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Variant-DB: A Tool for Efficiently Exploring Millions of Human Genetic Variants and Their Annotations
Kutzera, Joachim; May, Patrick
2017In Da Silveira, Marcos; Pruski, Cédric; Schneider, Reinhard (Eds.) DILS 2017: Data Integration in the Life Sciences
Peer reviewed
 

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Keywords :
Genetics; NGS
Abstract :
[en] Next Generation Sequencing (NGS) allows sequencing of a human genome within hours, enabling large scale applications such as sequencing the genome of each patient in a clinical study. Each individual human genome has about 3.5 Million genetic differences to the so called reference genome, the consensus genome of a healthy human. These differences, called variants, determine individual phenotypes, and certain variants are known to indicate disease predispositions. Finding associations from variant patterns and affected genes to these diseases requires combined analysis of variants from multiple individuals and hence, efficient solutions for accessing and filtering the variant data. We present Variant-DB, our in-house database solution that allows such efficient access to millions of variants from hundreds to thousands of individuals. Variant-DB stores individual variant genotypes and annotations. It features a REST-API and a web-based front-end for filtering variants based on annotations, individuals, families and studies. We explain Variant-DB and its front-end and demonstrate how the Variant-DB API can be included in data integration workflows.
Research center :
- Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group)
Disciplines :
Genetics & genetic processes
Computer science
Author, co-author :
Kutzera, Joachim ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
May, Patrick  ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
External co-authors :
no
Language :
English
Title :
Variant-DB: A Tool for Efficiently Exploring Millions of Human Genetic Variants and Their Annotations
Publication date :
24 October 2017
Event name :
Data Integration in the Life Sciences 2017
Event organizer :
Marcos DA SILVEIRA, Luxembourg Institute of Science and Technology
Cédric PRUSKI, Luxembourg Institute of Science and Technology
Reinhard SCHNEIDER, University of Luxembourg
Event place :
Luxembourg, Luxembourg
Event date :
from 14-11-2017 to 15-11-2017
Audience :
International
Main work title :
DILS 2017: Data Integration in the Life Sciences
Author, co-author :
Da Silveira, Marcos
Pruski, Cédric
Schneider, Reinhard 
Publisher :
Springer
ISBN/EAN :
978-3-319-69751-2
Collection name :
Lecture Notes in Computer Science, Vol. 10649; Lecture Notes in Bioinformatics
Pages :
22-28
Peer reviewed :
Peer reviewed
Focus Area :
Systems Biomedicine
Name of the research project :
NCER-PD
Available on ORBilu :
since 06 November 2017

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