Users who have been granted access to Foundation Medicine data can now visualize somatic mutations using GDC Data Analysis, Visualization, and Exploration (DAVE) tools.
The GDC released a new version of the GDC Data Portal with new visualization tools for copy number variations (CNVs).
The NCI's Genomic Data Commons (GDC) released new features allowing users to build and compare custom cohorts and perform operations on case, gene, or mutation sets.
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.
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