Chris Evelo Maastricht University.Pdf

• • • •

Academic Government Research Forensic & Pharmaceutical Drug testing Cancer Chemical & Diagnostics Energy Cytogenetic Environment research Genomics for FoodFood Molecular Analysis

CORE TECHNOLOGY PLATFORMS

26/11/13 22 About 100 active university collaborations annually

U of Washington Technical U of Denmark UC Davis U of Calgary Karolinska Inst., Sweden UCSF U of Michigan Karlsruhe U, Germany UC Berkeley U of Illinois Yale MIT Maastricht U, NL U of Twente, NL Tsinghua U, China Stanford CU Boulder Princeton U of Kent, UK U of Manchester, UK Harvard Arizona State NIBRT, Ireland Charles U, Czech Republic Seoul Nat’l U, Korea Johns Hopkins UC San Diego U of Oviedo, Spain Technion, Israel Chungnam Nat’l U, Korea U of Maryland Baylor U U of Alicante, Spain Tohoku U, Japan U of Texas Hamner Inst. Southeast U, China U of Houston U Teknologi MARA, Malaysia NUS, Singapore NTU, Singapore U of São Paulo, Brazil UNICAMP, Brazil U of Queensland Macquarie U U of Pretoria, S. Africa U of W. Australia Curtin U. Electronics U of Sydney U Tech, Sydney Chemical Analysis RMIT U Monash U Life Sciences U of Tasmania

26/11/13 23 TL Network http://www.agilent.com/univ_relation/TLP/index.shtml Thought Leader Awards

Promote fundamental advances in life science through contribution to research of thought leaders

• Align societal trends, academic research and rapidly advancing Agilent measurement platforms:

Synthetic Biology, Structural Biology, OMICS & Integrated Biology, in vitro Toxicology, and Environemntal & Food Safety

• Candidates selected based on scientific Establish strong collaborative leadership, productivity, project significance relationships with highly promising (invitational program) early career professors

• High-level executive sponsorship and active support 2013 focus: throughout Agilent enable breakthrough research Contributions to cancer diagnostics

26/11/13 24 LC/MS MassHunter Qual/Quant GC/MS ChemStation AMDIS

Microarrays Feature Extraction GeneSpring Platform Biological Pathways

Alignment to Reference Genome NGS Agilent’s Platform for Multi-Omics Data Analysis mRNA, miRNA, Exon arrays GWAS, CNV via SNP arrays

SureSelect Target Enrichment Whole Genome Sequencing

Proteomics Metabolomics mRNA microRNA QPCR NGS (Next-Gen Alternative Splicing Sequencing) SureSelect Target Enrichment GWAS & CNV via SNP arrays Whole Genome Sequencing MPP (Mass Profiler Pro) Proteomics Metabolomics

PA (Pathway Analysis) GX (Gene Expression) SureSelect Target Enrichment Whole Genome Sequencing DNA-Seq

RNA-Seq SureSelect Target Enrichment Methyl-Seq Whole Genome Sequencing ChIP-Seq MPP (Mass Profiler Pro) Proteomics small RNA-Seq Metabolomics

PA (Pathway Analysis) NGS Analysis Workflow: 1. Align data 2. Load BAM/SAM into GS NGS 3. Measure Gene Expression, Find variants, methyl calls 4. Biological Contextualization (Integrated Genomics, GO, Pathways) GX (Gene Expression)

• Import, store, and visualize Agilent Metabolomics & Proteomics data NGS (Next-Gen (LC/MS, GC/MS) Sequencing) SureSelect Target Enrichment • Generic file import Whole Genome Sequencing • Statistical analysis Proteomics • ID Browser for compound identification Metabolomics

PA (Pathway Analysis) (Gene Expression) Multi-Omic Analysis GX Canonical Pathways Network Discovery NGS (Next-Gen Sequencing) SureSelect Target Enrichment Whole Genome Sequencing MPP (Mass Profiler Pro) Proteomics Metabolomics • Map and visualize data from one or two types of –omic data on pathways

Metabolite Data • Search, browse and filter pathways Overlay

Supports pathways from: •WikiPathways •BioCyc

•Supported pathway formats • BioPAX 3 – Pathway Commons, Reactome, NCI Nature Pathway List of all pathway entities, dynamically • GPML – PathVisio –custom drawing linked to pathway selection Export compound list from pathways metabolites proteins Proteomics Genomics Proteomics and Genomics Select View overlaid Import of WikiPathways WikiPathways data on for analysis WikiPathways Examine Experimental Data

Export Pathway Entities Propose new experiments based on pathway analysis Build custom metabolite PCDL • Re-examine acquired untargeted database metabolomics data based on pathway analysis • Design new experiments (metabolite, Custom microarray or NGS eArray protein or genes) based on pathway design results interpretation

Targeted MS/MS Spectrum Mill Typical workflow used for identification of a relevant pathway using GeneSpring

Curated pathway Network analysis using Identification of Statistical analysis and analysis using NLP to identify differential expression filtering Wikipathways interaction of pathways Identification of Candidate Genes

Step 2) Volcano plot of showing Step 1) Identification of significantly differentially expressed differentially expressed between two conditions genes via hierarchical cluster analysis From Differential Expression to Pathways

Step 3) Significantly changed Step 4) The Protein-Protein Interactions pathways in Müller cells identified analysis was further performed to identify using pathway analysis in the direct interaction of these genes GeneSpring products in GeneSpring Pathway analysis showed significant changes in MAPK signaling at both conditions. Network analysis shows interaction of MAPK with other gene products. Compare network analysis/extension in Cytoscape.

OPS Framework OPS GUI Architecture. Dec 2011

Web Services

Identity & Vocabulary Management

Chemistry Normalisation & Registration

Public Vocabularies