Description
This track displays structural variants (SVs) in
dbVar with somatic origin,
aggregated from six dbVar studies.
Source studies:
- COSMIC
(estd192) —
the Catalogue Of Somatic Mutations In Cancer.
- Clinical Structural Variants
(nstd102) —
somatic subset of ClinVar SVs.
- Ghazali et al. 2021
(nstd202).
- Helman et al. 2014
(nstd94).
- Walter et al. 2009
(nstd11).
- Wills et al. 2016
(nstd125).
This track is updated with every monthly dbVar release.
Display Conventions and Configuration
Variants are colored by type, using the dbVar color scheme described in the
dbVar Overview
page:
| Color |
Variant Type(s) |
| deletion, copy number loss |
|---|
| duplication, copy number gain, insertion, mobile element insertion |
|---|
| inversion |
|---|
| complex substitution |
|---|
| tandem duplication |
|---|
Mouseover on items shows gene(s) affected, size, variant type, source dbVar study, and
discovery method.
The track can be filtered by:
- Variant Type
- Variant Size (Under 10KB, 10KB to 100KB, 100KB to 1MB, Over 1MB)
- Discovery Method (Curated, Multiple, SNP array, Sequencing)
- Pathogenic Reciprocal Overlap (none, 10 to 25, 25 to 50, 50 to 75, 75 to 90, 90 to 100)
— range of reciprocal overlap with pathogenic variants in nstd102
Methods
Per NCBI's dbVar processing pipeline, somatic variant calls are extracted from the
variant_calls.somatic.gvf files on the dbVar FTP site, reciprocally overlapped
with the pathogenic clinical SV file using bedtools, and converted to bigBed format. See the
dbVar
Overview for full methods.
Data Access
The raw data can be explored interactively with the
Table Browser, or the
Data Integrator. For automated analysis,
the data may be queried from our
REST API.
The data can also be downloaded from the
dbVar Track Hub,
or via the dbVar FTP in VCF, GVF, or tab-delimited formats. For questions about dbVar track data,
please contact
dbvar@ncbi.nlm.nih.gov.
Credits
Thanks to the dbVar team at NCBI, especially John Lopez and Timothy Hefferon for technical
coordination and consultation.
References
Lappalainen I, Lopez J, Skipper L, Hefferon T, Spalding JD, Garner J, Chen C, Maguire M, Corbett M,
Zhou G et al.
DbVar and DGVa: public archives for genomic structural variation.
Nucleic Acids Res. 2013 Jan;41(Database issue):D936-41.
PMID: 23193291;
PMC: PMC3531204
Tate JG, Bamford S, Jubb HC, Sondka Z, Beare DM, Bindal N, Boutselakis H, Cole CG, Creatore C,
Dawson E et al.
COSMIC: the Catalogue Of Somatic Mutations In Cancer.
Nucleic Acids Res. 2019 Jan 8;47(D1):D941-D947.
PMID: 30371878;
PMC: PMC6323903