VNTR alleles can be determined by fragment analysis on the 3730 XL DNA Sequencer. A 5-color system uses four fluorescent-labeled primers to multiplex PCR products in the same well. At minimum, four genotypes can be determined per sample in less than an hour for about $110 (96 samples in a 96-well plate).
Multiplexing different products with the same color can double or even quadruple the number of genotypes per sample (due to resolution of different-sized products with one base resolution). Allele or peak size is determined by using software such as Genemapper. Peak Scanner is another useful software program, and is available for free download from Applied Biosystems.
SNPs can be determined by several techniques, including standard allelic discrimination (Taqman assays), open-array technology, and high-resolution melt curve analysis. Open-array technology can be used to determine 3072 SNPs for about 15-20 cents per SNP. High-resolution melt curve uses a dsDNA intercalator to determine homozygotes and heterozygotes by detecting small differences in PCR melting curves.