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

TLDR

In vitro cancer cell cultures are widely used experimental models, yet the large number of lines, incomplete and inconsistent annotations, and lost relationships between patient‑matched and derivative models make accessing relevant information time‑consuming and difficult. The authors present Cell Model Passports, a database that details cell‑model relationships, patient and clinical information, and provides access to associated genetic and functional datasets. The database curates standardized annotations for over 1,200 models, is continuously updated, allows navigation by tissue, cancer type, genetic features and data availability, and offers a flexible REST‑API for programmatic access. Cell Model Passports facilitates rapid access to high‑dimensional genomic and phenotypic datasets, thereby empowering diverse cancer research applications.

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.