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Kopal J, Kumar K, Saltoun K, Modenato C, Moreau CA, Martin-Brevet S, Huguet G, Jean-Louis M, Martin CO, Saci Z, Younis N, Tamer P, Douard E, Maillard AM, Rodriguez-Herreros B, Pain A, Richetin S, Kushan L, Silva AI, van den Bree MBM, Linden DEJ, Owen MJ, Hall J, Lippé S, Draganski B, Sønderby IE, Andreassen OA, Glahn DC, Thompson PM, Bearden CE, Jacquemont S, Bzdok D. Rare CNVs and phenome-wide profiling highlight brain structural divergence and phenotypical convergence. Nat Hum Behav 2023; 7:1001-1017. [PMID: 36864136 PMCID: PMC7615290 DOI: 10.1038/s41562-023-01541-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 01/30/2023] [Indexed: 03/04/2023]
Abstract
Copy number variations (CNVs) are rare genomic deletions and duplications that can affect brain and behaviour. Previous reports of CNV pleiotropy imply that they converge on shared mechanisms at some level of pathway cascades, from genes to large-scale neural circuits to the phenome. However, existing studies have primarily examined single CNV loci in small clinical cohorts. It remains unknown, for example, how distinct CNVs escalate vulnerability for the same developmental and psychiatric disorders. Here we quantitatively dissect the associations between brain organization and behavioural differentiation across 8 key CNVs. In 534 CNV carriers, we explored CNV-specific brain morphology patterns. CNVs were characteristic of disparate morphological changes involving multiple large-scale networks. We extensively annotated these CNV-associated patterns with ~1,000 lifestyle indicators through the UK Biobank resource. The resulting phenotypic profiles largely overlap and have body-wide implications, including the cardiovascular, endocrine, skeletal and nervous systems. Our population-level investigation established brain structural divergences and phenotypical convergences of CNVs, with direct relevance to major brain disorders.
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Affiliation(s)
- Jakub Kopal
- Department of Biomedical Engineering, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
- Mila - Quebec Artificial Intelligence Institute, Montréal, Quebec, Canada
| | - Kuldeep Kumar
- Centre de recherche CHU Sainte-Justine and University of Montréal, Montréal, Quebec, Canada
| | - Karin Saltoun
- Department of Biomedical Engineering, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
- Mila - Quebec Artificial Intelligence Institute, Montréal, Quebec, Canada
| | - Claudia Modenato
- LREN - Department of Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
| | - Clara A Moreau
- Human Genetics and Cognitive Functions, CNRS UMR 3571: Genes, Synapses and Cognition, Institut Pasteur, Paris, France
| | - Sandra Martin-Brevet
- LREN - Department of Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
| | - Guillaume Huguet
- Centre de recherche CHU Sainte-Justine and University of Montréal, Montréal, Quebec, Canada
| | - Martineau Jean-Louis
- Centre de recherche CHU Sainte-Justine and University of Montréal, Montréal, Quebec, Canada
| | - Charles-Olivier Martin
- Centre de recherche CHU Sainte-Justine and University of Montréal, Montréal, Quebec, Canada
| | - Zohra Saci
- Centre de recherche CHU Sainte-Justine and University of Montréal, Montréal, Quebec, Canada
| | - Nadine Younis
- Centre de recherche CHU Sainte-Justine and University of Montréal, Montréal, Quebec, Canada
| | - Petra Tamer
- Centre de recherche CHU Sainte-Justine and University of Montréal, Montréal, Quebec, Canada
| | - Elise Douard
- Centre de recherche CHU Sainte-Justine and University of Montréal, Montréal, Quebec, Canada
| | - Anne M Maillard
- Service des Troubles du Spectre de l'Autisme et apparentés, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
| | - Borja Rodriguez-Herreros
- Service des Troubles du Spectre de l'Autisme et apparentés, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
| | - Aurèlie Pain
- Service des Troubles du Spectre de l'Autisme et apparentés, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
| | - Sonia Richetin
- Service des Troubles du Spectre de l'Autisme et apparentés, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
| | - Leila Kushan
- Semel Institute for Neuroscience and Human Behavior, Departments of Psychiatry and Biobehavioral Sciences and Psychology, UCLA, Los Angeles, CA, USA
| | - Ana I Silva
- School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Marianne B M van den Bree
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
- Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, UK
| | - David E J Linden
- School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
- Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, UK
| | - Michael J Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Jeremy Hall
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Sarah Lippé
- Centre de recherche CHU Sainte-Justine and University of Montréal, Montréal, Quebec, Canada
| | - Bogdan Draganski
- LREN - Department of Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
- Neurology Department, Max-Planck-Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Ida E Sønderby
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital and University of Oslo, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo, Oslo, Norway
| | - Ole A Andreassen
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital and University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo, Oslo, Norway
| | - David C Glahn
- Department of Psychiatry, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Paul M Thompson
- Imaging Genetics Center, Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Carrie E Bearden
- Semel Institute for Neuroscience and Human Behavior, Departments of Psychiatry and Biobehavioral Sciences and Psychology, UCLA, Los Angeles, CA, USA
| | - Sébastien Jacquemont
- Centre de recherche CHU Sainte-Justine and University of Montréal, Montréal, Quebec, Canada
| | - Danilo Bzdok
- Department of Biomedical Engineering, Faculty of Medicine, McGill University, Montreal, Quebec, Canada.
- Mila - Quebec Artificial Intelligence Institute, Montréal, Quebec, Canada.
- TheNeuro - Montreal Neurological Institute (MNI), McConnell Brain Imaging Centre, Faculty of Medicine, McGill University, Montreal, Quebec, Canada.
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2
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Mortillo M, Mulle JG. A cross-comparison of cognitive ability across 8 genomic disorders. Curr Opin Genet Dev 2021; 68:106-116. [PMID: 34082144 DOI: 10.1016/j.gde.2021.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/01/2021] [Accepted: 04/08/2021] [Indexed: 12/23/2022]
Abstract
Genomic disorders result from rearrangement of the human genome. Most genomic disorders are caused by copy number variants (CNV), deletions or duplications of several hundred kilobases. Many CNV loci are associated with autism, schizophrenia, and most commonly, intellectual disability (ID). However, there is little comparison of cognitive ability measures across these CNV disorders. This study aims to understand whether existing data can be leveraged for a cross-comparison of cognitive ability among multiple CNV. We found there is a lack of harmonization among assessment instruments and little standardization for reporting summary data across studies. Despite these limitations, we identified a differential impact of CNV loci on cognitive ability. Our data suggest that future cross-comparisons of CNV disorders will reveal meaningful differences across the phenotypic spectrum, especially if standardized phenotypic assessment is achieved.
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Affiliation(s)
- Michael Mortillo
- Department of Human Genetics, Emory University, Atlanta, GA, United States
| | - Jennifer G Mulle
- Department of Human Genetics, Emory University, Atlanta, GA, United States.
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3
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Harich B, van der Voet M, Klein M, Čížek P, Fenckova M, Schenck A, Franke B. From Rare Copy Number Variants to Biological Processes in ADHD. Am J Psychiatry 2020; 177:855-866. [PMID: 32600152 DOI: 10.1176/appi.ajp.2020.19090923] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
OBJECTIVE Attention deficit hyperactivity disorder (ADHD) is a highly heritable psychiatric disorder. The objective of this study was to define ADHD-associated candidate genes and their associated molecular modules and biological themes, based on the analysis of rare genetic variants. METHODS The authors combined data from 11 published copy number variation studies in 6,176 individuals with ADHD and 25,026 control subjects and prioritized genes by applying an integrative strategy based on criteria including recurrence in individuals with ADHD, absence in control subjects, complete coverage in copy number gains, and presence in the minimal region common to overlapping copy number variants (CNVs), as well as on protein-protein interactions and information from cross-species genotype-phenotype annotation. RESULTS The authors localized 2,241 eligible genes in the 1,532 reported CNVs, of which they classified 432 as high-priority ADHD candidate genes. The high-priority ADHD candidate genes were significantly coexpressed in the brain. A network of 66 genes was supported by ADHD-relevant phenotypes in the cross-species database. Four significantly interconnected protein modules were found among the high-priority ADHD genes. A total of 26 genes were observed across all applied bioinformatic methods. Lookup in the latest genome-wide association study for ADHD showed that among those 26 genes, POLR3C and RBFOX1 were also supported by common genetic variants. CONCLUSIONS Integration of a stringent filtering procedure in CNV studies with suitable bioinformatics approaches can identify ADHD candidate genes at increased levels of credibility. The authors' analytic pipeline provides additional insight into the molecular mechanisms underlying ADHD and allows prioritization of genes for functional validation in validated model organisms.
