DGV Struct Var Track Settings
 
Database of Genomic Variants: Structural Variation (CNV, Inversion, In/del)   (All Variation and Repeats tracks)

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Filter by publication reference: include exclude
Alkan et al 2009 Conrad et al 2006 Cooper et al 2008 De Smith et al 2007
Feuk et al 2005 Giglio et al 2002 Hinds et al 2006 Itsara et al 2009
Kidd et al 2008 Kidd et al 2010 Locke et al 2006 McCarroll et al 2006
McCarroll et al 2008 Mills et al 2006 Perry et al 2008 Pinto et al 2007
Redon et al 2006 Schuster et al 2010 Sebat et al 2004 Shaikh et al 2009
Sharp et al 2005 Simon-Sanchez et al 2007 Stefansson et al 2005 Teague et al 2010
Tuzun et al 2005 Wang et al 2007 Wong et al 2007
Data schema/format description and download
Source data version: beta (Nov. 23, 2012)
Assembly: Human May 2004 (NCBI35/hg17)
Data last updated at UCSC: 2013-02-11

Description

This track displays copy number variants (CNVs), insertions/deletions (InDels), inversions and inversion breakpoints annotated by the Database of Genomic Variants (DGV), which contains genomic variations observed in healthy individuals. DGV focuses on structural variation, defined as genomic alterations that involve segments of DNA that are larger than 1000 bp. Insertions/deletions of 100 bp or larger are also included.

Display Conventions

Color is used to indicate the type of variation.
Please note that variants now link to DGV's new browser as of February 2013.

  • inversions and inversion breakpoints are purple.
  • CNVs and InDels are blue if there is a gain in size relative to the reference.
  • CNVs and InDels are red if there is a loss in size relative to the reference.
  • CNVs and InDels are brown if there are reports of both a loss and a gain in size relative to the reference.
  • CNVs and InDels are black if there is an unknown change relative to the reference.

Variants are displayed with accession numbers with the following DGV nomenclature. When possible, DGV uses accessions from peer archives of structural variation (dbVar at NCBI or DGVa at EBI). These accessions begin with either "essv", "esv", "nssv", or "nsv", followed by a number. Variant submissions processed by EBI begin with "e" and those processed by NCBI begin with "n".

Accessions with ssv are for variant calls on a particular sample, and if they are copy number variants, they generally indicate whether the change is a gain or loss. Accessions with sv are for regions asserted by submitters to contain structural variants, and often span ssv elements for both losses and gains. dbVar and DGVa do not record numbers of losses and gains encompassed within sv regions.

DGV merges clusters of variants that share at least 70% reciprocal overlap in size/location, and provides an sv-like record with an accession that begins with "dgv_". For most sv and dgv variants, DGV displays the total number of gains and/or losses at the bottom of their variant detail page. Since each ssv variant is for one sample, its total is 1.

Methods

DGV collects these variants by ongoing manual curation of the literature. A brief description of the method and sample used for a particular variant is included on the details page, along with a link to the PubMed abstract for the study from which the variants were collected.

For data sets where the variation calls are reported at a sample-by-sample level, DGV merges calls with similar boundaries across the sample set. Only variants of the same type (i.e. CNVs, Indels, inversions) are merged, and gains and losses are merged separately. In addition, if several different platforms/approaches are used within the same study, these datasets are merged separately. Sample level calls that overlap by ≥ 70% are merged in this process.

Data Access

The raw data can be explored interactively with the Table Browser, or the Data Integrator. For automated access, this track, like all others, is available via our API. However, for bulk processing, it is recommended to download the dataset. The genome annotation is stored in a bigBed file that can be downloaded from the download server. The exact filenames can be found in the track configuration file. Annotations can be converted to ASCII text by our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, for example:

bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/gnomAD/structuralVariants/gnomad_v2.1_sv.sites.bb -chrom=chr6 -start=0 -end=1000000 stdout

Credits

Thanks to the Database of Genomic Variants for providing these data. In citing the Database of Genomic Variants please refer to Iafrate et al..

References

Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y, Scherer SW, Lee C. Detection of large-scale variation in the human genome. Nat Genet. 2004 Sep;36(9):949-51. PMID:15286789.

Zhang J, Feuk L, Duggan GE, Khaja R, Scherer SW. Development of bioinformatics resources for display and analysis of copy number and other structural variants in the human genome. Cytogenet Genome Res. 2006;115(3-4):205-14. PMID:17124402.