The American Association for Cancer Research Project Genomics Evidence Neoplasia Information Exchange Biopharma Collaborative (GENIE BPC) is an effort to aggregate comprehensive clinical data linked to genomic sequencing data to create a pan-cancer, publicly available data repository. These data detail clinical characteristics and drug regimen treatment information, along with high-throughput sequencing data and clinical outcomes, for cancer patients across multiple institutions. The GENIE BPC data repository forms a unique observational database of comprehensive clinical annotation with molecularly characterized tumors that can be used to advance precision medicine research in oncology. Linking multiple clinical and genomic datasets that vary in structure introduces an inherent complexity for data users. Therefore, use of the GENIE BPC data requires a rigorous process for preparing and merging the data to build analytic models. The {genieBPC} package is a user-friendly data processing pipeline to streamline the process for developing analytic cohorts that are ready for clinico-genomic analyses.
Install {genieBPC} from CRAN:
Install the development version of {genieBPC} with:
Data import: pull_data_synapse() imports GENIE BPC data from ‘Synapse’ into the R environment
Data processing
create_analytic_cohort() selects an analytic cohort based on cancer diagnosis information and/or cancer-directed drug regimen informationselect_unique_ngs() selects a unique next generation sequencing (NGS) test corresponding to the selected diagnosesData visualization: drug_regimen_sunburst() creates a sunburst figure of drug regimen information corresponding to the selected diagnoses in the order that the regimens were administered
Access to the GENIE BPC data release folders on ‘Synapse’ is required in order to use this function. To obtain access:
For public data releases:
Register for a ‘Synapse’ account. Be sure to create a username and password. Note: do NOT connect via your Google account.
Accept the Synapse account terms of use.
Navigate to GENIE Biopharma Collaborative Public page.
In the Files folder, navigate to Data Releases and click on the cancer cohort and data release version of choice.
Select Request Access, review the terms of data use, and select Accept.
For consortium data releases (restricted to GENIE consortium members & BPC pharmaceutical partners):
Register for a ‘Synapse’ account. Be sure to create a username and password. Note: do NOT connect via your Google account.
Accept the Synapse account terms of use.
Use this link to access the GENIE BPC team list and request to join the team. Please include your full name and affiliation in the message before sending out the request. (Note: Please allow up to a week to review and grant access.)
Once the request is accepted, you may access the data in the GENIE Biopharma Collaborative projects.
In the Files folder, navigate to Data Releases and click on the cancer cohort and data release version of choice.
Select Request Access, review the terms of data use, and select Accept.
Note: permissions for Synapse and permissions for each data release are distinct. Both permissions must be accepted to successfully access the data.
Authenticate yourself
Whether you are using public or consortium data, you will need to authenticate yourself at the beginning of each R session in which you use {genieBPC} to pull data (see set_synapse_credentials()), or store your credentials as environmental variables. See Tutorial: pull_data_synapse for more details.
The analytic data guides provide details on each analytic dataset and its corresponding variables for each data release.
Public Data Releases
NSCLC v2.0-Public Analytic Data Guide Released May 2022
CRC v2.0-Public Analytic Data Guide Released August 2022
Consortium Data Releases
Note that only GENIE BPC consortium users have access to the consortium releases.
The following example creates an analytic cohort of patients diagnosed with Stage IV adenocarcinoma NSCLC.
Pull data for NSCLC version 2.0-public:
Select stage IV adenocarcinoma NSCLC diagnoses:
nsclc_stg_iv_adeno <- create_analytic_cohort(data_synapse = nsclc_2_0$NSCLC_v2.0,
stage_dx = "Stage IV",
histology = "Adenocarcinoma")Select one unique metastatic lung adenocarcinoma genomic sample per patient in the analytic cohort returned above:
Create a visualization of the treatment patterns for the first 3 regimens received by patients diagnosed with stage IV adenocarcinoma:
sunplot <- drug_regimen_sunburst(data_synapse = nsclc_2_0$NSCLC_v2.0,
data_cohort = nsclc_stg_iv_adeno,
max_n_regimens = 3)Example of a sunburst plot showing 3 treatment regimens, highlighting the first treatment regimen:
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