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Espinosa-Mojica AA, Varo Varo C. Determining the Linguistic Profile of Children With Rare Genetic Disorders. JOURNAL OF SPEECH, LANGUAGE, AND HEARING RESEARCH : JSLHR 2024; 67:170-186. [PMID: 38085694 DOI: 10.1044/2023_jslhr-23-00101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
PURPOSE Language studies on populations with rare genetic disorders are limited. Hence, there is little data on commonly found or expected developmental linguistic traits and cognitive mechanisms that may be impaired. Based on the hypothesis that there is a close connection between language and cognition and the relevance of specific genetic changes in the development of each, our goal was to provide linguistic data on relationships with other executive functioning mechanisms. METHOD This study assessed language skills, communicative behaviors, and executive functions in four children, aged 7-9 years, with rare genetic disorders, using standardized protocols and tests. RESULTS The findings revealed different levels of language impairment and executive functioning problems in each case. The overall executive function index performance for each of the four cases studied was clinically significantly high, indicating executive dysfunction. CONCLUSIONS The cases analyzed illustrate different types of atypical development that affect both language and other cognitive mechanisms and underscore the importance of executive skills and the various ways in which they are involved in diverse levels of language that might be affected to a greater or lesser degree in rare genetic disorders. In conclusion, we found that language dysfunction is a salient feature of the rare genetic disorders included in our study, although this is not necessarily true for all genetic disorders. Along with these conclusive results, we performed a qualitative analysis of the linguistic and cognitive components that enable functional communication in order to allow optimal interpretation of the data we have collected, laying the foundations for a more effective therapeutic approach.
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Peter B, Bruce L, Finestack L, Dinu V, Wilson M, Klein-Seetharaman J, Lewis CR, Braden BB, Tang YY, Scherer N, VanDam M, Potter N. Precision Medicine as a New Frontier in Speech-Language Pathology: How Applying Insights From Behavior Genomics Can Improve Outcomes in Communication Disorders. AMERICAN JOURNAL OF SPEECH-LANGUAGE PATHOLOGY 2023; 32:1397-1412. [PMID: 37146603 PMCID: PMC10484627 DOI: 10.1044/2023_ajslp-22-00205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 11/07/2022] [Accepted: 03/01/2023] [Indexed: 05/07/2023]
Abstract
PURPOSE Precision medicine is an emerging intervention paradigm that leverages knowledge of risk factors such as genotypes, lifestyle, and environment toward proactive and personalized interventions. Regarding genetic risk factors, examples of interventions informed by the field of medical genomics are pharmacological interventions tailored to an individual's genotype and anticipatory guidance for children whose hearing impairment is predicted to be progressive. Here, we show how principles of precision medicine and insights from behavior genomics have relevance for novel management strategies of behaviorally expressed disorders, especially disorders of spoken language. METHOD This tutorial presents an overview of precision medicine, medical genomics, and behavior genomics; case examples of improved outcomes; and strategic goals toward enhancing clinical practice. RESULTS Speech-language pathologists (SLPs) see individuals with various communication disorders due to genetic variants. Ways of using insights from behavior genomics and implementing principles of precision medicine include recognizing early signs of undiagnosed genetic disorders in an individual's communication patterns, making appropriate referrals to genetics professionals, and incorporating genetic findings into management plans. Patients benefit from a genetics diagnosis by gaining a deeper and more prognostic understanding of their condition, obtaining more precisely targeted interventions, and learning about their recurrence risks. CONCLUSIONS SLPs can achieve improved outcomes by expanding their purview to include genetics. To drive this new interdisciplinary framework forward, goals should include systematic training in clinical genetics for SLPs, enhanced understanding of genotype-phenotype associations, leveraging insights from animal models, optimizing interprofessional team efforts, and developing novel proactive and personalized interventions.
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Affiliation(s)
- Beate Peter
- College of Health Solutions, Arizona State University, Tempe
| | - Laurel Bruce
- College of Health Solutions, Arizona State University, Tempe
| | - Lizbeth Finestack
- Department of Speech-Language-Hearing Sciences, University of Minnesota, Twin Cities, Minneapolis
| | - Valentin Dinu
- College of Health Solutions, Arizona State University, Tempe
| | - Melissa Wilson
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe
| | | | - Candace R. Lewis
- School of Life Sciences, Arizona State University, Tempe
- Department of Psychology, Arizona State University, Tempe
| | - B. Blair Braden
- College of Health Solutions, Arizona State University, Tempe
| | - Yi-Yuan Tang
- College of Health Solutions, Arizona State University, Tempe
| | - Nancy Scherer
- College of Health Solutions, Arizona State University, Tempe
| | - Mark VanDam
- Department of Speech and Hearing Sciences, Elson S. Floyd College of Medicine, Washington State University, Spokane
| | - Nancy Potter
- Department of Speech and Hearing Sciences, Elson S. Floyd College of Medicine, Washington State University, Spokane
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Andres EM, Earnest KK, Xuan H, Zhong C, Rice ML, Raza MH. Innovative Family-Based Genetically Informed Series of Analyses of Whole-Exome Data Supports Likely Inheritance for Grammar in Children with Specific Language Impairment. CHILDREN (BASEL, SWITZERLAND) 2023; 10:1119. [PMID: 37508616 PMCID: PMC10378399 DOI: 10.3390/children10071119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023]
Abstract
Individuals with specific language impairment (SLI) struggle with language acquisition despite average non-verbal intelligence and otherwise typical development. One SLI account focuses on grammar acquisition delay. The current study aimed to detect novel rare genetic variants associated with performance on a grammar assessment, the Test of Early Grammatical Impairment (TEGI), in English-speaking children. The TEGI was selected due to its sensitivity and specificity, consistently high heritability estimates, and its absence from all but one molecular genetic study. We performed whole exome sequencing (WES) in eight families with SLI (n = 74 total) and follow-up Sanger sequencing in additional unrelated probands (n = 146). We prioritized rare exonic variants shared by individuals with low TEGI performance (n = 34) from at least two families under two filtering workflows: (1) novel and (2) previously reported candidate genes. Candidate variants were observed on six new genes (PDHA2, PCDHB3, FURIN, NOL6, IQGAP3, and BAHCC1), and two genes previously reported for overall language ability (GLI3 and FLNB). We specifically suggest PCDHB3, a protocadherin gene, and NOL6 are critical for ribosome synthesis, as they are important targets of SLI investigation. The proposed SLI candidate genes associated with TEGI performance emphasize the utility of precise phenotyping and family-based genetic study.
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Affiliation(s)
- Erin M Andres
- Thompson Center for Autism and Neurodevelopment, University of Missouri, Columbia, MO 65201, USA
| | | | - Hao Xuan
- Department of Electrical Engineering and Computer Science, University of Kansas, Lawrence, KS 66045, USA
| | - Cuncong Zhong
- Department of Electrical Engineering and Computer Science, University of Kansas, Lawrence, KS 66045, USA
| | - Mabel L Rice
- Language Acquisition Studies Lab, University of Kansas, Lawrence, KS 66045, USA
- Child Language Doctoral Program, University of Kansas, Lawrence, KS 66045, USA
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Nudel R, Christensen RV, Kalnak N, Schwinn M, Banasik K, Dinh KM, Erikstrup C, Pedersen OB, Burgdorf KS, Ullum H, Ostrowski SR, Hansen TF, Werge T. Developmental language disorder - a comprehensive study of more than 46,000 individuals. Psychiatry Res 2023; 323:115171. [PMID: 36963307 DOI: 10.1016/j.psychres.2023.115171] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 02/16/2023] [Accepted: 03/14/2023] [Indexed: 03/26/2023]
Abstract
Developmental language disorder (DLD) is characterized by enduring low language abilities with a significant functional impact, in the absence of biomedical conditions in which language impairment is part of a complex of impairments. There is a lack of awareness of DLD even among healthcare professionals. Here we estimated the prevalence of DLD and its links to reading and learning difficulties and physical and mental health in the Danish Blood Donor Study (N = 46,547), where DLD-related information is based on questionnaires (self-report). We compared the questionnaire-derived DLD status with the relevant language-related diagnoses from hospital registers. We also investigated the genetic architecture of DLD in a subset of the cohort (N = 18,380). DLD was significantly associated with reading and learning difficulties and poorer mental and physical health. DLD prevalence was 3.36%-3.70% based on questionnaires, compared with 0.04% in hospital registers. Our genetic analyses identified one genome-wide significant locus, but not a significant heritability estimate. Our study shows that DLD has health-related implications that may last into adulthood, and that DLD may be undiagnosed in general healthcare. Furthermore, DLD is likely more genetically heterogeneous than narrower developmental language phenotypes. Our results emphasize the need to raise awareness of DLD and consider criteria for molecular studies of DLD to reduce case heterogeneity.
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Affiliation(s)
- Ron Nudel
- CORE - Copenhagen Research Centre for Mental Health, Mental Health Centre Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark.
| | - Rikke Vang Christensen
- Department of Nordic Studies and Linguistics, University of Copenhagen, Emil Holms Kanal 2, Copenhagen 2300, Denmark.
| | - Nelli Kalnak
- Department of Women's and Children's Health, Karolinska Institute, Stockholm, Sweden; Department of Speech-Language Pathology, Helsingborg Hospital, Helsingborg, Sweden.
| | - Michael Schwinn
- Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Karina Banasik
- Novo Nordisk foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Khoa Manh Dinh
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
| | | | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark; Department of Clinical Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Ole Birger Pedersen
- Department of Immunology, Næstved Hospital, Næstved, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kristoffer Sølvsten Burgdorf
- Department of Immunology, Rigshospitalet, Copenhagen, Denmark; Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Sisse Rye Ostrowski
- Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Folkmann Hansen
- Novo Nordisk foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Danish Headache Center, Rigshospitalet Glostrup, Glostrup, Denmark
| | - Thomas Werge
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Institute of Biological Psychiatry, Roskilde, Denmark
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Moore MW, Rambo-Hernandez KE, McDonald TL. Consonant Age of Acquisition Reveals Nonlinear Effects in Nonword Repetition Performance. JOURNAL OF PSYCHOLINGUISTIC RESEARCH 2022; 51:1347-1370. [PMID: 35871210 DOI: 10.1007/s10936-022-09901-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Recent work has shown significant sublexical effects of long-term memory in nonword repetition (NWR) using a dichotomous consonant age of acquisition (CAoA) variable (Moore, 2018; Moore, Fiez, and Tompkins, 2017). Performance consistently decreased when stimuli comprised consonants acquired later versus earlier in speech development. To address potential confounds related to stimulus design and linearity, the purpose of this study was to test whether performance decreases as the CAoA value of stimuli increases in various linguistic tasks using a continuous CAoA variable. Thirty-one college students completed NWR and other linguistic tasks in which the stimuli varied in average CAoA values. Data were analyzed using multilevel modeling. After accounting for phonotactic probability, CAoA was a statistically significant predictor of performance across the models reported. The relationship was more complex in some of the models in which CAoA showed a statistically significant nonlinear relationship with the outcome measure. Results from this study support previous work showing that CAoA affects performance on NWR and other linguistic tasks that vary in their memory, auditory perceptual, and articulatory demands. Importantly, this line of work was extended here by demonstrating that the CAoA effect is robust across novel stimulus sets and study designs, and may be more complex than previously understood when using a dichotomous CAoA variable. Quadratic results suggest that the CAoA variable has a differential effect on performance for low to moderate CAoA values, but for higher CAoA values the effect is similarly negative. The nonlinear relationship between CAoA and measures of speed and accuracy on some of the tasks warrants further study into the complex relationship between various predictive factors that contribute to language performance.
