A number of options exist for high throughput genotyping in our Core and what is best for your project depends mostly on the number of SNPs to be interrogated and the number of samples to be assayed over the course of the project.  There is also flexibility in the number of samples processed, although economies of scale dictate the lowest optimum sample size.  Here are some rough guidelines matching assay type to desired SNP multiplex level:

24, 48, 96, 192, 384 SNPs/sample:  Fluidigm EP1.  This System offers a cost-effective alternative to the Illumina Golden Gate assay (discontinued by Illumina in 2014).
~3,000-~70,000 SNPs/sample (non-human):  iSelect (custom) Infinium assay.  For large projects the custom iSelect Infinium assay can be exploited to carry out very high throughput genotyping at the multiplex levels indicated for any set of provided SNP sequences.  The minimum order is for 1152 individuals, or 48 x 24-array chips.  At the lowest multiplex level the entry price is approximately $200,000. More information about the assay can be found on our Infinium web site.
~6,000-1,000,000 (non-human and human): Catalog arrays with Infinium assay.  For human assays there is very wide variety of array types that can be exploited to look at particular SNP subsets related to, e.g., cancer, copy number variation, or methylation, as well as multiplex levels that go to 5,000,000 SNPs/sample for genome wide association studies (see the selection of “Omni Family” microarrays).  There are also “off-the-shelf” commercial and consortium Infinium chips for investigation of a number of experimental models including canine, porcine, bovine, ovine and maize (commercial BeadChips), and wheat, apple/peach/cherry, tomato, potato and goat (consortium BeadChips); more details can be found here. After reading through the documentation here and on the other sites, contact us so we can get into the specifics of pricing materials and designing a strategy for your particular project.

For more information on the specifics of each genotyping technology, please consult the relevant web page:

Fluidigm EP1 – 24, 48, 96 SNPs and up
Illumina Golden Gate Assay – Discontinued by Illumina, October 2014
Illumina Infinium Assay – 3000 SNPs and up