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SNP determination
SNPs can be determined by several techniques, including SNaPShot, SNPlex and Allelic Discrimination (Taqman Assays).
SNPlex
SNPlex is a high-throughput genotyping method that can call up to 450,000 SNPs per day. Up to 48 SNPs can be genotyped against a single biological sample.
This technique requires the 3730XL sequencer and Genemapper software.
Oligo Ligation/PCR technology is used for allelic discrimination. Ligation products are amplified and encoded into a universal set of dye-labelled fragments (Zipchute fragments). These fragments can be detected by the 3730XL.
The same set of Zipchute fragments are used for every SNPlex pool regardless of which SNPs are chosen. This results in extremely reducible detection and identification of assay products.
The SNPlex Bioninformatics design pipleline can optimize multiplexes of the SNPs you're interested in. SNPBrowser software is free and can be used to select sets of SNPs you are interested in. More than 6million SNPs (those associated with TaMan or SNPlex System assays) can be accessed with this software.
SNaPShot
SNaPShot is a primer extension-based method that can be used for SNP screening and validation. Up to 10 primer-template combinations can be combined in a single tube. Therefore, in the 3730XL 96 capillary machine, 96 samples can be screened for 10 SNPs in about an hour for a charge of about $120. The DNA fragments are generated with a kit and are run with a size standard that we add. The size of the labeled fragments is generated using that internal standard. Then you can use the Genemapper software available at the facility to analyze and generate the allele calls.