GDC Gene Model Updated to GENCODE 36
The gene model used as a reference across GDC has been updated from GENCODE 22 to GENCODE 36. GENCODE gene sets are continuously updated to improve the coverage and accuracy.
Access Data
Data from Landmark Chernobyl studies, New Methylation Pipeline, and More
Highlights from the GDC's recent Data Release 30 include data from major studies exploring the effects of Chernobyl radiation and methylation arrays processed via a new pipeline at the GDC.
Browse Data from Rare Cancers in the Data Portal
A recent data release offers new ways to access data from the Count Me In project.
Where can I find clinical data elements specific to my cancer research of interest?
Submitted by Anonymous
on
The GDC supports the submission of clinical and biospecimen supplements. Supplemental files can be downloaded from the GDC by searching for the Data Type "Clinical Supplement" or "Biospecimen Supplement" from the facet search in the GDC Data Portal Repository. For TCGA data, the supplement data is provided in XML documents and tab delimited files (biotabs). These files, in varying degrees, provide information on marker status (e.g.
What is the difference between tissue "collection" and tissue "procurement" in TCGA data?
Submitted by Anonymous
on
TCGA “collection” represents the collection of the sample for TCGA, whereas “procurement” represents the removal of tissue from the patient.
Why is the data maintained in cBioPortal, Broad Firehose, or the Seven Bridges Cancer Genomics Cloud different from the GDC data?
Submitted by Anonymous
on
The GDC harmonizes data across projects. This includes aligning the genomic data to a common reference genome (HG38) and generating higher level data using GDC bioinformatics pipelines. Other repositories may process the data differently.
How do I access data from TCGA marker or other landmark cancer genomics papers?
Submitted by Anonymous
on
The TCGA marker and other landmark cancer genomics papers, as well as associated supplemental files, are available on the GDC Publication Pages. The Publication Pages provide access to publication information and supplementary files.
Why does the treatment data appear to be incomplete and what treatment data is available in the GDC?
Submitted by Anonymous
on
Submitting treatment data is optional as not all projects are associated with treatment studies. For TCGA projects, for example, not all projects and cases have treatment data. For TCGA projects with treatment data, information is available in applicable clinical supplement files (i.e. clinical XML, biotabs). For other project associated with treatment studies in which the treatment data has been submitted to the GDC, treatment data is available for download in JSON and TSV format. These studies may also contain clinical supplement files.
Does the GDC provide access to follow-up (i.e. longitudinal) data?
Submitted by Anonymous
on
The availability of follow-up data is specific to the project and associated study.
For the Multiple Myeloma Research Foundation (MMRF) Clinical Outcomes in Multiple Myeloma to Personal Assessment of Genetic Profile (CoMMpass) study, longitudinal information was generated to track patients over the course of their disease. This data is available in the GDC by viewing the clinical follow-up data available for download on each case page in the GDC Data Portal or by querying the GDC API.
Explore MMRF Mutations in the Data Portal
The GDC’s Data Release 26 features updates allowing Multiple Myeloma Research Foundation (MMRF) CoMMpass data to be explored directly in the GDC Data Portal.