introduction to analysis of genomic data using r lecture12...

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Introduction to Analysis of Genomic Data Using RLecture12: Introduction to Microarray Technology

(Chapter 5 in Gondro’s book )

Dr. Yen-Yi Ho (hoyen@stat.sc.edu)

March 15, 2017

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Objectives of Lecture 12

I Types of ArraysI Expression Microarrays

I General Experiment ProtocolI Hybridization, Target, Probe, Probe SetI Commercial MicroarraysI Common Issues

I aCGH

I ChIP-chip

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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.

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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

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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

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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

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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

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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)

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On Type of Microarray Experimental Procedure

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Target

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Probes

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On Type of Microarray Experimental Procedure

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Platforms that dominate market

I Affymetrix

I Agilent

I Illumina

I NimbleGen

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Affymetrix GeneChip R©

source: Affymatrix

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Affymetrix GeneChip R©

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Affymetrix GeneChip R©

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Probe Set

A probe set is a collection of probes designed to interrogate agiven sequence.

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PM versus MM

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Affymetrix GeneChip R© Experiment Protocol

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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

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Illumina BeadArrays

• RefSeq BeadChip (left) 8 arrays per chip, 1 strip= 1 array

• Whole Genome (right) 6 arrays per chip, 2 strip= 1 array

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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

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Spatial Effect

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Spatial Effect

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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

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Array-comparative genomic hybridization (aCGH)

Nature Education1(1). Microarray-based Comparative Genomic Hybridization (aCGH)

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array CGH

Brian and Development 31(6):629:633.

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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

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ChIP-chipChromatin immunoprecipitation (”ChIP”) with microarraytechnology (”chip”)

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ChIP-chip

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Readings

Primer to Analysis of Genomic Data Using R (page 163 – 200).

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