CGCI Data Set¶
About the Cancer Genome Characterization Initiative¶
The Cancer Genome Characterization Initiative is a series of studies sponsored by the Office of Cancer Genomics (OCG) at the National Cancer Institute (NCI). This program utilizes molecular characterization to uncover distinct features of rare cancers such as HIV+ associated cancers and rare pediatric cancers. The Burkitt Lymphoma Genome Sequencing Project (BLGSP) is one of the projects available through GDC. It explores genetic changes in patients with Burkitt lymphoma (BL) that could lead to better prevention, detection, and treatment of this rare and aggressive cancer.
About the Cancer Genome Characterization Initiative Data¶
CGCI data consists of 120 cases with RNA sequencing, miRNA sequencing, and whole-genome sequencing data. The NCI GDC houses all the clinical, biospecimen, and molecular characterization data with over 589 BAM, 339 TXT, 402 TSV, 237 BRC XML, 120 BRC PPS XML, and 93 BCR SSF XML files in around 50.28 TB of data. The Project ID in the GDC Data Portal is CGCI-BLGSP.
For more information on the CGCI data, please refer to these sites:
Accessing Cancer Genome Characterization Initiative Data on the Cloud¶
Besides accessing the files on the GDC Data Portal, you can also access them from the GDC Google Cloud Storage Bucket, which means that you don’t need to download them to perform analysis. ISB-CGC stores the cloud file locations in tables in the
isb-cgc-bq.GDC_case_file_metadata data set in BigQuery.
To access these metadata files, go to the Google BigQuery console.
Perform SQL queries to find the CGCI files. Here is an example:
SELECT active.*, file_gdc_url FROM `isb-cgc-bq.GDC_case_file_metadata.fileData_active_current` as active, `isb-cgc-bq.GDC_case_file_metadata.GDCfileID_to_GCSurl_current` as GCSurl WHERE program_name = 'CGCI' AND active.file_gdc_id = GCSurl.file_gdc_id
Accessing the CGCI Data in Google BigQuery¶
ISB-CGC has CGCI data, such as clinical, RNA-seq and masked somatic mutations, stored in Google BigQuery tables. Information about these tables can be found using the ISB-CGC BigQuery Table Search with CGCI selected for filter PROGRAM. To learn more about this tool, see the ISB-CGC BigQuery Table Search documentation.
The CGCI tables are in project isb-cgc-bq. To learn more about how to view and query tables in the Google BigQuery console, see the ISB-CGC BigQuery Tables documentation.
isb-cgc-bq.CGCIcontains the latest tables for each data type.
isb-cgc-bq.CGCI_versionedcontains previously released tables, as well as the most current table.