Systematic Phenomics Analysis Deconvolutes Genes Mutated in Intellectual Disability into Biologically Coherent Modules
Intellectual disability (ID) disorders are genetically and phenotypically extremely heterogeneous. Can this complexity be depicted in a comprehensive way as a means of facilitating the understanding of ID disorders and their underlying biology? We provide a curated database of 746 currently known ge...
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| Published in | American journal of human genetics Vol. 98; no. 1; pp. 149 - 164 |
|---|---|
| Main Authors | , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
Elsevier Inc
07.01.2016
Cell Press Elsevier |
| Subjects | |
| Online Access | Get full text |
| ISSN | 0002-9297 1537-6605 1537-6605 |
| DOI | 10.1016/j.ajhg.2015.11.024 |
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| Abstract | Intellectual disability (ID) disorders are genetically and phenotypically extremely heterogeneous. Can this complexity be depicted in a comprehensive way as a means of facilitating the understanding of ID disorders and their underlying biology? We provide a curated database of 746 currently known genes, mutations in which cause ID (ID-associated genes [ID-AGs]), classified according to ID manifestation and associated clinical features. Using this integrated resource, we show that ID-AGs are substantially enriched with co-expression, protein-protein interactions, and specific biological functions. Systematic identification of highly enriched functional themes and phenotypes revealed typical phenotype combinations characterizing process-defined groups of ID disorders, such as chromatin-related disorders and deficiencies in DNA repair. Strikingly, phenotype classification efficiently breaks down ID-AGs into subsets with significantly elevated biological coherence and predictive power. Custom-made functional Drosophila datasets revealed further characteristic phenotypes among ID-AGs and specific clinical classes. Our study and resource provide systematic insights into the molecular and clinical landscape of ID disorders, represent a significant step toward overcoming current limitations in ID research, and prove the utility of systematic human and cross-species phenomics analyses in highly heterogeneous genetic disorders. |
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| AbstractList | Intellectual disability (ID) disorders are genetically and phenotypically extremely heterogeneous. Can this complexity be depicted in a comprehensive way as a means of facilitating the understanding of ID disorders and their underlying biology? We provide a curated database of 746 currently known genes, mutations in which cause ID (ID-associated genes [ID-AGs]), classified according to ID manifestation and associated clinical features. Using this integrated resource, we show that ID-AGs are substantially enriched with co-expression, protein-protein interactions, and specific biological functions. Systematic identification of highly enriched functional themes and phenotypes revealed typical phenotype combinations characterizing process-defined groups of ID disorders, such as chromatin-related disorders and deficiencies in DNA repair. Strikingly, phenotype classification efficiently breaks down ID-AGs into subsets with significantly elevated biological coherence and predictive power. Custom-made functional Drosophila datasets revealed further characteristic phenotypes among ID-AGs and specific clinical classes. Our study and resource provide systematic insights into the molecular and clinical landscape of ID disorders, represent a significant step toward overcoming current limitations in ID research, and prove the utility of systematic human and cross-species phenomics analyses in highly heterogeneous genetic disorders.Intellectual disability (ID) disorders are genetically and phenotypically extremely heterogeneous. Can this complexity be depicted in a comprehensive way as a means of facilitating the understanding of ID disorders and their underlying biology? We provide a curated database of 746 currently known genes, mutations in which cause ID (ID-associated genes [ID-AGs]), classified according to ID manifestation and associated clinical features. Using this integrated resource, we show that ID-AGs are substantially enriched with co-expression, protein-protein interactions, and specific biological functions. Systematic identification of highly enriched functional themes and phenotypes revealed typical phenotype combinations characterizing process-defined groups of ID disorders, such as chromatin-related disorders and deficiencies in DNA repair. Strikingly, phenotype classification efficiently breaks down ID-AGs into subsets with significantly elevated biological coherence and predictive power. Custom-made functional Drosophila datasets revealed further characteristic phenotypes among ID-AGs and specific clinical classes. Our study and resource provide systematic insights into the molecular and clinical landscape of ID disorders, represent a significant step toward overcoming current limitations in ID research, and prove the utility of systematic human and cross-species phenomics analyses in highly heterogeneous genetic disorders. Intellectual disability (ID) disorders are genetically and phenotypically extremely heterogeneous. Can this complexity be depicted in a comprehensive way as a means of facilitating the understanding of ID disorders and their underlying biology? We provide a curated database of 746 currently known genes, mutations in which cause ID (ID-associated genes [ID-AGs]), classified according to ID manifestation and associated clinical features. Using