Welcome!

Introduction to High Throughput Genomics December 2011

Norwegian Microarray ConsortiumFUGE Bioinformatics platform

Rita HoldhusKjell Petersen

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oCourse program – Day 1

Thursday 1st December 2011Lille Auditorium 2nd floor HiB

09.00 – 09.20: Welcome - Introduction09.20 – 09.50: Different microarray applications09.50 – 10.05: Break10.05 – 10.35: Microarray technologies10.35 – 10.50: Break10.50 – 11.35: Microarray pipeline11.35 – 12.20: Lunch12.20 – 12.50: Case study I: Gene expression in rat brain12.50 – 13.10: Case study II: DNA copy number changes (Array-CGH and SNP-analysis) 13.20 – 13.35: Break 13.35 – 15.00: Experimental design with practical exercise15.00 – 15.30: Questions and summary day 1

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oCourse program – Day 2

Friday 2nd December 2011Lille Auditorium 2nd floor HiB

09.00 – 10.00: Introduction Next Generation Sequencing technology10.00 – 10.15: Break10.15 – 11.00: Different NGS applications11.00 – 11.15: Break11.15 – 11.45: Case III: A gene centric NGS case study12.00 – 12.45: Lunch12.45 – 13.45: Quality Control and outlier detection13.45 – 14.00: Break14.00 – 15.00: Pre-processing (filtering, normalization)15.00 – 15.30: Questions and evaluation

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oThe Norwegian Microarray Consortium (NMC)

• A national platform for microarray technology and high- throughput genomics

• A collaboration between groups from:– 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.

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• Three regional microarray core facilities

Bergen node:

Center for Medical Genetics and molecular Medicine

The Laboratory Building, Haukeland University Hospital

CBU – Computational Biology Unit

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oThe Norwegian Microarray Consortium (NMC)

• Microarray services and soon NGS services to both national and foreign Microarray services and soon NGS services to both national and foreign usersusers

• Design meetings (how to get focussed, reliable results, randomization, Design meetings (how to get focussed, reliable results, randomization, experimental design..) experimental design..)

• Courses as:Courses as:

• Introduction to highthroughput genomics (2 days) Introduction to highthroughput genomics (2 days) • Analysis course (3 days)Analysis course (3 days)

– J-expressJ-express– R/BioConductorR/BioConductor

• WorkshopsWorkshops• Data analysis Data analysis

– Every last Friday of the monthEvery last Friday of the month– Participants should have their own datasetParticipants should have their own dataset

• BASEBASE (BioArray Software Environment)

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oShort introduction to microarrays

What?

Why?

How?

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oWhat is a microarray?

(As an example: DNA microarray)

Gene A

Gene B

Gene C

etc….

Microscopic slide

Specific DNA-probes

- DNA probe binds to complementary region- Sample of interest labelled with a fluorophore- Visualized and quantified

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oEvolution of microarrays

Multiple Northern blotsMultiple Northern blots

MacroarraysMacroarrays

cDNA microarrayscDNA microarrays

Oligonucleotide arraysOligonucleotide arrays

Todays technology – High density arraysTodays technology – High density arrays

Next-generationNext-generation

1977

1987

1995

1996

2003

2005

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Multiple Northern blotsMultiple Northern blots

Evolution of microarrays – Northern blots

1977

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Multiple Northern blots

Macroarrays (spotted cDNAs, nylon filters, ~1000 genes)Macroarrays (spotted cDNAs, nylon filters, ~1000 genes)

Evolution of microarrays – Macroarrays

1987

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Multiple Northern blots

Macroarrays (spotted cDNAs, nylon filters, ~1000 genes)

cDNA microarrays

Evolution of microarrays – Microarrays

(cDNA probes> 200 nt, (cDNA probes> 200 nt,

PCR produced)PCR produced)

1995

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Multiple Northern blots

Macroarrays (spotted cDNAs, nylon filters, ~1000 genes)

cDNA microarrays

Oligonucleotide arrays (oligos ~50 – 80 nt, more than 10 000 genes)

Evolution of microarrays – Microarrays

1996

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Todays technology – High density arraysTodays technology – High density arrayse.g. Illumina Bead arrays; 50 nt probes; e.g. Illumina Bead arrays; 50 nt probes; 1 000 000s of probes1 000 000s of probes

Evolution of microarrays – High density arrays

2003

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Next-generation; single-molecule sequencingNext-generation; single-molecule sequencing

Evolution of microarrays – High throughput sequencing

2005

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oWhy/How use HT genomics technology

• Each cell type expresses ~ 10- 20 000 genes

• Physiological and pathophysiological responses are linked to changes in gene expression/genetic features

• Knowledge of gene expression variation at different states may create new hypotheses about gene function and underlying mechanisms

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oWhy/How use HT genomics technology

Biology Genomics

Cell culture

Organ

Organism

~ 30 000 genes

DNA sequence

Protein sequence

Which genes are involved in a given biological process?

What are their functions?

Functional genomics

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oWhy/How use HT genomics technology

Biology Genomics

Cell culture

Organ

Organism

~ 30 000 genes

DNA sequence

Protein sequence

Which genes are involved in a given biological

process?

What are their functions?

Functional genomics

High-throughput analyses

Parallel analysis of 1000s of genes and proteins

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oHigh- throughput analysis

• Gene expression (gene activity)

• Sequence variations (SNPs/mutations)

• Chromosome copy numbers

• DNA-binding proteins (transcription factors)

• DNA methylation

• Protein profiles

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oCourse program – Day 1

Thursday 1st December 2011Lille Auditorium 2nd floor HiB

09.00 – 09.20: Welcome - Introduction09.20 – 09.50: Different microarray applications09.50 – 10.05: Break10.05 – 10.35: Microarray technologies10.35 – 10.50: Break10.50 – 11.35: Microarray pipeline11.35 – 12.20: Lunch12.20 – 12.50: Case study I: Gene expression in rat brain12.50 – 13.10: Case study II: DNA copy number changes (Array-CGH and SNP-analysis) 13.20 – 13.35: Break 13.35 – 15.00: Experimental design with practical exercise15.00 – 15.30: Questions and summary day 1