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Protocols

DbVar specifications

Information


Unique identifier OMICS_05334
Name DbVar
Alternative name Database of Genomic Structural Variation
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Allowed
Maintained Yes

Maintainer


  • person_outline Dean M. Church

Publications for Database of Genomic Structural Variation

DbVar citations

 (21)
library_books

Complement receptor 1 gene (CR1) intragenic duplication and risk of Alzheimer’s disease

2018
Hum Genet
PMCID: 5937907
PMID: 29675612
DOI: 10.1007/s00439-018-1883-2

[…] for each cohort. This represents the degree of clustering of the raw normalised data about integer copy number values (Barnes et al. ). PRT data from the 1000 Genomes samples analysed is available at dbvar accession nstd159 at ncbi.nlm.nih.gov/dbvar. […]

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

[…] arious public 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 […]

library_books

Mapping genetic variations to three dimensional protein structures to enhance variant interpretation: a proposed framework

2017
Genome Med
PMCID: 5735928
PMID: 29254494
DOI: 10.1186/s13073-017-0509-y

[…] ncy in control or general populations, as already mentioned. Public databases are burgeoning with information about genetic variants in humans and in many model organisms. Resources such as dbSNP [], dbVar [], COSMIC [], cBioPortal [], UniProt [], Kaviar [], Clinvar [], HGMD [], ExAC, and gnomAD [] provide data on hundreds of millions of single-nucleotide variants (SNVs) and other types of genetic […]

library_books

The 2018 Nucleic Acids Research database issue and the online molecular biology database collection

2017
Nucleic Acids Res
PMCID: 5753253
PMID: 29316735
DOI: 10.1093/nar/gkx1235

[…] ls. A major new resource is the Genome Variation Map () from the BIG Data Center covering 19 species. Its arrival is particularly timely with the announcement that comparable NCBI resources dbSNP and dbVar are to stop accepting non-human submissions (https://ncbiinsights.ncbi.nlm.nih.gov/2017/05/09/phasing-out-support-for-non-human-genome-organism-data-in-dbsnp-and-dbvar/).The well-used ClinVar re […]

library_books

Tools for annotation and comparison of structural variation

2017
F1000Res
PMCID: 5668921
PMID: 29123647
DOI: 10.5256/f1000research.13552.r26608

[…] tools/tree/master/resources/stratification-bed-files. Furthermore, we downloaded the gene annotations for GRCh37 from ensembl. Population genomic data was downloaded for the 1000 Genomes Project from dbVar (estd219) ( ) and filtered to produce a unique set of variant sites. SURVIVOR_ant (Version 0.0.1) was used to annotate the merged SVs with all the annotation data sets. The merged SVs are referr […]

library_books

Genome wide mapping of large deletions and their population genetic properties in dairy cattle

2017
PMCID: 5824824
PMID: 28985340
DOI: 10.1093/dnares/dsx037

[…] (BovineHD chip) based study, reflecting the resolution of our sequence-based calls. Only 18% of the deletion calls have overlap (≥1 bp) with previously reported bovine deletions (or CNV-loss) in the dbVar database (accessed on 27 January 2017), while remaining 82% are novel. However, ∼72% of our deletion regions remained unique when compared with all CNVs (gain or loss) and copy number variable r […]

Citations

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DbVar institution(s)
European Bioinformatics Institute, Hinxton, UK; National Center for Biotechnology Information, Bethesda, MD, USA
DbVar 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 for the DGVa.

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