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Lal D, May P, Perez-Palma E, Samocha KE, Kosmicki JA, Robinson EB, Møller RS, Krause R, Nürnberg P, Weckhuysen S, De Jonghe P, Guerrini R, Niestroj LM, Du J, Marini C, Ware JS, Kurki M, Gormley P, Tang S, Wu S, Biskup S, Poduri A, Neubauer BA, Koeleman BPC, Helbig KL, Weber YG, Helbig I, Majithia AR, Palotie A, Daly MJ. Gene family information facilitates variant interpretation and identification of disease-associated genes in neurodevelopmental disorders. Genome Med 2020; 12:28. [PMID: 32183904 PMCID: PMC7079346 DOI: 10.1186/s13073-020-00725-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 02/21/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Classifying pathogenicity of missense variants represents a major challenge in clinical practice during the diagnoses of rare and genetic heterogeneous neurodevelopmental disorders (NDDs). While orthologous gene conservation is commonly employed in variant annotation, approximately 80% of known disease-associated genes belong to gene families. The use of gene family information for disease gene discovery and variant interpretation has not yet been investigated on a genome-wide scale. We empirically evaluate whether paralog-conserved or non-conserved sites in human gene families are important in NDDs. METHODS Gene family information was collected from Ensembl. Paralog-conserved sites were defined based on paralog sequence alignments; 10,068 NDD patients and 2078 controls were statistically evaluated for de novo variant burden in gene families. RESULTS We demonstrate that disease-associated missense variants are enriched at paralog-conserved sites across all disease groups and inheritance models tested. We developed a gene family de novo enrichment framework that identified 43 exome-wide enriched gene families including 98 de novo variant carrying genes in NDD patients of which 28 represent novel candidate genes for NDD which are brain expressed and under evolutionary constraint. CONCLUSION This study represents the first method to incorporate gene family information into a statistical framework to interpret variant data for NDDs and to discover new NDD-associated genes.
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Affiliation(s)
- Dennis Lal
- Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA.
- Stanley Center for Psychiatric Research, The Broad Institute of Harvard and M.I.T, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, USA.
- Cologne Center for Genomics, University of Cologne, Cologne, Germany.
- Genomic Medicine Institute, Lerner Research Institute Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH, 44195, USA.
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6, Avenue du Swing, 4367, Belvaux, Luxembourg.
| | - Eduardo Perez-Palma
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Genomic Medicine Institute, Lerner Research Institute Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH, 44195, USA
| | - Kaitlin E Samocha
- Stanley Center for Psychiatric Research, The Broad Institute of Harvard and M.I.T, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, USA
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Jack A Kosmicki
- Stanley Center for Psychiatric Research, The Broad Institute of Harvard and M.I.T, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, USA
| | - Elise B Robinson
- Stanley Center for Psychiatric Research, The Broad Institute of Harvard and M.I.T, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Rikke S Møller
- The Danish Epilepsy Centre, Dianalund, Denmark
- Institute for Regional Health research, University of Southern Denmark, Odense, Denmark
| | - Roland Krause
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6, Avenue du Swing, 4367, Belvaux, Luxembourg
| | - Peter Nürnberg
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Sarah Weckhuysen
- Division of Neurology, Antwerp University Hospital, Antwerp, Belgium
- Neurogenetics Group, Center for Molecular Neurology, VIB, Antwerp, Belgium
- Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Peter De Jonghe
- Division of Neurology, Antwerp University Hospital, Antwerp, Belgium
| | - Renzo Guerrini
- Pediatric Neurology and Neuroscience Department, Children's Hospital Anna Meyer, University of Florence, Florence, Italy
| | - Lisa M Niestroj
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Juliana Du
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Carla Marini
- Pediatric Neurology and Neuroscience Department, Children's Hospital Anna Meyer, University of Florence, Florence, Italy
| | - James S Ware
- National Heart & Lung Institute and MRC London Institute of Medical Science, Imperial College London, London, UK
| | - Mitja Kurki
- Stanley Center for Psychiatric Research, The Broad Institute of Harvard and M.I.T, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, USA
| | - Padhraig Gormley
- Stanley Center for Psychiatric Research, The Broad Institute of Harvard and M.I.T, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, USA
| | - Sha Tang
- Division of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, USA
| | - Sitao Wu
- Division of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, USA
| | - Saskia Biskup
- CeGat and Practice for Human Genetics, Tübingen, Germany
| | - Annapurna Poduri
- Epilepsy Genetics Program, Boston Children's Hospital, Boston, MA, USA
| | - Bernd A Neubauer
- Department of Neuropediatrics UKGM, University of Giessen, Giessen, Germany
| | - Bobby P C Koeleman
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Katherine L Helbig
- Division of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, USA
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Yvonne G Weber
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- Department of Epileptology and Neurology, University of Aachen, Aachen, Germany
| | - Ingo Helbig
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Neurology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Amit R Majithia
- Division of Endocrinology, Department of Medicine, University of California, San Diego, CA, USA
| | - Aarno Palotie
- Stanley Center for Psychiatric Research, The Broad Institute of Harvard and M.I.T, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, USA
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Mark J Daly
- Stanley Center for Psychiatric Research, The Broad Institute of Harvard and M.I.T, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, USA.
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland.
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