DNA Microarrays for DNA Genotyping and Gene Expression Profiling
This course will be held prior to the Advances in Microarray Technology conference.
This course will explore design, fabrication and use of DNA microarrays for SNP genotyping and gene expression analysis. The course will be based on examples from the literature and methodology will be compared and discussed to give a deeper understanding of the workings and performance of DNA microarrays.
Topics and Course Organisation
SNP GENOTYPING/MUTATIONAL ANALYSIS
I. Understanding allele specific hybridization
- Principle of allele specific hybridization
- Predicting probe behaviour/assay condition for probes linked to surfaces
- Allele specific hybridization by dissociation kinetics
- Assay development strategies (trial and error vs. high throughput screening)
II. Understanding alleles specific primer extension and minisequencing
- Principles
- Examples of genotyping arrays from the literature (Genome wide SNP scans)
III. Comparing primer extension/minisequencing with allele specific hybridization
- Size and prize of different platforms (Affymetrix, Illumina and others)
- Throughout/automation
- Fabrication methods suitable for primer extension/minisequencing.
- Comparison with high throughput sequencing
GENE EXPRESSION STUDIES
I. Examples where microarrays are used in research and diagnostics
- Explaining cell function
- Systems biology
- Diagnostics
II. Platforms (microarrays and hardware)
- Comparison of different platforms commercial platforms (Affymetrix, Agilent, Niblegene; Illumina)
- Home made arrays - benefits and challenges
III. Considerations about the methodology
- Target preparation/labelling
- Hybridization
- Detection
IV. Data analysis and validation
- Basic methods to determine which gene that are expressed
- Validating microarray assay results by other methods
- Data mining/pathway analysis
V. Quality control and reproducibility of DNA microarrays for gene expression studies
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