introduction to dna microarray technologies sandrine dudoit, robert gentleman, rafael irizarry, and...
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Introduction to DNA microarray technologies
Sandrine Dudoit, Robert Gentleman, Rafael Irizarry, and Yee Hwa Yang
Bioconductor short course
Summer 2002
© Copyright 2002, all rights reserved
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Outline
• Basic principles
• cDNA microarrays
• Affymetrix oligonucleotide chips
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DNA microarrays
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DNA microarrays
DNA microarrays rely on the hybridization properties of nucleic acids to monitor DNA or RNA abundance on a genomic scale in different types of cells.
The ancestor of cDNA microarrays: the Northern blot.
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Hybridization
• Hybridization refers to the annealing of two nucleic acid strands following the base-pairing rules.
• Nucleic acid strands in a duplex can be separated, or denatured, by heating to destroy the hydrogen bonds.
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Hybridization
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Hybridization
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Gene expression assays
The main types of gene expression assays:– Serial analysis of gene expression (SAGE);– Short oligonucleotide arrays
(Affymetrix);– Long oligonucleotide arrays (Agilent Inkjet);– Fibre optic arrays (Illumina);– cDNA arrays (Brown/Botstein).
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Applications of microarrays
• Measuring transcript abundance (cDNA arrays);
• Genotyping;• Estimating DNA copy number (CGH);• Determining identity by descent (GMS);• Measuring mRNA decay rates;• Identifying protein binding sites;• Determining sub-cellular localization of gene
products;• …
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Transcriptome
• mRNA or transcript levels sensitively reflect the state of a cell.
• Measuring protein levels (translation) would be more direct but more difficult.
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Transcriptome
• The transcriptome reflects– Tissue source: cell type, organ.– Tissue activity and state:
• Stage of development, growth, death.• Cell cycle.• Disease vs. healthy.• Response to therapy, stress.
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Applications of microarrays
• Cancer research: Molecular characterization of tumors on a genomic scale
more reliable diagnosis and effective treatment of cancer.
• Immunology: Study of host genomic responses to bacterial infections; reversing immunity.
• …
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Applications of microarrays
• Compare mRNA (transcript) levels in different types of cells, i.e., vary– Tissue: liver vs. brain;– Treatment: drugs A, B, and C;– State: tumor vs. non-tumor, development;– Organism: different yeast strains;– Timepoint;– etc.
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cDNA microarrays
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cDNA microarraysPrepare cDNA target
Hybridizetarget to microarray
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cDNA microarrays
• The relative abundance of a spotted DNA sequence in two DNA or RNA samples may be assessed by monitoring the differential hybridization of these two samples to the sequence on the array.
• Probes: DNA sequences spotted on the array, immobile substrate.
• Targets: Nucleic acid samples hybridized to the array, mobile substrate.
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cDNA microarrays
• The ratio of the red and green fluorescence intensities for each spot is indicative of the relative abundance of the corresponding DNA probe in the two nucleic acid target samples.
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cDNA microarrays
M = log2 R/G = log2R - log2G
• M < 0, gene is over-expressed in green-labeled sample compared to red-labeled sample.
• M = 0, gene is equally expressed in both samples.
• M > 0, gene is over-expressed in red-labeled sample compared to green-labeled sample.
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The processBuilding the microarray:
MASSIVE PCR PCR PURIFICATION AND PREPARATION
PREPARING SLIDES
PRINTING
RNA preparation:
CELL CULTURE AND HARVEST
RNA ISOLATION
cDNA PRODUCTION
Hybing the array:
ARRAY HYBRIDIZATIONAND SCANNING
TARGET LABELING DATA ANALYSIS
POST PROCESSING
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Ngai Lab arrayer, UC Berkeley
The arrayer
Print-head
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96-well plate
Contains cDNA probes
Glass slide
Array of bound cDNA probes
4x4 blocks = 16 print-tip-groups
Print-tip group 7
cDNA clones
Print-tip group 1
Print-tips collect cDNA from wells
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Sample preparation
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Hybridization
cover
slip
Hybridize for
5-12 hours
Binding of cDNA target samples to cDNA probes on the slide
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LABEL
3XSSC
HYB CHAMBER
ARRAY
SLIDE
LIFTER SLIP
SLIDE LABEL
• Humidity• Temperature• Formamide
(Lowers the Tmp)
Hybridization chamber
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ScanningDetector
PMT
Image
Duplicate spots
Cy5: 635nmCy3: 532nm
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RGB overlay of Cy3 and Cy5 images
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Raw data
E.g. Human cDNA arrays• ~43K spots;• 16–bit TIFFs: ~ 20Mb per channel;• ~ 2,000 x 5,500 pixels per image;• Spot separation: ~ 136um;• For a “typical” array, the spot area has
– mean = 43 pixels, – med = 32 pixels, – SD = 26 pixels.
