The microarray format has been proven to be a successful tool for multiplexed SNP genotyping, providing medium to high throughput. With a basic level of laboratory automation it is feasible to produce around 960 genotypes for 96 samples in 8 h, depending on the multiplexing level of the assay. In comparison to other currently used genotyping technologies, allele-specific primer extension on microarrays is typically quickly adaptable for novel SNP markers and has very low limitations on the context of the genotyped locus. Whilst the genotyping throughput is not as high as in most robust technologies, the method is highly applicable for smaller-scale projects, involving for example rapid custom candidate gene genotyping. The special advantage of the method is that it does not require expensive investments on instrumentation.

Since multiple fluorescent nucleotides are added in the extension reaction, the amount of emitted fluorescence is higher than in minisequencing where only a single fluorescent nucleotide is added to the detection. In the minisequencing reaction, the detection primer bound to the array is only extended by a single nucleotide using fluorescently labeled dideoxy nucleotides. By using four different fluorophores for the four ddNTPs, all different alleles can be detected.

The interpretation of the allele signal is often easier with the allele-specific primer extension chemistry. When compared to allele-specific primer extension, minisequencing chemistry however doubles the amount of information that can be retrieved from the same number of probes on the array. With rare SNPs having more than two alleles, this difference is even greater.

Together with the current high-quality microarray technologies and intelligent allele-calling and genotyping software, the reliability of the produced genotypes is high, which is of utmost importance for the downstream analysis of the genotype information.

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