MP2PRT Data Set
About MP2PRT
The Molecular Profiling to Predict Response to Treatment (MP2PRT) program is part of the NCI’s Cancer Moonshot Initiative. This study “Identification of Genetic Changes Associated with Relapse and/or Adaptive Resistance in Patients Registered as Favorable Histology Wilms Tumor on AREN03B2” performs genomic characterization on trio cases (normal tissue, tumor tissue at time of diagnosis, tumor tissue at time of relapse) from patients who relapsed with Favorable Histology Wilms Tumor.
About MP2PRT Data
The MP2PRT data set includes one project MP2PRT-WT with 52 cases. Data categories include sequencing reads, transcriptome profiling, simple nucleotide variation and copy number variation.
For more information on MP2PRT data, please refer to the site below:
Accessing the MP2PRT 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 MP2PRT 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 = 'MP2PRT'
AND active.file_gdc_id = GCSurl.file_gdc_id
Accessing the MP2PRT Data in Google BigQuery
ISB-CGC has MP2PRT data, such as clinical and metadata, stored in Google BigQuery tables. Information about these tables can be found using the ISB-CGC BigQuery Table Search with MP2PRT selected for filter PROGRAM. To learn more about this tool, see the ISB-CGC BigQuery Table Search documentation.
The MP2PRT 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.
Data set
isb-cgc-bq.MP2PRTcontains the latest tables for each data type.Data set
isb-cgc-bq.MP2PRT_versionedcontains previously released tables, as well as the most current table.