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Affiliation(s)
- Michelle W Moore
- Division of Communication Sciences and Disorders, West Virginia University, P.O. Box 9226, Morgantown, WV, 26506, USA.
| | - Karen E Rambo-Hernandez
- Department of Teaching, Learning, and Culture, Texas A&M University, College Station, Texas, 77843, USA
| | - Taylor L McDonald
- Division of Communication Sciences and Disorders, West Virginia University, P.O. Box 9226, Morgantown, WV, 26506, USA
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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; 9:586. [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;
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Family-Based Whole-Exome Analysis of Specific Language Impairment (SLI) Identifies Rare Variants in BUD13, a Component of the Retention and Splicing (RES) Complex. Brain Sci 2021; 12:brainsci12010047. [PMID: 35053791 PMCID: PMC8773923 DOI: 10.3390/brainsci12010047] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/18/2021] [Accepted: 12/27/2021] [Indexed: 12/12/2022] Open
Abstract
Specific language impairment (SLI) is a common neurodevelopmental disorder (NDD) that displays high heritability estimates. Genetic studies have identified several loci, but the molecular basis of SLI remains unclear. With the aim to better understand the genetic architecture of SLI, we performed whole-exome sequencing (WES) in a single family (ID: 489; n = 11). We identified co-segregating rare variants in three new genes: BUD13, APLP2, and NDRG2. To determine the significance of these genes in SLI, we Sanger sequenced all coding regions of each gene in unrelated individuals with SLI (n = 175). We observed 13 additional rare variants in 18 unrelated individuals. Variants in BUD13 reached genome-wide significance (p-value < 0.01) upon comparison with similar variants in the 1000 Genomes Project, providing gene level evidence that BUD13 is involved in SLI. Additionally, five BUD13 variants showed cohesive variant level evidence of likely pathogenicity. Bud13 is a component of the retention and splicing (RES) complex. Additional supportive evidence from studies of an animal model (loss-of-function mutations in BUD13 caused a profound neural phenotype) and individuals with an NDD phenotype (carrying a CNV spanning BUD13), indicates BUD13 could be a target for investigation of the neural basis of language.
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Nudel R, Appadurai V, Buil A, Nordentoft M, Werge T. Pleiotropy between language impairment and broader behavioral disorders-an investigation of both common and rare genetic variants. J Neurodev Disord 2021; 13:54. [PMID: 34773992 PMCID: PMC8590378 DOI: 10.1186/s11689-021-09403-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 10/22/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Language plays a major role in human behavior. For this reason, neurodevelopmental and psychiatric disorders in which linguistic ability is impaired could have a big impact on the individual's social interaction and general wellbeing. Such disorders tend to have a strong genetic component, but most past studies examined mostly the linguistic overlaps across these disorders; investigations into their genetic overlaps are limited. The aim of this study was to assess the potential genetic overlap between language impairment and broader behavioral disorders employing methods capturing both common and rare genetic variants. METHODS We employ polygenic risk scores (PRS) trained on specific language impairment (SLI) to evaluate genetic overlap across several disorders in a large case-cohort sample comprising ~13,000 autism spectrum disorder (ASD) cases, including cases of childhood autism and Asperger's syndrome, ~15,000 attention deficit/hyperactivity disorder (ADHD) cases, ~3000 schizophrenia cases, and ~21,000 population controls. We also examine rare variants in SLI/language-related genes in a subset of the sample that was exome-sequenced using the SKAT-O method. RESULTS We find that there is little evidence for genetic overlap between SLI and ADHD, schizophrenia, and ASD, the latter being in line with results of linguistic analyses in past studies. However, we observe a small, significant genetic overlap between SLI and childhood autism specifically, which we do not observe for SLI and Asperger's syndrome. Moreover, we observe that childhood autism cases have significantly higher SLI-trained PRS compared to Asperger's syndrome cases; these results correspond well to the linguistic profiles of both disorders. Our rare variant analyses provide suggestive evidence of association for specific genes with ASD, childhood autism, and schizophrenia. CONCLUSIONS Our study provides, for the first time, to our knowledge, genetic evidence for ASD subtypes based on risk variants for language impairment.
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Affiliation(s)
- Ron Nudel
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- CORE - Copenhagen Research Centre for Mental Health, Mental Health Centre Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
| | - Vivek Appadurai
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - Alfonso Buil
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - Merete Nordentoft
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- CORE - Copenhagen Research Centre for Mental Health, Mental Health Centre Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Werge
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark.
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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Andres EM, Neely HL, Hafeez H, Yasmin T, Kausar F, Basra MAR, Raza MH. Study of rare genetic variants in TM4SF20, NFXL1, CNTNAP2, and ATP2C2 in Pakistani probands and families with language impairment. Meta Gene 2021; 30. [PMID: 34540591 DOI: 10.1016/j.mgene.2021.100966] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Language impairment (LI) is highly heritable and aggregates in families. Genetic investigation of LI has revealed many chromosomal regions and genes of interest, though very few studies have focused on rare variant analysis in non-English speaking or non-European samples. We selected four candidate genes (TM4SF20, NFXL1, CNTNAP2 and ATP2C2) strongly suggested for specific language impairment (SLI), a subtype of LI, and investigated rare protein coding variants through Sanger sequencing of probands with LI ascertained from Pakistan. The probands and their family members completed a speech and language family history questionnaire and a vocabulary measure, the Peabody Picture Vocabulary Test-fourth edition (PPVT-4), translated to Urdu, the national language of Pakistan. Our study aimed to determine the significance of rare variants in these SLI candidate genes through segregation analysis in a novel population with a high rate of consanguinity. In total, we identified 16 rare variants (according to the rare MAF in the global population in gnomAD v2.1.1 database exomes), including eight variants with a MAF <0.5 % in the South Asian population. Most of the identified rare variants aggregated in proband's families, one rare variant (c.*9T>C in CNTNAP2) co-segregated in a small family (PKSLI-64) and another (c.2465C>T in ATP2C2) co-segregated in the proband branch (PKSLI-27). The lack of complete co-segregation of most of the identified rare variants indicates that while these genes could be involved in overall risk for LI, other genes are likely involved in LI in this population. Future investigation of these consanguineous families has the potential to expand our understanding of gene function related to language acquisition and impairment.
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Affiliation(s)
- Erin M Andres
- University of Kansas, Child Language Doctoral Program
| | | | - Huma Hafeez
- School of Chemistry, University of the Punjab
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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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11
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Andres EM, Earnest KK, Smith SD, Rice ML, Raza MH. Pedigree-Based Gene Mapping Supports Previous Loci and Reveals Novel Suggestive Loci in Specific Language Impairment. JOURNAL OF SPEECH, LANGUAGE, AND HEARING RESEARCH : JSLHR 2020; 63:4046-4061. [PMID: 33186502 PMCID: PMC8608229 DOI: 10.1044/2020_jslhr-20-00102] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Purpose Specific language impairment (SLI) is characterized by a delay in language acquisition despite a lack of other developmental delays or hearing loss. Genetics of SLI is poorly understood. The purpose of this study is to identify SLI genetic loci through family-based linkage mapping. Method We performed genome-wide parametric linkage analysis in six families segregating with SLI. An age-appropriate standardized omnibus language measure was used to categorically define the SLI phenotype. Results A suggestive linkage region replicated a previous region of interest with the highest logarithm of odds (LOD) score of 2.40 at 14q11.2-q13.3 in Family 489. A paternal parent-of-origin effect associated with SLI and language phenotypes on a nonsynonymous single nucleotide polymorphism (SNP) in NOP9 (14q12) was reported previously. Linkage analysis identified a new SLI locus at 15q24.3-25.3 with the highest parametric LOD score of 3.06 in Family 315 under a recessive mode of inheritance. Suggestive evidence of linkage was also revealed at 4q31.23-q35.2 in Family 300, with the highest LOD score of 2.41. Genetic linkage was not identified in the other three families included in parametric linkage analysis. Conclusions These results are the first to report genome-wide suggestive linkage with a total language standard score on an age-appropriate omnibus language measure across a wide age range. Our findings confirm previous reports of a language-associated locus on chromosome 14q, report new SLI loci, and validate the pedigree-based parametric linkage analysis approach to mapping genes for SLI. Supplemental Material https://doi.org/10.23641/asha.13203218.
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Affiliation(s)
- Erin M. Andres
- Child Language Doctoral Program, University of Kansas, Lawrence
| | | | - Shelley D. Smith
- Department of Neurological Sciences, University of Nebraska Medical Center, Omaha
| | - Mabel L. Rice
- Child Language Doctoral Program, University of Kansas, Lawrence
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12
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Thompson PA, Bishop DVM, Eising E, Fisher SE, Newbury DF. Generalized Structured Component Analysis in candidate gene association studies: applications and limitations. Wellcome Open Res 2020; 4:142. [PMID: 33521327 PMCID: PMC7818107 DOI: 10.12688/wellcomeopenres.15396.2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2020] [Indexed: 12/04/2022] Open
Abstract
Background: Generalized Structured Component Analysis (GSCA) is a component-based alternative to traditional covariance-based structural equation modelling. This method has previously been applied to test for association between candidate genes and clinical phenotypes, contrasting with traditional genetic association analyses that adopt univariate testing of many individual single nucleotide polymorphisms (SNPs) with correction for multiple testing. Methods: We first evaluate the ability of the GSCA method to replicate two previous findings from a genetics association study of developmental language disorders. We then present the results of a simulation study to test the validity of the GSCA method under more restrictive data conditions, using smaller sample sizes and larger numbers of SNPs than have previously been investigated. Finally, we compare GSCA performance against univariate association analysis conducted using PLINK v1.9. Results: Results from simulations show that power to detect effects depends not just on sample size, but also on the ratio of SNPs with effect to number of SNPs tested within a gene. Inclusion of many SNPs in a model dilutes true effects. Conclusions: We propose that GSCA is a useful method for replication studies, when candidate SNPs have been identified, but should not be used for exploratory analysis.
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Affiliation(s)
- Paul A. Thompson
- Experimental Psychology, University of Oxford, Anna Watts Building, Radcliffe Observatory Quarter, Woodstock Road, Oxford, OX2 6GG, UK
| | - Dorothy V. M. Bishop
- Experimental Psychology, University of Oxford, Anna Watts Building, Radcliffe Observatory Quarter, Woodstock Road, Oxford, OX2 6GG, UK
| | - Else Eising
- Max Planck Institute for Psycholinguistics, Wundtlaan 1, Nijmegen, 6525 XD, The Netherlands
| | - Simon E. Fisher
- Max Planck Institute for Psycholinguistics, Wundtlaan 1, Nijmegen, 6525 XD, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Montessorilaan 3, Nijmegen, 6525 HR, The Netherlands
| | - Dianne F. Newbury
- Department of Biological and Medical Sciences, Oxford Brookes University, Headington Campus, Oxford, OX3 0BP, UK
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13
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Walters CE, Nitin R, Margulis K, Boorom O, Gustavson DE, Bush CT, Davis LK, Below JE, Cox NJ, Camarata SM, Gordon RL. Automated Phenotyping Tool for Identifying Developmental Language Disorder Cases in Health Systems Data (APT-DLD): A New Research Algorithm for Deployment in Large-Scale Electronic Health Record Systems. JOURNAL OF SPEECH, LANGUAGE, AND HEARING RESEARCH : JSLHR 2020; 63:3019-3035. [PMID: 32791019 PMCID: PMC7890229 DOI: 10.1044/2020_jslhr-19-00397] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 04/23/2020] [Accepted: 05/19/2020] [Indexed: 05/13/2023]
Abstract
Purpose Data mining algorithms using electronic health records (EHRs) are useful in large-scale population-wide studies to classify etiology and comorbidities (Casey et al., 2016). Here, we apply this approach to developmental language disorder (DLD), a prevalent communication disorder whose risk factors and epidemiology remain largely undiscovered. Method We first created a reliable system for manually identifying DLD in EHRs based on speech-language pathologist (SLP) diagnostic expertise. We then developed and validated an automated algorithmic procedure, called, Automated Phenotyping Tool for identifying DLD cases in health systems data (APT-DLD), that classifies a DLD status for patients within EHRs on the basis of ICD (International Statistical Classification of Diseases and Related Health Problems) codes. APT-DLD was validated in a discovery sample (N = 973) using expert SLP manual phenotype coding as a gold-standard comparison and then applied and further validated in a replication sample of N = 13,652 EHRs. Results In the discovery sample, the APT-DLD algorithm correctly classified 98% (concordance) of DLD cases in concordance with manually coded records in the training set, indicating that APT-DLD successfully mimics a comprehensive chart review. The output of APT-DLD was also validated in relation to independently conducted SLP clinician coding in a subset of records, with a positive predictive value of 95% of cases correctly classified as DLD. We also applied APT-DLD to the replication sample, where it achieved a positive predictive value of 90% in relation to SLP clinician classification of DLD. Conclusions APT-DLD is a reliable, valid, and scalable tool for identifying DLD cohorts in EHRs. This new method has promising public health implications for future large-scale epidemiological investigations of DLD and may inform EHR data mining algorithms for other communication disorders. Supplemental Material https://doi.org/10.23641/asha.12753578.
