Description

This track shows genomic locations for variants in the CIViC (Clinical Interpretation of Variants in Cancer) database. These clinically relevant variant interpretations are expert- and crowd-sourced from peer-reviewed literature, clinical trials, and some conference abstracts.

Each variant's interpretation is in the context of a broader molecular profile: one or more variants grouped together. For example, clinical evidence may be relevant to a KRAS G12 mutation on its own, but other clinical evidence may relevant for cases with either a mutation in KRAS G12 or G13.

The primary points of data from the scientific literature are curated as Clinical Evidence, which connects to a molecular profile, which in turn connects to the variants shown in this track. Groups of evidence can become curator Assertions about the relevence of a molecular profile.

The detail for a feature will list diseases and therapies that have been associated with a genomic variant. Visiting the CIViC page for a variant will allow browsing the Molecular Profiles associated with that variant, and in turn each Molecular Profile shows the Clinical Evidence and Assertions for various diseases and therapies.

Display Conventions and Configuration

There are three types of variant feature types in CIViC: gene, fusion, and factor, of which only the gene and fusion fetaures have a genomic location.

Gene variants are shown as a single item, with a name indicating the variant's mode: sequence change, gene expression, gene deletion, etc.

Fusion variants connect two genes via a structural DNA rearrangement, typically in the introns or promotors of genes. For CIViC fusions that have an annotated transcript and exon, the exon will be shown as a thick bar. If there is an intron associated with the fusion, it will be annotated as a thin bar on the feature.

Data updates

This track reflects the monthly data summaries published by CIViC. The latest information is always available directly on the CIViC website or by its API.

Data access

The raw data can be explored interactively with the Table Browser or the Data Integrator. The data can be accessed from scripts through our API, via the track name "civic".

Methods

The monthly CIViC Variant Summaries were reformatted at UCSC to bigBed format. The data is updated every month, the week after CIViC data summary release. The diseases and therapies associated with a variant are collected from the corresponding TSV files from CIViC, using the molecular profile summaries as a mapping.

Credits

Thanks to the CIViC contributers and organizers for curating the database and making the data available for download.

Reference

Griffith M, Spies NC, Krysiak K, McMichael JF, Coffman AC, Danos AM, Ainscough BJ, Ramirez CA, Rieke DT, Kujan L et al. CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer. Nat Genet. 2017Jan31;49(2):170-174. PMID: 28138153; PMC: PMC5367263