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Affiliation(s)
- Benjamin Harich
- Department of Human Genetics (Harich, van der Voet, Klein, Fenckova, Schenck, Franke) and Department of Psychiatry (Franke), Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands; and Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands (Čížek)
| | - Monique van der Voet
- Department of Human Genetics (Harich, van der Voet, Klein, Fenckova, Schenck, Franke) and Department of Psychiatry (Franke), Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands; and Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands (Čížek)
| | - Marieke Klein
- Department of Human Genetics (Harich, van der Voet, Klein, Fenckova, Schenck, Franke) and Department of Psychiatry (Franke), Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands; and Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands (Čížek)
| | - Pavel Čížek
- Department of Human Genetics (Harich, van der Voet, Klein, Fenckova, Schenck, Franke) and Department of Psychiatry (Franke), Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands; and Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands (Čížek)
| | - Michaela Fenckova
- Department of Human Genetics (Harich, van der Voet, Klein, Fenckova, Schenck, Franke) and Department of Psychiatry (Franke), Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands; and Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands (Čížek)
| | - Annette Schenck
- Department of Human Genetics (Harich, van der Voet, Klein, Fenckova, Schenck, Franke) and Department of Psychiatry (Franke), Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands; and Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands (Čížek)
| | - Barbara Franke
- Department of Human Genetics (Harich, van der Voet, Klein, Fenckova, Schenck, Franke) and Department of Psychiatry (Franke), Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands; and Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands (Čížek)
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4
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Wiśniowiecka-Kowalnik B, Nowakowska BA. Genetics and epigenetics of autism spectrum disorder-current evidence in the field. J Appl Genet 2019; 60:37-47. [PMID: 30627967 PMCID: PMC6373410 DOI: 10.1007/s13353-018-00480-w] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 12/14/2018] [Accepted: 12/18/2018] [Indexed: 12/26/2022]
Abstract
Autism spectrum disorders (ASD) is a heterogenous group of neurodevelopmental disorders characterized by problems in social interaction and communication as well as the presence of repetitive and stereotyped behavior. It is estimated that the prevalence of ASD is 1–2% in the general population with the average male to female ratio 4–5:1. Although the causes of ASD remain largely unknown, the studies have shown that both genetic and environmental factors play an important role in the etiology of these disorders. Array comparative genomic hybridization and whole exome/genome sequencing studies identified common and rare copy number or single nucleotide variants in genes encoding proteins involved in brain development, which play an important role in neuron and synapse formation and function. The genetic etiology is recognized in ~ 25–35% of patients with ASD. In this article, we review the current state of knowledge about the genetic etiology of ASD and also propose a diagnostic algorithm for patients.
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5
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García JC, Bustos RH. The Genetic Diagnosis of Neurodegenerative Diseases and Therapeutic Perspectives. Brain Sci 2018; 8:brainsci8120222. [PMID: 30551598 PMCID: PMC6316116 DOI: 10.3390/brainsci8120222] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/26/2018] [Accepted: 12/07/2018] [Indexed: 12/12/2022] Open
Abstract
Genetics has led to a new focus regarding approaches to the most prevalent diseases today. Ascertaining the molecular secrets of neurodegenerative diseases will lead to developing drugs that will change natural history, thereby affecting the quality of life and mortality of patients. The sequencing of candidate genes in patients suffering neurodegenerative pathologies is faster, more accurate, and has a lower cost, thereby enabling algorithms to be proposed regarding the risk of neurodegeneration onset in healthy persons including the year of onset and neurodegeneration severity. Next generation sequencing has resulted in an explosion of articles regarding the diagnosis of neurodegenerative diseases involving exome sequencing or sequencing a whole gene for correlating phenotypical expression with genetic mutations in proteins having key functions. Many of them occur in neuronal glia, which can trigger a proinflammatory effect leading to defective proteins causing sporadic or familial mutations. This article reviews the genetic diagnosis techniques and the importance of bioinformatics in interpreting results from neurodegenerative diseases. Risk scores must be established in the near future regarding diseases with a high incidence in healthy people for defining prevention strategies or an early start for giving drugs in the absence of symptoms.
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Affiliation(s)
- Julio-César García
- Evidence-Based Therapeutics Group, Department of Clinical Pharmacology, Universidad de La Sabana, Chía 140013, Colombia.
- Department of Clinical Pharmacology, Clínica Universidad de La Sabana, Chía 140013, Colombia.
| | - Rosa-Helena Bustos
- Evidence-Based Therapeutics Group, Department of Clinical Pharmacology, Universidad de La Sabana, Chía 140013, Colombia.
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6
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Ji J, Qin Y, Wang R, Huang Z, Zhang Y, Zhou R, Song L, Ling X, Hu Z, Miao D, Shen H, Xia Y, Wang X, Lu C. Copy number gain of VCX, X-linked multi-copy gene, leads to cell proliferation and apoptosis during spermatogenesis. Oncotarget 2018; 7:78532-78540. [PMID: 27705943 PMCID: PMC5340235 DOI: 10.18632/oncotarget.12397] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 09/25/2016] [Indexed: 11/25/2022] Open
Abstract
Male factor infertility affects one-sixth of couples worldwide, and non-obstructive azoospermia (NOA) is one of the most severe forms. In recent years there has been increasing evidence to implicate the participation of X chromosome in the process of spermatogenesis. To uncover the roles of X-linked multi-copy genes in spermatogenesis, we performed systematic analysis of X-linked gene copy number variations (CNVs) and Y chromosome haplogrouping in 447 idiopathic NOA patients and 485 healthy controls. Interestingly, the frequency of individuals with abnormal level copy of Variable charge, X-linked (VCX) was significantly different between cases and controls after multiple test correction (p = 5.10 × 10−5). To discriminate the effect of gain/loss copies in these genes, we analyzed the frequency of X-linked multi-copy genes in subjects among subdivided groups. Our results demonstrated that individuals with increased copy numbers of Nuclear RNA export factor 2 (NXF2) (p = 9.21 × 10−8) and VCX (p = 1.97 × 10−4) conferred the risk of NOA. In vitro analysis demonstrated that increasing copy number of VCX could upregulate the gene expression and regulate cell proliferation and apoptosis. Our study establishes a robust association between the VCX CNVs and NOA risk.
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Affiliation(s)
- Juan Ji
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China.,Department of Children Health Care, Nanjing Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Yufeng Qin
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Rong Wang
- Research Center for Bone and Stem Cells, Department of Anatomy, Histology, and Embryology, Nanjing Medical University, Nanjing, China
| | - Zhenyao Huang
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yan Zhang
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Ran Zhou
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Ling Song
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xiufeng Ling
- Department of Children Health Care, Nanjing Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Zhibin Hu
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China.,Department of Epidemiology and Biostatistics and Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Dengshun Miao
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China.,Research Center for Bone and Stem Cells, Department of Anatomy, Histology, and Embryology, Nanjing Medical University, Nanjing, China
| | - Hongbing Shen
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China.,Department of Epidemiology and Biostatistics and Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yankai Xia
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xinru Wang
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Chuncheng Lu
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
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7
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Epistasis in Neuropsychiatric Disorders. Trends Genet 2017; 33:256-265. [PMID: 28268034 DOI: 10.1016/j.tig.2017.01.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 01/25/2017] [Accepted: 01/27/2017] [Indexed: 12/12/2022]
Abstract
The contribution of epistasis to human disease remains unclear. However, several studies have now identified epistatic interactions between common variants that increase the risk of a neuropsychiatric disorder, while there is growing evidence that genetic interactions contribute to the pathogenicity of rare, multigenic copy-number variants (CNVs) that have been observed in patients. This review discusses the current evidence for epistatic events and genetic interactions in neuropsychiatric disorders, how paradigm shifts in the phenotypic classification of patients would empower the search for epistatic effects, and how network and cellular models might be employed to further elucidate relevant epistatic interactions.
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8
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Yeh E, Weiss LA. If genetic variation could talk: What genomic data may teach us about the importance of gene expression regulation in the genetics of autism. Mol Cell Probes 2016; 30:346-356. [PMID: 27751841 DOI: 10.1016/j.mcp.2016.10.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 10/09/2016] [Accepted: 10/13/2016] [Indexed: 11/25/2022]
Abstract
Autism spectrum disorder (ASD) has been long known to have substantial genetic etiology. Much research has attempted to identify specific genes contributing to ASD risk with the goal of tying gene function to a molecular pathological explanation for ASD. A unifying molecular pathology would potentially increase understanding of what is going wrong during development, and could lead to diagnostic biomarkers or targeted preventative or therapeutic directions. We review past and current genetic mapping approaches and discuss major results, leading to the hypothesis that global dysregulation of gene or protein expression may be implicated in ASD rather than disturbance of brain-specific functions. If substantiated, this hypothesis might indicate the need for novel experimental and analytical approaches in order to understand this neurodevelopmental disorder, develop biomarkers, or consider treatment approaches.
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Affiliation(s)
- Erika Yeh
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Lauren A Weiss
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, 94143, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, 94143, USA.
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9
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Bone WP, Washington NL, Buske OJ, Adams DR, Davis J, Draper D, Flynn ED, Girdea M, Godfrey R, Golas G, Groden C, Jacobsen J, Köhler S, Lee EMJ, Links AE, Markello TC, Mungall CJ, Nehrebecky M, Robinson PN, Sincan M, Soldatos AG, Tifft CJ, Toro C, Trang H, Valkanas E, Vasilevsky N, Wahl C, Wolfe LA, Boerkoel CF, Brudno M, Haendel MA, Gahl WA, Smedley D. Computational evaluation of exome sequence data using human and model organism phenotypes improves diagnostic efficiency. Genet Med 2016; 18:608-17. [PMID: 26562225 PMCID: PMC4916229 DOI: 10.1038/gim.2015.137] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Accepted: 08/27/2015] [Indexed: 01/18/2023] Open
Abstract
PURPOSE Medical diagnosis and molecular or biochemical confirmation typically rely on the knowledge of the clinician. Although this is very difficult in extremely rare diseases, we hypothesized that the recording of patient phenotypes in Human Phenotype Ontology (HPO) terms and computationally ranking putative disease-associated sequence variants improves diagnosis, particularly for patients with atypical clinical profiles. METHODS Using simulated exomes and the National Institutes of Health Undiagnosed Diseases Program (UDP) patient cohort and associated exome sequence, we tested our hypothesis using Exomiser. Exomiser ranks candidate variants based on patient phenotype similarity to (i) known disease-gene phenotypes, (ii) model organism phenotypes of candidate orthologs, and (iii) phenotypes of protein-protein association neighbors. RESULTS Benchmarking showed Exomiser ranked the causal variant as the top hit in 97% of known disease-gene associations and ranked the correct seeded variant in up to 87% when detectable disease-gene associations were unavailable. Using UDP data, Exomiser ranked the causative variant(s) within the top 10 variants for 11 previously diagnosed variants and achieved a diagnosis for 4 of 23 cases undiagnosed by clinical evaluation. CONCLUSION Structured phenotyping of patients and computational analysis are effective adjuncts for diagnosing patients with genetic disorders.Genet Med 18 6, 608-617.