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Affiliation(s)
- Courtney E. Walters
- Department of Otolaryngology, Vanderbilt University Medical Center, Nashville, TN
- Neuroscience Program, College of Arts and Science, Vanderbilt University, Nashville, TN
| | - Rachana Nitin
- Department of Otolaryngology, Vanderbilt University Medical Center, Nashville, TN
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN
| | - Katherine Margulis
- Department of Hearing and Speech Sciences, Vanderbilt University Medical Center, Nashville, TN
- Kennedy Krieger Institute, Baltimore, MD
| | - Olivia Boorom
- Department of Hearing and Speech Sciences, Vanderbilt University Medical Center, Nashville, TN
| | - Daniel E. Gustavson
- Department of Otolaryngology, Vanderbilt University Medical Center, Nashville, TN
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN
| | - Catherine T. Bush
- Department of Hearing and Speech Sciences, Vanderbilt University Medical Center, Nashville, TN
| | - Lea K. Davis
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Jennifer E. Below
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Nancy J. Cox
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Stephen M. Camarata
- Department of Hearing and Speech Sciences, Vanderbilt University Medical Center, Nashville, TN
| | - Reyna L. Gordon
- Department of Otolaryngology, Vanderbilt University Medical Center, Nashville, TN
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN
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14
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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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15
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The Association of Dyslexia and Developmental Speech and Language Disorder Candidate Genes with Reading and Language Abilities in Adults. Twin Res Hum Genet 2020; 23:23-32. [PMID: 32248883 DOI: 10.1017/thg.2020.7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Reading and language abilities are critical for educational achievement and success in adulthood. Variation in these traits is highly heritable, but the underlying genetic architecture is largely undiscovered. Genetic studies of reading and language skills traditionally focus on children with developmental disorders; however, much larger unselected adult samples are available, increasing power to identify associations with specific genetic variants of small effect size. We introduce an Australian adult population cohort (41.7-73.2 years of age, N = 1505) in which we obtained data using validated measures of several aspects of reading and language abilities. We performed genetic association analysis for a reading and spelling composite score, nonword reading (assessing phonological processing: a core component in learning to read), phonetic spelling, self-reported reading impairment and nonword repetition (a marker of language ability). Given the limited power in a sample of this size (~80% power to find a minimum effect size of 0.005), we focused on analyzing candidate genes that have been associated with dyslexia and developmental speech and language disorders in prior studies. In gene-based tests, FOXP2, a gene implicated in speech/language disorders, was associated with nonword repetition (p < .001), phonetic spelling (p = .002) and the reading and spelling composite score (p < .001). Gene-set analyses of candidate dyslexia and speech/language disorder genes were not significant. These findings contribute to the assessment of genetic associations in reading and language disorders, crucial for understanding their etiology and informing intervention strategies, and validate the approach of using unselected adult samples for gene discovery in language and reading.
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16
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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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17
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Nudel R, Christiani CAJ, Ohland J, Uddin MJ, Hemager N, Ellersgaard DV, Spang KS, Burton BK, Greve AN, Gantriis DL, Bybjerg-Grauholm J, Jepsen JRM, Thorup AAE, Mors O, Nordentoft M, Werge T. Language deficits in specific language impairment, attention deficit/hyperactivity disorder, and autism spectrum disorder: An analysis of polygenic risk. Autism Res 2019; 13:369-381. [PMID: 31577390 PMCID: PMC7078922 DOI: 10.1002/aur.2211] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/04/2019] [Indexed: 12/27/2022]
Abstract
Language is one of the cognitive domains often impaired across many neurodevelopmental disorders. While for some disorders the linguistic deficit is the primary impairment (e.g., specific language impairment, SLI), for others it may accompany broader behavioral problems (e.g., autism). The precise nature of this phenotypic overlap has been the subject of debate. Moreover, several studies have found genetic overlaps across neurodevelopmental disorders. This raises the question of whether these genetic overlaps may correlate with phenotypic overlaps and, if so, in what manner. Here, we apply a genome‐wide approach to the study of the linguistic deficit in SLI, autism spectrum disorder (ASD), and attention deficit/hyperactivity disorder (ADHD). Using a discovery genome‐wide association study of SLI, we generate polygenic risk scores (PRS) in an independent sample which includes children with language impairment, SLI, ASD or ADHD and age‐matched controls and perform regression analyses across groups. The SLI‐trained PRS significantly predicted risk in the SLI case–control group (adjusted R2 = 6.24%; P = 0.024) but not in the ASD or ADHD case‐control groups (adjusted R2 = 0.0004%, 0.01%; P = 0.984, 0.889, respectively) nor for height, used as a negative control (R2 = 0.2%; P = 0.452). Additionally, there was a significant difference in the normalized PRS between children with SLI and children with ASD (common language effect size = 0.66; P = 0.044). Our study suggests no additive common‐variant genetic overlap between SLI and ASD and ADHD. This is discussed in the context of phenotypic studies of SLI and related disorders. Autism Res 2020, 13: 369–381. © 2019 The Authors. Autism Research published by International Society for Autism Research published by Wiley Periodicals, Inc. Lay Summary Language deficits are characteristic of specific language impairment (SLI), but may also be found in other neurodevelopmental disorders, such as autism spectrum disorder (ASD) and attention deficit/hyperactivity disorder (ADHD). Many studies examined the overlaps and differences across the language deficits in these disorders, but few studies have examined the genetic aspect thereof. In this study, we use a genome‐wide approach to evaluate whether common genetic variants increasing risk of SLI may also be associated with ASD and ADHD in the same manner. Our results suggest that this is not the case, and we discuss this finding in the context of theories concerning the etiologies of these disorders.
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Affiliation(s)
- Ron Nudel
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Camilla A J Christiani
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark
| | - Jessica Ohland
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark
| | - Md Jamal Uddin
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, 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, Aarhus, Denmark.,Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark
| | - Ditte V Ellersgaard
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark
| | - Katrine S Spang
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, 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, Aarhus, 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, Aarhus, Denmark.,Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
| | - Ditte L Gantriis
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
| | - Jonas Bybjerg-Grauholm
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, 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, Aarhus, 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, Aarhus, 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, Aarhus, Denmark.,Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
| | - Merete Nordentoft
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, 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
| | - Thomas Werge
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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18
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Thompson PA, Bishop DVM, Eising E, Fisher SE, Newbury DF. Generalized Structured Component Analysis in candidate gene association studies: applications and limitations. Wellcome Open Res 2019; 4:142. [PMID: 33521327 PMCID: PMC7818107 DOI: 10.12688/wellcomeopenres.15396.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2019] [Indexed: 02/15/2024] Open
Abstract
Background: Generalized Structured Component Analysis (GSCA) is a component-based alternative to traditional covariance-based structural equation modelling. This method has previously been applied to test for association between candidate genes and clinical phenotypes, contrasting with traditional genetic association analyses that adopt univariate testing of many individual single nucleotide polymorphisms (SNPs) with correction for multiple testing. Methods: We first evaluate the ability of the GSCA method to replicate two previous findings from a genetics association study of developmental language disorders. We then present the results of a simulation study to test the validity of the GSCA method under more restrictive data conditions, using smaller sample sizes and larger numbers of SNPs than have previously been investigated. Finally, we compare GSCA performance against univariate association analysis conducted using PLINK v1.9. Results: Results from simulations show that power to detect effects depends not just on sample size, but also on the ratio of SNPs with effect to number of SNPs tested within a gene. Inclusion of many SNPs in a model dilutes true effects. Conclusions: We propose that GSCA is a useful method for replication studies, when candidate SNPs have been identified, but should not be used for exploratory analysis.
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Affiliation(s)
- Paul A. Thompson
- Experimental Psychology, University of Oxford, Anna Watts Building, Radcliffe Observatory Quarter, Woodstock Road, Oxford, OX2 6GG, UK
| | - Dorothy V. M. Bishop
- Experimental Psychology, University of Oxford, Anna Watts Building, Radcliffe Observatory Quarter, Woodstock Road, Oxford, OX2 6GG, UK
| | - Else Eising
- Max Planck Institute for Psycholinguistics, Wundtlaan 1, Nijmegen, 6525 XD, The Netherlands
| | - Simon E. Fisher
- Max Planck Institute for Psycholinguistics, Wundtlaan 1, Nijmegen, 6525 XD, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Montessorilaan 3, Nijmegen, 6525 HR, The Netherlands
| | - Dianne F. Newbury
- Department of Biological and Medical Sciences, Oxford Brookes University, Headington Campus, Oxford, OX3 0BP, UK
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19
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Andres EM, Hafeez H, Yousaf A, Riazuddin S, Rice ML, Basra MAR, Raza MH. A genome-wide analysis in consanguineous families reveals new chromosomal loci in specific language impairment (SLI). Eur J Hum Genet 2019; 27:1274-1285. [PMID: 30976110 DOI: 10.1038/s41431-019-0398-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 03/19/2019] [Accepted: 03/26/2019] [Indexed: 12/31/2022] Open
Abstract
Language is a uniquely human ability, and failure to attain this ability can have a life-long impact on the affected individuals. This is particularly true for individuals with specific language impairment (SLI), which is defined as an impairment in normal language development in the absence of any other developmental disability. Although SLI displays high heritability, family-based linkage studies have been hampered by an unclear mode of Mendelian segregation, variable disease penetrance, and heterogeneity of diagnostic criteria. We performed genome-wide parametric linkage analysis and homozygosity mapping in 14 consanguineous families from Pakistan segregating SLI. Linkage analysis revealed a multipoint LOD score of 4.18 at chromosome 2q in family PKSLI05 under a recessive mode of inheritance. A second linkage score of 3.85 was observed in family PKSLI12 at a non-overlapping locus on chromosome 2q. Two other suggestive linkage loci were found in family PKSLI05 on 14q and 22q with LOD scores of 2.37 and 2.23, respectively, that were also identified in homozygosity mapping. Reduction to homozygosity was observed on chromosomes 2q, 5p, 8q, 14q, 17q, and 22q. Each homozygosity region occurred in multiple PKSLI families. We report new SLI loci on chromosomes 2 and 8 and confirm suggestive SLI linkage loci on chromosomes 5, 14, 17, and 22 reported previously in the population of Robinson Crusoe Island. These findings indicate that linkage and homozygosity mapping in consanguineous families can improve genetic analyses in SLI and suggest the involvement of additional genes in the causation of this disorder.
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Affiliation(s)
- Erin M Andres
- Child Language Doctoral Program (CLDP), University of Kansas, Lawrence, KS, USA
| | - Huma Hafeez
- Institute of Chemistry, University of the Punjab, Lahore, Pakistan
| | - Adnan Yousaf
- Child Language Doctoral Program (CLDP), University of Kansas, Lawrence, KS, USA.,Department of Biotechnology, International Islamic University, Islamabad, Pakistan
| | | | - Mabel L Rice
- Child Language Doctoral Program (CLDP), University of Kansas, Lawrence, KS, USA
| | | | - Muhammad Hashim Raza
- Child Language Doctoral Program (CLDP), University of Kansas, Lawrence, KS, USA.
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20
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Devanna P, Chen XS, Ho J, Gajewski D, Smith SD, Gialluisi A, Francks C, Fisher SE, Newbury DF, Vernes SC. Next-gen sequencing identifies non-coding variation disrupting miRNA-binding sites in neurological disorders. Mol Psychiatry 2018; 23:1375-1384. [PMID: 28289279 PMCID: PMC5474318 DOI: 10.1038/mp.2017.30] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 12/17/2016] [Accepted: 01/12/2017] [Indexed: 12/26/2022]
Abstract
Understanding the genetic factors underlying neurodevelopmental and neuropsychiatric disorders is a major challenge given their prevalence and potential severity for quality of life. While large-scale genomic screens have made major advances in this area, for many disorders the genetic underpinnings are complex and poorly understood. To date the field has focused predominantly on protein coding variation, but given the importance of tightly controlled gene expression for normal brain development and disorder, variation that affects non-coding regulatory regions of the genome is likely to play an important role in these phenotypes. Herein we show the importance of 3 prime untranslated region (3'UTR) non-coding regulatory variants across neurodevelopmental and neuropsychiatric disorders. We devised a pipeline for identifying and functionally validating putatively pathogenic variants from next generation sequencing (NGS) data. We applied this pipeline to a cohort of children with severe specific language impairment (SLI) and identified a functional, SLI-associated variant affecting gene regulation in cells and post-mortem human brain. This variant and the affected gene (ARHGEF39) represent new putative risk factors for SLI. Furthermore, we identified 3'UTR regulatory variants across autism, schizophrenia and bipolar disorder NGS cohorts demonstrating their impact on neurodevelopmental and neuropsychiatric disorders. Our findings show the importance of investigating non-coding regulatory variants when determining risk factors contributing to neurodevelopmental and neuropsychiatric disorders. In the future, integration of such regulatory variation with protein coding changes will be essential for uncovering the genetic causes of complex neurological disorders and the fundamental mechanisms underlying health and disease.
