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