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Affiliation(s)
- William P. Bone
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - Nicole L. Washington
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Orion J. Buske
- Centre for Computational Medicine Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - David R. Adams
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
- Medical Genetics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Joie Davis
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - David Draper
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - Elise D. Flynn
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - Marta Girdea
- Centre for Computational Medicine Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Rena Godfrey
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - Gretchen Golas
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - Catherine Groden
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - Julius Jacobsen
- Skarnes Faculty group, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Sebastian Köhler
- Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Elizabeth M. J. Lee
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - Amanda E. Links
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - Thomas C. Markello
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Michele Nehrebecky
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - Peter N. Robinson
- Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Murat Sincan
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - Ariane G. Soldatos
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - Cynthia J. Tifft
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
- Medical Genetics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Camilo Toro
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - Heather Trang
- Centre for Computational Medicine Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Elise Valkanas
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - Nicole Vasilevsky
- Library; and Department of Medical Informatics and Epidemiology, Oregon Health & Science University, Portland, Oregon, USA
| | - Colleen Wahl
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - Lynne A. Wolfe
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - Cornelius F. Boerkoel
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael Brudno
- Centre for Computational Medicine Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Melissa A. Haendel
- Library; and Department of Medical Informatics and Epidemiology, Oregon Health & Science University, Portland, Oregon, USA
| | - William A. Gahl
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
- Medical Genetics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Damian Smedley
- Skarnes Faculty group, Wellcome Trust Sanger Institute, Hinxton, UK
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10
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Preikšaitienė E, Ambrozaitytė L, Maldžienė Ž, Morkūnienė A, Cimbalistienė L, Rančelis T, Utkus A, Kučinskas V. Identification of genetic causes of congenital neurodevelopmental disorders using genome wide molecular technologies. Acta Med Litu 2016; 23:73-85. [PMID: 28356794 PMCID: PMC5088740 DOI: 10.6001/actamedica.v23i2.3324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Background. Intellectual disability affects about 1–2% of the general population worldwide, and this is the leading socio-economic problem of health care. The evaluation of the genetic causes of intellectual disability is challenging because these conditions are genetically heterogeneous with many different genetic alterations resulting in clinically indistinguishable phenotypes. Genome wide molecular technologies are effective in a research setting for establishing the new genetic basis of a disease. We describe the first Lithuanian experience in genome-wide CNV detection and whole exome sequencing, presenting the results obtained in the research project UNIGENE. Materials and methods. The patients with developmental delay/intellectual disability have been investigated (n = 66). Diagnostic screening was performed using array-CGH technology. FISH and real time-PCR were used for the confirmation of gene-dose imbalances and investigation of parental samples. Whole exome sequencing using the next generation high throughput NGS technique was used to sequence the samples of 12 selected families. Results. 14 out of 66 patients had pathogenic copy number variants, and one patient had novel likely pathogenic aberration (microdeletion at 4p15.2). Twelve families have been processed for whole exome sequencing. Two identified sequence variants could be classified as pathogenic (in MECP2, CREBBP genes). The other families had several candidate intellectual disability gene variants that are of unclear clinical significance and must be further investigated for possible effect on the molecular pathways of intellectual disability. Conclusions. The genetic heterogeneity of intellectual disability requires genome wide approaches, including detection of chromosomal aberrations by chromosomal microarrays and whole exome sequencing capable of uncovering single gene mutations. This study demonstrates the benefits and challenges that accompany the use of genome wide molecular technologies and provides genotype-phenotype information on 32 patients with chromosomal imbalances and ID candidate sequence variants.
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Affiliation(s)
- Eglė Preikšaitienė
- Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Laima Ambrozaitytė
- Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Živilė Maldžienė
- Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Aušra Morkūnienė
- Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Loreta Cimbalistienė
- Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Tautvydas Rančelis
- Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Algirdas Utkus
- Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
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11
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Prioritizing Clinically Relevant Copy Number Variation from Genetic Interactions and Gene Function Data. PLoS One 2015; 10:e0139656. [PMID: 26437450 PMCID: PMC4593641 DOI: 10.1371/journal.pone.0139656] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 09/16/2015] [Indexed: 11/19/2022] Open
Abstract
It is becoming increasingly necessary to develop computerized methods for identifying the few disease-causing variants from hundreds discovered in each individual patient. This problem is especially relevant for Copy Number Variants (CNVs), which can be cheaply interrogated via low-cost hybridization arrays commonly used in clinical practice. We present a method to predict the disease relevance of CNVs that combines functional context and clinical phenotype to discover clinically harmful CNVs (and likely causative genes) in patients with a variety of phenotypes. We compare several feature and gene weighing systems for classifying both genes and CNVs. We combined the best performing methodologies and parameters on over 2,500 Agilent CGH 180k Microarray CNVs derived from 140 patients. Our method achieved an F-score of 91.59%, with 87.08% precision and 97.00% recall. Our methods are freely available at https://github.com/compbio-UofT/cnv-prioritization. Our dataset is included with the supplementary information.
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12
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Smedley D, Robinson PN. Phenotype-driven strategies for exome prioritization of human Mendelian disease genes. Genome Med 2015; 7:81. [PMID: 26229552 PMCID: PMC4520011 DOI: 10.1186/s13073-015-0199-2] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Whole exome sequencing has altered the way in which rare diseases are diagnosed and disease genes identified. Hundreds of novel disease-associated genes have been characterized by whole exome sequencing in the past five years, yet the identification of disease-causing mutations is often challenging because of the large number of rare variants that are being revealed. Gene prioritization aims to rank the most probable candidate genes towards the top of a list of potentially pathogenic variants. A promising new approach involves the computational comparison of the phenotypic abnormalities of the individual being investigated with those previously associated with human diseases or genetically modified model organisms. In this review, we compare and contrast the strengths and weaknesses of current phenotype-driven computational algorithms, including Phevor, Phen-Gen, eXtasy and two algorithms developed by our groups called PhenIX and Exomiser. Computational phenotype analysis can substantially improve the performance of exome analysis pipelines.
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Affiliation(s)
- Damian Smedley
- />Skarnes Faculty Group, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Peter N. Robinson
- />Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
- />Max Planck Institute for Molecular Genetics, Ihnestrasse, 14195 Berlin, Germany
- />Berlin Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Augustenburger Platz, 13353 Berlin, Germany
- />Institute for Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, Takustrasse, 14195 Berlin, Germany
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13
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Haendel MA, Vasilevsky N, Brush M, Hochheiser HS, Jacobsen J, Oellrich A, Mungall CJ, Washington N, Köhler S, Lewis SE, Robinson PN, Smedley D. Disease insights through cross-species phenotype comparisons. Mamm Genome 2015; 26:548-55. [PMID: 26092691 PMCID: PMC4602072 DOI: 10.1007/s00335-015-9577-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 05/20/2015] [Indexed: 11/30/2022]
Abstract
New sequencing technologies have ushered in a new era for diagnosis and discovery of new causative mutations for rare diseases. However, the sheer numbers of candidate variants that require interpretation in an exome or genomic analysis are still a challenging prospect. A powerful approach is the comparison of the patient’s set of phenotypes (phenotypic profile) to known phenotypic profiles caused by mutations in orthologous genes associated with these variants. The most abundant source of relevant data for this task is available through the efforts of the Mouse Genome Informatics group and the International Mouse Phenotyping Consortium. In this review, we highlight the challenges in comparing human clinical phenotypes with mouse phenotypes and some of the solutions that have been developed by members of the Monarch Initiative. These tools allow the identification of mouse models for known disease-gene associations that may otherwise have been overlooked as well as candidate genes may be prioritized for novel associations. The culmination of these efforts is the Exomiser software package that allows clinical researchers to analyse patient exomes in the context of variant frequency and predicted pathogenicity as well the phenotypic similarity of the patient to any given candidate orthologous gene.
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Affiliation(s)
- Melissa A Haendel
- University Library and Department of Medical Informatics and Epidemiology, Oregon Health & Science University, Portland, OR, USA
| | - Nicole Vasilevsky
- University Library and Department of Medical Informatics and Epidemiology, Oregon Health & Science University, Portland, OR, USA
| | - Matthew Brush
- University Library and Department of Medical Informatics and Epidemiology, Oregon Health & Science University, Portland, OR, USA
| | - Harry S Hochheiser
- Department of Biomedical Informatics and Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA, 15206, USA
| | - Julius Jacobsen
- Skarnes Faculty Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Anika Oellrich
- Skarnes Faculty Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Christopher J Mungall
- Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Nicole Washington
- Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Sebastian Köhler
- Computational Biology Group, Institute for Medical Genetics and Human Genetics, Universitatsklinikum Charité, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Suzanna E Lewis
- Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Peter N Robinson
- Computational Biology Group, Institute for Medical Genetics and Human Genetics, Universitatsklinikum Charité, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Damian Smedley
- Skarnes Faculty Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
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14
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Groza T, Tudorache T, Robinson PN, Zankl A. Capturing domain knowledge from multiple sources: the rare bone disorders use case. J Biomed Semantics 2015; 6:21. [PMID: 25926964 PMCID: PMC4414390 DOI: 10.1186/s13326-015-0008-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 03/02/2015] [Indexed: 12/13/2022] Open
Abstract
Background Lately, ontologies have become a fundamental building block in the process of formalising and storing complex biomedical information. The community-driven ontology curation process, however, ignores the possibility of multiple communities building, in parallel, conceptualisations of the same domain, and thus providing slightly different perspectives on the same knowledge. The individual nature of this effort leads to the need of a mechanism to enable us to create an overarching and comprehensive overview of the different perspectives on the domain knowledge. Results We introduce an approach that enables the loose integration of knowledge emerging from diverse sources under a single coherent interoperable resource. To accurately track the original knowledge statements, we record the provenance at very granular levels. We exemplify the approach in the rare bone disorders domain by proposing the Rare Bone Disorders Ontology (RBDO). Using RBDO, researchers are able to answer queries, such as: “What phenotypes describe a particular disorder and are common to all sources?” or to understand similarities between disorders based on divergent groupings (classifications) provided by the underlying sources. Availability RBDO is available at http://purl.org/skeletome/rbdo. In order to support lightweight query and integration, the knowledge captured by RBDO has also been made available as a SPARQL Endpoint at http://bio-lark.org/se_skeldys.html.
