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30-3-2015
R2: Biologist friendly web-based genomics
analysis & visualization platform
Power to the biomedical researcher
Jan Koster
Department of Oncogenomics
Academic Medical Center (AMC)
UvA, the Netherlands
jankoster@amc.uva.nl
The problem
• High throughput technologies have become part of the every
day biomedical laboratory standards
• Working with these data can be challenging and is often
done via external collaboration (bioinformatics group)
• As a consequence the wetlab researchers are out of touch
with their own data, while external data analysts that are not
in touch with the experiment are analyzing the data in stead.
jankoster@amc.uva.nl
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What is R2?
• R2 genomics analysis and visualization platform
– Web based (http://r2.amc.nl)
• No installation required
• Works everywhere (lab / home /
conference room)
– (Public) collection datasets
• Uniform normalization
– Analysis/Visualization tools
• Intended users
– Biomedical researchers
– Wetlab biologists
• Queries
– Targeted by users interests
– Graphical representations
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Overview of R2 core
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Before we start
• Neuroblastoma
– Childhood tumor
– MYCN oncogene amplified (++ DNA copies) in 20%
patients
• Bad prognosis on their survival
• Amplification is measured in clinical setting and used in risk
stratification
• Most of the options in R2 will be demonstrated in a
neuroblastoma dataset generated within the
department of Oncogenomics (NB88), and in
addition focus on the MYCN gene or its
amplification status
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R2 main window
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R2 main window
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R2 main window
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View a gene
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View a gene
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View a gene
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View a gene
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TranscriptView
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Differential Expression
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Differential Expression
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Differential Expression
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Detailed View
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Detailed View
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Detailed View
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KaplanScan
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Differential Expression
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2 groups plotter
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Differential Expression
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Gene Ontology
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Differential Expression
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Scavenger / gene set analysis
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Differential Expression
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Also in R2
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Across datasets
• One of the Powers of R2 is the large database of
diverse (public) datasets and the possibility to
combine them for analysis / visualizations
Cell Lines
Pediatric Cancers
Normal Tissues
RMS
OS
NRBL
MB
GBM
Ewing
Leukemia
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Adult Cancers
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Integrative Analyses (different data types)
+
jankoster@amc.uva.nl
Hovestadt
et al, Nature, 2014
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4: Whole genome sequencing data in R2
Neuroblastoma primary tumors (n=87 pairs)
Only ~12 aa affecting mutations
Chromothripsis frequent in high stage disease
Structural variations affecting single genes
jankoster@amc.uva.nl
Molenaar
& Koster et al, Nature, 2012
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Whole genome sequencing data in R2
Cohort
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Patient
Variants
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R2 usage overview
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Acknowledgements
Development/Concepts/Support
Jan Koster
Richard Volckmann
Piet Molenaar
Danny Zwijnenburg
Jan Molenaar
Marcel Kool
Linda Valentijn
Rogier Versteeg
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