Universität zu Köln

Perez-Palma, Eduardo ORCID: 0000-0003-0546-5141, Gramm, Marie, Nuernberg, Peter, May, Patrick ORCID: 0000-0001-8698-3770 and Lal, Dennis (2019). Simple ClinVar: an interactive web server to explore and retrieve gene and disease variants aggregated in ClinVar database. Nucleic Acids Res., 47 (W1). S. W99 - 7. OXFORD: OXFORD UNIV PRESS. ISSN 1362-4962

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Abstract

Clinical genetic testing has exponentially expanded in recent years, leading to an overwhelming amount of patient variants with high variability in pathogenicity and heterogeneous phenotypes. A large part of the variant level data is aggregated in public databases such as ClinVar. However, the ability to explore this rich resource and answer general questions such as 'How many genes inside ClinVar are associated with a specific disease? or 'In which part of the protein are patient variants located?' is limited and requires advanced bioinformatics processing. Here, we present Simple ClinVar (http://simpleclinvar.broadinstitute.org/) a web server application that is able to provide variant, gene and disease level summary statistics based on the entire ClinVar database in a dynamic and user-friendly web-interface. Overall, our web application is able to interactively answer basic questions regarding genetic variation and its known relationships to disease. By typing a disease term of interest, the user can identify in seconds the genes and phenotypes most frequently reported to ClinVar. Subsets of variants can then be further explored, filtered or mapped and visualized in the corresponding protein sequences. Our website will follow ClinVar monthly releases and provide easy access to ClinVar resources to a broader audience including basic and clinical scientists.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Perez-Palma, Eduardo UNSPECIFIED orcid.org/0000-0003-0546-5141 UNSPECIFIED Gramm, Marie UNSPECIFIED UNSPECIFIED UNSPECIFIED Nuernberg, Peter UNSPECIFIED UNSPECIFIED UNSPECIFIED May, Patrick UNSPECIFIED orcid.org/0000-0001-8698-3770 UNSPECIFIED Lal, Dennis UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-135677
DOI:	10.1093/nar/gkz411
Journal or Publication Title:	Nucleic Acids Res.
Volume:	47
Number:	W1
Page Range:	S. W99 - 7
Date:	2019
Publisher:	OXFORD UNIV PRESS
Place of Publication:	OXFORD
ISSN:	1362-4962
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language SEQUENCE VARIANTS Multiple languages Biochemistry & Molecular Biology Multiple languages
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/13567