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Affiliation(s)
- P Devanna
- Neurogenetics of Vocal Communication
Group, Max Planck Institute for Psycholinguistics, Nijmegen,
The Netherlands
| | - X S Chen
- Language and Genetics Department, Max
Planck Institute for Psycholinguistics, Nijmegen, The
Netherlands
| | - J Ho
- Neurogenetics of Vocal Communication
Group, Max Planck Institute for Psycholinguistics, Nijmegen,
The Netherlands
- Language and Genetics Department, Max
Planck Institute for Psycholinguistics, Nijmegen, The
Netherlands
| | - D Gajewski
- Neurogenetics of Vocal Communication
Group, Max Planck Institute for Psycholinguistics, Nijmegen,
The Netherlands
| | - S D Smith
- Department of Developmental Neuroscience,
Munroe Meyer Institute, University of Nebraska Medical Center,
Omaha, NE, USA
| | - A Gialluisi
- Language and Genetics Department, Max
Planck Institute for Psycholinguistics, Nijmegen, The
Netherlands
- Department of Translational Research in
Psychiatry, Max Planck Institute of Psychiatry, Munich,
Germany
| | - C Francks
- Language and Genetics Department, Max
Planck Institute for Psycholinguistics, Nijmegen, The
Netherlands
- Donders Institute for Brain, Cognition
and Behaviour, 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, Nijmegen, The Netherlands
| | - D F Newbury
- Wellcome Trust Centre for Human Genetics,
University of Oxford, Oxford, UK
- Department of Biological and Medical
Sciences, Faculty of Health and Life Sciences, Oxford Brookes University,
Oxford, UK
| | - S C Vernes
- Neurogenetics of Vocal Communication
Group, Max Planck Institute for Psycholinguistics, Nijmegen,
The Netherlands
- Donders Institute for Brain, Cognition
and Behaviour, Nijmegen, The Netherlands
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21
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De Barbieri Z, Fernández MA, Newbury DF, Villanueva P. Family aggregation of language impairment in an isolated Chilean population from Robinson Crusoe Island. INTERNATIONAL JOURNAL OF LANGUAGE & COMMUNICATION DISORDERS 2018; 53:643-655. [PMID: 29575355 DOI: 10.1111/1460-6984.12377] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 01/18/2018] [Accepted: 01/20/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND It has been reported that the inhabitants of the Chilean Robinson Crusoe Island have an increased frequency of specific language impairment (SLI) or developmental language disorder (DLD). AIMS To explore the familial aggregation of DLD in this community. METHODS & PROCEDURES We assessed the frequency of DLD amongst colonial children between the ages of 3 and 8;11 years (50 individuals from 45 nuclear families). Familial aggregation rates of language disorder were calculated by assessing all available first-degree relatives (n = 107, 77 parents, 25 siblings, five half-siblings) of the probands. OUTCOMES & RESULTS We found that 71% of the child population performed significantly below expected in measures of phonological production or expressive and receptive morphology. The majority of these children presented with severe expressive and/or receptive language difficulties. One-quarter of language-disordered probands primarily had phonological difficulties. Family members of affected probands experienced a higher risk of language disorder than those of typically developing probands. This increased risk was apparent regardless of non-verbal IQ. CONCLUSIONS & IMPLICATIONS The study substantiates the existence of a familial form of speech and language disorder on Robinson Crusoe Island. Furthermore, we find that the familiarity is stable regardless of non-verbal IQ, supporting the recent movement to reduce the importance of non-verbal IQ criterion in DLD diagnoses.
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Affiliation(s)
- Zulema De Barbieri
- Department of Speech language and Hearing Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - María Angélica Fernández
- Department of Speech language and Hearing Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Dianne F Newbury
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Pía Villanueva
- Department of Speech language and Hearing Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- Institute of Biomedical Sciences, Human Genetics Division, Faculty of Medicine, Universidad de Chile, Santiago, Chile
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22
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Moore MW, Fiez JA, Tompkins CA. Consonant Age-of-Acquisition Effects in Nonword Repetition Are Not Articulatory in Nature. JOURNAL OF SPEECH, LANGUAGE, AND HEARING RESEARCH : JSLHR 2017; 60:3198-3212. [PMID: 29052729 PMCID: PMC5945079 DOI: 10.1044/2017_jslhr-l-16-0359] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 05/08/2017] [Indexed: 05/12/2023]
Abstract
PURPOSE Most research examining long-term-memory effects on nonword repetition (NWR) has focused on lexical-level variables. Phoneme-level variables have received little attention, although there are reasons to expect significant sublexical effects in NWR. To further understand the underlying processes of NWR, this study examined effects of sublexical long-term phonological knowledge by testing whether performance differs when the stimuli comprise consonants acquired later versus earlier in speech development. METHOD Thirty (Experiment 1) and 20 (Experiment 2) college students completed tasks that investigated whether an experimental phoneme-level variable (consonant age of acquisition) similarly affects NWR and lexical-access tasks designed to vary in articulatory, auditory-perceptual, and phonological short-term-memory demands. The lexical-access tasks were performed in silence or with concurrent articulation to explore whether consonant age-of-acquisition effects arise before or after articulatory planning. RESULTS NWR accuracy decreased on items comprising later- versus earlier-acquired phonemes. Similar consonant age-of-acquisition effects were observed in accuracy measures of nonword reading and lexical decision performed in silence or with concurrent articulation. CONCLUSION Results indicate that NWR performance is sensitive to phoneme-level phonological knowledge in long-term memory. NWR, accordingly, should not be regarded as a diagnostic tool for pure impairment of phonological short-term memory. SUPPLEMENTAL MATERIALS https://doi.org/10.23641/asha.5435137.
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Affiliation(s)
- Michelle W. Moore
- West Virginia University, Morgantown
- University of Pittsburgh, Pennsylvania
| | - Julie A. Fiez
- University of Pittsburgh, Pennsylvania
- Learning Research and Development Center, Pittsburgh, PA
- Center for the Neural Basis of Cognition, Pittsburgh, PA
| | - Connie A. Tompkins
- University of Pittsburgh, Pennsylvania
- Center for the Neural Basis of Cognition, Pittsburgh, PA
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23
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Luo M, Fan J, Wenger TL, Harr MH, Racobaldo M, Mulchandani S, Dubbs H, Zackai EH, Spinner NB, Conlin LK. CMIP haploinsufficiency in two patients with autism spectrum disorder and co-occurring gastrointestinal issues. Am J Med Genet A 2017; 173:2101-2107. [PMID: 28504353 DOI: 10.1002/ajmg.a.38277] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 04/10/2017] [Indexed: 12/20/2022]
Abstract
Autism spectrum disorder (ASD) is a genetically heterogeneous group of disorders characterized by impairments in social communication and restricted interests. Though some patients with ASD have an identifiable genetic cause, the cause of most ASD remains elusive. Many ASD susceptibility loci have been identified through clinical studies. We report two patients with syndromic ASD and persistent gastrointestinal issues who carry de novo deletions involving the CMIP gene detected by genome-wide SNP microarray and fluorescence in situ hybridization (FISH) analysis. Patient 1 has a 517 kb deletion within 16q23.2q23.3 including the entire CMIP gene. Patient 2 has a 1.59 Mb deletion within 16q23.2q23.3 that includes partial deletion of CMIP in addition to 12 other genes, none of which have a known connection to ASD or other clinical phenotypes. The deletion of CMIP is rare in general population and was not found among a reference cohort of approximately 12,000 patients studied in our laboratory who underwent SNP array analysis for various indications. A 280 kb de novo deletion containing the first 3 exons of CMIP was reported in one patient who also demonstrated ASD and developmental delay. CMIP has previously been identified as a susceptibility locus for specific language impairment (SLI). It is notable that both patients in this study had significant gastrointestinal issues requiring enteral feedings, which is unusual for patients with ASD, in addition to unusually elevated birth length, further supporting a shared causative gene. These findings suggest that CMIP haploinsufficiency is the likely cause of syndromic ASD in our patients.
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Affiliation(s)
- Minjie Luo
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jinbo Fan
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Tara L Wenger
- Department of Pediatrics, Seattle Children's Hospital, Seattle, Washington
| | - Margaret H Harr
- Division of Craniofacial Medicine, Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Melissa Racobaldo
- Department of Pediatrics, Division of Genetics and Metabolism, University of South Florida College of Medicine, Tampa, Florida
| | - Surabhi Mulchandani
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Holly Dubbs
- Division of Neurology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Elaine H Zackai
- Division of Craniofacial Medicine, Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Nancy B Spinner
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Laura K Conlin
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
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24
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Chen XS, Reader RH, Hoischen A, Veltman JA, Simpson NH, Francks C, Newbury DF, Fisher SE. Next-generation DNA sequencing identifies novel gene variants and pathways involved in specific language impairment. Sci Rep 2017; 7:46105. [PMID: 28440294 PMCID: PMC5404330 DOI: 10.1038/srep46105] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 03/08/2017] [Indexed: 12/22/2022] Open
Abstract
A significant proportion of children have unexplained problems acquiring proficient linguistic skills despite adequate intelligence and opportunity. Developmental language disorders are highly heritable with substantial societal impact. Molecular studies have begun to identify candidate loci, but much of the underlying genetic architecture remains undetermined. We performed whole-exome sequencing of 43 unrelated probands affected by severe specific language impairment, followed by independent validations with Sanger sequencing, and analyses of segregation patterns in parents and siblings, to shed new light on aetiology. By first focusing on a pre-defined set of known candidates from the literature, we identified potentially pathogenic variants in genes already implicated in diverse language-related syndromes, including ERC1, GRIN2A, and SRPX2. Complementary analyses suggested novel putative candidates carrying validated variants which were predicted to have functional effects, such as OXR1, SCN9A and KMT2D. We also searched for potential “multiple-hit” cases; one proband carried a rare AUTS2 variant in combination with a rare inherited haplotype affecting STARD9, while another carried a novel nonsynonymous variant in SEMA6D together with a rare stop-gain in SYNPR. On broadening scope to all rare and novel variants throughout the exomes, we identified biological themes that were enriched for such variants, including microtubule transport and cytoskeletal regulation.
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Affiliation(s)
- Xiaowei Sylvia Chen
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Rose H Reader
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Joris A Veltman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Clinical Genetics, University of Maastricht, Maastricht, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Nuala H Simpson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Clyde Francks
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Dianne F Newbury
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.,Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Simon E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
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25
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Truong DT, Shriberg LD, Smith SD, Chapman KL, Scheer-Cohen AR, DeMille MMC, Adams AK, Nato AQ, Wijsman EM, Eicher JD, Gruen JR. Multipoint genome-wide linkage scan for nonword repetition in a multigenerational family further supports chromosome 13q as a locus for verbal trait disorders. Hum Genet 2016; 135:1329-1341. [PMID: 27535846 PMCID: PMC5065602 DOI: 10.1007/s00439-016-1717-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 07/22/2016] [Indexed: 12/19/2022]
Abstract
Verbal trait disorders encompass a wide range of conditions and are marked by deficits in five domains that impair a person's ability to communicate: speech, language, reading, spelling, and writing. Nonword repetition is a robust endophenotype for verbal trait disorders that is sensitive to cognitive processes critical to verbal development, including auditory processing, phonological working memory, and motor planning and programming. In the present study, we present a six-generation extended pedigree with a history of verbal trait disorders. Using genome-wide multipoint variance component linkage analysis of nonword repetition, we identified a region spanning chromosome 13q14-q21 with LOD = 4.45 between 52 and 55 cM, spanning approximately 5.5 Mb on chromosome 13. This region overlaps with SLI3, a locus implicated in reading disability in families with a history of specific language impairment. Our study of a large multigenerational family with verbal trait disorders further implicates the SLI3 region in verbal trait disorders. Future studies will further refine the specific causal genetic factors in this locus on chromosome 13q that contribute to language traits.
