PDX Finder team will be in AACR Annual Meeting 2019 in Atlanta, Georgia! on 29th March-3rd April 2019
Come and see our poster ! Monday Apr 1, 2019 1:00 PM – 5:00 PM, Poster Section 31
Session Category: Bioinformatics and Systems Biology
Session Title: Databases and Computational Tools for Cancer Discovery
Session Date and Time: Monday Apr 1, 2019 1:00 PM – 5:00 PM
Location: Georgia World Congress Center, Exhibit Hall B, Poster Section 31
PDX Finder: A free and Global Catalogue of Patient Tumour Derived Xenograft Models.
- Conte1 , J. Mason1, C. Halmagyi1, A. Mosaku1 , S. Neuhauser2, D.A. Begley2, D.M. Krupke2, H. Parkinson1, T. Meehan1, C. Bult2
- EMBL-EBI, Hinxton, Cambridge, UK;
- The Jackson laboratory, Bar Harbor, USA
Patient-derived tumor xenograft (PDX) mouse models are an important oncology platform for cancer research, drug development and personalized medicine. PDX models are made available in repositories managed by academic labs, large research consortia and contract research organizations (CROs). Because of the distributed and heterogeneous nature of repositories, finding models of interest is a challenge. To address this issue, The Jackson Laboratory and EMBL-EBI have co-developed the PDX Finder†, a comprehensive free and global catalogue of PDX models and their associated data across resources. In support this initiative, we coordinated the community initiative to develop the PDX Minimal Information standard (PDX-MI) that defines the metadata necessary for describing key elements of a PDX model including clinical attributes of a patient’s tumor, xenograft methods of implantation, host strain and quality assurance methods used for model validation††. PDX-MI serves as the basis for PDX Finder’s comprehensive search and filtering options. In addition to metadata, PDX Finder can store and display associated data like Omics and/or drug dosing studies which can be filtered for, making the models more discoverable. Within PDX Finder, model attributes are harmonized and integrated into a cohesive ontological data model that supports consistent searching across the resources. Advanced search and filtering options allow researchers to find PDX models based on multiple attributes like diagnosis (e.g. invasive ductal carcinoma), various tumour attributes (e.g. metastasis or primary), availability of specific datasets (e.g. mutation, dosing studies), markers (e.g. KRAS V600E) or results from drug resistance/sensitivity studies (e.g. resistance to cetuximab). From PDX Finder, direct links to originating resources are provided to allow users to contact the relevant institution for model acquisition and collaboration. PDX Finder is formally collaborating and providing critical software components to support several worldwide consortia including PDXnet and EurOPDX. We aim to promote standardisation and harmonisation of the (meta)data and accelerate global integration and sharing of PDX models to accelerate cancer research and drug discovery. PDX Finder is a free global catalog currently displaying data from over 2000 PDX models for a wide variety of cancers from both academia and CROs. The community is actively invited to submit their PDX models, explore and provide feedback as we build this rich resource at: www.pdxfinder.org. Software components developed by the PDX Finder team are freely available under an Apache 2 license and source code is available at GitHub github.com/pdxfinder.
† Conte et al, 2019. PDX Finder: A Portal for Patient-Derived tumor Xenograft Model Discovery. NAR, in press.
†† Meehan, Conte et al, 2017. PDX-MI: Minimal
Information for Patient-Derived Tumor Xenograft Models. Cancer Res. 2017 Nov.