Sanger DepMap Websites

The Cell Model Passports provides manual and programmatic access to a cancer cell model database containing curated patient, sample and model relationship information as well as genomic and functional datasets. Over 1700 cancer cell models have been incorporated covering all models used within the Sanger Cancer Dependency Map.

Large scale genomic datasets exist for the majority of models in the database including somatic nucleotide variant, gene expression, copy number variation and methylation data. Links to raw data are provided and direct downloads of processed genomic data enable and improve accessibility for non-computational, wet-lab scientists.

The Cell Model Passports exploits these genomic and functional datasets to provide users with additional model specific information. Genomic characteristics such as microsatellite stability status, ploidy, mutational burden are reported in addition to top drug sensitivities determined from the GDSC project.

As an evolving platform the Cell Model Passports is designed to incorporate new datasets and models. This will include organoids derived at the Sanger as part of the Human Cancer Model Initiative and datasets such as whole-genome CRISPR-knockout screens generated for the Sanger Cancer Dependency Map.

Publication reference: van der Meer, D; Barthorpe, S; Yang, W; Lightfoot, H; Hall, C; Gilbert, G, Francies, HE; Garnett, MJ Cell Model Passports—a hub for clinical, genetic and functional datasets of preclinical cancer models, Nucleic Acids Research 2019.

The DepMap Miner is platform to analyse & explore multiomic and functional datasets within the Dependency Map at Sanger.

The website integrates the datasets available from the Cell Model Passports and provides tools to examine gene dependencies and context specificity. In addition the website provides tools to explore the explore the GDSC drug sensitivity data.

Genomics of Drug Sensitivity in Cancer

The Genomics of Drug Sensitivity in Cancer website's datasets and features have now been integrated into the Cell Model Passports & DepMap Miner..

The Genomics of Drug Sensitivity in Cancer (GDSC) datasets are available to download on the Cell Model Passports.

This data can be explored using the DepMap Miner.

Publication references:

Yang W et al. Genomics of Drug Sensitivity in Cancer (GDSC): a resource for therapeutic biomarker discovery in cancer cells. Nucleic Acids Res. 2013 Jan

Garnett, M. et al. Systematic identification of genomic markers of drug sensitivity in cancer cells. Nature 2012.

Francesco Iorio et al. A Landscape of Pharmacogenomic Interactions in Cancer, Cell, 2016.

Project Score

The Project Score website's datasets and features have now been integrated into the Cell Model Passports & DepMap Miner.

An updated CRISPR dependency dataset is available to download on the Cell Model Passports. This data can be visualised and explored using the DepMap Miner.

Access to Project Score archived datasets is available via the Cell Model Passports download pages.

Publication references:

Dwane L, et al. Project Score database: a resource for investigating cancer cell dependencies and prioritizing therapeutic targets. Nucleic Acids Res. 2021

Behan, F.M., Iorio, F., Picco, G. et al. Prioritization of cancer therapeutic targets using CRISPR–Cas9 screens. Nature 2019

Clare Pacini, et al. A comprehensive clinically informed map of dependencies in cancer cells and framework for target prioritization, Cancer Cell, 2024.