The Database of Genomic Variants: a curated collection of structural variation in the human genome
By J. MacDonald, R. Ziman, R. Yuen, L. Feuk, Stephen W. Scherer. Nucleic Acids Res., 2013
1,239 citations recorded by the source corpus.
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.
Subfields: Genetics, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/eddc172a618775a7cb19ca822c03743409035642
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Citations in the corpus
- The Intolerance of Regulatory Sequence to Genetic Variation Predicts Gene Dosage Sensitivity (2015, methodology): “Finally, to look at the opposite end of the dosage sensitivity spectrum, we identified genes that are tolerant to copy number variations (CNVs) based on the CNV data from two large Database of Genomic Variants (DGV) studies [17–19].”
- Oxford Nanopore MinION Sequencing and Genome Assembly (2016, methodology): “Currently, variants of size P 50 bp in length are all considered as SVs [65–68].”
- Variation Interpretation Predictors: Principles, Types, Performance, and Choice (2016, background): “, 2014], chromosomal structural variation databases such as The Database of Genomic Variants (DGV) [MacDonald et al., 2014], Database of Genomic Variants archive (DGVa, http://www.”
- Insights into Autism Spectrum Disorder Genomic Architecture and Biology from 71 Risk Loci (2015, methodology): “Rare variation was defined as a population frequency % 0.1% in either the Database of Genomic Variation (DGV) (MacDonald et al., 2014) or among all 5,382 SSC parents.”
- The UCSC Genome Browser database: 2021 update (2020, methodology): “On the configuration page for several tracks (ClinVar Variants, Database of Genomic Variants (6), and Leiden Open Variation Database Public Variants (7)), filters were added to allow the display of specified subsets of the data: Variant type, molecular consequence and clinical significance.”