The DGV database: non-pathological structural variations in humans

Database of Genomic Variants

There is an online database of which aim is to collect all DNA structural variations which can be considered as normal polymorphisms in humans (DGV – Database of Genomic Variants). The consultation of this database is particularly important because it allows to know whether a particular CNV (copy number variation) can be pathogenic or not.

In collaboration with DGVa (EBI) and dbVar (NCBI)

The database contains structural variations defined as ” genomic alterations that involve segments of DNA that are larger than 50bp“. The database is continuously fed by new data coming from peer reviewed research studies and it’s part of a collaboration with two archival CNV databases at EBI and NCBI, called DGVa and dbVar, respectively.  The three databases are synchronized, so to allow for an official accessioning of variants (actually any new submission must be done at DGVa and dbVar before being accepted and published in DGV).

The consulting of any entry of the database is quite intuitive. For example, if we want to see the structural variations of the LRRK2 gene (Parkinson disease 8), we can simply input “LRRK2” in the searching window and we’ll get a graphical representation of the gene, with some colored bars (see the picture below): the blue bars indicate the extension of the gained regions (duplications/multiplications) whereas the red bars indicate the extension of the possible (deletions) so far detected in large subsets of genomes of healthy humans.

Gains (blue bars) and losses (red bars) of genomic material as displayed in the DGV browser (click image to enlarge).

Also available in UCSC Genome and Ensembl browsers

Of note, all DGV entries can be accessed also in the UCSC Genome Browser and Ensembl browser. With the standard settings, DGV entries aren’t displayed in the UCSC browser, but they can be recalled by selecting the relevant option in the menu below the map (see picture below). We think, however, that the representation in the DGV browser may be clearer as less crowded and with variations displayed on different lines.

The option to be selected to show the DGV data in UCSC Genome Browser.

Breda Genetics srl and DGV

The deep curation of the DGV entries, its synchronization with DGVa and dbVAR and its foundations on a very large amount of data (the current version comprises more than 2.5 million entries identified in more than 22,300 genomes) makes DGV a standard data resource for copy number variation testing in clinical settings. At Breda Genetics we therefore consult DGV regularly to check the likelihood of non-pathogenic CNVs in certain genomic regions (which might explain, for instance, an unusual extension of homozigosity for a long genomic stretch).

References:, PMID: 24174537

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