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. 2022 Feb 22;23(1):156.
doi: 10.1186/s12864-022-08367-1.

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

Zdenka Dudová #  1 , Nathalie Conte #  2 , Jeremy Mason  2 , Dalibor Stuchlík  1 , Radim Peša  1 , Csaba Halmagyi  2 , Zinaida Perova  2 , Abayomi Mosaku  2 , Ross Thorne  2 , Alex Follette  2 , Ľuboslav Pivarč  1 , Radim Šašinka  1 , Muhammad Usman  1 , Steven Neuhauser  3 , Dale A Begley  3 , Debra M Krupke  3 , Massimiliano Frassà  4 , Alessandro Fiori  4 , Riccardo Corsi  5 , Luca Vezzadini  5 , Claudio Isella  4   6 , Andrea Bertotti  4 , Carol Bult  3 , Helen Parkinson  2 , Enzo Medico  4   6 , Terrence Meehan #  2 , Aleš Křenek #  7
Affiliations

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

Zdenka Dudová et al. BMC Genomics. .

Abstract

Background: Patient-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 body: In 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) conclusion: EurOPDX 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.

Keywords: Data harmonization; Database; Molecular data analysis; PDX; Research infrastructure.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
EurOPDX Data Portal data flows. Four layers are described: (i) Input layer for metadata and processed molecular data provided by partners from the consortium. These data are collected via templates and laboratory information management systems (LIMS); (ii) Data processing layer where the data are collected, semi-automatically standardized and harmonized to be aligned with PDX Finder data services utilized in the Portal as well; (iii) Storage layer consists of the Data Hub where the EurOPDX data are stored; (iv) Data analysis layer is then a graphical user interface enabling (meta)data browsing and further analysis
Fig. 2
Fig. 2
Visualization of data types available in the Data Portal, by percentage. Out of 1010 deposited models, 653 include gene mutation data (65%), 505 include copy number alteration data (50%), for 283 models there are available drug dosing studies (28%), 270 models include gene expression data (27%), 103 models cytogenetics (10%), and 69 models include patient treatment data (7%)
Fig. 3
Fig. 3
EurOPDX Data Hub schema. The Hub includes the Neo4J database containing data accessible via the Data Portal Search page, and the MySQL database providing temporary operational data. There is a REST API available within the Hub accessible to the chaining tools
Fig. 4
Fig. 4
Schema of the Neo4J Database. Each node of the graph database schema is an entity or event captured in the data. Arrows, so called edges, show the relationships between the nodes
Fig. 5
Fig. 5
EurOPDX data visualization in the EurOPDX cBioPortal instance. A Example of plots which can be designed according to the user’s needs. This is a plot showing EGFR gene mutations compared with age of the patient within a selected study; B OncoPrint of queried genes. Provides information about number of samples per patient within a selected study, data types availability per each sample and gene mutations or alterations; C Example of mutation analysis of a chosen dataset – MutationMapper tool. It is possible to browse mutations within the selected gene - mutations mapping on a linear protein and its domains, type of the mutation – and get detailed sample information in which mutations are present. 3D visualizations of the protein interactions and other mutation information is available by linking external databases
Fig. 6
Fig. 6
Screenshot of the Search page from the EurOPDX Data Portal
See this image and copyright information in PMC

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