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.

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.