SNP: SNPlex

Paul Berg

Since summer 2005 we have been running the SNPlex system from Applied Biosystems for SNP genotyping. SNPlex is a relatively new technology that we will utilize in instances where it turns out to be more economical than running the Sequenom system. This will in essence be projects where the numbers of samples are close to 5000 and the numbers of SNPs are in amplicons of 48, as this is the size of the kits from Applied Biosystems. In addition, it would be an advantage to know that most of the SNPs are real and informative, as the 48 panels are fixed once they have been ordered. See here for more information on our prices.

In total, this system is a powerful, high-throughput genotyping technology for identifying genetic variations and providing a combination of accuracy, throughput, and economy. We are currently running SNPlex on a routine basis in our lab with good and confident results.

The SNPlex system uses Oligonucleotide Ligation Assay (OLA) and PCR technology for allelic discrimination and ligation product amplification. The genotype information is then encoded into a universal set of fluorescently dye-labeled, mobility modified fragments (Zipchutes), for rapid detection by capillary electrophoresis on our ABI 3730. As the same set of Zipchutes is used for every SNPlex setup, regardless of which SNPs you have chosen, one can achieve extremely reproducible detection and identification of assay products on the ABI 3730.

Updated: 21.04.06
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