SNP genotyping with arrays

Single nucleotide polymorphisms (SNPs) are sequence variants in which two alternate bases occur at one position. The SNP Consortium is developing a dense map of SNPs in the hope that certain variants can be associated with disease states. With hundreds of thousands of SNPs identified, the scoring of these SNPs in patient populations has become the limiting factor. Hirschhorn et al. provide a possible solution in the October 24 Proceedings of the National Academy of Sciences by making the existing technique of single-base extension (SBE) a parallel process (Proc Natl Acad Sci USA 2000, 97:12164-12169). The technique begins with target amplification and the annealing of a primer next to a SNP site. A single fluorescently labeled nucleotide is incorporated as the next base; the identity of the fluorescent label identifies the variant base. Hirschhorn et al. modify this basic SBE technique by adding generic sequence tags...