Content: Overview


The majority of models within the Cancer Dependency Map at Sanger have undergone extensive characterisation including: sequencing, copy number, methylation, gene expression and drug screening. These large scale genomic and functional datasets can be explored using dedicated resources such as the Cell Model Passports, Project Score and GDSC. Processed downloads are available here and via the DepMap API. Links to repositories holding raw data are provided in the Cell Model Passports and within each dataset's documentation page.

Dataset Overview

Genomic Datasets

Dataset Type Description Documentation
Mutation All sequencing data including WES, WGS & TGS used to generate mutation data for the cell line and organoid models. Mutation
Copy Number Copy number data obtained using the Affymetrix SNP6 array processed using PICNIC and GISTIC. Copy Number
Gene Expression Gene expression generated from RNASeq data and processed by the iRAP pipeline. Gene Expression
Fusions Gene fusions predicted using Sanger and CCLE RNASeq data. Fusions
Proteomics Protein intensity values acquired using data-independent acquisition mass spectrometry (DIA-MS). Proteomics
Methylation Methylation profiling of cell lines using the Illumina Human Methylation 450 BeadChip. Methlyation

Functional Datasets

Dataset Type Description Documentation
CRISPR WG Drop-out CRISPR-Cas9 drop-out screens in cell models identifying genes required for cell fitness. CRISPR Drop-out
Drug Sensitivity Drug response data and genomic markers of sensitivity generated through large scale cell viability screens. Drug Sensitivity
Growth rate Cell model growth rates derived from the GDSC drug sensitivity screens. Growth Rate

Gene Lists & Driver Annotations

Gene & Driver Lists Description Documentation
Full Gene List Includes the DepMap cancer gene list and HUGO, Ensembl, Entrez and Refseq annotations. Gene List
Driver Gene List Cancer gene list used in Cell Model Passports with tumour suppressor / oncogene annotation. Driver Gene List
Content Overview