VarFish: comprehensive DNA variant analysis for diagnostics and research.

Autor:	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., 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., Nieminen M; CUBI - Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany.; Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany., 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., Knaus A; Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn 53127, Germany., 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., 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., 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., 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., 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., 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., 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., 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., Beule D; CUBI - Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany.; Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany.
Jazyk:	angličtina
Zdroj:	Nucleic acids research [Nucleic Acids Res] 2020 Jul 02; Vol. 48 (W1), pp. W162-W169.
DOI:	10.1093/nar/gkaa241
Abstrakt:	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. (© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.)
Databáze:	MEDLINE
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