PDX Finder: A portal for patient-derived tumor xenograft model discovery

Abstract

Patient-derived tumor xenograft (PDX) mouse models are a versatile oncology research platform for studying tumor biology and for testing chemotherapeutic approaches tailored to genomic characteristics of individual patients' tumors. PDX models are generated and distributed by a diverse group of academic labs, multi-institution consortia and contract research organizations. The distributed nature of PDX repositories and the use of different metadata standards for describing model characteristics presents a significant challenge to identifying PDX models relevant to specific cancer research questions. The Jackson Laboratory and EMBL-EBI are addressing these challenges by co-developing PDX Finder, a comprehensive open global catalog of PDX models and their associated datasets. Within PDX Finder, model attributes are harmonized and integrated using a previously developed community minimal information standard to support consistent searching across the originating resources. Links to repositories are provided from the PDX Finder search results to facilitate model acquisition and/or collaboration. The PDX Finder resource currently contains information for 1985 PDX models of diverse cancers including those from large resources such as the Patient-Derived Models Repository, PDXNet and EurOPDX. Individuals or organizations that generate and distribute PDXs are invited to increase the 'findability' of their models by participating in the PDX Finder initiative at www.pdxfinder.org.

Figure 1.

PDX Model Search page. Example of a search output corresponding to a query for colorectal cancer PDX model with KRAS G12D mutations and resistance to cetuximab.

Figure 2.

PDX Model and Patient Detail Pages. (A) Example of a PDX model detail page. A tabulated section beneath the overview provides summary views of clinical, model and validation information. Contact links at the top right allow users to directly contact the PDX Producer for further collaboration. (B) Example of a Patient Detail page that contains key clinical attributes about the tumor collection event(s) used to generate PDX models.

Figure 3.

PDX Data pages. (A) The Molecular data page contains genomic data analysis files that where provided by the resources. A table summarises the types of data and files accessible, with links to the datasets. The results can be exported in a tabular format using the ‘Download Results’ icon. (B) The Drug dosing page summarise the drug-response results generated for a particular model. Links to protocols and platforms description are provided for all datasets to allow the user to understand how the data was generated and analysed.