Course Tutor:
Prof. Martin Dufva
This course will be held prior to the Advances in Microarray Technology Conference.
Who Should Attend?
The course will be suitable for scientists, technicians and engineers that plan to start making genotyping arrays. The focus will be on mutation analysis and SNP analysis but the course content may also apply for designing siRNA array designs and to some extent viral/bacterial DNA microarrays. The course will be discussing strategies for probe design and assay development using allele specific hybridization techniques and allele specific primer extension/minisequencing.
Learning Objectives
1. Understand allele specific hyridization
2. Understand allele specific primer extension/minisequencing
3. Drawbacks and strengths of the respective techniques
4. Assay development
5. Probes behaviour on surfaces
Topics and Course Organisation
Understanding allele specific hybridization
(1/2 of the course)
1. Principle of allele specific hybridization
2. Predicting probe behaviour/assay condition for probes linked to surfaces
a. Dissociation curves (effects on shape by surfaces and probes density)
b. Melting temperature (predicted vs. observed)
c. Effect of hairpins in target and probes
d. Temperature of optimal classification
3. Allele specific hybridization by dissociation kinetics
a. Real time dissociation hardware
b. Examples
4. Example of an assay development (beta globin gene)
Understanding alleles specific primer extension and minisequencing
(1/4 of the course)
1. Principles
a. On chip genotyping
b. Genotyping using universal array for sorting genotypings performed in solution
c. Priming strategy
2. Examples of arrays from the literature
Comparing primer extension/minisequencing with allele specific hybridization
(1/4 of the course)
1. Size and prize of different platforms (Affymetrix, Illumina and others)
2. Throughout/automation
3. Fabrication methods suitable for primer extension/minisequencing
Kaynak: http://www.selectbiosciences.com/conferences/Dufva_pmAMT2008/index.aspx?utm_source=SBTrngFeb08
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