The Database of Genomic Variants: a curated collection of structural variation in the human genome

Abstract

Over the past decade, the Database of Genomic Variants (DGV; http://dgv.tcag.ca/) has provided a publicly accessible, comprehensive curated catalogue of structural variation (SV) found in the genomes of control individuals from worldwide populations. Here, we describe updates and new features, which have expanded the utility of DGV for both the basic research and clinical diagnostic communities. The current version of DGV consists of 55 published studies, comprising >2.5 million entries identified in >22,300 genomes. Studies included in DGV are selected from the accessioned data sets in the archival SV databases dbVar (NCBI) and DGVa (EBI), and then further curated for accuracy and validity. The core visualization tool (gbrowse) has been upgraded with additional functions to facilitate data analysis and comparison, and a new query tool has been developed to provide flexible and interactive access to the data. The content from DGV is regularly incorporated into other large-scale genome reference databases and represents a standard data resource for new product and database development, in particular for copy number variation testing in clinical labs. The accurate cataloguing of variants in DGV will continue to enable medical genetics and genome sequencing research.

Figure 1.

Content of the DGV. Increase in variants reported in DGV since inception, highlighting the recent transition towards NGS-based approaches for variant discovery (numbers based on year of publication).

Figure 2.

Functionality and navigation options for accessing entries in DGV. (A) An example of search options available in the DGV query tool, which identify sample level deletions in study nstd65 mapped to the GRCh37 assembly. (B) Links for each variant in the query tool result, allow for navigation to the variant details page, which includes a summary of all available attributes. (C) Links from the variant details page provide access to the genome browser to allow for evaluation of selected variants in their respective genomic region.

Figure 2.

Functionality and navigation options for accessing entries in DGV. (A) An example of search options available in the DGV query tool, which identify sample level deletions in study nstd65 mapped to the GRCh37 assembly. (B) Links for each variant in the query tool result, allow for navigation to the variant details page, which includes a summary of all available attributes. (C) Links from the variant details page provide access to the genome browser to allow for evaluation of selected variants in their respective genomic region.