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MetaDome: Pathogenicity analysis of genetic variants through aggregation of homologous human protein domains

Authors: Laurens Wiel; Coos Baakman; Daan Gilissen; Joris A. Veltman; Gerrit Vriend; Christian Gilissen;

MetaDome: Pathogenicity analysis of genetic variants through aggregation of homologous human protein domains

Abstract

AbstractThe growing availability of human genetic variation has given rise to novel methods of measuring genetic tolerance that better interpret variants of unknown significance. We recently developed a novel concept based on protein domain homology in the human genome to improve variant interpretation. For this purpose we mapped population variation from the Exome Aggregation Consortium (ExAC) and pathogenic mutations from the Human Gene Mutation Database (HGMD) onto Pfam protein domains. The aggregation of these variation data across homologous domains into meta-domains allowed us to generate base-pair resolution of genetic intolerance profiles for human protein domains.Here we developed MetaDome, a fast and easy-to-use web service that visualizes meta-domain information and gene-wide profiles of genetic tolerance. We updated the underlying data of MetaDome to contain information from 56,319 human transcripts, 71,419 protein domains, 12,164,292 genetic variants from gnomAD, and 34,076 pathogenic mutations from ClinVar. MetaDome allows researchers to easily investigate their variants of interest for the presence or absence of variation at corresponding positions within homologous domains. We illustrate the added value of MetaDome by an example that highlights how it may help in the interpretation of variants of unknown significance. The MetaDome web server is freely accessible at https://stuart.radboudumc.nl/metadome.

Country
Netherlands
Subjects by Vocabulary

Microsoft Academic Graph classification: Protein domain Human genetic variation Computational biology Gene mutation Biology Homology (biology) Genetic variation Homologous chromosome Exome Genetic variants Human genome

Keywords

Informatics, web server, Bioinformatics, homologous protein domains, human genome, All institutes and research themes of the Radboud University Medical Center, Protein Domains, Databases, Genetic, Genetics, genetic tolerance, pathogenicity, Humans, Genetic Predisposition to Disease, Genetics (clinical), protein domain homology, Internet, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Radboudumc 7: Neurodevelopmental disorders DCMN: Donders Center for Medical Neuroscience, Genome, Human, Radboudumc 19: Nanomedicine RIMLS: Radboud Institute for Molecular Life Sciences, Computational Biology, Genetic Variation, Proteins, Metabolic Disorders Radboud Institute for Molecular Life Sciences [Radboudumc 6], ClinVar, gnomAD, Structural Homology, Protein, meta‐domains, Radboudumc 6: Metabolic Disorders RIMLS: Radboud Institute for Molecular Life Sciences, Pfam, Nanomedicine Radboud Institute for Molecular Life Sciences [Radboudumc 19], Software

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citations
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
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popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
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