Work package leader:

Jan Koster (AMC), Louis Stancato (Eli Lilly).
Co-lead: Natalie Jäger (DKFZ)

Objectives of the work package:

Information technology infrastructure and data analysis

Description of the tasks:

Centralized data repository including results of the project such as precompetitive model characteristics (i.e., all data associated with model molecular and pharmacological characterization using commercially-available agents) and SOC testing data with custom informatics tools to visualize and analyze data.

For dissemination of processed genomics and drug-testing data, the consortium proposes to build on the existing IT infrastructure that is available at the AMC (R2; and which is used extensively in the pediatric cancer research community. R2 already has an extensive track record in providing biomedical researchers insight into their high-throughput data (390+ Pubmed citations and serving data on 100,000+ samples, Aug. 2016). R2 allows for many different types of investigations on pre-processed genomics data ranging from correlative/differential analyses up to working with whole genome sequencing results in real-time. It contains a wealth of analysis and visualizations that are easily accessible. In addition, R2 hosts a growing set of tools for integrative analyses over different types of data (e.g. correlating gene expression to DNA methylation, DNA copy-number, or mutation status). R2 will host pre-processed genomics data in various ways to allow for ‘browsing’, analysis, and visualization of the diverse types of information obtained throughout this project.

Overview of R2: Genomics Analysis and Visualization Platform – Left panel: Data storage types within the platform. Right panel: Example data visualization and correlation capabilities for mRNA data.