Genotyping – SNP and Microsatellite Assays

Genotyping – SNP and Microsatellite Assays

Service Description

We provide all-inclusive genotyping services on a fee-for-service basis with the goal of generating high-quality single nucleotide polymorphisms (SNPs) and microsatellite data. We work with our UW system and external collaborators to interrogate SNPs and microsatellite assays using several different platforms for fluorescence, capillary electrophoresis, or next-generation sequencing to provide meaningful biological information in a time-sensitive manner.

Genotyping by Sequencing (GBS) is a more comprehensive SNP analysis service that we offer.

SNP Assays

  • KASPar

    KASPar (KBioscience Competitive Allele-Specific Polymerase chain reaction) genotyping is an allele-specific PCR fluorescence based genotyping service for SNP analysis. We provide a cost-effective, high throughput assay that requires only a small amount of sample. Please email for a list of validated SNPs. If the SNP is not listed, we will work with you to determine genotype-specific primers and validate them prior to starting your project.

  • TaqMan Assays

    TaqMan® Assays (Thermo Fisher Scientific) use the 5′ nuclease activity of Taq DNA polymerase to cleave a fluorescently labeled probe (FAM) that increases the specificity of specific alleles in genomic DNA detection. Up to seven different SNPs can be multiplexed and run in one reaction.

  • RFLP Assays

    RFLP (Restriction Fragment Length Polymorphism) Assays use restriction enzymes to digest DNA into different length fragments that we then separate out by gel electrophoresis. RFLP is highly locus-specific for restriction sites and each fragment length is considered an allele. We can use this assay in genetic analysis for your genome mapping, genetic linkage, and variation analysis projects.

Microsatellite Analyses

  • Overview<

We offer microsatellite analyses of Simple Sequence Repeats (SSR) and Variable Number Tandem Repeat (VNTR), along with Fragment Analysis. Using microsattelite analyses, we interrogate polymorphic DNA loci, which contain repeat nucleotide regions of 2-6 nucleotides. We typically use this in population genetics and genetic linkage studies. Microsatellite marker analysis is measured using capillary electrophoresis.

  • SSRs

    SSRs are tandemly arranged repeated regions about 1-6 nucleotides long for an individual microsatellite at a specific locus. During PCR, we use primers labeled with fluorescent dye to multiplex (if the SSRs are far enough apart). We separate amplified fragments by electrophoresis or assess on a Next Gen Sequencer. Each band will represent an allele specific size in base pairs. We use SSRs in assessing genetic variation, evolutionary studies, and genetic mapping

  • VNTRs

    VNTRs are locations on a genome where short nucleotide sequences are organized as a tandem repeat caused by recombination or replication errors. Variations in repeat lengths are specific to different alleles. We use PCR to amplify VNTRs and determine the size by gel electrophoresis. We can also multiplex multiple VNTRs. We use VNTRs for linkage analysis of diploid genomes, genetic diversity and breeding patterns in populations.

  • Fragment Analysis

    Fragment Analysis is the sizing of fluorescently labeled products of 100-600bp. The primers are typically labeled with fluorescent dyes (6-FAM, HEX and NED) and have an internal ladder of ROX or LIZ. For more information visit Fragment Analysis here.

    Instruments/platforms used for microsatellite fragment analysis:

    • ABI 3730XL Genetic Analyzer (Thermo Fisher)
    • 5200 Fragment Analyzer System (Agilent)
    • QIAxcel Advanced System (Qiagen)
    • Next Gen Sequencing (Illumina)

Getting Started

To discuss a project or acquire a quote, please contact us! For new clients, please set up an account (see New Lab or Customer Access below). All projects must be discussed before samples are submitted.

If you would like to initiate a project or get more information, please use the following contact information, and a member of our group will get in touch with you directly.

Next Generation Sequencing:

New Lab or Customer Access

We MUST have this information before we can proceed with your request.

Adding a new lab:

    • Name, address, phone number, UW NetID and email of the Principal Investigator (PI) or Primary scientific contact person.
    • Name, address, phone number, FAX number and email of he financial contact person.
    • Name, UW NetID, phone number and email of all individuals who will be using our service.
    • Payment information: For campus users this should be a direct charge number, e.g. a 144 or 133 prefixed account (please send the whole string of characters). For off campus users you can set up a PO or we can send the financial contact person a bill — your choice. Non-UW system users are charged an additional institutional overhead.

Adding a member to an existing lab:

    • Name of the PI whose lab you are joining.
    • Your name, UW NetID, phone number and email.

Sample Submission

Please contact to arrange all sample submissions. Samples and submission forms must be submitted before a project can be entered into our queue.

Submission Forms and Guidelines

Please check the service page guidelines for specific Submission Forms and Guidelines that need to be included with your samples.

Submitting Samples/ Shipping Instructions

After setting up a customer account, filling out submission form, and reviewing submission guidelines, you can now submit or send samples. *We require customers to submit electronic Submission Forms!*

In Person Submission

Please give advance notice of submission date and time so staff can be prepared to receive samples. Schedule a time for drop off with a staff member at

Shipping Submission

Please send the tracking information to:

Next Generation Sequencing:

*Samples that are being shipped must have a hard copy of the submission form and guidelines in the package! This way we know what the samples are and where they are from.*

If shipping samples from outside UWBC, ship via express shipping carrier on dry ice to the address below:

Next Generation Sequencing
UW DNA Sequencing Facility
Attn: Next Generation Sequencing
425 Henry Mall
1250 Biotechnology
Madison WI, 53706

SNP Assay Pricing

Microsatellite/SSR/RFLP Pricing

EXTERNAL RATES: Clients not affiliated with UW Madison or the University of Wisconsin system are charged a 55% surcharge for all labor and incidentals provided; prices are as listed above.  This surcharge is subject to change.

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.