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Protocols

DGVa specifications

Information


Unique identifier OMICS_05335
Name DGVa
Alternative name Database of Genomic Variants archive
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Maintainers


  • person_outline DGVa
  • person_outline Dean M. Church

Publications for Database of Genomic Variants archive

DGVa citations

 (5)
call_split

Late diagnosis of a truncating WISP3 mutation entails a severe phenotype of progressive pseudorheumatoid dysplasia

2018
PMCID: 5793772
PMID: 29258992
DOI: 10.1101/mcs.a002139
call_split See protocol

[…] lic databases: dbSNP (), 1000 Genomes Project (The 1000 Genomes Project Consortium et al. 2010), Exome Variant Server (EVS http://evs.gs.washington.edu/EVS/), HGMD professional database (), dbVAR and DGVa (), GERP (), and Ensembl (). The functional effect of variants were predicted using PolyPhen (), SIFT (), and RVIS (). All of this downstream analysis has been assembled together with a few scrip […]

call_split

Identification of copy number variation in French dairy and beef breeds using next generation sequencing

2017
PMCID: 5655909
PMID: 29065859
DOI: 10.1186/s12711-017-0352-z
call_split See protocol

[…] We compared our CNV dataset with those previously published for cattle [, , –] and with the publicly available Genomic Variants archive (DGVa) database of EMBL-EBI (http://www.ebi.ac.uk/dgva). These publicly available CNV were detected using array-based CGH [], SNP genotyping arrays [, ], and whole-genome sequencing [, , , ]. The compa […]

library_books

A deep intronic CLRN1 (USH3A) founder mutation generates an aberrant exon and underlies severe Usher syndrome on the Arabian Peninsula

2017
Sci Rep
PMCID: 5431179
PMID: 28469144
DOI: 10.1038/s41598-017-01577-8

[…] ng the variant <3). The remaining variants were annotated with their presence in public databases (dbSNP, 1000 Genomes Project, Exome Variant Server (EVS http://evs.gs.washington.edu/EVS/), dbVAR and DGVa, GERP, ENSEMBL, and the commercial HGMD professional database) as well as a CCG inhouse exome collection of 511 samples. Effects on splicing were predicted using the maximum entropy approach from […]

library_books

Leveraging the Power of High Performance Computing for Next Generation Sequencing Data Analysis: Tricks and Twists from a High Throughput Exome Workflow

2015
PLoS One
PMCID: 4420499
PMID: 25942438
DOI: 10.1371/journal.pone.0126321

[…] , , (10)). Several databases are parsed to annotate known variants during this step as well (dbSNP [], 1000 Genomes Project [], Exome Variant Server (EVS http://evs.gs.washington.edu/EVS/), dbVAR and DGVa [], GERP [], ENSEMBL [], and the commercial HGMD professional database []). Next, a functional assessment of the variants is performed by combining various third party tools (POLYPHEN [], SIFT [] […]

library_books

Ensembl BioMarts: a hub for data retrieval across taxonomic space

2011
PMCID: 3170168
PMID: 21785142
DOI: 10.1093/database/bar030

[…] esources include those in dbSNP () as well as variation data created by the project in the context of genome analysis (). Close collaboration with other projects at the EBI including InterPro (), the Database of Genomic Variants archive (DGVa) () and HGNC () ensures that Ensembl resources are integrated and available through other important bioinformatics resources. Recently somatic mutation data […]

Citations

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DGVa institution(s)
European Bioinformatics Institute, Hinxton, Cambridgeshire, UK; National Center for Biotechnology Information, Bethesda, MD, USA
DGVa funding source(s)
Supported by the Intramural Research Program of the National Institutes of Health, National Library of Medicine for the work on dbVar; the Wellcome Trust (grant number WT084107MA) and by the European Molecular Biology Laboratory.

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