Variant-DB: A Tool for Efficiently Exploring Millions of Human Genetic Variants and Their Annotations

Abstract

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.