Abstract LB017: PDX Finder: An open and global catalogue of patient-derived xenograft models
Authors: Zinaida Perova, Csaba Halmagyi, Abayomi Mosaku, Nathalie Conte, Jeremy Mason, Alex Follette, Ross Thorne, Mauricio Martinez, Steven Neuhauser, Dale Begley, Debra Krupke, Helen Parkinson, Terrence Meehan, Carol Bult
Journal: Cancer Research (2021)

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 PDXs 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 millions of phenomic information from over 4300 models (www.pdxfinder.org, PMID: 30535239). In support of this initiative, we developed the PDX Minimal Information standard (PDX-MI) which defines metadata necessary to describe models (PMID: 29092942). 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 search and faceted search interface allow 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 detail pages where all available information can be browsed and downloaded. To further facilitate user's model selection, we are linking key external resources like publication platforms and cancer-specific annotation tools enabling exploration and prioritization of PDX variation data (COSMIC, CIViC, OncoMx, 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 informatics tools integrating PDX data. It has been re-used by different initiatives in the context of data collection and data modeling 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, maximizing 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 (ended 31Aug2020), U24 CA253539, and R01 CA089713. Citation Format: Zinaida Perova, Csaba Halmagyi, Abayomi Mosaku, Nathalie Conte, Jeremy Mason, Alex Follette, Ross Thorne, Mauricio Martinez, Steven Neuhauser, Dale Begley, Debra Krupke, Helen Parkinson, Terrence Meehan, Carol Bult. PDX Finder: An open and global catalogue of patient-derived xenograft models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr LB017.