Welcome! Introduction to High Throughput Genomics December Norwegian Microarray Consortium FUGE Bioinformatics platform
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1 Introduction to High Throughput Genomics December 2011 Norwegian Microarray Consortium FUGE Bioinformatics platform Rita Holdhus Kjell Petersen Welcome!
2 Course program Day 1 Thursday 1st December 2011 Lille Auditorium 2nd floor HiB : Welcome - Introduction : Different microarray applications : Break : Microarray technologies : Break : Microarray pipeline : Lunch : Case study I: Gene expression in rat brain : Case study II: DNA copy number changes (Array-CGH and SNP-analysis) : Break : Experimental design with practical exercise : Questions and summary day 1
3 Course program Day : Introduction Next Generation Sequencing technology : Break : Different NGS applications : Break : Case III: A gene centric NGS case study : Lunch : Quality Control and outlier detection : Break : Pre-processing (filtering, normalization) : Questions and evaluation Friday 2nd December 2011 Lille Auditorium 2nd floor HiB
4 The Norwegian Microarray Consortium (NMC) University of Oslo and the Radiumhospital Norwegian University of Science and Technology in Trondheim (NTNU) University of Bergen (UiB) Founded in year 2000 (Norwegian cancer society) National microarray technology platform under the Functional Genomics (FUGE) program of the Research Council of Norway. A national platform for microarray technology and high- throughput genomics A collaboration between groups from:
5 Three regional microarray core facilities Center for Medical Genetics and molecular Medicine The Laboratory Building, Haukeland University Hospital CBU Computational Biology Unit Bergen node:
6 The Norwegian Microarray Consortium (NMC) Microarray services and soon NGS services to both national and foreign users Courses as: Introduction to highthroughput genomics (2 days) Analysis course (3 days) J-express R/BioConductor Workshops Data analysis Every last Friday of the month Participants should have their own dataset BASE (BioArray Software Environment) Design meetings (how to get focussed, reliable results, randomization, experimental design..)
7 Short introduction to microarrays Why? How? What?
8 What is a microarray? (As an example: DNA microarray) Specific DNA-probes Gene A Gene B etc. Microscopic slide - DNA probe binds to complementary region - Sample of interest labelled with a fluorophore - Visualized and quantified Gene C
9 Evolution of microarrays Multiple Northern blots 1987 Macroarrays 1995 cdna microarrays 1996 Oligonucleotide arrays 2003 Todays technology High density arrays 2005 Next-generation 1977
10 Evolution of microarrays Northern blots 1977 Multiple Northern blots
11 Evolution of microarrays Macroarrays Multiple Northern blots Macroarrays (spotted cdnas, nylon filters, ~1000 genes) 1987
12 Evolution of microarrays Microarrays Multiple Northern blots 1995 cdna microarrays (cdna probes> 200 nt, PCR produced) Macroarrays (spotted cdnas, nylon filters, ~1000 genes)
13 Evolution of microarrays Microarrays Multiple Northern blots cdna microarrays 1996 Oligonucleotide arrays (oligos ~50 80 nt, more than genes) Macroarrays (spotted cdnas, nylon filters, ~1000 genes)
14 Evolution of microarrays High density arrays 2003 Todays technology High density arrays e.g. Illumina Bead arrays; 50 nt probes; s of probes
15 Evolution of microarrays High throughput sequencing 2005 Next-generation; single-molecule sequencing
16 Why/How use HT genomics technology Each cell type expresses ~ genes Knowledge of gene expression variation at different states may create new hypotheses about gene function and underlying mechanisms Physiological and pathophysiological responses are linked to changes in gene expression/genetic features
17 Why/How use HT genomics technology Functional genomics Biology Which genes are involved in a given biological process? Organ Organism What are their functions? ~ genes DNA sequence Protein sequence Cell culture Genomics
18 Why/How use HT genomics technology Functional genomics Biology Genomics What are their functions? ~ genes DNA sequence Organ Organism High-throughput analyses Parallel analysis of 1000s of genes and proteins Protein sequence Cell culture Which genes are involved in a given biological process?
19 High- throughput analysis Gene expression (gene activity) Chromosome copy numbers DNA-binding proteins (transcription factors) DNA methylation Protein profiles Sequence variations (SNPs/mutations)
20 Course program Day 1 Thursday 1st December 2011 Lille Auditorium 2nd floor HiB : Welcome - Introduction : Different microarray applications : Break : Microarray technologies : Break : Microarray pipeline : Lunch : Case study I: Gene expression in rat brain : Case study II: DNA copy number changes (Array-CGH and SNP-analysis) : Break : Experimental design with practical exercise : Questions and summary day 1
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