1, ROBO2, and CNTNAP2 non-coding changes rose to high frequency after the separation from archaic hominins. These variants are promising candidates for association studies in LI and DD.
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Affiliation(s)
- Alessandra Mozzi
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842 Bosisio Parini, Italy
| | - Diego Forni
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842 Bosisio Parini, Italy
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, 20090 Milan, Italy
- Don C. Gnocchi Foundation ONLUS, IRCCS, 20100 Milan, Italy
| | - Uberto Pozzoli
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842 Bosisio Parini, Italy
| | - Sara Mascheretti
- Child Psychopathology Unit, Scientific Institute IRCCS E. MEDEA, 23842 Bosisio Parini, Lecco, Italy
| | | | - Stefania Riva
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842 Bosisio Parini, Italy
| | - Nereo Bresolin
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842 Bosisio Parini, Italy
- Dino Ferrari Centre, Department of Physiopathology and Transplantation, University of Milan, Fondazione Ca’ Granda IRCCS Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Rachele Cagliani
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842 Bosisio Parini, Italy
| | - Manuela Sironi
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842 Bosisio Parini, Italy
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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.
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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
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Plomin R, DeFries JC, Knopik VS, Neiderhiser JM. Top 10 Replicated Findings From Behavioral Genetics. PERSPECTIVES ON PSYCHOLOGICAL SCIENCE 2016; 11:3-23. [PMID: 26817721 PMCID: PMC4739500 DOI: 10.1177/1745691615617439] [Citation(s) in RCA: 188] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
In the context of current concerns about replication in psychological science, we describe 10 findings from behavioral genetic research that have replicated robustly. These are "big" findings, both in terms of effect size and potential impact on psychological science, such as linearly increasing heritability of intelligence from infancy (20%) through adulthood (60%). Four of our top 10 findings involve the environment, discoveries that could have been found only with genetically sensitive research designs. We also consider reasons specific to behavioral genetics that might explain why these findings replicate.
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Affiliation(s)
- Robert Plomin
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London
| | - John C DeFries
- Institute for Behavioral Genetics, University of Colorado
| | - Valerie S Knopik
- Department of Psychiatry, Rhode Island Hospital, Providence, Rhode Island, and Departments of Psychiatry and Human Behavior and Behavioral and Social Sciences, Brown University
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Paracchini S, Diaz R, Stein J. Advances in Dyslexia Genetics—New Insights Into the Role of Brain Asymmetries. ADVANCES IN GENETICS 2016; 96:53-97. [DOI: 10.1016/bs.adgen.2016.08.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Pediatric asthma and autism-genomic perspectives. Clin Transl Med 2015; 4:37. [PMID: 26668064 PMCID: PMC4678135 DOI: 10.1186/s40169-015-0078-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 11/29/2015] [Indexed: 02/06/2023] Open
Abstract
High-throughput technologies, ranging from microarrays to NexGen sequencing of RNA and genomic DNA, have opened new avenues for exploration of the pathobiology of human disease. Comparisons of the architecture of the genome, identification of mutated or modified sequences, and pre-and post- transcriptional regulation of gene expression as disease specific biomarkers are revolutionizing our understanding of the causes of disease and are guiding the development of new therapies. There is enormous heterogeneity in types of genomic variation that occur in human disease. Some are inherited, while others are the result of new somatic or germline mutations or errors in chromosomal replication. In this review, we provide examples of changes that occur in the human genome in two of the most common chronic pediatric disorders, autism and asthma. The incidence and economic burden of both of these disorders are increasing worldwide. Genomic variations have the potential to serve as biomarkers for personalization of therapy and prediction of outcomes.
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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.
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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;
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Copy Number Variation Screen Identifies a Rare De Novo Deletion at Chromosome 15q13.1-13.3 in a Child with Language Impairment. PLoS One 2015; 10:e0134997. [PMID: 26262844 PMCID: PMC4532445 DOI: 10.1371/journal.pone.0134997] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 07/17/2015] [Indexed: 01/15/2023] Open
Abstract
A significant proportion of children (up to 7% in the UK) present with pronounced language difficulties that cannot be explained by obvious causes like other neurological and medical conditions. A substantial genetic component is predicted to underlie such language problems. Copy number variants (CNVs) have been implicated in neurodevelopmental and psychiatric conditions, such as autism and schizophrenia, but it is not fully established to what extent they might contribute to language disorders. We conducted a CNV screen in a longitudinal cohort of young children with language-related difficulties (n = 85), focusing on single events at candidate loci. We detected a de novo deletion on chromosome 15q13.1–13.3. The adjacent 15q11-13.1 locus is disrupted in Prader-Willi and Angelman syndromes, while disruptions across the breakpoints (BP1-BP6) have previously been implicated in different neurodevelopmental phenotypes including autism, intellectual disability (ID), seizures and developmental delay (DD). This is the first report of a deletion at BP3-BP5 being linked to a deficit confined to language impairment, in the absence of ID, expanding the range of phenotypes that implicate the chromosome 15q13 locus.
