The Huck Institutes of the Life Sciences

Genotyping

Information about genotyping services provided by the Genomics Core Facility at University Park

 

VNTRs

VNTR alleles can be determined by Fragment Analysis on the 3730 XL DNA Sequencer.

A 5-color system uses 4 fluorescent-labeled primers to multiplex PCR products in the same well.

At minimum, 4 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.

 

SNP determination

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.

 

Instrumentation

Applied Biosystems 3730XL