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Affiliation(s)
- D T Truong
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, 06510, USA
| | - L D Shriberg
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - S D Smith
- Department of Pediatrics, University of Nebraska at Omaha, Omaha, NE, 68182, USA
| | - K L Chapman
- Department of Communication Sciences and Disorders, University of Utah, Salt Lake City, UT, 84112, USA
| | - A R Scheer-Cohen
- Department of Speech-Language Pathology, California State University, San Marcos, CA, 92096, USA
| | - M M C DeMille
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, 06510, USA
| | - A K Adams
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA
| | - A Q Nato
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, 98195, USA
| | - E M Wijsman
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, 98195, USA
- Department of Biostatistics and Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - J D Eicher
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA
| | - J R Gruen
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, 06510, USA.
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA.
- Investigative Medicine Program, Yale School of Medicine, New Haven, CT, 06510, USA.
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26
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Tager-Flusberg H. Defining language impairments in a subgroup of children with autism spectrum disorder. SCIENCE CHINA-LIFE SCIENCES 2016; 58:1044-52. [PMID: 26335733 DOI: 10.1007/s11427-012-4297-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Autism spectrum disorder (ASD) is diagnosed on the basis of core impairments in pragmatic language skills, which are found across all ages and subtypes. In contrast, there is significant heterogeneity in language phenotypes, ranging from nonverbal to superior linguistic abilities, as defined on standardized tests of vocabulary and grammatical knowledge. The majority of children are verbal but impaired in language, relative to age-matched peers. One hypothesis is that this subgroup has ASD and co-morbid specific language impairment (SLI). An experiment was conducted comparing children with ASD to children with SLI and typically developing controls on aspects of language processing that have been shown to be impaired in children with SLI: repetition of nonsense words. Patterns of performance among the children with ASD and language impairment were similar to those with SLI, and contrasted with the children with ASD and no language impairment and typical controls, providing further evidence for the hypothesis that a subgroup of children with ASD has co-morbid SLI. The findings are discussed in the context of brain imaging studies that have explored the neural bases of language impairment in ASD and SLI, and overlap in the genes associated with elevated risk for these disorders.
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27
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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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28
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Kornilov SA, Rakhlin N, Koposov R, Lee M, Yrigollen C, Caglayan AO, Magnuson JS, Mane S, Chang JT, Grigorenko EL. Genome-Wide Association and Exome Sequencing Study of Language Disorder in an Isolated Population. Pediatrics 2016; 137:peds.2015-2469. [PMID: 27016271 PMCID: PMC4811310 DOI: 10.1542/peds.2015-2469] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/26/2016] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND AND OBJECTIVE Developmental language disorder (DLD) is a highly prevalent neurodevelopmental disorder associated with negative outcomes in different domains; the etiology of DLD is unknown. To investigate the genetic underpinnings of DLD, we performed genome-wide association and whole exome sequencing studies in a geographically isolated population with a substantially elevated prevalence of the disorder (ie, the AZ sample). METHODS DNA samples were collected from 359 individuals for the genome-wide association study and from 12 severely affected individuals for whole exome sequencing. Multifaceted phenotypes, representing major domains of expressive language functioning, were derived from collected speech samples. RESULTS Gene-based analyses revealed a significant association between SETBP1 and complexity of linguistic output (P = 5.47 × 10(-7)). The analysis of exome variants revealed coding sequence variants in 14 genes, most of which play a role in neural development. Targeted enrichment analysis implicated myocyte enhancer factor-2 (MEF2)-regulated genes in DLD in the AZ population. The main findings were successfully replicated in an independent cohort of children at risk for related disorders (n = 372). CONCLUSIONS MEF2-regulated pathways were identified as potential candidate pathways in the etiology of DLD. Several genes (including the candidate SETBP1 and other MEF2-related genes) seem to jointly influence certain, but not all, facets of the DLD phenotype. Even when genetic and environmental diversity is reduced, DLD is best conceptualized as etiologically complex. Future research should establish whether the signals detected in the AZ population can be replicated in other samples and languages and provide further characterization of the identified pathway.
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Affiliation(s)
- Sergey A. Kornilov
- Child Study Center, School of Medicine, Yale University, New Haven, Connecticut;,Department of Psychology, University of Connecticut, Storrs, Connecticut;,Haskins Laboratories, New Haven, Connecticut;,Department of Psychology, Moscow State University, Moscow, Russia;,Department of Psychology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Natalia Rakhlin
- Child Study Center, School of Medicine, Yale University, New Haven, Connecticut;,Department of Communication Sciences and Disorders, Wayne State University, Detroit, Michigan
| | - Roman Koposov
- Regional Centre for Child and Youth Mental Health and Child Welfare, UiT The Arctic University of Norway, Tromsø, Norway
| | - Maria Lee
- Child Study Center, School of Medicine, Yale University, New Haven, Connecticut
| | - Carolyn Yrigollen
- The Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ahmet Okay Caglayan
- Child Study Center, School of Medicine, Yale University, New Haven, Connecticut;,Department of Medical Genetics, Istanbul Bilim University, Istanbul, Turkey; and
| | - James S. Magnuson
- Department of Psychology, University of Connecticut, Storrs, Connecticut;,Haskins Laboratories, New Haven, Connecticut
| | - Shrikant Mane
- Child Study Center, School of Medicine, Yale University, New Haven, Connecticut
| | - Joseph T. Chang
- Child Study Center, School of Medicine, Yale University, New Haven, Connecticut
| | - Elena L. Grigorenko
- Child Study Center, School of Medicine, Yale University, New Haven, Connecticut;,Haskins Laboratories, New Haven, Connecticut;,Department of Psychology, Saint Petersburg State University, Saint Petersburg, Russia;,Moscow State University for Psychology and Education, Moscow, Russia
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29
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Evans PD, Mueller KL, Gamazon ER, Cox NJ, Tomblin JB. A genome-wide sib-pair scan for quantitative language traits reveals linkage to chromosomes 10 and 13. GENES BRAIN AND BEHAVIOR 2016; 14:387-97. [PMID: 25997078 DOI: 10.1111/gbb.12223] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 05/06/2015] [Accepted: 05/06/2015] [Indexed: 02/03/2023]
Abstract
Although there is considerable evidence that individual differences in language development are highly heritable, there have been few genome-wide scans to locate genes associated with the trait. Previous analyses of language impairment have yielded replicable evidence for linkage to regions on chromosomes 16q, 19q, 13q (within lab) and at 13q (between labs). Here we report the first linkage study to screen the continuum of language ability, from normal to disordered, as found in the general population. 383 children from 147 sib-ships (214 sib-pairs) were genotyped on the Illumina(®) Linkage IVb Marker Panel using three composite language-related phenotypes and a measure of phonological memory (PM). Two regions (10q23.33; 13q33.3) yielded genome-wide significant peaks for linkage with PM. A peak suggestive of linkage was also found at 17q12 for the overall language composite. This study presents two novel genetic loci for the study of language development and disorders, but fails to replicate findings by previous groups. Possible reasons for this are discussed.
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Affiliation(s)
- P D Evans
- Department of Medicine, The University of Chicago, IL, USA
| | - K L Mueller
- Murdoch Childrens Research Institute, Melbourne, Australia.,Department of Communication Sciences and Disorders, The University of Iowa, IA, USA
| | - E R Gamazon
- Department of Medicine, The University of Chicago, IL, USA.,Present address: Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN, USA
| | - N J Cox
- Department of Medicine, The University of Chicago, IL, USA.,Department of Communication Sciences and Disorders, The University of Iowa, IA, USA.,Present address: Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN, USA
| | - J B Tomblin
- Department of Communication Sciences and Disorders, The University of Iowa, IA, USA
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Redmond SM. Markers, Models, and Measurement Error: Exploring the Links Between Attention Deficits and Language Impairments. JOURNAL OF SPEECH, LANGUAGE, AND HEARING RESEARCH : JSLHR 2016; 59:62-71. [PMID: 26501406 PMCID: PMC4867933 DOI: 10.1044/2015_jslhr-l-15-0088] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Accepted: 06/15/2015] [Indexed: 05/12/2023]
Abstract
PURPOSE The empirical record regarding the expected co-occurrence of attention-deficit/hyperactivity disorder (ADHD) and specific language impairment is confusing and contradictory. A research plan is presented that has the potential to untangle links between these 2 common neurodevelopmental disorders. METHOD Data from completed and ongoing research projects examining the relative value of different clinical markers for separating cases of specific language impairment from ADHD are presented. RESULTS The best option for measuring core language impairments in a manner that does not potentially penalize individuals with ADHD is to focus assessment on key grammatical and verbal memory skills. Likewise, assessment of ADHD symptoms through standardized informant rating scales is optimized when they are adjusted for overlapping language and academic symptoms. CONCLUSION As a collection, these clinical metrics set the stage for further examination of potential linkages between attention deficits and language impairments.
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Lee JC, Mueller KL, Tomblin JB. Examining Procedural Learning and Corticostriatal Pathways for Individual Differences in Language: Testing Endophenotypes of DRD2/ANKK1. LANGUAGE, COGNITION AND NEUROSCIENCE 2016; 31:1098-1114. [PMID: 31768398 PMCID: PMC6876848 DOI: 10.1080/23273798.2015.1089359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The aim of the study was to explore whether genetic variation in the dopaminergic system is associated with procedural learning and the corticostriatal pathways in individuals with developmental language impairment (DLI). We viewed these two systems as endophenotypes and hypothesized that they would be more sensitive indicators of genetic effects than the language phenotype itself. Thus, we genotyped two SNPs in the DRD2/ANKK1 gene complex, and tested for their associations to the phenotype of DLI and the two endophenotypes. Results showed that individuals with DLI revealed poor procedural learning abilities and abnormal structures of the basal ganglia. Genetic variation in DRD2/ANKK1 was associated with procedural learning abilities and with microstructural differences of the caudate nucleus. The association of the language phenotype with these DRD2/ANKK1 polymorphisms was not significant, but the phenotype was significantly associated with the two endophenotypes. We suggest that procedural learning and the corticostriatal pathways could be used as effective endophenotypes to aid molecular genetic studies searching for genes predisposing to DLI.
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Affiliation(s)
- Joanna C. Lee
- Department of Communication Sciences and Disorders, University of Iowa, Iowa City, IA, USA
| | - Kathryn L. Mueller
- Department of Communication Sciences and Disorders, University of Iowa, Iowa City, IA, USA
| | - J. Bruce Tomblin
- Department of Communication Sciences and Disorders, University of Iowa, Iowa City, IA, USA
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Pettigrew KA, Fajutrao Valles SF, Moll K, Northstone K, Ring S, Pennell C, Wang C, Leavett R, Hayiou-Thomas ME, Thompson P, Simpson NH, Fisher SE, Whitehouse AJO, Snowling MJ, Newbury DF, Paracchini S. Lack of replication for the myosin-18B association with mathematical ability in independent cohorts. GENES BRAIN AND BEHAVIOR 2015; 14:369-76. [PMID: 25778778 PMCID: PMC4672701 DOI: 10.1111/gbb.12213] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 03/12/2015] [Accepted: 03/12/2015] [Indexed: 12/20/2022]
Abstract
Twin studies indicate that dyscalculia (or mathematical disability) is caused partly by a genetic component, which is yet to be understood at the molecular level. Recently, a coding variant (rs133885) in the myosin-18B gene was shown to be associated with mathematical abilities with a specific effect among children with dyslexia. This association represents one of the most significant genetic associations reported to date for mathematical abilities and the only one reaching genome-wide statistical significance. We conducted a replication study in different cohorts to assess the effect of rs133885 maths-related measures. The study was conducted primarily using the Avon Longitudinal Study of Parents and Children (ALSPAC), (N = 3819). We tested additional cohorts including the York Cohort, the Specific Language Impairment Consortium (SLIC) cohort and the Raine Cohort, and stratified them for a definition of dyslexia whenever possible. We did not observe any associations between rs133885 in myosin-18B and mathematical abilities among individuals with dyslexia or in the general population. Our results suggest that the myosin-18B variant is unlikely to be a main factor contributing to mathematical abilities.
