Genotyping

The facility has a SNPstream Ultra High Throughput system for ascertaining SNP genotypes. We have generated 40,000 SNPs in a single day with a single technician. In order to attain this high throughput, DNAs are arranged in 384 well plates, PCR reactions are run with 12 pairs of primers and the alternative nucleotides at the SNP are identified in a miniarray containing 16 spots for the 12 SNPs of interest and 4 internal controls. The software necessary for designing the primer sets is available with an appropriate password at a restricted web site. The Applied Biosystems 3730XL also offers a high throughput platform with which to analyze SNPs. Using the Applied Biosystems SNPlex reagents, up to 48 SNPs can be analyzed in a single well in a 384 well format.