SNP: MassArray

Paul Berg

As of summer 2003 we have been using Sequenom's MassARRAY system for genotyping. In the beginning we were quite happy with running 4 plexes and we were thrilled when we managed to run 12 plexes by the end of 2003. After Sequenom launched their iPLEX technology in 2005, we are routinely running 29 plexes with good and confident results.

The Sequenom MassARRAY system utilizes a MALDI-TOF (Matrix-assisted laser desorption ionization - time of flight) mass spectrometry for genotyping.

This system is a powerful, flexible, high-throughput genotyping technology for identifying genetic variations, providing a combination of accuracy, throughput, simplicity and economy.

The system combines the benefits of rapid and highly efficient assay design and development tools with an economical homogenous assay that quickly generates accurate genotype calls. The system is based on an allele-specific primer extension reaction where short primers are extended according to the base composition in the template sequence and then separated by mass (See e.g. N. Storm et al. 2003. Methods Mol.Biol., 212 p.241-262.) The differences in mass between the two extension products are large compared to the resolution of the Mass Spec, this allows for completely automated calling of the genotype.

Since genotypes are separated by mass and all assays are computer-designed, it is possible to multiplex several independent SNP sites in a single typing assay without any fluorescent labelling.

We typically multiplex at a level of 25 to 29 (depending on the project). See here for more information on our prices.

If assays do not work or turn out to be monomorphic, it is possible to re-plex the remaining SNPs or simply just remove the unwanted SNPs. In this way, you don’t spend your money on non-informative genotyping.

Our service includes primer and assay design all the way through to production of genotypes. All steps involved are highly automated. Specialized equipment for this work includes a Beckman Biomek Fx pipetting robot, a Beckman Multimek96 pipetting robot, a nandispenser chip-printing robot, a mass spectrometer, a LIMS system, etc.



Updated: 21.04.06
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