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Affiliation(s)
- Tudor Groza
- School of ITEE, The University of Queensland, St Lucia, Australia
| | - Tania Tudorache
- Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, USA
| | - Peter N Robinson
- Institut für Medizinische Genetik und Humangenetik, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Andreas Zankl
- Children's Hospital, Westmead, The University of Sydney, Sydney, New South Wales Australia
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15
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The clustering of functionally related genes contributes to CNV-mediated disease. Genome Res 2015; 25:802-13. [PMID: 25887030 PMCID: PMC4448677 DOI: 10.1101/gr.184325.114] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 04/13/2015] [Indexed: 12/20/2022]
Abstract
Clusters of functionally related genes can be disrupted by a single copy number variant (CNV). We demonstrate that the simultaneous disruption of multiple functionally related genes is a frequent and significant characteristic of de novo CNVs in patients with developmental disorders (P = 1 × 10−3). Using three different functional networks, we identified unexpectedly large numbers of functionally related genes within de novo CNVs from two large independent cohorts of individuals with developmental disorders. The presence of multiple functionally related genes was a significant predictor of a CNV's pathogenicity when compared to CNVs from apparently healthy individuals and a better predictor than the presence of known disease or haploinsufficient genes for larger CNVs. The functionally related genes found in the de novo CNVs belonged to 70% of all clusters of functionally related genes found across the genome. De novo CNVs were more likely to affect functional clusters and affect them to a greater extent than benign CNVs (P = 6 × 10−4). Furthermore, such clusters of functionally related genes are phenotypically informative: Different patients possessing CNVs that affect the same cluster of functionally related genes exhibit more similar phenotypes than expected (P < 0.05). The spanning of multiple functionally similar genes by single CNVs contributes substantially to how these variants exert their pathogenic effects.
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16
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Andrews T, Meader S, Vulto-van Silfhout A, Taylor A, Steinberg J, Hehir-Kwa J, Pfundt R, de Leeuw N, de Vries BBA, Webber C. Gene networks underlying convergent and pleiotropic phenotypes in a large and systematically-phenotyped cohort with heterogeneous developmental disorders. PLoS Genet 2015; 11:e1005012. [PMID: 25781962 PMCID: PMC4362763 DOI: 10.1371/journal.pgen.1005012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 01/17/2015] [Indexed: 12/05/2022] Open
Abstract
Readily-accessible and standardised capture of genotypic variation has revolutionised our understanding of the genetic contribution to disease. Unfortunately, the corresponding systematic capture of patient phenotypic variation needed to fully interpret the impact of genetic variation has lagged far behind. Exploiting deep and systematic phenotyping of a cohort of 197 patients presenting with heterogeneous developmental disorders and whose genomes harbour de novo CNVs, we systematically applied a range of commonly-used functional genomics approaches to identify the underlying molecular perturbations and their phenotypic impact. Grouping patients into 408 non-exclusive patient-phenotype groups, we identified a functional association amongst the genes disrupted in 209 (51%) groups. We find evidence for a significant number of molecular interactions amongst the association-contributing genes, including a single highly-interconnected network disrupted in 20% of patients with intellectual disability, and show using microcephaly how these molecular networks can be used as baits to identify additional members whose genes are variant in other patients with the same phenotype. Exploiting the systematic phenotyping of this cohort, we observe phenotypic concordance amongst patients whose variant genes contribute to the same functional association but note that (i) this relationship shows significant variation across the different approaches used to infer a commonly perturbed molecular pathway, and (ii) that the phenotypic similarities detected amongst patients who share the same inferred pathway perturbation result from these patients sharing many distinct phenotypes, rather than sharing a more specific phenotype, inferring that these pathways are best characterized by their pleiotropic effects. Developmental disorders occur in ∼3% of live births, and exhibit a broad range of abnormalities including: intellectual disability, autism, heart defects, and other neurological and morphological problems. Often, patients are grouped into genetic syndromes which are defined by a specific set of mutations and a common set of abnormalities. However, many mutations are unique to a single patient and many patients present a range of abnormalities which do not fit one of the recognized genetic syndromes, making diagnosis difficult. Using a dataset of 197 patients with systematically described abnormalities, we identified molecular pathways whose disruption was associated with specific abnormalities among many patients. Importantly, patients with mutations in the same pathway often exhibited similar co-morbid symptoms and thus the commonly disrupted pathway appeared responsible for the broad range of shared abnormalities amongst these patients. These findings support the general concept that patients with mutations in distinct genes could be etiologically grouped together through the common pathway that these mutated genes participate in, with a view to improving diagnoses, prognoses and therapeutic outcomes.
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Affiliation(s)
- Tallulah Andrews
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Stephen Meader
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | | | - Avigail Taylor
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Julia Steinberg
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Jayne Hehir-Kwa
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Nicole de Leeuw
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Bert B. A. de Vries
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- * E-mail: (BBAdV); (CW)
| | - Caleb Webber
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
- * E-mail: (BBAdV); (CW)
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17
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Oellrich A, Walls RL, Cannon EKS, Cannon SB, Cooper L, Gardiner J, Gkoutos GV, Harper L, He M, Hoehndorf R, Jaiswal P, Kalberer SR, Lloyd JP, Meinke D, Menda N, Moore L, Nelson RT, Pujar A, Lawrence CJ, Huala E. An ontology approach to comparative phenomics in plants. PLANT METHODS 2015; 11:10. [PMID: 25774204 PMCID: PMC4359497 DOI: 10.1186/s13007-015-0053-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 02/05/2015] [Indexed: 05/29/2023]
Abstract
BACKGROUND Plant phenotype datasets include many different types of data, formats, and terms from specialized vocabularies. Because these datasets were designed for different audiences, they frequently contain language and details tailored to investigators with different research objectives and backgrounds. Although phenotype comparisons across datasets have long been possible on a small scale, comprehensive queries and analyses that span a broad set of reference species, research disciplines, and knowledge domains continue to be severely limited by the absence of a common semantic framework. RESULTS We developed a workflow to curate and standardize existing phenotype datasets for six plant species, encompassing both model species and crop plants with established genetic resources. Our effort focused on mutant phenotypes associated with genes of known sequence in Arabidopsis thaliana (L.) Heynh. (Arabidopsis), Zea mays L. subsp. mays (maize), Medicago truncatula Gaertn. (barrel medic or Medicago), Oryza sativa L. (rice), Glycine max (L.) Merr. (soybean), and Solanum lycopersicum L. (tomato). We applied the same ontologies, annotation standards, formats, and best practices across all six species, thereby ensuring that the shared dataset could be used for cross-species querying and semantic similarity analyses. Curated phenotypes were first converted into a common format using taxonomically broad ontologies such as the Plant Ontology, Gene Ontology, and Phenotype and Trait Ontology. We then compared ontology-based phenotypic descriptions with an existing classification system for plant phenotypes and evaluated our semantic similarity dataset for its ability to enhance predictions of gene families, protein functions, and shared metabolic pathways that underlie informative plant phenotypes. CONCLUSIONS The use of ontologies, annotation standards, shared formats, and best practices for cross-taxon phenotype data analyses represents a novel approach to plant phenomics that enhances the utility of model genetic organisms and can be readily applied to species with fewer genetic resources and less well-characterized genomes. In addition, these tools should enhance future efforts to explore the relationships among phenotypic similarity, gene function, and sequence similarity in plants, and to make genotype-to-phenotype predictions relevant to plant biology, crop improvement, and potentially even human health.
