VarFish: comprehensive DNA variant analysis for diagnostics and research.

Genetic Variation Humans Molecular Sequence Annotation Rare Diseases / diagnosis Research Software User-Computer Interface

Journal

Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011

Informations de publication

Date de publication:
02 07 2020
Historique:
accepted: 16 04 2020
revised: 27 03 2020
received: 06 02 2020
pubmed: 28 4 2020
medline: 2 10 2020
entrez: 28 4 2020
Statut: ppublish

Résumé

VarFish is a user-friendly web application for the quality control, filtering, prioritization, analysis, and user-based annotation of DNA variant data with a focus on rare disease genetics. It is capable of processing variant call files with single or multiple samples. The variants are automatically annotated with population frequencies, molecular impact, and presence in databases such as ClinVar. Further, it provides support for pathogenicity scores including CADD, MutationTaster, and phenotypic similarity scores. Users can filter variants based on these annotations and presumed inheritance pattern and sort the results by these scores. Variants passing the filter are listed with their annotations and many useful link-outs to genome browsers, other gene/variant data portals, and external tools for variant assessment. VarFish allows users to create their own annotations including support for variant assessment following ACMG-AMP guidelines. In close collaboration with medical practitioners, VarFish was designed for variant analysis and prioritization in diagnostic and research settings as described in the software's extensive manual. The user interface has been optimized for supporting these protocols. Users can install VarFish on their own in-house servers where it provides additional lab notebook features for collaborative analysis and allows re-analysis of cases, e.g. after update of genotype or phenotype databases.

Identifiants

DOI: 10.1093/nar/gkaa241 PMID: 32338743 PMC: PMC7319464
pubmed: 32338743
pii: 5825625
doi: 10.1093/nar/gkaa241
pmc: PMC7319464
doi:

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

W162-W169

Informations de copyright

© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.

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Auteurs

Manuel Holtgrewe (M)

CUBI - Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany.
Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany.

Oliver Stolpe (O)

CUBI - Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany.
Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany.

Mikko Nieminen (M)

CUBI - Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany.
Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany.

Stefan Mundlos (S)

Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 13353, Germany.
Development and Disease Group, Max Planck Institute for Medical Genetics, Berlin 14195, Germany.

Alexej Knaus (A)

Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn 53127, Germany.

Uwe Kornak (U)

Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 13353, Germany.
Development and Disease Group, Max Planck Institute for Medical Genetics, Berlin 14195, Germany.

Dominik Seelow (D)

Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 13353, Germany.
Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Str. 2, 10178 Berlin, Germany.

Lara Segebrecht (L)

Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 13353, Germany.

Malte Spielmann (M)

Development and Disease Group, Max Planck Institute for Medical Genetics, Berlin 14195, Germany.
Institut für Humangenetik Lübeck, Universität zu Lübeck, 23538 Lübeck, Germany.

Björn Fischer-Zirnsak (B)

Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 13353, Germany.
Development and Disease Group, Max Planck Institute for Medical Genetics, Berlin 14195, Germany.

Felix Boschann (F)

Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 13353, Germany.

Ute Scholl (U)

Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Str. 2, 10178 Berlin, Germany.
Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Nephrology and Medical Intensive Care, BCRT - Berlin Institute of Health Center for Regenerative Therapies, 13353 Berlin, Germany.

Nadja Ehmke (N)

Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 13353, Germany.

Dieter Beule (D)

CUBI - Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany.
Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany.

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Classifications MeSH

questionsmedicales.fr › Phénomènes génétiques › Variation génétique › VarFish: comprehensive DNA variant analysis...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › VarFish: comprehensive DNA variant analysis...
questionsmedicales.fr › Sciences de l'information › Sources d'information › Services d'information › Documentation › Données de séquences moléculaires › Annotation de séquence moléculaire › VarFish: comprehensive DNA variant analysis...
questionsmedicales.fr › États, signes et symptômes pathologiques › Processus pathologiques › Caractéristiques de la maladie › Maladies rares › VarFish: comprehensive DNA variant analysis...
questionsmedicales.fr › Disciplines des sciences naturelles › Science › Recherche › VarFish: comprehensive DNA variant analysis...
questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Logiciel › VarFish: comprehensive DNA variant analysis...
questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Logiciel › Interface utilisateur › VarFish: comprehensive DNA variant analysis...