Cell Model Passports-a hub for clinical, genetic and functional datasets of preclinical cancer models

Abstract

In vitro cancer cell cultures are facile experimental models used widely for research and drug development. Many cancer cell lines are available and efforts are ongoing to derive new models representing the histopathological and molecular diversity of tumours. Cell models have been generated by multiple laboratories over decades and consequently their annotation is incomplete and inconsistent. Furthermore, the relationships between many patient-matched and derivative cell lines have been lost, and accessing information and datasets is time-consuming and difficult. Here, we describe the Cell Model Passports database; cellmodelpassports.sanger.ac.uk, which provides details of cell model relationships, patient and clinical information, as well as access to associated genetic and functional datasets. The Passports database currently contains curated details and standardized annotation for >1200 cell models, including cancer organoid cultures. The Passports will be updated with newly derived cell models and datasets as they are generated. Users can navigate the database via tissue, cancer-type, genetic feature and data availability to select a model most suitable for specific applications. A flexible REST-API provides programmatic data access and exploration. The Cell Model Passports are a valuable tool enabling access to high-dimensional genomic and phenotypic cancer cell model datasets empowering diverse research applications.

Figure 1.

A schematic of the hierarchy used by the Cell Model Passports to capture the relationships that exist between cell models. The patient is at the pinnacle of the hierarchy (Patient 1) followed by the samples obtained (Sample 1 and 2) and models established (Model 1, 2 and 3). Establishment of further cell models from a pre-existing cell model are recorded by a parent-child link (Model 4). Image elements were obtained and adapted from Servier Medical Art under a Creative Commons Attribution 3.0 Unported License.

Figure 2.

An overview of the availability of various genomic and functional datasets. Currently, mutation, copy number variation (CNV), methylation, gene expression and drug sensitivity datasets are available. To emphasize the lack of sparsity, a subset of 956 models has been highlighted for which all five datasets are available.

Figure 3.

An example of a Passport Model Page. The model features and datasets are provided by the multiple information panels. Links are provided to NCI-Thesaurus definitions as well as raw and processed genomic and drug sensitivity data.