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Affiliation(s)
- Anika Oellrich
- />Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA UK
| | - Ramona L Walls
- />iPlant Collaborative, University of Arizona, 1657 E. Helen St., Tucson, Arizona 85721 USA
| | - Ethalinda KS Cannon
- />Department of Electrical and Computer Engineering Iowa State University, 1018 Crop Informatics Lab, Ames, Iowa 50011 USA
| | - Steven B Cannon
- />USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Crop Genome Informatics Lab, Iowa State University, Ames, IA 50011 USA
- />Department of Agronomy, Agronomy Hall, Iowa State University, Ames, IA 50010 USA
| | - Laurel Cooper
- />Department of Botany and Plant Pathology, 2082 Cordley Hall, Oregon State University, Corvallis, OR 97331 USA
| | - Jack Gardiner
- />Department of Genetics, Development and Cell Biology, Roy J Carver Co-Laboratory, Iowa State University, Ames, IA 50010 USA
| | - Georgios V Gkoutos
- />Department of Computer Science, Aberystwyth University, Llandinam Building, Aberystwyth, SY23 3DB UK
| | - Lisa Harper
- />USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Crop Genome Informatics Lab, Iowa State University, Ames, IA 50011 USA
| | - Mingze He
- />Department of Genetics, Development and Cell Biology, Roy J Carver Co-Laboratory, Iowa State University, Ames, IA 50010 USA
| | - Robert Hoehndorf
- />Computer, Electrical and Mathematical Sciences & Engineering Division and Computational Bioscience Research Center, King Abdullah University of Science and Technology, 4700 King Abdullah University of Science and Technology, P.O. Box 2882, Thuwal, 23955-6900 Kingdom of Saudi Arabia
| | - Pankaj Jaiswal
- />Department of Botany and Plant Pathology, 2082 Cordley Hall, Oregon State University, Corvallis, OR 97331 USA
| | - Scott R Kalberer
- />USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Crop Genome Informatics Lab, Iowa State University, Ames, IA 50011 USA
| | - John P Lloyd
- />Department of Plant Biology, Michigan State University, 220 Trowbridge Rd, East Lansing, MI 48824 USA
| | - David Meinke
- />Department of Botany, Oklahoma State University, 301 Physical Sciences, Stillwater, OK 74078 USA
| | - Naama Menda
- />Boyce Thompson Institute for Plant Research, 533 Tower Road, Ithaca, NY 14853 USA
| | - Laura Moore
- />Department of Botany and Plant Pathology, 2082 Cordley Hall, Oregon State University, Corvallis, OR 97331 USA
| | - Rex T Nelson
- />USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Crop Genome Informatics Lab, Iowa State University, Ames, IA 50011 USA
| | - Anuradha Pujar
- />Boyce Thompson Institute for Plant Research, 533 Tower Road, Ithaca, NY 14853 USA
| | - Carolyn J Lawrence
- />Department of Agronomy, Agronomy Hall, Iowa State University, Ames, IA 50010 USA
- />Department of Genetics, Development and Cell Biology, Roy J Carver Co-Laboratory, Iowa State University, Ames, IA 50010 USA
| | - Eva Huala
- />Phoenix Bioinformatics, 643 Bair Island Rd Suite 403, Redwood City, CA 94063 USA
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18
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Collier N, Oellrich A, Groza T. Toward knowledge support for analysis and interpretation of complex traits. Genome Biol 2015; 14:214. [PMID: 24079802 PMCID: PMC4053827 DOI: 10.1186/gb-2013-14-9-214] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The systematic description of complex traits, from the organism to the cellular level, is important for hypothesis generation about underlying disease mechanisms. We discuss how intelligent algorithms might provide support, leading to faster throughput.
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19
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Köhler S, Schoeneberg U, Czeschik JC, Doelken SC, Hehir-Kwa JY, Ibn-Salem J, Mungall CJ, Smedley D, Haendel MA, Robinson PN. Clinical interpretation of CNVs with cross-species phenotype data. J Med Genet 2014; 51:766-772. [PMID: 25280750 DOI: 10.1136/jmedgenet-2014-102633] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
BACKGROUND Clinical evaluation of CNVs identified via techniques such as array comparative genome hybridisation (aCGH) involves the inspection of lists of known and unknown duplications and deletions with the goal of distinguishing pathogenic from benign CNVs. A key step in this process is the comparison of the individual's phenotypic abnormalities with those associated with Mendelian disorders of the genes affected by the CNV. However, because often there is not much known about these human genes, an additional source of data that could be used is model organism phenotype data. Currently, almost 6000 genes in mouse and zebrafish are, when knocked out, associated with a phenotype in the model organism, but no disease is known to be caused by mutations in the human ortholog. Yet, searching model organism databases and comparing model organism phenotypes with patient phenotypes for identifying novel disease genes and medical evaluation of CNVs is hindered by the difficulty in integrating phenotype information across species and the lack of appropriate software tools. METHODS Here, we present an integrated ranking scheme based on phenotypic matching, degree of overlap with known benign or pathogenic CNVs and the haploinsufficiency score for the prioritisation of CNVs responsible for a patient's clinical findings. RESULTS We show that this scheme leads to significant improvements compared with rankings that do not exploit phenotypic information. We provide a software tool called PhenogramViz, which supports phenotype-driven interpretation of aCGH findings based on multiple data sources, including the integrated cross-species phenotype ontology Uberpheno, in order to visualise gene-to-phenotype relations. CONCLUSIONS Integrating and visualising cross-species phenotype information on the affected genes may help in routine diagnostics of CNVs.
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Affiliation(s)
- Sebastian Köhler
- Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin,Berlin, Germany.,Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Berlin, Germany
| | - Uwe Schoeneberg
- Foundation Institute Molecular Biology and Bioinformatics, Freie Universitaet Berlin, Berlin, Germany
| | | | - Sandra C Doelken
- Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin,Berlin, Germany
| | - Jayne Y Hehir-Kwa
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Jonas Ibn-Salem
- Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin,Berlin, Germany
| | | | - Damian Smedley
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Melissa A Haendel
- Department of Medical Informatics and Epidemiology and OHSU Library, Oregon Health & Science University, Portland, USA
| | - Peter N Robinson
- Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin,Berlin, Germany.,Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Berlin, Germany.,Max Planck Institute for Molecular Genetics, Berlin, Germany.,Department of Mathematics and Computer Science, Institute for Bioinformatics, Freie Universitaet Berlin, Berlin, Germany
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20
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Belizário JE. The humankind genome: from genetic diversity to the origin of human diseases. Genome 2014; 56:705-16. [PMID: 24433206 DOI: 10.1139/gen-2013-0125] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Genome-wide association studies have failed to establish common variant risk for the majority of common human diseases. The underlying reasons for this failure are explained by recent studies of resequencing and comparison of over 1200 human genomes and 10 000 exomes, together with the delineation of DNA methylation patterns (epigenome) and full characterization of coding and noncoding RNAs (transcriptome) being transcribed. These studies have provided the most comprehensive catalogues of functional elements and genetic variants that are now available for global integrative analysis and experimental validation in prospective cohort studies. With these datasets, researchers will have unparalleled opportunities for the alignment, mining, and testing of hypotheses for the roles of specific genetic variants, including copy number variations, single nucleotide polymorphisms, and indels as the cause of specific phenotypes and diseases. Through the use of next-generation sequencing technologies for genotyping and standardized ontological annotation to systematically analyze the effects of genomic variation on humans and model organism phenotypes, we will be able to find candidate genes and new clues for disease's etiology and treatment. This article describes essential concepts in genetics and genomic technologies as well as the emerging computational framework to comprehensively search websites and platforms available for the analysis and interpretation of genomic data.
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Affiliation(s)
- Jose E Belizário
- Departamento de Farmacologia, Instituto de Ciências Biomédicas da Universidade de São Paulo, Avenida Lineu Prestes, 1524 CEP 05508-900, São Paulo, SP, Brazil
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21
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Ibn-Salem J, Köhler S, Love MI, Chung HR, Huang N, Hurles ME, Haendel M, Washington NL, Smedley D, Mungall CJ, Lewis SE, Ott CE, Bauer S, Schofield PN, Mundlos S, Spielmann M, Robinson PN. Deletions of chromosomal regulatory boundaries are associated with congenital disease. Genome Biol 2014; 15:423. [PMID: 25315429 PMCID: PMC4180961 DOI: 10.1186/s13059-014-0423-1] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 07/24/2014] [Indexed: 12/21/2022] Open
Abstract
Background Recent data from genome-wide chromosome conformation capture analysis indicate that the human genome is divided into conserved megabase-sized self-interacting regions called topological domains. These topological domains form the regulatory backbone of the genome and are separated by regulatory boundary elements or barriers. Copy-number variations can potentially alter the topological domain architecture by deleting or duplicating the barriers and thereby allowing enhancers from neighboring domains to ectopically activate genes causing misexpression and disease, a mutational mechanism that has recently been termed enhancer adoption. Results We use the Human Phenotype Ontology database to relate the phenotypes of 922 deletion cases recorded in the DECIPHER database to monogenic diseases associated with genes in or adjacent to the deletions. We identify combinations of tissue-specific enhancers and genes adjacent to the deletion and associated with phenotypes in the corresponding tissue, whereby the phenotype matched that observed in the deletion. We compare this computationally with a gene-dosage pathomechanism that attempts to explain the deletion phenotype based on haploinsufficiency of genes located within the deletions. Up to 11.8% of the deletions could be best explained by enhancer adoption or a combination of enhancer adoption and gene-dosage effects. Conclusions Our results suggest that enhancer adoption caused by deletions of regulatory boundaries may contribute to a substantial minority of copy-number variation phenotypes and should thus be taken into account in their medical interpretation. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0423-1) contains supplementary material, which is available to authorized users.
