1. Galaxy course EMC TraIT Nov 2014_Jenster
Data analysis and integration
How to get from a pile of unprocessed data to knowledge:
The user’s perspective
Guido Jenster, Ph.D.
Professor of Experimental Urological Oncology
Department of Urology
Erasmus MC

2. Experimental Research
Prostate Cancer Molecular Medicine
Clinical Research
Biobanking
Experimental Research
Imaging
DATA
QUERY
VIEWING
DATA INTEGRATION
DATA PROCESSING
NEW KNOWLEDGE
DATA STORAGE
DATA GENERATION
FAIR: Findable, Accessible, Interoperable, Reusable

3. Prostate Cancer Molecular Medicine
What do we want?
Use case:
Identify novel fusion genes from DNA and RNA sequencing data
PUSH TO
START

4. Experimental Research
Prostate Cancer Molecular Medicine
Clinical Research
Biobanking
Experimental Research
Imaging
DATA INTEGRATION
DATA PROCESSING
DATA STORAGE
DATA GENERATION

5. The TraIT mansion requires good support
Adopt, Adapt, Develop

6. Copy Number Abberations
DNAseq Data Analysis
SNVs / InDels
Copy Number Abberations
TF Binding
B-Allele Frequency
DNAseq data
Chromatin Interactions
Structural Variations
Methylation
Active Chromatin
MetaGenomics
Identify
Integration Sites
Read
Barcode

7. Differential expression MetaTranscriptomics
RNAseq Data Analysis
Differential expression
MetaTranscriptomics
SNVs / InDels
RNAseq data
Alternative splicing &
Promoters
Novel Transcripts
Read-Through & Fusion Transcripts

8. Prostate Cancer Molecular Medicine
What do we want?
Use case:
Identify novel fusion genes from DNA and RNA sequencing data
PUSH TO
START

9. Intrachromosomal fusions from RNAseq and WGS DNAseq from a selection of 266 Breast Cancers
Smid et al., Nat Commun Sep 26;7:12910
Nik-Zainal et al., Nature Jun 2;534(7605):47-54.

10. Comparison of WGS and RNAseq DNA breaks in 266 Breast Cancers
Whole Genome
Sequencing
Random-primed
RNA sequencing

11. TraIT Galaxy

12. Work Flows

13. Galaxy course EMC TraIT Nov 2014_Jenster
Data Mining: Query & Viewing Tools
Platform
Level:
Which level do I want to mine?
Between-Study Level
Study Level
Patient/Sample Level
Molecular Level
Single gene
Explain how our Use Case evolved and got complex and big, but also covers many NGS pipelines to serve a large community
Tool:
What is the best query
& viewing tool?

15. Erasmus MC Cancer Research Facilities