HCMI Data Set¶
About the Human Cancer Models Initiative¶
The Human Cancer Models Initiative (HCMI) is a collaborative international consortium that is generating novel, next-generation, tumor-derived culture models annotated with genomic and clinical data. The collaborating institutions are the National Cancer Institute (NCI), Cancer Research UK (CRUK), Wellcome Sanger Institute (WSI), and foundation Hubrecht Organoid Technology (HUB). The four Cancer Model Development Centers (CMDCs), which are supported by the NCI as part of the HCMI, are Broad Institute of MIT and Harvard (BROAD), Cold Spring Harbor Laboratory (CSHL), Stanford University, and Weill Cornell Medical College.
About the Human Cancer Models Initiative Data¶
HCMI data consists of 23 cases with over 450 phenotyped subjects with whole-exome sequencing, RNA sequencing, and whole-genome sequencing data. The NCI GDC houses all the clinical, biospecimen, and molecular characterization data with over 460 VCF, 261 BAM, 123 TXT, 57 TSV, and 23 BRC XML files. The Project ID in the GDC Data Portal is HCMI-CMDC.
For more information on the HCMI data, please refer to these sites:
Accessing the Human Cancer Models 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 HCMI 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 = 'HCMI' AND active.file_gdc_id = GCSurl.file_gdc_id
Accessing the HCMI Data in Google BigQuery¶
ISB-CGC has HCMI data, such as clinical, RNA-seq and somatic mutation, stored in Google BigQuery tables. Information about these tables can be found using the ISB-CGC BigQuery Table Search with HCMI selected for filter PROGRAM. To learn more about this tool, see the ISB-CGC BigQuery Table Search documentation.
The HCMI 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.HCMIcontains the latest tables for each data type.
isb-cgc-bq.HCMI_versionedcontains previously released tables, as well as the most current table.