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22
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Zemojtel T, Köhler S, Mackenroth L, Jäger M, Hecht J, Krawitz P, Graul-Neumann L, Doelken S, Ehmke N, Spielmann M, Oien NC, Schweiger MR, Krüger U, Frommer G, Fischer B, Kornak U, Flöttmann R, Ardeshirdavani A, Moreau Y, Lewis SE, Haendel M, Smedley D, Horn D, Mundlos S, Robinson PN. Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome. Sci Transl Med 2014; 6:252ra123. [PMID: 25186178 PMCID: PMC4512639 DOI: 10.1126/scitranslmed.3009262] [Citation(s) in RCA: 187] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Less than half of patients with suspected genetic disease receive a molecular diagnosis. We have therefore integrated next-generation sequencing (NGS), bioinformatics, and clinical data into an effective diagnostic workflow. We used variants in the 2741 established Mendelian disease genes [the disease-associated genome (DAG)] to develop a targeted enrichment DAG panel (7.1 Mb), which achieves a coverage of 20-fold or better for 98% of bases. Furthermore, we established a computational method [Phenotypic Interpretation of eXomes (PhenIX)] that evaluated and ranked variants based on pathogenicity and semantic similarity of patients' phenotype described by Human Phenotype Ontology (HPO) terms to those of 3991 Mendelian diseases. In computer simulations, ranking genes based on the variant score put the true gene in first place less than 5% of the time; PhenIX placed the correct gene in first place more than 86% of the time. In a retrospective test of PhenIX on 52 patients with previously identified mutations and known diagnoses, the correct gene achieved a mean rank of 2.1. In a prospective study on 40 individuals without a diagnosis, PhenIX analysis enabled a diagnosis in 11 cases (28%, at a mean rank of 2.4). Thus, the NGS of the DAG followed by phenotype-driven bioinformatic analysis allows quick and effective differential diagnostics in medical genetics.
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Affiliation(s)
- Tomasz Zemojtel
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany. Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland. Labor Berlin-Charité Vivantes GmbH, Humangenetik, Föhrer Straße 15, 13353 Berlin, Germany
| | - Sebastian Köhler
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Luisa Mackenroth
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Marten Jäger
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Jochen Hecht
- Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany. Berlin-Brandenburg Center for Regenerative Therapies, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Peter Krawitz
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany. Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Luitgard Graul-Neumann
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Sandra Doelken
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Nadja Ehmke
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Malte Spielmann
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany. Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Nancy Christine Oien
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany. Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Michal R Schweiger
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany. Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany. Cologne Center for Genomics, University of Cologne, D-50931 Cologne, Germany
| | - Ulrike Krüger
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Götz Frommer
- Agilent Technologies, Hewlett-Packard-Straße 8, 76337 Waldbronn, Germany
| | - Björn Fischer
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany. Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Uwe Kornak
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany. Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Ricarda Flöttmann
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Amin Ardeshirdavani
- Department of Electrical Engineering, STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics, KU Leuven, 3001 Leuven, Belgium
| | - Yves Moreau
- Department of Electrical Engineering, STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics, KU Leuven, 3001 Leuven, Belgium
| | - Suzanna E Lewis
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Melissa Haendel
- University Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Sciences University, Portland, OR 97327, USA
| | - Damian Smedley
- Mouse Informatics Group, Wellcome Trust Sanger Institute, CB10 1SA Hinxton, UK
| | - Denise Horn
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Stefan Mundlos
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany. Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany. Berlin-Brandenburg Center for Regenerative Therapies, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Peter N Robinson
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany. Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany. Berlin-Brandenburg Center for Regenerative Therapies, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany. Institute for Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, Takustr. 9, 14195 Berlin, Germany.
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23
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Human symptoms-disease network. Nat Commun 2014; 5:4212. [PMID: 24967666 DOI: 10.1038/ncomms5212] [Citation(s) in RCA: 316] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 05/27/2014] [Indexed: 12/19/2022] Open
Abstract
In the post-genomic era, the elucidation of the relationship between the molecular origins of diseases and their resulting phenotypes is a crucial task for medical research. Here, we use a large-scale biomedical literature database to construct a symptom-based human disease network and investigate the connection between clinical manifestations of diseases and their underlying molecular interactions. We find that the symptom-based similarity of two diseases correlates strongly with the number of shared genetic associations and the extent to which their associated proteins interact. Moreover, the diversity of the clinical manifestations of a disease can be related to the connectivity patterns of the underlying protein interaction network. The comprehensive, high-quality map of disease-symptom relations can further be used as a resource helping to address important questions in the field of systems medicine, for example, the identification of unexpected associations between diseases, disease etiology research or drug design.
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24
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Haendel MA, Balhoff JP, Bastian FB, Blackburn DC, Blake JA, Bradford Y, Comte A, Dahdul WM, Dececchi TA, Druzinsky RE, Hayamizu TF, Ibrahim N, Lewis SE, Mabee PM, Niknejad A, Robinson-Rechavi M, Sereno PC, Mungall CJ. Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. J Biomed Semantics 2014; 5:21. [PMID: 25009735 PMCID: PMC4089931 DOI: 10.1186/2041-1480-5-21] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 03/25/2014] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Elucidating disease and developmental dysfunction requires understanding variation in phenotype. Single-species model organism anatomy ontologies (ssAOs) have been established to represent this variation. Multi-species anatomy ontologies (msAOs; vertebrate skeletal, vertebrate homologous, teleost, amphibian AOs) have been developed to represent 'natural' phenotypic variation across species. Our aim has been to integrate ssAOs and msAOs for various purposes, including establishing links between phenotypic variation and candidate genes. RESULTS Previously, msAOs contained a mixture of unique and overlapping content. This hampered integration and coordination due to the need to maintain cross-references or inter-ontology equivalence axioms to the ssAOs, or to perform large-scale obsolescence and modular import. Here we present the unification of anatomy ontologies into Uberon, a single ontology resource that enables interoperability among disparate data and research groups. As a consequence, independent development of TAO, VSAO, AAO, and vHOG has been discontinued. CONCLUSIONS The newly broadened Uberon ontology is a unified cross-taxon resource for metazoans (animals) that has been substantially expanded to include a broad diversity of vertebrate anatomical structures, permitting reasoning across anatomical variation in extinct and extant taxa. Uberon is a core resource that supports single- and cross-species queries for candidate genes using annotations for phenotypes from the systematics, biodiversity, medical, and model organism communities, while also providing entities for logical definitions in the Cell and Gene Ontologies. THE ONTOLOGY RELEASE FILES ASSOCIATED WITH THE ONTOLOGY MERGE DESCRIBED IN THIS MANUSCRIPT ARE AVAILABLE AT: http://purl.obolibrary.org/obo/uberon/releases/2013-02-21/ CURRENT ONTOLOGY RELEASE FILES ARE AVAILABLE ALWAYS AVAILABLE AT: http://purl.obolibrary.org/obo/uberon/releases/
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Affiliation(s)
- Melissa A Haendel
- Department of Medical Informatics & Epidemiology, Oregon Health & Science University, Portland, OR, USA
| | - James P Balhoff
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA ; National Evolutionary Synthesis Center, Durham, NC, USA
| | - Frederic B Bastian
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland ; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - David C Blackburn
- Department of Vertebrate Zoology and Anthropology, California Academy of Sciences, San Francisco, CA 94118, USA
| | | | - Yvonne Bradford
- The Zebrafish Model Organism Database, University of Oregon, Eugene, OR 97403, USA
| | - Aurelie Comte
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland ; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Wasila M Dahdul
- National Evolutionary Synthesis Center, Durham, NC, USA ; Department of Biology, University of South Dakota, Vermillion, SD 57069, USA
| | - Thomas A Dececchi
- Department of Biology, University of South Dakota, Vermillion, SD 57069, USA
| | - Robert E Druzinsky
- Department of Oral Biology, University of Illinois-Chicago, Chicago, IL 60612, USA
| | | | - Nizar Ibrahim
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL 60637, USA
| | - Suzanna E Lewis
- Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA
| | - Paula M Mabee
- Department of Biology, University of South Dakota, Vermillion, SD 57069, USA
| | - Anne Niknejad
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland ; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland ; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Paul C Sereno
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL 60637, USA
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25
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Abstract
The use of model organisms as tools for the investigation of human genetic variation has significantly and rapidly advanced our understanding of the aetiologies underlying hereditary traits. However, while equivalences in the DNA sequence of two species may be readily inferred through evolutionary models, the identification of equivalence in the phenotypic consequences resulting from comparable genetic variation is far from straightforward, limiting the value of the modelling paradigm. In this review, we provide an overview of the emerging statistical and computational approaches to objectively identify phenotypic equivalence between human and model organisms with examples from the vertebrate models, mouse and zebrafish. Firstly, we discuss enrichment approaches, which deem the most frequent phenotype among the orthologues of a set of genes associated with a common human phenotype as the orthologous phenotype, or phenolog, in the model species. Secondly, we introduce and discuss computational reasoning approaches to identify phenotypic equivalences made possible through the development of intra- and interspecies ontologies. Finally, we consider the particular challenges involved in modelling neuropsychiatric disorders, which illustrate many of the remaining difficulties in developing comprehensive and unequivocal interspecies phenotype mappings.
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Affiliation(s)
- Peter N. Robinson
- Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Berlin, Germany
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
- * E-mail: (PNR); (CW)
| | - Caleb Webber
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
- * E-mail: (PNR); (CW)
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26
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Van Slyke CE, Bradford YM, Westerfield M, Haendel MA. The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio. J Biomed Semantics 2014; 5:12. [PMID: 24568621 PMCID: PMC3944782 DOI: 10.1186/2041-1480-5-12] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 02/07/2014] [Indexed: 01/07/2023] Open
Abstract
Background The Zebrafish Anatomy Ontology (ZFA) is an OBO Foundry ontology that is used in conjunction with the Zebrafish Stage Ontology (ZFS) to describe the gross and cellular anatomy and development of the zebrafish, Danio rerio, from single cell zygote to adult. The zebrafish model organism database (ZFIN) uses the ZFA and ZFS to annotate phenotype and gene expression data from the primary literature and from contributed data sets. Results The ZFA models anatomy and development with a subclass hierarchy, a partonomy, and a developmental hierarchy and with relationships to the ZFS that define the stages during which each anatomical entity exists. The ZFA and ZFS are developed utilizing OBO Foundry principles to ensure orthogonality, accessibility, and interoperability. The ZFA has 2860 classes representing a diversity of anatomical structures from different anatomical systems and from different stages of development. Conclusions The ZFA describes zebrafish anatomy and development semantically for the purposes of annotating gene expression and anatomical phenotypes. The ontology and the data have been used by other resources to perform cross-species queries of gene expression and phenotype data, providing insights into genetic relationships, morphological evolution, and models of human disease.
