Galaxy course EMC TraIT Nov 2014_Jenster

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Presentation transcript:

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 g.jenster@erasmusmc.nl

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

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

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

The TraIT mansion requires good support https://trait.health-ri.nl/trait-tools Adopt, Adapt, Develop

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

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

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

Intrachromosomal fusions from RNAseq and WGS DNAseq from a selection of 266 Breast Cancers Smid et al., Nat Commun. 2016 Sep 26;7:12910 Nik-Zainal et al., Nature. 2016 Jun 2;534(7605):47-54.

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

TraIT Galaxy

Work Flows

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?

https://www.symbaloo.com/shared/AAAAB69x5lwAA42ARlAylQ==

Erasmus MC Cancer Research Facilities http://cancerportal.erasmusmc.nl/ https://intranet.erasmusmc.nl/pathologie/CRS1/Services1/