Genotyping of Single Nucleotide Polymorphisms by Arrayed Primer Extension

Although the majority of microarray studies have been directed toward RNA expression profiling (functional genomics) and increasingly toward proteomics, a steady increase in the use of microarrays as platforms for DNA genotyping has occurred over the past 5 yr. Multiple array-based chemistries have been developed in order to genotype single nucleotide polymorphisms. Conceptually, the simplest of these microarray genotyping technologies is based on the dideoxynucleotide chemistry of mini-sequencing by arrayed primer extension, whereby oligonucleotide probes (preprinted on the array) are extended by a single nucleotide base. This enzymecatalyzed single base extension reaction is dependent on the sequence (genotype) of the template nucleic acid (sample) that is temporarily hybridized to the probes. Utilization of all four dideoxynucleotides, each conjugated to a different fluorophore, allows genotyping by spectral differentiation of the single base extension reaction products.