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Biotechniques. 1999 Sep;27(3):538-40, 542, 544 passim.

High-throughput single nucleotide polymorphism genotyping by fluorescent 5' exonuclease assay.

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Axys Pharmaceuticals, La Jolla, CA, USA.


Single nucleotide polymorphisms (SNPs) are the class of DNA variants that are most common in the genome. Technologies are needed that allow relatively high-throughput, high-quality genotyping of SNPs, with rapid assay development for individual SNPs of interest. We have implemented an accurate and high-throughput SNP genotyping system using a commercially available fluorescent 5' exonuclease assay. Optimization of the assay system for low-volume reactions and low-probe concentrations has reduced assay costs by 75%. Using a simple assay optimization process, we successfully developed genotyping assays for 92% of assays attempted (309 out of 335) and have generated over 200,000 genotypes.

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