How do I find models with variants in the gene(s) of interest?

Answer: 

Users can identify models with research somatic and/or clinical variants in the gene(s) of interest by using the “Search by Gene” search box in the filter panel on the left-hand side of the HCMI Searchable Catalog. As gene(s) of interest are selected, the list of models containing any variants in the gene(s) of interest will appear within the main viewing table. The example below shows the list of models that contain research somatic and/or clinical variants in the BRAF gene. Additionally, the “Most Frequently Mutated Genes” bar graph at the top of the Catalog can be used to identify models with research somatic and/or clinical variants in the gene(s) of interest by clicking on any data column within the graph.

Note: The open-access masked somatic MAF data shown in the Catalog is generated at NCI’s Genomic Data Commons (GDC). These data are highly processed to remove low frequency somatic variants and potential germline variants (for more information see: https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format/). If omission of true-positive somatic mutations is a concern, we recommend accessing controlled-access MAFs through GDC, which requires user certification through dbGaP. The clinical variant data provided is reported from the  Case Report Forms (CRF).

Image showing a searchable feature on HCMI Searchable Catalog

Associated Program: 
Human Cancer Models Initiative
PGDI: 
No
Last updated: April 21, 2021