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Affiliation(s)
- K A Pettigrew
- School of Medicine, University of St Andrews, St Andrews, UK
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Smith AW, Holden KR, Dwivedi A, Dupont BR, Lyons MJ. Deletion of 16q24.1 supports a role for the ATP2C2 gene in specific language impairment. J Child Neurol 2015; 30:517-21. [PMID: 25296922 DOI: 10.1177/0883073814545113] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
A 10-year-old boy presented with a history of significant delay in language acquisition as well as receptive and expressive language impairment that persisted into elementary school. In school, he exhibited difficulty with reading comprehension, telling and understanding narratives, and making inferences. Other aspects of his neurodevelopment were normal, with no history of significant medical concerns. He did not have hearing impairment, oromotor dysfunction, or specific neurologic abnormalities. He did not meet testing criteria for autism. Chromosomal microarray analysis and quantitative polymerase chain reaction determined that he had a de novo 159-kilobase deletion of chromosome 16q24.1 that included the ATP2C2 gene. ATP2C2 is a known candidate gene for specific language impairment and is postulated to have neurobiological significance in memory-related circuits. Our patient's language deficits were consistent with a global type of specific language impairment impacting language comprehension, formulation, semantics, syntax, and phonology attributed to his de novo chromosome deletion.
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Affiliation(s)
- Amena W Smith
- Department of Neurosciences (Neurology), Medical University of South Carolina, Charleston, SC, USA
| | - Kenton R Holden
- Department of Neurosciences (Neurology), Medical University of South Carolina, Charleston, SC, USA Department of Pediatrics, Medical University of South Carolina, Charleston, SC, USA Greenwood Genetic Center, Greenwood, SC, USA
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34
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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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35
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Simpson NH, Ceroni F, Reader RH, Covill LE, Knight JC, Hennessy ER, Bolton PF, Conti-Ramsden G, O'Hare A, Baird G, Fisher SE, Newbury DF. Genome-wide analysis identifies a role for common copy number variants in specific language impairment. Eur J Hum Genet 2015; 23:1370-7. [PMID: 25585696 PMCID: PMC4592089 DOI: 10.1038/ejhg.2014.296] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 12/08/2014] [Accepted: 12/12/2014] [Indexed: 11/29/2022] Open
Abstract
An exploratory genome-wide copy number variant (CNV) study was performed in 127 independent cases with specific language impairment (SLI), their first-degree relatives (385 individuals) and 269 population controls. Language-impaired cases showed an increased CNV burden in terms of the average number of events (11.28 vs 10.01, empirical P=0.003), the total length of CNVs (717 vs 513 Kb, empirical P=0.0001), the average CNV size (63.75 vs 51.6 Kb, empirical P=0.0005) and the number of genes spanned (14.29 vs 10.34, empirical P=0.0007) when compared with population controls, suggesting that CNVs may contribute to SLI risk. A similar trend was observed in first-degree relatives regardless of affection status. The increased burden found in our study was not driven by large or de novo events, which have been described as causative in other neurodevelopmental disorders. Nevertheless, de novo CNVs might be important on a case-by-case basis, as indicated by identification of events affecting relevant genes, such as ACTR2 and CSNK1A1, and small events within known micro-deletion/-duplication syndrome regions, such as chr8p23.1. Pathway analysis of the genes present within the CNVs of the independent cases identified significant overrepresentation of acetylcholine binding, cyclic-nucleotide phosphodiesterase activity and MHC proteins as compared with controls. Taken together, our data suggest that the majority of the risk conferred by CNVs in SLI is via common, inherited events within a ‘common disorder–common variant' model. Therefore the risk conferred by CNVs will depend upon the combination of events inherited (both CNVs and SNPs), the genetic background of the individual and the environmental factors.
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Affiliation(s)
- Nuala H Simpson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Fabiola Ceroni
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Rose H Reader
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Laura E Covill
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Julian C Knight
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | | | - Patrick F Bolton
- Departments of Child and Adolescent Psychiatry, Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, UK
| | - Gina Conti-Ramsden
- School of Psychological Sciences, University of Manchester, Manchester, UK
| | - Anne O'Hare
- Department of Reproductive and Developmental Sciences, University of Edinburgh, Edinburgh, UK
| | - Gillian Baird
- Children's Neurosciences Department, Evelina Children's Hospital and King's Health Partners, London, UK
| | - Simon E Fisher
- Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Dianne F Newbury
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.,St John's College, University of Oxford, Oxford, UK
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36
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Peña ED, Bedore LM, Kester ES. Discriminant accuracy of a semantics measure with Latino English-speaking, Spanish-speaking, and English-Spanish bilingual children. JOURNAL OF COMMUNICATION DISORDERS 2015; 53:30-41. [PMID: 25573288 PMCID: PMC5858189 DOI: 10.1016/j.jcomdis.2014.11.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 10/18/2014] [Accepted: 11/23/2014] [Indexed: 05/19/2023]
Abstract
UNLABELLED We explored classification accuracy of English and Spanish versions of an experimental semantic language measure with functional monolingual-bilingual children with and without language impairment. A total of 441 children participated, including 78 balanced bilinguals (15 with language impairment, 63 with typical development); 179 monolingual Spanish (36 with language impairment, 143 with typical development); and 183 monolingual English (49 with language impairment, 134 with typical development) children between 4;0 and 6;11 years. Cut points derived for functionally monolingual children were applied to bilinguals to assess the predictive accuracy of English and Spanish semantics. Correct classification of English monolinguals and Spanish monolinguals was 81%. Discriminant analysis yielded 76% and 90% correct classification for balanced bilingual children in English and Spanish respectively. This semantics-based measure has fair to good classification accuracy for functional monolinguals and for Spanish-English bilingual children when one language is tested. LEARNING OUTCOMES As a result of this study, the reader will describe advantages of lexical-semantic tasks for identification of language impairment. They will be able to describe procedures for conceptual scoring and identify its benefits. Readers will also gain an understanding of similarities and differences in bilingual and monolingual performance on a semantics task in Spanish and English.
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Affiliation(s)
- Elizabeth D Peña
- Communication Sciences and Disorders, University of Texas at Austin, United States.
| | - Lisa M Bedore
- Communication Sciences and Disorders, University of Texas at Austin, United States
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37
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Eicher JD, Gruen JR. Language impairment and dyslexia genes influence language skills in children with autism spectrum disorders. Autism Res 2014; 8:229-34. [PMID: 25448322 DOI: 10.1002/aur.1436] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 10/01/2014] [Indexed: 12/27/2022]
Abstract
Language and communication development is a complex process influenced by numerous environmental and genetic factors. Many neurodevelopment disorders include deficits in language and communication skills in their diagnostic criteria, including autism spectrum disorders (ASD), language impairment (LI), and dyslexia. These disorders are polygenic and complex with a significant genetic component contributing to each. The similarity of language phenotypes and comorbidity of these disorders suggest that they may share genetic contributors. To test this, we examined the association of genes previously implicated in dyslexia, LI, and/or language-related traits with language skills in children with ASD. We used genetic and language data collected in the Autism Genome Research Exchange (AGRE) and Simons Simplex Collection (SSC) cohorts to perform a meta-analysis on performance on a receptive vocabulary task. There were associations with LI risk gene ATP2C2 and dyslexia risk gene MRPL19. Additionally, we found suggestive evidence of association with CMIP, GCFC2, KIAA0319L, the DYX2 locus (ACOT13, GPLD1, and FAM65B), and DRD2. Our results show that LI and dyslexia genes also contribute to language traits in children with ASD. These associations add to the growing literature of generalist genes that contribute to multiple related neurobehavioral traits. Future studies should examine whether other genetic contributors may be shared among these disorders and how risk variants interact with each other and the environment to modify clinical presentations.
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Affiliation(s)
- John D Eicher
- Department of Genetics, Yale University, New Haven, Connecticut
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38
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Ceroni F, Simpson NH, Francks C, Baird G, Conti-Ramsden G, Clark A, Bolton PF, Hennessy ER, Donnelly P, Bentley DR, Martin H, Parr J, Pagnamenta AT, Maestrini E, Bacchelli E, Fisher SE, Newbury DF. Homozygous microdeletion of exon 5 in ZNF277 in a girl with specific language impairment. Eur J Hum Genet 2014; 22:1165-71. [PMID: 24518835 PMCID: PMC4169542 DOI: 10.1038/ejhg.2014.4] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 10/28/2013] [Accepted: 12/18/2013] [Indexed: 01/22/2023] Open
Abstract
Specific language impairment (SLI), an unexpected failure to develop appropriate language skills despite adequate non-verbal intelligence, is a heterogeneous multifactorial disorder with a complex genetic basis. We identified a homozygous microdeletion of 21,379 bp in the ZNF277 gene (NM_021994.2), encompassing exon 5, in an individual with severe receptive and expressive language impairment. The microdeletion was not found in the proband's affected sister or her brother who had mild language impairment. However, it was inherited from both parents, each of whom carries a heterozygous microdeletion and has a history of language problems. The microdeletion falls within the AUTS1 locus, a region linked to autistic spectrum disorders (ASDs). Moreover, ZNF277 is adjacent to the DOCK4 and IMMP2L genes, which have been implicated in ASD. We screened for the presence of ZNF277 microdeletions in cohorts of children with SLI or ASD and panels of control subjects. ZNF277 microdeletions were at an increased allelic frequency in SLI probands (1.1%) compared with both ASD family members (0.3%) and independent controls (0.4%). We performed quantitative RT-PCR analyses of the expression of IMMP2L, DOCK4 and ZNF277 in individuals carrying either an IMMP2L_DOCK4 microdeletion or a ZNF277 microdeletion. Although ZNF277 microdeletions reduce the expression of ZNF277, they do not alter the levels of DOCK4 or IMMP2L transcripts. Conversely, IMMP2L_DOCK4 microdeletions do not affect the expression levels of ZNF277. We postulate that ZNF277 microdeletions may contribute to the risk of language impairments in a manner that is independent of the autism risk loci previously described in this region.
