Based Genotyping

The major reaction principles that form the basis of the genotyping technologies available today are primer extension, ligation, and hybridization. Many of the methods for SNP genotyping rely on PCR amplification of the sequence of interest prior to allele determination. Primer design and assay optimization for multiplexed and reproducible genotyping of SNPs in large sample sets have become major bottle necks in most methods used today. 

In minisequencing single nucleotide primer extension (SNE) or single base extension (SBE), a DNA polymerase is used to extend a detection primer, which anneals immediately adjacent to the site of the SNP, with a labeled nucleotide analog (23,24). In the microarray format of 

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Tang K, Fu DJ, Julien D, Braun A, Cantor CR, Koster H. Chip-based genotyping by mass spectrometry. Proc Natl Acad Sci USA 1999 96 10016-10020. 

Johansson I, Lundqvist E, Dahl ML, Ingelman-Sundberg M. PCR-based genotyping for duplicated and deleted CYP2D6 genes. Pharmacogenetics 1996 6 351-5. 

Kai Tang, Dong-Jing Fu, Dominique Julien, Andreas Braun, Charles R. Cantor and Hubert Koster, Chip-based genotyping by mass spectrometry. Proceedings of the National Academy of Sciences USA, 96 (1999), 10016-10020. 

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