MALDI-TOF analysis of DNA methylation patterns separating and arraying DNA fragments. This platform gained favor because it was reliable for the analysis of one or a few genes, but difficulties in automation weighed against it, and it has been replaced in many applications by other separation methods40 such as capillary electrophoresis,41 high-performance liquid chromatography (HPLC),42,43 and mass spectrometry.44-47 Homogeneous assays eliminated the need for the separation of reaction components and increased the popularity of assays based on this platform. The demand for large-scale analysis of sequence variation presented new challenges and led to the development of the platform of solid-phase systems. Solid-phase systems include gene chip/ microarray,48 bead, and microtiter plate assay formats.49,50 Adoption of one or another of these platforms has improved the readout of genotyping results, but usually does not alter the fundamental biochemistry that determines the specificity of the approach.38
The technique selected for analysis should take account of the expected nature of the variant, its size and the structure of the gene of interest, the availability of mRNA, the degree of sensitivity required, and other resources available. The underlying principle of each procedure, its salient features, and its primary advantages and disadvantages are summarized below. Additional details are available in the references cited.
Procedures used primarily to scan DNA sequences are considered first and separately from those used primarily to score variants.
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