The Analyzing Data using GDC Data Analysis, Visualization, and Exploration (DAVE) Tools webinar will help introduce users to GDC tools for analyzing data from cancer genomic studies.
To search for a mutation, you can utilize the Quick Search bar at the top right portion of the GDC Portal by entering in either a dbSNP reference cluster ID (rs#) or the coordinates of the chromosomal change. For example entering in 'rs121912651' or 'chr17:g.7674221G>A' will bring the user to the mutation entity page for that mutation.
The GDC is not normalizing frequency by gene length. This is currently under discussion. As such, these genes are appearing in the mutated genes table. Users can filter by the COSMIC Cancer Gene Census to display only genes for which mutations have been causally implicated in cancer.
The “# Mutations” column in the Project or Mutation Frequency > Gene tab displays the number of distinct (unique) mutations within the affected cases and not necessarily the total number of all mutations within the project or query filter.
The NCI's Genomic Data Commons (GDC) officially launched Data Analysis, Visualization, and Exploration (DAVE) tools transforming the GDC from a cancer genomics data repository into an interactive k
Please refer to the GDC MAF File Specification to obtain detailed information on the format of GDC MAF files.
Yes. The GDC provides additional analysis endpoints to retrieve data sets associated with visualizations. Analysis endpoints include: survival, top_cases_counts_by_genes, top_mutated_genes_by_project, top_mutated_cases_by_gene, top_mutated_cases_by_ssm, and mutated_cases_count_by_project.
Please refer to the GDC API User's Guide Analysis Section for additional information.
The IMPACT is categorized by the Sequencing Ontology type of the variants that is also compatible to snpEff. The VEP IMPACT rating is a separate rating given for compatibility with other variant annotation tools (e.g. snpEff). Basically, each category is associated with a set of SO terms:
Data analysis and visualization features are only available for projects which maintain open-access MAF files. Programs such as the Molecular Analysis for Therapy Choice (MATCH) trial maintain controlled-access MAF files only. As such, data analysis and visualization cannot be applied to MATCH projects.
