DNA Microarray Introduction

Microarray introduction
1
DNA Microarray Introduction
Huai-Kuang Tsai
Department of Computer Science &
Information Engineering
National Taiwan University
[email protected]
2002.03.28
Microarray introduction
2
Contents
Introduction to Microarray
Gene-wide cluster analysis
Software demo
Classification (If we have time)
Genetic network (Optional)
Microarray introduction
3
Introduction to Microarray
What Is microarray
Instruments
Life Cycle
Applications
Microarray introduction
4
What Is Microarray
A new powerful technology for biological exploration which enable one to simultaneously measure the level of activity of up to 60,000 genes. In particular, the amount of mRNA for each gene in a given sample (or a pair of samples) is measured
Parallel
High-throughput
Large-scale
Genomic scale
Microarray introduction
5
Basic Idea
Central dogma
Complementary hybridization
Microarray introduction
6
ATATCGGCATCAGTCGATCGATCATCGATCGAT
UAUAGCCGUAGUCAGCUAGCUAGUAGCUAGCUA
ATATCGGCATCAGTCGATCGATCATCGATCGAT
DNA
mRNA
cDNA
Central Dogma
Microarray introduction
7
Microarray introduction
8
Microarray introduction
9
What Is Microarray
Different Approaches
Microarray introduction
10
Stanford Approach
Use robot to spot glass slides
Able to measure qualitatively relative expression levels of genes
Differential expression by use of simultaneous, two-color fluorescence hybridisation
Cheaper with DIY ($60,000)
Also called home-made system
Microarray introduction
11
Microarray introduction
12
Microarray introduction
13
Microarray introduction
14
Microarray introduction
15
Microarray introduction
16
Microarray introduction
17
Affymetrix
Probe Array (Photolithography)
Synthesis of probe




Microarray introduction
18
Instruments
Arrayer
Scanner
Laser Confocal Microscope
Microarray introduction
19
Arrayer
Microarray introduction
20
Scanner
GenPix 4000
Microarray introduction
21
Life Cycle
Biological
Question
Sample
Preparation
Microarray
Reaction
Microarray
Detection
Data Analysis
& Modeling
Microarray introduction
22
Life cycle
Cy3
(green)
Cy5
(red)
Microarray introduction
23
Procedures
Preparation
Target DNA (reference and test samples)
Slides
Reaction(Droplet or Pin Spotting)
Hybridization
Scanning
Analysis
Image processing
Data mining
Modeling
Microarray introduction
24
Applications
Gene expression studies
Gene function for cell state change in various conditions (clustering, classification)
Disease diagnosis (classification)
Inferring regulatory networks
Pathogen analysis
Microarray introduction
25
Applications(Cont.)
Drug Discovery
identify appropriate molecular targets for therapeutic intervention
monitor changes in gene expression in response to drug treatments
Targeted Drug Treatment
Microarray introduction
26
The Basic System Computational Tasks
Gene set selection
Probe design
Image analysis
Normalization of chip, sample….
…more….
Microarray introduction
27
The Analysis
Computational Tasks
Clustering genes: which genes seem to be regulated together
Classifying genes: which functional class does a given gene fall into
Classifying cell samples: does this patient have ALL or AML
Inferring regulatory networks: what is the “circuitry” of the cell
Microarray introduction
28
Probe design system(一)
A method of hybridization of short synthetic oligonucleotide probes to cloned DNA sequences to derive genetic sequence information.
Application field
oligonucleotide array
Polymerase Chain Reaction : primer design
Microarray introduction
29
Probe design system(二)
Probe design issue
Unique probe for each gene
Different probe sets for each genes : fingerprints
Probes (or a unique probe) of each gene should have the ability of representing the gene.
The similarities between probes should very low.