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Moralli D, Nudel R, Chan MTM, Green CM, Volpi EV, Benítez-Burraco A, Newbury DF, García-Bellido P. Language impairment in a case of a complex chromosomal rearrangement with a breakpoint downstream of FOXP2. Mol Cytogenet 2015; 8:36. [PMID: 26060509 PMCID: PMC4460787 DOI: 10.1186/s13039-015-0148-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 05/20/2015] [Indexed: 01/12/2023] Open
Abstract
Background We report on a young female, who presents with a severe speech and language disorder and a balanced de novo complex chromosomal rearrangement, likely to have resulted from a chromosome 7 pericentromeric inversion, followed by a chromosome 7 and 11 translocation. Results Using molecular cytogenetics, we mapped the four breakpoints to 7p21.1-15.3 (chromosome position: 20,954,043-21,001,537, hg19), 7q31 (chromosome position: 114,528,369-114,556,605, hg19), 7q21.3 (chromosome position: 93,884,065-93,933,453, hg19) and 11p12 (chromosome position: 38,601,145-38,621,572, hg19). These regions contain only non-coding transcripts (ENSG00000232790 on 7p21.1 and TCONS_00013886, TCONS_00013887, TCONS_00014353, TCONS_00013888 on 7q21) indicating that no coding sequences are directly disrupted. The breakpoint on 7q31 mapped 200 kb downstream of FOXP2, a well-known language gene. No splice site or non-synonymous coding variants were found in the FOXP2 coding sequence. We were unable to detect any changes in the expression level of FOXP2 in fibroblast cells derived from the proband, although this may be the result of the low expression level of FOXP2 in these cells. Conclusions We conclude that the phenotype observed in this patient either arises from a subtle change in FOXP2 regulation due to the disruption of a downstream element controlling its expression, or from the direct disruption of non-coding RNAs. Electronic supplementary material The online version of this article (doi:10.1186/s13039-015-0148-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniela Moralli
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Headington, Oxford, OX3 7BN UK
| | - Ron Nudel
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Headington, Oxford, OX3 7BN UK
| | - May T M Chan
- Faculty of Linguistics, Philology and Phonetics, University of Oxford, Walton Street, Oxford, OX1 2HG UK ; Worcester College, University of Oxford, Oxford, OX1 2HB, UK
| | - Catherine M Green
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Headington, Oxford, OX3 7BN UK
| | - Emanuela V Volpi
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Headington, Oxford, OX3 7BN UK ; Department of Biomedical Sciences, University of Westminster, 115 New Cavendish Street, London, W1W 6UW UK
| | - Antonio Benítez-Burraco
- Faculty of Modern languages, University of Oxford, 47 Wellington Square, Oxford, OX1 2JF UK ; Department of Spanish Philology and its Didactics, University of Huelva, Huelva, Spain
| | - Dianne F Newbury
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Headington, Oxford, OX3 7BN UK
| | - Paloma García-Bellido
- Faculty of Linguistics, Philology and Phonetics, University of Oxford, Walton Street, Oxford, OX1 2HG UK ; Faculty of Modern languages, University of Oxford, 47 Wellington Square, Oxford, OX1 2JF 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] [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.
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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
| | - 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
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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: 18] [Impact Index Per Article: 2.0] [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.
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The Generation R Study: Biobank update 2015. Eur J Epidemiol 2014; 29:911-27. [PMID: 25527369 DOI: 10.1007/s10654-014-9980-6] [Citation(s) in RCA: 174] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Accepted: 12/06/2014] [Indexed: 12/14/2022]
Abstract
The Generation R Study is a population-based prospective cohort study from fetal life until adulthood. The study is designed to identify early environmental and genetic causes and causal pathways leading to normal and abnormal growth, development and health from fetal life, childhood and young adulthood. In total, 9,778 mothers were enrolled in the study. Data collection in children and their parents include questionnaires, interviews, detailed physical and ultrasound examinations, behavioural observations, Magnetic Resonance Imaging and biological samples. Efforts have been conducted for collecting biological samples including blood, hair, faeces, nasal swabs, saliva and urine samples and generating genomics data on DNA, RNA and microbiome. In this paper, we give an update of the collection, processing and storage of these biological samples and available measures. Together with detailed phenotype measurements, these biological samples provide a unique resource for epidemiological studies focused on environmental exposures, genetic and genomic determinants and their interactions in relation to growth, health and development from fetal life onwards.
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Benítez-Burraco A, Boeckx C. FOXP2, retinoic acid, and language: a promising direction. Front Cell Neurosci 2014; 8:387. [PMID: 25431551 PMCID: PMC4230053 DOI: 10.3389/fncel.2014.00387] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Accepted: 10/30/2014] [Indexed: 11/13/2022] Open
Affiliation(s)
| | - Cedric Boeckx
- Catalan Institute for Advanced Studies and Research (ICREA) Barcelona, Spain ; Department of Linguistics, Universitat de Barcelona Barcelona, Spain
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Boeckx C, Benítez-Burraco A. Globularity and language-readiness: generating new predictions by expanding the set of genes of interest. Front Psychol 2014; 5:1324. [PMID: 25505436 PMCID: PMC4243498 DOI: 10.3389/fpsyg.2014.01324] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 10/31/2014] [Indexed: 12/30/2022] Open
Abstract
This study builds on the hypothesis put forth in Boeckx and Benítez-Burraco (2014), according to which the developmental changes expressed at the levels of brain morphology and neural connectivity that resulted in a more globular braincase in our species were crucial to understand the origins of our language-ready brain. Specifically, this paper explores the links between two well-known 'language-related' genes like FOXP2 and ROBO1 implicated in vocal learning and the initial set of genes of interest put forth in Boeckx and Benítez-Burraco (2014), with RUNX2 as focal point. Relying on the existing literature, we uncover potential molecular links that could be of interest to future experimental inquiries into the biological foundations of language and the testing of our initial hypothesis. Our discussion could also be relevant for clinical linguistics and for the interpretation of results from paleogenomics.
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Affiliation(s)
- Cedric Boeckx
- Catalan Institute for Advanced Studies and Research (ICREA)Barcelona, Spain
- Department of Linguistics, Universitat de BarcelonaBarcelona, Spain
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