Importing Gene Panels

This page describes how to import a gene panel into the cBioPortal database. It assumes the following requirements have been satisfied:

  1. The cBioPortal software has been correctly built from source.

  2. The gene panel to import is in the proper file format. See Gene Panel File format for more information.

  3. The PORTAL_HOME environment variable has been properly defined. See Loading a Sample Study for more information.

Gene panel file format

The gene panel file follows the format of a meta file with the following fields: 1. stable_id: The name of the gene panel. This should be unique across all studies, as gene panels can be globally applied to any sample and any genetic profile. 2. description: A description of the gene panel. 3. gene_list: Tab separated genes, represented either by all gene symbols or all Entrez gene IDs.

An example gene panel file would be:

stable_id: IMPACT410
description: Targeted (410 cancer genes) sequencing of various tumor types via MSK-IMPACT on Illumina HiSeq sequencers.
gene_list: ABL1 ACVR1 AKT1 AKT3 ...

Import command

In this example, we are loading the example gene panels which resides in the sample dataset study_es_0.

cd <cbioportal_source_folder>/core/src/main/scripts
./importGenePanel.pl --data ../../test/scripts/test_data/study_es_0/data_gene_panel_testpanel1.txt
./importGenePanel.pl --data ../../test/scripts/test_data/study_es_0/data_gene_panel_testpanel2.txt

After loading gene panels into the database, please restart Tomcat so that the validator can retrieve gene panel information from the cBioPortal API.

Update existing gene panel

If a gene panel exists in the database with the same name as the one being imported, and there exists cancer study data that refers to this gene panel, the ImportGenePanel command will abort. In order to reimport the gene panel in this situation, run the UpdateGenePanel command.

If the incoming gene panel is the same as the original gene panel, whether through importing or updating, then no changes shall be made to the gene panel. If the incoming gene panel is empty, then the script will abort. Genes in the incoming gene panel that were not in the original shall be added to the existing gene panel. Conversely, genes not in the incoming gene panel that were in the original shall be removed from the existing gene panel. The UpdateGenePanel command will prompt twice to confirm changes made to the gene panel, such as genes to be added or removed.

cd <cbioportal_source_folder>/core/src/main/scripts
./updateGenePanel.pl --data ../../test/scripts/test_data/study_es_0/data_gene_panel_testpanel1.txt