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Animation
http://www.bio.davidson.edu/courses/genomics/chip/chip.html
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Oligonucleotide chips
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Probe sets
• Each gene is represented by 16-20 oligonucleotides of 25 base-pairs, i.e., 25-mers.
• Perfect match probe, PM: A 25-mer complementary to the reference sequence.
• Mismatch probe, MM: same as PM but with a single homomeric base change for the middle (13th) base.
• Probe pair. A (PM,MM) pair.• Probe set. 16-20 probe pairs. • The purpose of the MM probe design is to measure
non-specific binding and background noise.
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Probe sets
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Oligonucleotide chips
24µm24µm
Millions of copies of a specificMillions of copies of a specificoligonucleotide probeoligonucleotide probe
Image of Hybridized Probe ArrayImage of Hybridized Probe Array
>200,000 different>200,000 differentcomplementary probes complementary probes
Single stranded, Single stranded, labeled RNA targetlabeled RNA target
Oligonucleotide probeOligonucleotide probe
**
**
*
1.28cm1.28cm
GeneChipGeneChip Probe ArrayProbe ArrayHybridized Probe CellHybridized Probe Cell
Compliments of D. Gerhold
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Oligonucleotide chips
• The probes are synthesized in situ, using combinatorial chemistry and photolithography.
• Probe cells are square-shaped features on the chip containing millions of copies of a single 25-mer probe. Sides are 18-50 microns.
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Oligonucleotide chips
The manufacturing of GeneChip® probe arrays is a combination of photolithography and combinational chemistry.
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Image analysis
•About 100 pixels per probe cell.•These intensities are combined to form one number representing the expression level for the probe cell oligo.• CEL file with PM or MM intensity for each cell.
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Expression measures
• Most expression measures are based on differences of PM-MM.
• The intention if to correct for background and non-specific binding.
• E.g. MarrayArray Suite® (MAS) v. 4.0 uses Average Difference Intensity (ADI) or
AvDiff = average of PM-MM.• Problem: MM may also measure signal.• More on this in lecture Pre-processing in DNA
microarray experiments.
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What is the evidence?
Lockhart et. al. Nature Biotechnology 14 (1996)
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Testing
Biological verification and interpretation
Microarray experiment
Estimation
Experimental design
Image analysis
Normalization
Clustering Discrimination
Biological question
Statistics andMicroarrays
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Everywhere …
• for statistical design and analysis: – pre-processing, estimation, testing, clustering,
prediction, etc.
• for integration with biological information resources (in house and external databases)– gene annotation (GenBank, LocusLink);– literature (PubMed);– graphical (pathways, chromosome maps).
Statistical computing
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Integration of biological metadata
• Expression, sequence, structure, annotation, literature.
• Integration will depend on our using a common language and will rely on database methodology as well as statistical analyses.
• This area is largely unexplored.
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WWW resources
• Complete guide to “microarraying” http://cmgm.stanford.edu/pbrown/mguide/ http://www.microarrays.org
– Parts and assembly instructions for printer and scanner;– Protocols for sample prep;– Software;– Forum, etc.
• cDNA microarray animation http://www.bio.davidson.edu/courses/genomics/chip/chip.html
• Affymetrix http://www.affymetrix.com
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Next …
Pre-processing in DNA microarray experiments
• cDNA microarrays– Image analysis; – Normalization.
• Affymetrix oligonucleotide chips– Image analysis;– Normalization;– Expression measures.