Introduction to Analysis of Genomic Data Using R Lecture10:...
Transcript of Introduction to Analysis of Genomic Data Using R Lecture10:...
- - :
Introduction to Analysis of Genomic Data Using RLecture10: Introduction to Microarray Technology
(Chapter 5 in Gondro’s book )
Dr. Yen-Yi Ho ([email protected])
March 21, 2018
1/35
- - :
Objectives of Lecture 10
I Types of ArraysI Expression Microarrays
I General Experiment ProtocolI Hybridization, Target, Probe, Probe SetI Commercial MicroarraysI Common Issues
I aCGH
I ChIP-chip
2/35
- - :
Microarrays
I Microarrays (or just arrays) allow the simultaneousmeasurement of the mRNA of thousands of genes (geneexpression)
I Why “micro”? Measuring things on a small scale means lessmRNA is necessary to be extracted
I The simultaneous measurement is important, so that variousfactors/conditions are all common to the array, and relativegene expression can be measured with less variability
I Still microarray? Microarray is still widely used because oflower costs, easier experimental procedure and moreestablished analysis methods.
I Similar problems are presented in newer technologies such asRNA-seq, and similar statistical approaches can be applied.
3/35
- - :
Microarrays
Microarrays can be used for many purpose including:
I genotyping:
SNP arrays
I measure gene expression
I determine DNA copy number: aCGH
I determining transcription factor binding sties: Chip-chip
4/35
- - :
Microarrays
Microarrays can be used for many purpose including:
I genotyping: SNP arrays
I measure gene expression
I determine DNA copy number:
aCGH
I determining transcription factor binding sties: Chip-chip
5/35
- - :
Microarrays
Microarrays can be used for many purpose including:
I genotyping: SNP arrays
I measure gene expression
I determine DNA copy number: aCGH
I determining transcription factor binding sties:
Chip-chip
6/35
- - :
Microarrays
Microarrays can be used for many purpose including:
I genotyping: SNP arrays
I measure gene expression
I determine DNA copy number: aCGH
I determining transcription factor binding sties: Chip-chip
7/35
- - :
Co$t
MicorarrayAffymetrix Cost: $425/per arrayIllumina BeadChip Cost: $ 80 ∼ $250 /per strip × 12 = $960 ∼$3,000 /chip
Next-Generation SequencingIllumina ∼$2,000 per samples (for 1-7 samples)
8/35
- - :
On Type of Microarray Experimental Procedure
9/35
- - :
10/35
- - :
11/35
- - :
Target
12/35
- - :
Probes
13/35
- - :
On Type of Microarray Experimental Procedure
14/35
- - :
Platforms that dominate market
I Affymetrix
I Agilent
I Illumina
I NimbleGen
15/35
- - :
Affymetrix GeneChip R©
source: Affymatrix
16/35
- - :
Affymetrix GeneChip R©
source: Affymatrix17/35
- - :
Affymetrix GeneChip R©
18/35
- - :
Probe Set
A probe set is a collection of probes designed to interrogate agiven sequence.
19/35
- - :
PM versus MM
20/35
- - :
Affymetrix GeneChip R© Experiment Protocol
21/35
- - :
Illumina BeadArrays
• Each silica bead is 3 µ in diameter
• 700,000 copies of same probe sequence attached to each bead
• May have more than one bead for a particular gene
22/35
- - :
Illumina BeadArrays
• RefSeq BeadChip (left) 8 arrays per chip, 1 strip= 1 array
• Whole Genome (right) 6 arrays per chip, 2 strip= 1 array
23/35
- - :
Commons Issues
I Background: print-tip, plate, print-order, spatial effects
I Between arrays: batches, plates, cross platform comparison,experiment protocols
I Within arrays: background noise, intensity dependent effect
24/35
- - :
Spatial Effect
25/35
- - :
Spatial Effect
26/35
- - :
27/35
- - :
28/35
- - :
Microarrays
Microarrays can be used for many purpose including:
I genotyping: SNP arrays
I measure gene expression
I determine DNA copy number: aCGH
I determining transcription factor binding sties: Chip-chip
29/35
- - :
Array-comparative genomic hybridization (aCGH)
Nature Education1(1). Microarray-based Comparative Genomic Hybridization (aCGH)
30/35
- - :
array CGH
Brian and Development 31(6):629:633.
31/35
- - :
Microarrays
Microarrays can be used for many purpose including:
I genotyping: SNP arrays
I measure gene expression
I determine DNA copy number: aCGH
I determining transcription factor binding sties: Chip-Chip
32/35
- - :
ChIP-chipChromatin immunoprecipitation (”ChIP”) with microarraytechnology (”chip”)
33/35
- - :
ChIP-chip
34/35
- - :
Readings
Primer to Analysis of Genomic Data Using R (page 163 – 200).
35/35