BEATAML1.0 Data Set¶
About the BEATAML1.0¶
The BEATAML1.0 data is from several studies focused on acute myeloid leukemia (AML) and the effect of different therapies such as the drug Crenolanib. The implementation of targeted therapies for AML was challenging due to two reasons. The first was due to the intricate mutational patterns within and across patients and the second, was a shortage of pharmacologic agents for most mutational events.
The Crenolanib drug was studied because it is a potent type I pan-FLT3 (GeneID:2322) inhibitor, and FLT3 mutations are associated with poor prognosis and commonly detected in AML patients.
About the BEATAML1.0 Data¶
The BEATAML1.0 consists of over 220 files with 56 phenotyped subjects, 672 tumor specimens collected from 562 cases, and over 36 TB of data. The data is made up of mainly BAM, VCF, TXT, and TSV files. The majority of the data is whole-exome sequencing along with RNA sequencing. The Project ID in the GDC is BEATAML1.0-CRENOLANIB and BEATAML1.0-COHORT.
For more information on the BEATAML1.0 data, please refer to these sites:
Accessing the BEATAML1.0 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 BEATAML1.0 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 = 'BEATAML1.0' AND active.file_gdc_id = GCSurl.file_gdc_id
Accessing the BEATAML1.0 Data in Google BigQuery¶
ISB-CGC has BEATAML data, such as clinical and RNA-seq, stored in Google BigQuery tables. Information about these tables can be found using the ISB-CGC BigQuery Table Search with BEATAML selected for filter PROGRAM. To learn more about this tool, see the ISB-CGC BigQuery Table Search documentation.
The BEATAML 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.BEATAMLcontains the latest tables for each data type.
- Data set
isb-cgc-bq.BEATAML_versionedcontains previously released tables, as well as the most current table.