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University of Wisconsin–Madison

DNA Sequencing Facility


The DNA Sequencing Facility provides all-inclusive genotyping services on a rolling-submission, fee-for-service basis, with the goal of generating high-quality SNP and microsatellite data.  We work with our UW system and external collaborators to interrogate SNPs using allele-specific PCR (KASPar) and TaqMan® assays, and microsatellite, SSR, VNTR and RFLP assays via capillary electrophoresis or next-generation sequencing to provide meaningful biological information in a time-sensitive manner.

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.

Acknowledging UWBC and the DNA Sequencing Facility

A visible measure of a core's impact is made through proper acknowledgement of usage in publications.  To acknowledge our core, please use the following statement: "The author(s) thank the University of Wisconsin Biotechnology Center DNA Sequencing Facility for providing ________ facilities and services”.

Getting started

To discuss a project or acquire a quote, please contact our genotyping team.  To submit a project please review our submission guidelines and contact us to set up an account and coordinate sample delivery.

There are a number of commonly-requested SNP and microsatellite assays that we have evaluated and optimized in order to expedite projects. Please contact us for an updated list.

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.

Validated SNP Assays

(Please email UWBC staff for list of validated SNPs)

Validated Microsatellite Assays

5'HTTLPR/rs25531 Fluorescent Analysis
Human AVPR1a Fluorescent Analysis
Human MAOA Fluorescent Analysis
Human DAT1 Fluorescent Analysis
Human DRD4 Fluorescent Analysis
Human DRD2 Fluorescent Analysis


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

Genotype Pricing

  • SNP Genotyping

  • Microsatellite/SSR/RFLP Genotyping

Unless otherwise specified, all data and reagents distributed by the University of Wisconsin Biotechnology Center DNA Sequencing Facility are intended for research purposes only. They are not intended nor certified for diagnostic or clinical use.  Clinical services are provided through our collaboration with the UW Collaborative Genomics Core.