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Affiliation(s)
- Fabiola Ceroni
- Dipartimento di Farmacia e Biotecnologie, University of Bologna, Bologna, Italy
| | - Nuala H Simpson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Clyde Francks
- Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
- Donders Institute for Brain, Cognition & Behaviour, Nijmegen, Netherlands
| | - Gillian Baird
- Guy's & St Thomas NHS Foundation Trust, Newcomen Children's Neurosciences Centre, St Thomas' Hospital, London, UK
| | - Gina Conti-Ramsden
- School of Psychological Sciences, The University of Manchester, Manchester, UK
| | - Ann Clark
- Speech and Hearing Sciences, Queen Margaret University, Edinburgh, UK
| | - Patrick F Bolton
- Departments of Child & Adolescent Psychiatry & Social Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Kings College London, London, UK
| | | | - Peter Donnelly
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - David R Bentley
- Illumina Cambridge Ltd., Chesterford Research Park, Little Chesterford, Essex, UK
| | - Hilary Martin
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - IMGSAC1113
- Dipartimento di Farmacia e Biotecnologie, University of Bologna, Bologna, Italy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
- Donders Institute for Brain, Cognition & Behaviour, Nijmegen, Netherlands
- Guy's & St Thomas NHS Foundation Trust, Newcomen Children's Neurosciences Centre, St Thomas' Hospital, London, UK
- School of Psychological Sciences, The University of Manchester, Manchester, UK
- Speech and Hearing Sciences, Queen Margaret University, Edinburgh, UK
- Departments of Child & Adolescent Psychiatry & Social Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Kings College London, London, UK
- University Child Health and DMDE, University of Aberdeen, Aberdeen, UK
- Illumina Cambridge Ltd., Chesterford Research Park, Little Chesterford, Essex, UK
- Institute of Neuroscience and Health and Society, Newcastle University, Newcastle, UK
- NIHR Biomedical Research Centre, Oxford and Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - SLI Consortium213
- Dipartimento di Farmacia e Biotecnologie, University of Bologna, Bologna, Italy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
- Donders Institute for Brain, Cognition & Behaviour, Nijmegen, Netherlands
- Guy's & St Thomas NHS Foundation Trust, Newcomen Children's Neurosciences Centre, St Thomas' Hospital, London, UK
- School of Psychological Sciences, The University of Manchester, Manchester, UK
- Speech and Hearing Sciences, Queen Margaret University, Edinburgh, UK
- Departments of Child & Adolescent Psychiatry & Social Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Kings College London, London, UK
- University Child Health and DMDE, University of Aberdeen, Aberdeen, UK
- Illumina Cambridge Ltd., Chesterford Research Park, Little Chesterford, Essex, UK
- Institute of Neuroscience and Health and Society, Newcastle University, Newcastle, UK
- NIHR Biomedical Research Centre, Oxford and Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - WGS500 Consortium213
- Dipartimento di Farmacia e Biotecnologie, University of Bologna, Bologna, Italy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
- Donders Institute for Brain, Cognition & Behaviour, Nijmegen, Netherlands
- Guy's & St Thomas NHS Foundation Trust, Newcomen Children's Neurosciences Centre, St Thomas' Hospital, London, UK
- School of Psychological Sciences, The University of Manchester, Manchester, UK
- Speech and Hearing Sciences, Queen Margaret University, Edinburgh, UK
- Departments of Child & Adolescent Psychiatry & Social Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Kings College London, London, UK
- University Child Health and DMDE, University of Aberdeen, Aberdeen, UK
- Illumina Cambridge Ltd., Chesterford Research Park, Little Chesterford, Essex, UK
- Institute of Neuroscience and Health and Society, Newcastle University, Newcastle, UK
- NIHR Biomedical Research Centre, Oxford and Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Jeremy Parr
- Institute of Neuroscience and Health and Society, Newcastle University, Newcastle, UK
| | - Alistair T Pagnamenta
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- NIHR Biomedical Research Centre, Oxford and Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Elena Maestrini
- Dipartimento di Farmacia e Biotecnologie, University of Bologna, Bologna, Italy
| | - Elena Bacchelli
- Dipartimento di Farmacia e Biotecnologie, University of Bologna, Bologna, Italy
| | - Simon E Fisher
- Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
- Donders Institute for Brain, Cognition & Behaviour, Nijmegen, Netherlands
| | - Dianne F Newbury
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
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Abstract
Specific language impairment (SLI) is a multifactorial neurodevelopmental disorder which occurs unexpectedly and without an obvious cause. Over a decade of research suggests that SLI is highly heritable. Several genes and loci have already been implicated in SLI through linkage and targeted association methods. Recently, genome-wide association studies (GWAS) of SLI and language traits in the general population have been reported and, consequently, new candidate genes have been identified. This review aims to summarise the literature concerning genome-wide studies of SLI. In addition, this review highlights the methodologies that have been used to research the genetics of SLI to date, and also considers the current, and future, contributions that GWAS can offer.
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Affiliation(s)
- Rose H Reader
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN UK
| | - Laura E Covill
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN UK
| | - Ron Nudel
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN UK
| | - Dianne F Newbury
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN UK ; St John's College, University of Oxford, Oxford, OX1 3JP UK
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40
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Gialluisi A, Newbury DF, Wilcutt EG, Olson RK, DeFries JC, Brandler WM, Pennington BF, Smith SD, Scerri TS, Simpson NH, Luciano M, Evans DM, Bates TC, Stein JF, Talcott JB, Monaco AP, Paracchini S, Francks C, Fisher SE. Genome-wide screening for DNA variants associated with reading and language traits. GENES BRAIN AND BEHAVIOR 2014; 13:686-701. [PMID: 25065397 PMCID: PMC4165772 DOI: 10.1111/gbb.12158] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 07/20/2014] [Accepted: 07/24/2014] [Indexed: 01/04/2023]
Abstract
Reading and language abilities are heritable traits that are likely to share some genetic influences with each other. To identify pleiotropic genetic variants affecting these traits, we first performed a genome-wide association scan (GWAS) meta-analysis using three richly characterized datasets comprising individuals with histories of reading or language problems, and their siblings. GWAS was performed in a total of 1862 participants using the first principal component computed from several quantitative measures of reading- and language-related abilities, both before and after adjustment for performance IQ. We identified novel suggestive associations at the SNPs rs59197085 and rs5995177 (uncorrected P ≈ 10–7 for each SNP), located respectively at the CCDC136/FLNC and RBFOX2 genes. Each of these SNPs then showed evidence for effects across multiple reading and language traits in univariate association testing against the individual traits. FLNC encodes a structural protein involved in cytoskeleton remodelling, while RBFOX2 is an important regulator of alternative splicing in neurons. The CCDC136/FLNC locus showed association with a comparable reading/language measure in an independent sample of 6434 participants from the general population, although involving distinct alleles of the associated SNP. Our datasets will form an important part of on-going international efforts to identify genes contributing to reading and language skills.
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Affiliation(s)
- A Gialluisi
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
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Kraft SJ, DeThorne LS. The Brave New World of Epigenetics: Embracing Complexity in the Study of Speech and Language Disorders. CURRENT DEVELOPMENTAL DISORDERS REPORTS 2014. [DOI: 10.1007/s40474-014-0024-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Kato M, Okanoya K, Koike T, Sasaki E, Okano H, Watanabe S, Iriki A. Human speech- and reading-related genes display partially overlapping expression patterns in the marmoset brain. BRAIN AND LANGUAGE 2014; 133:26-38. [PMID: 24769279 DOI: 10.1016/j.bandl.2014.03.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 03/02/2014] [Accepted: 03/22/2014] [Indexed: 06/03/2023]
Abstract
Language is a characteristic feature of human communication. Several familial language impairments have been identified, and candidate genes for language impairments already isolated. Studies comparing expression patterns of these genes in human brain are necessary to further understanding of these genes. However, it is difficult to examine gene expression in human brain. In this study, we used a non-human primate (common marmoset; Callithrix jacchus) as a biological model of the human brain to investigate expression patterns of human speech- and reading-related genes. Expression patterns of speech disorder- (FoxP2, FoxP1, CNTNAP2, and CMIP) and dyslexia- (ROBO1, DCDC2, and KIAA0319) related genes were analyzed. We found the genes displayed overlapping expression patterns in the ocular, auditory, and motor systems. Our results enhance understanding of the molecular mechanisms underlying language impairments.
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Affiliation(s)
- Masaki Kato
- Laboratory for Symbolic Cognitive Development, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Laboratory for Biolinguistics, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Center for Advanced Research on Logic and Sensibility (CARLS), Keio University, 2-15-45 Mita, Minato-ku, Tokyo 108-8345, Japan.
| | - Kazuo Okanoya
- Laboratory for Biolinguistics, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Taku Koike
- Laboratory for Symbolic Cognitive Development, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Erika Sasaki
- Department of Applied Developmental Biology, Central Institute for Experimental Animals, 3-25-12 Tonomachi, Kawasaki, Kanagawa 210-0821, Japan; Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan; KEIO-RIKEN Research Center for Human Cognition, Keio University, 2-15-45 Mita, Minato-ku, Tokyo 108-8345, Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan; KEIO-RIKEN Research Center for Human Cognition, Keio University, 2-15-45 Mita, Minato-ku, Tokyo 108-8345, Japan; Keio University Joint Research Laboratory, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Shigeru Watanabe
- KEIO-RIKEN Research Center for Human Cognition, Keio University, 2-15-45 Mita, Minato-ku, Tokyo 108-8345, Japan; Center for Advanced Research on Logic and Sensibility (CARLS), Keio University, 2-15-45 Mita, Minato-ku, Tokyo 108-8345, Japan
| | - Atsushi Iriki
- Laboratory for Symbolic Cognitive Development, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; KEIO-RIKEN Research Center for Human Cognition, Keio University, 2-15-45 Mita, Minato-ku, Tokyo 108-8345, Japan; Center for Advanced Research on Logic and Sensibility (CARLS), Keio University, 2-15-45 Mita, Minato-ku, Tokyo 108-8345, Japan.
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Reading and language disorders: the importance of both quantity and quality. Genes (Basel) 2014; 5:285-309. [PMID: 24705331 PMCID: PMC4094934 DOI: 10.3390/genes5020285] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 03/11/2014] [Accepted: 03/12/2014] [Indexed: 01/25/2023] Open
Abstract
Reading and language disorders are common childhood conditions that often co-occur with each other and with other neurodevelopmental impairments. There is strong evidence that disorders, such as dyslexia and Specific Language Impairment (SLI), have a genetic basis, but we expect the contributing genetic factors to be complex in nature. To date, only a few genes have been implicated in these traits. Their functional characterization has provided novel insight into the biology of neurodevelopmental disorders. However, the lack of biological markers and clear diagnostic criteria have prevented the collection of the large sample sizes required for well-powered genome-wide screens. One of the main challenges of the field will be to combine careful clinical assessment with high throughput genetic technologies within multidisciplinary collaborations.
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Nudel R, Simpson NH, Baird G, O'Hare A, Conti-Ramsden G, Bolton PF, Hennessy ER, Ring SM, Davey Smith G, Francks C, Paracchini S, Monaco AP, Fisher SE, Newbury DF. Genome-wide association analyses of child genotype effects and parent-of-origin effects in specific language impairment. GENES BRAIN AND BEHAVIOR 2014; 13:418-29. [PMID: 24571439 PMCID: PMC4114547 DOI: 10.1111/gbb.12127] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 01/30/2014] [Accepted: 02/22/2014] [Indexed: 12/19/2022]
Abstract
Specific language impairment (SLI) is a neurodevelopmental disorder that affects linguistic abilities when development is otherwise normal. We report the results of a genome-wide association study of SLI which included parent-of-origin effects and child genotype effects and used 278 families of language-impaired children. The child genotype effects analysis did not identify significant associations. We found genome-wide significant paternal parent-of-origin effects on chromosome 14q12 (P = 3.74 × 10−8) and suggestive maternal parent-of-origin effects on chromosome 5p13 (P = 1.16 × 10−7). A subsequent targeted association of six single-nucleotide-polymorphisms (SNPs) on chromosome 5 in 313 language-impaired individuals and their mothers from the ALSPAC cohort replicated the maternal effects, albeit in the opposite direction (P = 0.001); as fathers’ genotypes were not available in the ALSPAC study, the replication analysis did not include paternal parent-of-origin effects. The paternally-associated SNP on chromosome 14 yields a non-synonymous coding change within the NOP9 gene. This gene encodes an RNA-binding protein that has been reported to be significantly dysregulated in individuals with schizophrenia. The region of maternal association on chromosome 5 falls between the PTGER4 and DAB2 genes, in a region previously implicated in autism and ADHD. The top SNP in this association locus is a potential expression QTL of ARHGEF19 (also called WGEF) on chromosome 1. Members of this protein family have been implicated in intellectual disability. In summary, this study implicates parent-of-origin effects in language impairment, and adds an interesting new dimension to the emerging picture of shared genetic etiology across various neurodevelopmental disorders.
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Affiliation(s)
- R Nudel
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
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Harlaar N, Meaburn EL, Hayiou-Thomas ME, Davis OSP, Docherty S, Hanscombe KB, Haworth CMA, Price TS, Trzaskowski M, Dale PS, Plomin R. Genome-wide association study of receptive language ability of 12-year-olds. JOURNAL OF SPEECH, LANGUAGE, AND HEARING RESEARCH : JSLHR 2014; 57:96-105. [PMID: 24687471 PMCID: PMC3974169 DOI: 10.1044/1092-4388(2013/12-0303)] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
PURPOSE Researchers have previously shown that individual differences in measures of receptive language ability at age 12 are highly heritable. In the current study, the authors attempted to identify some of the genes responsible for the heritability of receptive language ability using a genome-wide association approach. METHOD The authors administered 4 Internet-based measures of receptive language (vocabulary, semantics, syntax, and pragmatics) to a sample of 2,329 twelve-year-olds for whom DNA and genome-wide genotyping were available. Nearly 700,000 single-nucleotide polymorphisms (SNPs) and 1 million imputed SNPs were included in a genome-wide association analysis of receptive language composite scores. RESULTS No SNP associations met the demanding criterion of genome-wide significance that corrects for multiple testing across the genome ( p < 5 × 10 -8). The strongest SNP association did not replicate in an additional sample of 2,639 twelve-year-olds. CONCLUSIONS These results indicate that individual differences in receptive language ability in the general population do not reflect common genetic variants that account for more than 3% of the phenotypic variance. The search for genetic variants associated with language skill will require larger samples and additional methods to identify and functionally characterize the full spectrum of risk variants.
