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SNP typing with DNA chips
8/1/03. By Richard Twyman
Microarrays can be used to determine the particular base present in a single nucleotide polymorphism (SNP).
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Oligonucleotide chips contain thousands of short DNA sequences immobilised at different positions. Such chips can be used to discriminate between alternative bases at the site of a SNP.
Chips allow many SNPs to be analysed in parallel, which is necessary for large-scale association or pharmacogenomic studies.
Key principles
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DNA chips are miniature devices with thousands of different DNA sequences immobilised at different positions on the surface. Oligonucleotide chips contain very short DNA sequences (~25 nucleotides).
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A DNA sequence containing a single nucleotide polymorphism is hybridised to the chip.
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A method is employed to discriminate between alternative bases at the polymorphic site. This is known as typing the polymorphism.
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A signal, corresponding to the specific identified base, is detected.
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A chip can be used to type many SNPs simultaneously.
How does it work?
Two chip-based typing methods are widely used. One method relies on allele-specific hybridisation. Short DNA sequences on the chip represent all possible variations at a polymorphic site; a labelled DNA will only stick if there is an exact match. The base is identified by the location of the fluorescent signal.
Alternatively, the oligonucleotide on the chip may stop one base before the variable site. In this case typing relies on allele-specific primer extension. A DNA sample stuck onto the chip is used as a template for DNA synthesis, with the immobilised oligonucleotide as a primer. The four nucleotides, containing different fluorescent labels, are added along with DNA polymerase. The
incorporated base, which is inserted opposite to the polymorphic site on the template, is identified by the nature of its fluorescent signal. In a variation of this technique, the added nucleotide is identified not by a fluorescent label but by mass spectrometry.
How is it used?
The chip-based methods discussed above are particularly suitable for high-throughput SNP typing which is required for large-scale studies of populations. Two of the most important applications are 'association studies', which attempt to correlate SNP profiles with predisposition to disease, and pharmacogenomic studies, which attempt to correlate SNP profiles with drug
response patterns.
A disadvantage of chip-based assays is that they are somewhat inflexible - new SNPs cannot easily be incorporated onto a chip, requiring a new chip to be made. This is being overcome by the use of bead arrays.
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