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Smedley D, Kohler S, Bone W, Oellrich A, Jacobsen J, Wang K, Mungall C, Washington N, Bauer S, Seelow D, Krawitz P, Boerkel C, Gilissen C, Haendel M, Lewis SE, Robinson PN. Use of animal models for exome prioritization of rare disease genes. Orphanet J Rare Dis 2014. [PMCID: PMC4249606 DOI: 10.1186/1750-1172-9-s1-o19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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28
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Köhler S, Doelken SC, Mungall CJ, Bauer S, Firth HV, Bailleul-Forestier I, Black GCM, Brown DL, Brudno M, Campbell J, FitzPatrick DR, Eppig JT, Jackson AP, Freson K, Girdea M, Helbig I, Hurst JA, Jähn J, Jackson LG, Kelly AM, Ledbetter DH, Mansour S, Martin CL, Moss C, Mumford A, Ouwehand WH, Park SM, Riggs ER, Scott RH, Sisodiya S, Van Vooren S, Wapner RJ, Wilkie AOM, Wright CF, Vulto-van Silfhout AT, de Leeuw N, de Vries BBA, Washingthon NL, Smith CL, Westerfield M, Schofield P, Ruef BJ, Gkoutos GV, Haendel M, Smedley D, Lewis SE, Robinson PN. The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res 2013; 42:D966-74. [PMID: 24217912 PMCID: PMC3965098 DOI: 10.1093/nar/gkt1026] [Citation(s) in RCA: 519] [Impact Index Per Article: 47.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The Human Phenotype Ontology (HPO) project, available at http://www.human-phenotype-ontology.org, provides a structured, comprehensive and well-defined set of 10,088 classes (terms) describing human phenotypic abnormalities and 13,326 subclass relations between the HPO classes. In addition we have developed logical definitions for 46% of all HPO classes using terms from ontologies for anatomy, cell types, function, embryology, pathology and other domains. This allows interoperability with several resources, especially those containing phenotype information on model organisms such as mouse and zebrafish. Here we describe the updated HPO database, which provides annotations of 7,278 human hereditary syndromes listed in OMIM, Orphanet and DECIPHER to classes of the HPO. Various meta-attributes such as frequency, references and negations are associated with each annotation. Several large-scale projects worldwide utilize the HPO for describing phenotype information in their datasets. We have therefore generated equivalence mappings to other phenotype vocabularies such as LDDB, Orphanet, MedDRA, UMLS and phenoDB, allowing integration of existing datasets and interoperability with multiple biomedical resources. We have created various ways to access the HPO database content using flat files, a MySQL database, and Web-based tools. All data and documentation on the HPO project can be found online.
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Affiliation(s)
- Sebastian Köhler
- Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany, Berlin-Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany, Lawrence Berkeley National Laboratory, Mail Stop 84R0171, Berkeley, CA 94720, USA, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK, Department of Medical Genetics, Cambridge University Addenbrooke's Hospital, Cambridge CB2 2QQ, UK, Université Paul Sabatier, Faculté de Chirurgie Dentaire, CHU Toulouse, France, Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre (MAHSC), Manchester, UK, Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, MAHSC, Manchester M13 9WL, UK, Institute of Genetic Medicine. Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK, Department of Computer Science, University of Toronto, Ontario, Canada, Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada, Department of Clinical Genetics, Leeds Teaching Hospitals NHS Trust, Leeds LS2 9NS, UK, MRC Human Genetics Unit, MRC Institute of Genetic and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK, The Jackson Laboratory, Bar Harbor, ME 04609, USA, Center for Molecular and Vascular Biology, University of Leuven, Belgium, Department of Neuropediatrics, University Medical Center Schleswig-Holstein, Kiel Campus, 24105 Kiel, Germany, NE Thames Genetics Service, Great Ormond Street Hospital, London WC1N 3JH, UK, Drexel University College of Medicine, Philadelphia, PA 19102, USA, Department of Haematology, University of Cambridge and NHS Blood and Transplant Cambridge, CB2 0PT Cambridge, UK, Autism and Developmental Medicine Institute, Geisinger Health System
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29
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Dauber A, Golzio C, Guenot C, Jodelka FM, Kibaek M, Kjaergaard S, Leheup B, Martinet D, Nowaczyk MJM, Rosenfeld JA, Zeesman S, Zunich J, Beckmann JS, Hirschhorn JN, Hastings ML, Jacquemont S, Katsanis N. SCRIB and PUF60 are primary drivers of the multisystemic phenotypes of the 8q24.3 copy-number variant. Am J Hum Genet 2013; 93:798-811. [PMID: 24140112 DOI: 10.1016/j.ajhg.2013.09.010] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 09/10/2013] [Accepted: 09/16/2013] [Indexed: 11/19/2022] Open
Abstract
Copy-number variants (CNVs) represent a significant interpretative challenge, given that each CNV typically affects the dosage of multiple genes. Here we report on five individuals with coloboma, microcephaly, developmental delay, short stature, and craniofacial, cardiac, and renal defects who harbor overlapping microdeletions on 8q24.3. Fine mapping localized a commonly deleted 78 kb region that contains three genes: SCRIB, NRBP2, and PUF60. In vivo dissection of the CNV showed discrete contributions of the planar cell polarity effector SCRIB and the splicing factor PUF60 to the syndromic phenotype, and the combinatorial suppression of both genes exacerbated some, but not all, phenotypic components. Consistent with these findings, we identified an individual with microcephaly, short stature, intellectual disability, and heart defects with a de novo c.505C>T variant leading to a p.His169Tyr change in PUF60. Functional testing of this allele in vivo and in vitro showed that the mutation perturbs the relative dosage of two PUF60 isoforms and, subsequently, the splicing efficiency of downstream PUF60 targets. These data inform the functions of two genes not associated previously with human genetic disease and demonstrate how CNVs can exhibit complex genetic architecture, with the phenotype being the amalgam of both discrete dosage dysfunction of single transcripts and also of binary genetic interactions.
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Affiliation(s)
- Andrew Dauber
- Division of Endocrinology, Boston Children's Hospital, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02115, USA
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Robinson PN, Köhler S, Oellrich A, Wang K, Mungall CJ, Lewis SE, Washington N, Bauer S, Seelow D, Krawitz P, Gilissen C, Haendel M, Smedley D. Improved exome prioritization of disease genes through cross-species phenotype comparison. Genome Res 2013; 24:340-8. [PMID: 24162188 PMCID: PMC3912424 DOI: 10.1101/gr.160325.113] [Citation(s) in RCA: 239] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Numerous new disease-gene associations have been identified by whole-exome sequencing studies in the last few years. However, many cases remain unsolved due to the sheer number of candidate variants remaining after common filtering strategies such as removing low quality and common variants and those deemed unlikely to be pathogenic. The observation that each of our genomes contains about 100 genuine loss-of-function variants makes identification of the causative mutation problematic when using these strategies alone. We propose using the wealth of genotype to phenotype data that already exists from model organism studies to assess the potential impact of these exome variants. Here, we introduce PHenotypic Interpretation of Variants in Exomes (PHIVE), an algorithm that integrates the calculation of phenotype similarity between human diseases and genetically modified mouse models with evaluation of the variants according to allele frequency, pathogenicity, and mode of inheritance approaches in our Exomiser tool. Large-scale validation of PHIVE analysis using 100,000 exomes containing known mutations demonstrated a substantial improvement (up to 54.1-fold) over purely variant-based (frequency and pathogenicity) methods with the correct gene recalled as the top hit in up to 83% of samples, corresponding to an area under the ROC curve of >95%. We conclude that incorporation of phenotype data can play a vital role in translational bioinformatics and propose that exome sequencing projects should systematically capture clinical phenotypes to take advantage of the strategy presented here.
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Affiliation(s)
- Peter N Robinson
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
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Brinkley JF, Borromeo C, Clarkson M, Cox TC, Cunningham MJ, Detwiler LT, Heike CL, Hochheiser H, Mejino JLV, Travillian RS, Shapiro LG. The ontology of craniofacial development and malformation for translational craniofacial research. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2013; 163C:232-45. [PMID: 24124010 DOI: 10.1002/ajmg.c.31377] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We introduce the Ontology of Craniofacial Development and Malformation (OCDM) as a mechanism for representing knowledge about craniofacial development and malformation, and for using that knowledge to facilitate integrating craniofacial data obtained via multiple techniques from multiple labs and at multiple levels of granularity. The OCDM is a project of the NIDCR-sponsored FaceBase Consortium, whose goal is to promote and enable research into the genetic and epigenetic causes of specific craniofacial abnormalities through the provision of publicly accessible, integrated craniofacial data. However, the OCDM should be usable for integrating any web-accessible craniofacial data, not just those data available through FaceBase. The OCDM is based on the Foundational Model of Anatomy (FMA), our comprehensive ontology of canonical human adult anatomy, and includes modules to represent adult and developmental craniofacial anatomy in both human and mouse, mappings between homologous structures in human and mouse, and associated malformations. We describe these modules, as well as prototype uses of the OCDM for integrating craniofacial data. By using the terms from the OCDM to annotate data, and by combining queries over the ontology with those over annotated data, it becomes possible to create "intelligent" queries that can, for example, find gene expression data obtained from mouse structures that are precursors to homologous human structures involved in malformations such as cleft lip. We suggest that the OCDM can be useful not only for integrating craniofacial data, but also for expressing new knowledge gained from analyzing the integrated data.
