Abstract 3212: PDX Finder: Largest global catalog of patient tumor derived xenograft models
Authors: Nathalie Conte, Csaba Halmagyi, Abayomi Mosaku, Jeremy C. Mason, Alex W. Follette, Ross Thorne, Steven Neuhauser, Dale Begley, Debbie M. Krupke, Helen Parkinson, Terrence Meehan, Carol Bult
Journal: Cancer Research (2020)

Abstract Patient-derived tumor xenograft (PDX) models are a critical oncology platform for cancer research, drug development and personalized medicine. Because of the heterogeneous nature of PDX repositories, finding models of interest is a challenge. The Jackson Laboratory and EMBL-EBI are developing PDX Finder, the world's largest open PDX database containing phenomic information of over 2900 models (www.pdxfinder.org, †). In support of this initiative, we developed the PDX Minimal Information standard (PDX-MI) which defines the minimal necessary metadata required to describe models (††). Within PDX Finder, critical attributes like diagnosis, drug names or genes are harmonized into a cohesive ontological data model based on PDX-MI. An intuitive, faceted search interface allows users to select models based on clinical/PDX attributes, tumor markers, dataset availability and/or drug dosing results. We provide PDX, patient, drug and molecular data details pages where all available information can be browsed and downloaded. To further facilitate users' model selection, we link key external resources like publication platforms and cancer specific annotation tools, enabling exploration and prioritisation of PDX variation data (COSMIC, CivicDb, OpenCRAVAT). Links to originating resource protocols and contact information are provided, facilitating data understanding and further collaboration. Alongside database development activities, PDX Finder has undertaken activities to tackle areas of standards and tool development, data integration and outreach. PDX Finder provides key expertise and software components to support several worldwide consortia including PDXNet, PDMR and EurOPDX. We are driving the development of, and promoting the use of descriptive standards to facilitate data interoperability and promote global sharing of models. Our standard has become established in the community for data exchange, adopted by PDX providers, consortia, and informatic tools integrating PDX data. It has been re-used by different initiatives in the context of data collection and data modelling allowing adherence to the FAIR data principles - Findability, Accessibility, Interoperability and Reusability. PDX Finder is increasing awareness of PDX models, facilitating data integration, and enabling international collaboration, maximising the investment in, and translational capabilities of these important models of human cancer. PDX Finder is freely available under an Apache 2 license (github.com/pdxfinder). Work supported by NCI U24 CA204781 01, R01 CA089713 and the European Molecular Biology Laboratory. † Conte et al, 2019. PDX Finder: A Portal for Patient-Derived tumor Xenograft Model Discovery. NAR, 2019 Jan.†† Meehan, Conte et al, 2017. PDX-MI: Minimal Information for Patient-Derived Tumor Xenograft Models. Cancer Res. 2017 Nov.PDXNet: www.pdxnetwork.org, PDMR: pdmr.cancer.gov, EUROPDX: www.europdx.eu Citation Format: Nathalie Conte, Csaba Halmagyi, Abayomi Mosaku, Jeremy C. Mason, Alex W. Follette, Ross Thorne, Steven Neuhauser, Dale Begley, Debbie M. Krupke, Helen Parkinson, Terrence Meehan, Carol Bult. PDX Finder: Largest global catalog of patient tumor derived xenograft models [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3212.