The EurOPDX Data Portal: an open platform for patient-derived cancer xenograft data sharing and visualization

Zdenka Dudová,Ľuboslav Pivarč,Radim Šašinka,Aleš Křenek,Radim Peša,Alex Follette,Jeremy Mason,Dalibor Stuchlík,Massimiliano Frassà,Zinaida Perova,Ross Thorne,Carol J Bult ,Enzo Medico,Riccardo Corsi,Andrea Bertotti,Nathalie Conte,Dale A Begley,Muhammad Usman,Claudio Isella,Abayomi Mosaku,Helen Parkinson,Luca Vezzadini,Debra M Krupke,Csaba Halmagyi,Steven B Neuhauser ,Fabio Mammano ,Alessandro Fiori

doi:10.1186/s12864-022-08367-1

Abstract

BackgroundPatient-derived xenografts (PDX) mice models play an important role in preclinical trials and personalized medicine. Sharing data on the models is highly valuable for numerous reasons – ethical, economical, research cross validation etc. The EurOPDX Consortium was established 8 years ago to share such information and avoid duplicating efforts in developing new PDX mice models and unify approaches to support preclinical research. EurOPDX Data Portal is the unified data sharing platform adopted by the Consortium.Main bodyIn this paper we describe the main features of the EurOPDX Data Portal (https://dataportal.europdx.eu/), its architecture and possible utilization by researchers who look for PDX mice models for their research. The Portal offers a catalogue of European models accessible on a cooperative basis. The models are searchable by metadata, and a detailed view provides molecular profiles (gene expression, mutation, copy number alteration) and treatment studies. The Portal displays the data in multiple tools (PDX Finder, cBioPortal, and GenomeCruzer in future), which are populated from a common database displaying strictly mutually consistent views.(Short) ConclusionEurOPDX Data Portal is an entry point to the EurOPDX Research Infrastructure offering PDX mice models for collaborative research, (meta)data describing their features and deep molecular data analysis according to users’ interests.

Highlights

Patient-derived xenografts (PDX) mice models play an important role in preclinical trials and personalized medicine
Patient-derived xenografts (PDX) become increasingly important as they provide a new approach for preclinical cancer research
Since the number of researchers working with PDX mice models across Europe is rising quickly, as well as the number of models generated, there was a need to organize information about European PDX mice models

Summary

D ATA B A S E

The EurOPDX Data Portal: an open platform for patient-derived cancer xenograft data sharing and visualization. Zdenka Dudová1†, Nathalie Conte2†, Jeremy Mason, Dalibor Stuchlík, Radim Peša, Csaba Halmagyi, Zinaida Perova, Abayomi Mosaku, Ross Thorne, Alex Follette, Ľuboslav Pivarč, Radim Šašinka, Muhammad Usman, Steven Neuhauser, Dale A.

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