The Sequenom MassArray (compact) system at the DNA Sequencing and Genotyping core facility is designed for moderate to high-throughput (primarily fine-mapping) genotyping needs. It consists of a liquid handler, a nanodispenser, and a mass spectrometer. The method consists of the following steps:
1. Generation of a list of desired SNPs with short flanking regions,
2. Organization of them into multiplexed groups using the “iPlex Gold” application (up to 40-plex),
3. Purchase of three primers for each SNP (a pair to amplify each SNP region and one to extend into the SNP) from your vendor of choice,
4. Multiplex PCR amplification of each SNP group,
5. Inactivation of remaining dNTP’s using shrimp alkaline phosphatase (SAP),
6. Addition of primers for extending a single base into each SNP,
7. Extension of primers one base into each SNP using a mass-modified dideoxy terminator mix,
8. Cleanup of the reactions using a desalting resin,
9. Spotting products on a 384-position glass chip using the nanodispenser,
10. Separation and analysis of products by mass spectrometry.
For those who are interested in using the Sequenom MassArray system for genotyping, we have provided several of the manuals and the software documentation. All of the files are PDF format, so you should be able to drag each link to your desktop (or directory) and open it there with your PDF viewer of choice. Note that there is a lot of information here, so especially if you are a new user, we recommend that you start with the Application note first and work your way through the rest. Access to the iPlex Gold application (Windows only) is via the Sequenom website (www.sequenom.com) where you need to register for a RealSNP account (free), then use your password to download the software.