R2: Biologist friendly web-based genomics analysis & visualization

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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.
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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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Detailed View
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Detailed View
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Detailed View
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KaplanScan
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2 groups plotter
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Gene Ontology
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Scavenger / gene set analysis
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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)
+
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
Molenaar
& Koster et al, Nature, 2012
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Whole genome sequencing data in R2
Cohort
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Variants
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R2 usage overview
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http://r2.amc.nl
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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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R2: Biologist friendly web-based genomics analysis & visualization

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