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Oetting WS, Robinson PN, Greenblatt MS, Cotton RG, Beck T, Carey JC, Doelken SC, Girdea M, Groza T, Hamilton CM, Hamosh A, Kerner B, MacArthur JAL, Maglott DR, Mons B, Rehm HL, Schofield PN, Searle BA, Smedley D, Smith CL, Bernstein IT, Zankl A, Zhao EY. Getting ready for the Human Phenome Project: the 2012 forum of the Human Variome Project. Hum Mutat 2013; 34:661-6. [PMID: 23401191 DOI: 10.1002/humu.22293] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 02/05/2013] [Indexed: 11/05/2022]
Abstract
A forum of the Human Variome Project (HVP) was held as a satellite to the 2012 Annual Meeting of the American Society of Human Genetics in San Francisco, California. The theme of this meeting was "Getting Ready for the Human Phenome Project." Understanding the genetic contribution to both rare single-gene "Mendelian" disorders and more complex common diseases will require integration of research efforts among many fields and better defined phenotypes. The HVP is dedicated to bringing together researchers and research populations throughout the world to provide the resources to investigate the impact of genetic variation on disease. To this end, there needs to be a greater sharing of phenotype and genotype data. For this to occur, many databases that currently exist will need to become interoperable to allow for the combining of cohorts with similar phenotypes to increase statistical power for studies attempting to identify novel disease genes or causative genetic variants. Improved systems and tools that enhance the collection of phenotype data from clinicians are urgently needed. This meeting begins the HVP's effort toward this important goal.
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Affiliation(s)
- William S Oetting
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN, USA.
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Maynard SM, Mungall CJ, Lewis SE, Imam FT, Martone ME. A knowledge based approach to matching human neurodegenerative disease and animal models. Front Neuroinform 2013; 7:7. [PMID: 23717278 PMCID: PMC3653101 DOI: 10.3389/fninf.2013.00007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Accepted: 04/09/2013] [Indexed: 12/19/2022] Open
Abstract
Neurodegenerative diseases present a wide and complex range of biological and clinical features. Animal models are key to translational research, yet typically only exhibit a subset of disease features rather than being precise replicas of the disease. Consequently, connecting animal to human conditions using direct data-mining strategies has proven challenging, particularly for diseases of the nervous system, with its complicated anatomy and physiology. To address this challenge we have explored the use of ontologies to create formal descriptions of structural phenotypes across scales that are machine processable and amenable to logical inference. As proof of concept, we built a Neurodegenerative Disease Phenotype Ontology (NDPO) and an associated Phenotype Knowledge Base (PKB) using an entity-quality model that incorporates descriptions for both human disease phenotypes and those of animal models. Entities are drawn from community ontologies made available through the Neuroscience Information Framework (NIF) and qualities are drawn from the Phenotype and Trait Ontology (PATO). We generated ~1200 structured phenotype statements describing structural alterations at the subcellular, cellular and gross anatomical levels observed in 11 human neurodegenerative conditions and associated animal models. PhenoSim, an open source tool for comparing phenotypes, was used to issue a series of competency questions to compare individual phenotypes among organisms and to determine which animal models recapitulate phenotypic aspects of the human disease in aggregate. Overall, the system was able to use relationships within the ontology to bridge phenotypes across scales, returning non-trivial matches based on common subsumers that were meaningful to a neuroscientist with an advanced knowledge of neuroanatomy. The system can be used both to compare individual phenotypes and also phenotypes in aggregate. This proof of concept suggests that expressing complex phenotypes using formal ontologies provides considerable benefit for comparing phenotypes across scales and species.
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Affiliation(s)
- Sarah M Maynard
- Department of Neurosciences, Center for Research in Biological Systems, University of California San Diego, San Diego, CA, USA
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Köhler S, Doelken SC, Ruef BJ, Bauer S, Washington N, Westerfield M, Gkoutos G, Schofield P, Smedley D, Lewis SE, Robinson PN, Mungall CJ. Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research. F1000Res 2013; 2:30. [PMID: 24358873 DOI: 10.12688/f1000research.2-30.v1] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/22/2013] [Indexed: 12/30/2022] Open
Abstract
Phenotype analyses, e.g. investigating metabolic processes, tissue formation, or organism behavior, are an important element of most biological and medical research activities. Biomedical researchers are making increased use of ontological standards and methods to capture the results of such analyses, with one focus being the comparison and analysis of phenotype information between species. We have generated a cross-species phenotype ontology for human, mouse and zebrafish that contains classes from the Human Phenotype Ontology, Mammalian Phenotype Ontology, and generated classes for zebrafish phenotypes. We also provide up-to-date annotation data connecting human genes to phenotype classes from the generated ontology. We have included the data generation pipeline into our continuous integration system ensuring stable and up-to-date releases. This article describes the data generation process and is intended to help interested researchers access both the phenotype annotation data and the associated cross-species phenotype ontology. The resource described here can be used in sophisticated semantic similarity and gene set enrichment analyses for phenotype data across species. The stable releases of this resource can be obtained from http://purl.obolibrary.org/obo/hp/uberpheno/.
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Affiliation(s)
- Sebastian Köhler
- Institute for Medical and Human Genetics, Charité-Universitatsmedizin Berlin, Berlin, 13353, Germany ; Berlin-Brandenberg Center for Regenerative Therapies (BCRT), Charité-Universitatsmedizin Berlin, Berlin, 13353, Germany
| | - Sandra C Doelken
- Institute for Medical and Human Genetics, Charité-Universitatsmedizin Berlin, Berlin, 13353, Germany
| | - Barbara J Ruef
- ZFIN, Institute of Neuroscience, University of Oregon, Eugene OR, 97403-5291, USA
| | - Sebastian Bauer
- Institute for Medical and Human Genetics, Charité-Universitatsmedizin Berlin, Berlin, 13353, Germany
| | | | - Monte Westerfield
- ZFIN, Institute of Neuroscience, University of Oregon, Eugene OR, 97403-5291, USA
| | - George Gkoutos
- Department of Computer Science, University of Aberystwyth, Aberystwyth, SY23 2AX, UK
| | - Paul Schofield
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Damian Smedley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK
| | - Suzanna E Lewis
- Lawrence Berkeley National Laboratory, Berkeley CA, 94720, USA
| | - Peter N Robinson
- Institute for Medical and Human Genetics, Charité-Universitatsmedizin Berlin, Berlin, 13353, Germany ; Berlin-Brandenberg Center for Regenerative Therapies (BCRT), Charité-Universitatsmedizin Berlin, Berlin, 13353, Germany ; Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
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Köhler S, Doelken SC, Ruef BJ, Bauer S, Washington N, Westerfield M, Gkoutos G, Schofield P, Smedley D, Lewis SE, Robinson PN, Mungall CJ. Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research. F1000Res 2013; 2:30. [PMID: 24358873 PMCID: PMC3799545 DOI: 10.12688/f1000research.2-30.v2] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/20/2014] [Indexed: 12/11/2022] Open
Abstract
Phenotype analyses, e.g. investigating metabolic processes, tissue formation, or organism behavior, are an important element of most biological and medical research activities. Biomedical researchers are making increased use of ontological standards and methods to capture the results of such analyses, with one focus being the comparison and analysis of phenotype information between species. We have generated a cross-species phenotype ontology for human, mouse and zebrafish that contains classes from the Human Phenotype Ontology, Mammalian Phenotype Ontology, and generated classes for zebrafish phenotypes. We also provide up-to-date annotation data connecting human genes to phenotype classes from the generated ontology. We have included the data generation pipeline into our continuous integration system ensuring stable and up-to-date releases. This article describes the data generation process and is intended to help interested researchers access both the phenotype annotation data and the associated cross-species phenotype ontology. The resource described here can be used in sophisticated semantic similarity and gene set enrichment analyses for phenotype data across species. The stable releases of this resource can be obtained from
http://purl.obolibrary.org/obo/hp/uberpheno/.
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Affiliation(s)
- Sebastian Köhler
- Institute for Medical and Human Genetics, Charité-Universitatsmedizin Berlin, Berlin, 13353, Germany ; Berlin-Brandenberg Center for Regenerative Therapies (BCRT), Charité-Universitatsmedizin Berlin, Berlin, 13353, Germany
| | - Sandra C Doelken
- Institute for Medical and Human Genetics, Charité-Universitatsmedizin Berlin, Berlin, 13353, Germany
| | - Barbara J Ruef
- ZFIN, Institute of Neuroscience, University of Oregon, Eugene OR, 97403-5291, USA
| | - Sebastian Bauer
- Institute for Medical and Human Genetics, Charité-Universitatsmedizin Berlin, Berlin, 13353, Germany
| | | | - Monte Westerfield
- ZFIN, Institute of Neuroscience, University of Oregon, Eugene OR, 97403-5291, USA
| | - George Gkoutos
- Department of Computer Science, University of Aberystwyth, Aberystwyth, SY23 2AX, UK
| | - Paul Schofield
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Damian Smedley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK
| | - Suzanna E Lewis
- Lawrence Berkeley National Laboratory, Berkeley CA, 94720, USA
| | - Peter N Robinson
- Institute for Medical and Human Genetics, Charité-Universitatsmedizin Berlin, Berlin, 13353, Germany ; Berlin-Brandenberg Center for Regenerative Therapies (BCRT), Charité-Universitatsmedizin Berlin, Berlin, 13353, Germany ; Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
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