DNA Sequencing Facility: Genotyping

The DNA Sequencing Facility provides genotyping services for determination of SNPs, indels, or microsatellites (SSRs, VNTRs).  SNPs are interrogated using allele-specific PCR (KASPar) or TaqMan® assays.  Genotyping of indels or microsatellites is performed on agarose gels or via capillary electrophoresis.  Turnaround times are highly dependent on whether optimized assays are available at the DNA Sequencing Facility. There are a number of SNP and microsatellite assays that we have evaluated and optimized.   

All data and reagents distributed by the University of Wisconsin Biotechnology Center DNA Sequence Facility are intended for research purposes only.  They are not intended or certified for diagnostic or clinical use.

Pricing

Note: non-UW users are charged a 50.5% surcharge above rates listed below.

SNP Genotyping: KASPar Assay

Pricing for KASPar SNP genotyping is broken into two components, setup charges (primer design and synthesis) and run charges.  Setup is charged on a per SNP basis and run charges are based on the total number of genotype calls (#SNPs x #Samples).

Setup Charges: Primer Design and Synthesis

Run Charges per Genotype Call

SNP Genotyping: TaqMan Assay

Pricing for TaqMan SNP genotyping is broken into two components, setup charges (primer design and synthesis) and run charges.  Setup charges per SNP are based on the number of samples to be genotyped and run charges are based on the total number of genotype calls (#SNPs x #Samples). Minimum number of samples per assay is 48.

Setup Charges: Primer Design and Synthesis

Run Charges per Genotype Call

Fluorescent Fragment Analysis

For this service, the user generates fluorescently labeled PCR fragments (typically through use of fluorescently labeled primers, available through our DNA Synthesis facility, or through incorporation of fluorescent nucleotides) that are resolved and accurately sized on our automated sequencers using the Genescan software. Suitable for microsatellites, AFLP, RAPDs, and related procedures. Price depends on the number of samples. For more information, consult the "Fragment Analysis" document at the DNA files page.

Policy Statement

Every effort is made to provide our users with the best data in a timely fashion for the advancement of their research. Turnaround time for genotyping projects is dependent on the parameters of the specific project.  This can be estimated for projects involving assays that we have already optimised in-house but can be quite variable for assays that need development and optimization.  For requested assays that are not already optimised, we will do everything in our power to generate working assays, including testing different methods such as allele-specific-PCR or using Taqman probes. However, five to fifteen percent of SNPs and other polymorphisms cannot be converted into reliable assays.  In those cases, customers will still be responsible for the standard setup fee.

Validated SNP Assays

(Please email UWBC staff for list of validated SNPs)

Validated Microsatellite Assays