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Analyze Data

The GDC provides an array of interactive, web-based Analysis Tools for performing in-depth gene- and variant- level analyses. The workflow is cohort-centric, meaning analyses are specific to a researcher's cohort of interest.

  • Build cohorts and perform gene and variant level analysis on the cohort
  • Visualize most frequently mutated genes and somatic mutations for a cohort
  • Visualize a matrix of the top most mutated cases and genes affected by high impact mutations in a cohort
  • Perform a survival analysis for cases with a mutated form of a certain gene and cases without the mutation
  • Visualize mutations and their frequency across cases mapped to a graphical visualization of protein-coding regions
  • Visualize the top most variably expressed genes in a cohort
  • Visualize sequencing reads for a given gene, position, SNP, or variant
  • Use clinical variables to perform basic statistical analysis of a cohort
  • Compare custom gene or case sets by visualizing set similarities and differences

Documentation

Data Analysis Tools

The GDC provides interactive, cohort-centric tools for analyzing genomic and clinical data.

Data Analysis Policy

Policies and guidelines for appropriate use of data, are provided by the GDC whether open- or controlled- access.

Data Harmonization and Generation

The GDC developers best-in-practice pipelines for processing the most common molecular platforms. Variant calling, gene expression analysis, and other pipelines are implemented using software and algorithms selected in consultation with experts in the genomics community.

What’s New with GDC and Cancer Research

Cancer Research Highlights and Publications:

From the GDC FAQ

What considerations should be taken when comparing samples with different target capture kits?

Target capture kits are used to "target" specific regions of a given genome for the Whole Exome Sequencing (WXS) and Targeted Sequencing experimental strategies. Users should therefore take care when comparing data from different target capture kits for the WXS and Targeted Sequencing experimental strategies because of potential differences in genomic regions targeted, variant filtering, and subsequent variants recovered. Additionally, users should also consider that Whole Genome Sequencing (WGS) does not use target capture kits and may thus recover variants that are excluded in the WXS and Targeted Sequencing experimental strategies.

From the GDC Data Portal "Repository" page, the names of the target capture kits can be accessed by clicking the "Adding a File Filter" link and choosing "analysis.metadata.read_groups.target_capture_kit" from the menu. The GDC does not distribute target or bait files because they are intellectual property. Users should contact each individual project directly if detailed target capture region information is needed.

Need Assistance?

Need help with data retrieval, download, or submission?

Visit the GDC Support Page