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Epigenetic analysis of neurocognitive development at 1 year of age in a community-based pregnancy cohort. Behav Genet 2014; 44:113-25. [PMID: 24452678 DOI: 10.1007/s10519-014-9641-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 01/09/2014] [Indexed: 10/25/2022]
Abstract
Multiple studies show that molecular genetic changes and epigenetic modifications affect the risk of cognitive disability or impairment. However, the role of epigenetic variation in cognitive development of neurotypical young children remains largely unknown. Using data from a prospective, community-based study of mother-infant pairs, we investigated the association of DNA methylation patterns in neonatal umbilical cord blood with cognitive and language development at 1 year of age. No CpG loci achieved genome-wide significance, although a small number of weakly suggestive associations with Bayley-III Receptive Communication scales were noted. While umbilical cord blood is a convenient resource for genetic analyses of birth outcomes, our results do not provide conclusive evidence that its use for DNA methylation profiling yields epigenetic markers that are directly related to postnatal neurocognitive outcomes at 1 year of age.
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47
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Nudel R, Simpson NH, Baird G, O'Hare A, Conti-Ramsden G, Bolton PF, Hennessy ER, Monaco AP, Knight JC, Winney B, Fisher SE, Newbury DF. Associations of HLA alleles with specific language impairment. J Neurodev Disord 2014; 6:1. [PMID: 24433325 PMCID: PMC3906746 DOI: 10.1186/1866-1955-6-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 01/02/2014] [Indexed: 01/28/2023] Open
Abstract
Background Human leukocyte antigen (HLA) loci have been implicated in several neurodevelopmental disorders in which language is affected. However, to date, no studies have investigated the possible involvement of HLA loci in specific language impairment (SLI), a disorder that is defined primarily upon unexpected language impairment. We report association analyses of single-nucleotide polymorphisms (SNPs) and HLA types in a cohort of individuals affected by language impairment. Methods We perform quantitative association analyses of three linguistic measures and case-control association analyses using both SNP data and imputed HLA types. Results Quantitative association analyses of imputed HLA types suggested a role for the HLA-A locus in susceptibility to SLI. HLA-A A1 was associated with a measure of short-term memory (P = 0.004) and A3 with expressive language ability (P = 0.006). Parent-of-origin effects were found between HLA-B B8 and HLA-DQA1*0501 and receptive language. These alleles have a negative correlation with receptive language ability when inherited from the mother (P = 0.021, P = 0.034, respectively) but are positively correlated with the same trait when paternally inherited (P = 0.013, P = 0.029, respectively). Finally, case control analyses using imputed HLA types indicated that the DR10 allele of HLA-DRB1 was more frequent in individuals with SLI than population controls (P = 0.004, relative risk = 2.575), as has been reported for individuals with attention deficit hyperactivity disorder (ADHD). Conclusion These preliminary data provide an intriguing link to those described by previous studies of other neurodevelopmental disorders and suggest a possible role for HLA loci in language disorders.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Dianne F Newbury
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
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48
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Eicher JD, Powers NR, Miller LL, Akshoomoff N, Amaral DG, Bloss CS, Libiger O, Schork NJ, Darst BF, Casey BJ, Chang L, Ernst T, Frazier J, Kaufmann WE, Keating B, Kenet T, Kennedy D, Mostofsky S, Murray SS, Sowell ER, Bartsch H, Kuperman JM, Brown TT, Hagler DJ, Dale AM, Jernigan TL, St Pourcain B, Davey Smith G, Ring SM, Gruen JR. Genome-wide association study of shared components of reading disability and language impairment. GENES, BRAIN, AND BEHAVIOR 2013; 12:792-801. [PMID: 24024963 PMCID: PMC3904347 DOI: 10.1111/gbb.12085] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 08/16/2013] [Accepted: 09/09/2013] [Indexed: 11/29/2022]
Abstract
Written and verbal languages are neurobehavioral traits vital to the development of communication skills. Unfortunately, disorders involving these traits-specifically reading disability (RD) and language impairment (LI)-are common and prevent affected individuals from developing adequate communication skills, leaving them at risk for adverse academic, socioeconomic and psychiatric outcomes. Both RD and LI are complex traits that frequently co-occur, leading us to hypothesize that these disorders share genetic etiologies. To test this, we performed a genome-wide association study on individuals affected with both RD and LI in the Avon Longitudinal Study of Parents and Children. The strongest associations were seen with markers in ZNF385D (OR = 1.81, P = 5.45 × 10(-7) ) and COL4A2 (OR = 1.71, P = 7.59 × 10(-7) ). Markers within NDST4 showed the strongest associations with LI individually (OR = 1.827, P = 1.40 × 10(-7) ). We replicated association of ZNF385D using receptive vocabulary measures in the Pediatric Imaging Neurocognitive Genetics study (P = 0.00245). We then used diffusion tensor imaging fiber tract volume data on 16 fiber tracts to examine the implications of replicated markers. ZNF385D was a predictor of overall fiber tract volumes in both hemispheres, as well as global brain volume. Here, we present evidence for ZNF385D as a candidate gene for RD and LI. The implication of transcription factor ZNF385D in RD and LI underscores the importance of transcriptional regulation in the development of higher order neurocognitive traits. Further study is necessary to discern target genes of ZNF385D and how it functions within neural development of fluent language.
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Affiliation(s)
- J D Eicher
- Department of Genetics, Yale UniversityNew Haven, CT, USA
| | - N R Powers
- Department of Genetics, Yale UniversityNew Haven, CT, USA
| | - L L Miller
- MRC Integrative Epidemiology Unit (IEU), School of Social and Community Medicine, University of BristolBristol, UK
| | - N Akshoomoff
- Center for Human Development, University of California at San DiegoLa Jolla, CA, USA
- Department of Psychiatry, University of California at San DiegoLa Jolla, CA, USA
| | - D G Amaral
- Department of Psychiatry and Behavioral Sciences, University of CaliforniaDavis, CA, USA
| | - C S Bloss
- Scripps Genomic Medicine, Scripps Translational Science Institute and Scripps HealthLa Jolla, CA, USA
| | - O Libiger
- Scripps Genomic Medicine, Scripps Translational Science Institute and Scripps HealthLa Jolla, CA, USA
| | - N J Schork
- Scripps Genomic Medicine, Scripps Translational Science Institute and Scripps HealthLa Jolla, CA, USA
| | - B F Darst
- Scripps Genomic Medicine, Scripps Translational Science Institute and Scripps HealthLa Jolla, CA, USA
| | - B J Casey
- Sackler Institute for Developmental Psychobiology, Weil Cornell Medical CollegeNew York, NY, USA
| | - L Chang
- Department of Medicine, University of Hawaii and Queen's Medical CenterHonolulu, HI, USA
| | - T Ernst
- Department of Medicine, University of Hawaii and Queen's Medical CenterHonolulu, HI, USA
| | - J Frazier
- Department of Psychiatry, University of Massachusetts Medical SchoolBoston, MA, USA
| | - W E Kaufmann
- Kennedy Krieger InstituteBaltimore, MD, USA
- Department of Neurology, Children's Hospital Boston, Harvard Medical SchoolBoston, MA, USA
| | - B Keating
- Department of Medicine, University of Hawaii and Queen's Medical CenterHonolulu, HI, USA
| | - T Kenet
- Department of Neurology and Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General HospitalCharlestown, MA, USA
| | - D Kennedy
- Department of Psychiatry, University of Massachusetts Medical SchoolBoston, MA, USA
| | | | - S S Murray
- Scripps Genomic Medicine, Scripps Translational Science Institute and Scripps HealthLa Jolla, CA, USA
| | - E R Sowell
- Department of Pediatrics, University of Southern CaliforniaLos Angeles, CA, USA
- Developmental Cognitive Neuroimaging Laboratory, Children's HospitalLos Angeles, CA, USA
| | - H Bartsch
- Multimodal Imaging Laboratory, University of California at San DiegoLa Jolla, CA, USA
| | - J M Kuperman
- Multimodal Imaging Laboratory, University of California at San DiegoLa Jolla, CA, USA
- Department of Neurosciences, University of California at San DiegoLa Jolla, CA, USA
| | - T T Brown
- Center for Human Development, University of California at San DiegoLa Jolla, CA, USA
- Multimodal Imaging Laboratory, University of California at San DiegoLa Jolla, CA, USA
- Department of Neurosciences, University of California at San DiegoLa Jolla, CA, USA
| | - D J Hagler
- Multimodal Imaging Laboratory, University of California at San DiegoLa Jolla, CA, USA
- Department of Radiology, University of California at San DiegoLa Jolla, CA, USA
| | - A M Dale
- Department of Psychiatry, University of California at San DiegoLa Jolla, CA, USA
- Multimodal Imaging Laboratory, University of California at San DiegoLa Jolla, CA, USA
- Department of Neurosciences, University of California at San DiegoLa Jolla, CA, USA
- Department of Radiology, University of California at San DiegoLa Jolla, CA, USA
- Department of Cognitive Science, University of California at San DiegoLa Jolla, CA, USA
| | - T L Jernigan
- Center for Human Development, University of California at San DiegoLa Jolla, CA, USA
- Department of Psychiatry, University of California at San DiegoLa Jolla, CA, USA
- Department of Radiology, University of California at San DiegoLa Jolla, CA, USA
- Department of Cognitive Science, University of California at San DiegoLa Jolla, CA, USA
| | - B St Pourcain
- MRC Integrative Epidemiology Unit (IEU), School of Social and Community Medicine, University of BristolBristol, UK
- School of Oral and Dental Sciences, University of BristolBristol, UK
- School of Experimental Psychology, University of BristolBristol, UK
| | - G Davey Smith
- MRC Integrative Epidemiology Unit (IEU), School of Social and Community Medicine, University of BristolBristol, UK
| | - S M Ring
- MRC Integrative Epidemiology Unit (IEU), School of Social and Community Medicine, University of BristolBristol, UK
| | - J R Gruen
- Department of Genetics, Yale UniversityNew Haven, CT, USA
- Departments of Pediatrics and Investigative Medicine, Yale University School of MedicineNew Haven, CT, USA
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Carrion-Castillo A, Franke B, Fisher SE. Molecular genetics of dyslexia: an overview. DYSLEXIA (CHICHESTER, ENGLAND) 2013; 19:214-240. [PMID: 24133036 DOI: 10.1002/dys.1464] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 09/02/2013] [Indexed: 05/28/2023]
Abstract
Dyslexia is a highly heritable learning disorder with a complex underlying genetic architecture. Over the past decade, researchers have pinpointed a number of candidate genes that may contribute to dyslexia susceptibility. Here, we provide an overview of the state of the art, describing how studies have moved from mapping potential risk loci, through identification of associated gene variants, to characterization of gene function in cellular and animal model systems. Work thus far has highlighted some intriguing mechanistic pathways, such as neuronal migration, axon guidance, and ciliary biology, but it is clear that we still have much to learn about the molecular networks that are involved. We end the review by highlighting the past, present, and future contributions of the Dutch Dyslexia Programme to studies of genetic factors. In particular, we emphasize the importance of relating genetic information to intermediate neurobiological measures, as well as the value of incorporating longitudinal and developmental data into molecular designs.
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Affiliation(s)
- Amaia Carrion-Castillo
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
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50
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Nudel R, Newbury DF. FOXP2. WILEY INTERDISCIPLINARY REVIEWS. COGNITIVE SCIENCE 2013; 4:547-560. [PMID: 24765219 PMCID: PMC3992897 DOI: 10.1002/wcs.1247] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Revised: 06/04/2013] [Accepted: 07/06/2013] [Indexed: 11/30/2022]
Abstract
The forkhead box P2 gene, designated FOXP2, is the first gene implicated in a speech and language disorder. Since its discovery, many studies have been carried out in an attempt to explain the mechanism by which it influences these characteristically human traits. This review presents the story of the discovery of the FOXP2 gene, including early studies of the phenotypic implications of a disruption in the gene. We then discuss recent investigations into the molecular function of the FOXP2 gene, including functional and gene expression studies. We conclude this review by presenting the fascinating results of recent studies of the FOXP2 ortholog in other species that are capable of vocal communication. WIREs Cogn Sci 2013, 4:547–560. doi: 10.1002/wcs.1247
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Affiliation(s)
- Ron Nudel
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Dianne F Newbury
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
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