this integrated resource, we show that ID-AGs are substantially enriched with co-expression, protein-protein interactions, and specific biological functions. Systematic identification of highly enriched functional themes and phenotypes revealed typical phenotype combinations characterizing process-defined groups of ID disorders, such as chromatin-related disorders and deficiencies in DNA repair. Strikingly, phenotype classification efficiently breaks down ID-AGs into subsets with significantly elevated biological coherence and predictive power. Custom-made functional Drosophila datasets revealed further characteristic phenotypes among ID-AGs and specific clinical classes. Our study and resource provide systematic insights into the molecular and clinical landscape of ID disorders, represent a significant step toward overcoming current limitations in ID research, and prove the utility of systematic human and cross-species phenomics analyses in highly heterogeneous genetic disorders. |
| Author | Zweier, Christiane Nijhof, Bonnie Webber, Caleb Kramer, Jamie M. Honti, Frank Huynen, Martijn A. Kochinke, Korinna Cizek, Pavel Oortveld, Merel A.W. Keerthikumar, Shivakumar Fenckova, Michaela Schenck, Annette Kleefstra, Tjitske |
| AuthorAffiliation | 1 Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, 6525 GA Nijmegen, the Netherlands 2 Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany 4 Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3QX, UK 3 Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud university medical center, 6525 GA Nijmegen, the Netherlands |
| AuthorAffiliation_xml | – name: 2 Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany – name: 1 Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, 6525 GA Nijmegen, the Netherlands – name: 4 Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3QX, UK – name: 3 Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud university medical center, 6525 GA Nijmegen, the Netherlands |
| Author_xml | – sequence: 1 givenname: Korinna surname: Kochinke fullname: Kochinke, Korinna organization: Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, 6525 GA Nijmegen, the Netherlands – sequence: 2 givenname: Christiane surname: Zweier fullname: Zweier, Christiane organization: Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany – sequence: 3 givenname: Bonnie surname: Nijhof fullname: Nijhof, Bonnie organization: Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, 6525 GA Nijmegen, the Netherlands – sequence: 4 givenname: Michaela surname: Fenckova fullname: Fenckova, Michaela organization: Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, 6525 GA Nijmegen, the Netherlands – sequence: 5 givenname: Pavel surname: Cizek fullname: Cizek, Pavel organization: Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud university medical center, 6525 GA Nijmegen, the Netherlands – sequence: 6 givenname: Frank surname: Honti fullname: Honti, Frank organization: Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3QX, UK – sequence: 7 givenname: Shivakumar surname: Keerthikumar fullname: Keerthikumar, Shivakumar organization: Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud university medical center, 6525 GA Nijmegen, the Netherlands – sequence: 8 givenname: Merel A.W. surname: Oortveld fullname: Oortveld, Merel A.W. organization: Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, 6525 GA Nijmegen, the Netherlands – sequence: 9 givenname: Tjitske surname: Kleefstra fullname: Kleefstra, Tjitske organization: Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, 6525 GA Nijmegen, the Netherlands – sequence: 10 givenname: Jamie M. surname: Kramer fullname: Kramer, Jamie M. organization: Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, 6525 GA Nijmegen, the Netherlands – sequence: 11 givenname: Caleb surname: Webber fullname: Webber, Caleb organization: Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3QX, UK – sequence: 12 givenname: Martijn A. surname: Huynen fullname: Huynen, Martijn A. email: martijn.huijnen@radboudumc.nl organization: Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud university medical center, 6525 GA Nijmegen, the Netherlands – sequence: 13 givenname: Annette surname: Schenck fullname: Schenck, Annette email: annette.schenck@radboudumc.nl organization: Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, 6525 GA Nijmegen, the Netherlands |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/26748517$$D View this record in MEDLINE/PubMed |
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| Copyright | 2016 The American Society of Human Genetics Copyright © 2016 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved. Copyright Cell Press Jan 7, 2016 2016 by The American Society of Human Genetics. All rights reserved. 2016 The American Society of Human Genetics |
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| Language | English |
| License | http://www.elsevier.com/open-access/userlicense/1.0 Copyright © 2016 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved. publisher-specific-oa |
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| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 Present address: Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON N6G 2M1, Canada These authors contributed equally to this work Present address: Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora VIC 3086, Australia |
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| SubjectTerms | Animals DNA repair Drosophila - genetics Genes Genetic disorders Genotype & phenotype Humans Intellectual Disability - genetics Learning disabilities Mutation Phenotype |
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