Mutation frequency in the context of the OncoGrid represents total mutation occurrences in the gene (total count), while the # of Mutations listed on other portions of the GDC Portal represents the number of unique mutations on a gene or within a particular cohort.
There are less cases displayed with mutations in the 'Top Mutated Cancer Genes in Selected Projects' on the Project List Page because there is a filter on cases that have mutations on 1) Genes in the Cancer Gene Census and 2) Mutations with consequence types of {missense_variant, frameshift_variant, start_lost, stop_lost, initiator_codon_variant, stop_gained}.
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 cases in the OncoGrid are filtered by consequence type. Only cases that have mutations that have consequence types of: {missense_variant, frameshift_variant, start_lost, stop_lost, initiator_codon_variant, stop_gained} are displayed in the OncoGrid.
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.
Within the GDC data analysis workflow, both public (somatic) MAFs and protected MAFs generated are from the same pipeline and link back to the same cases. For example, For the TCGA-GBM project, the somatic MAF has the following header:
# in TCGA.GBM.muse.7e85de23-3855-4279-a3ac-a81827e4ccb6.DR6.0.somatic.maf.gz
#version gdc-1.0.0
#filedate 20170307
#n.analyzed.samples 393
The “# Mutations” column in the Project or Exploration/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.
