Genotyping Facility

What's Inside Genotyping Facility
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Introduction

The Genotyping Facility is located on the Minneapolis campus of the University of Minnesota.  The genotyping facility employs state of the art Sequenom System including Biomek and Multimek robotic pipetting devices, 384 well ABI PCR machines, a chip spotting device, and a MALDI-TOF mass spectrometry system for determining the absolute mass of short DNA sequences and an Affymetrix GeneChip MegAllele System including Affymetrix GeneChip 3000 7G Scanner, Fluidic Station 450, 640 GeneChip Hybridization oven, Computer work stations. These high-tech equipments form the core of the genotyping facility and enables throughputs in excess of 10,000 SNP genotypes per day to 0.5 million genotypes/day using a 10K SNP panel.

Genotyping Facility

• Sequenom System
  The Genotyping Facility, part of the BioMedical Genomics Center, provides flexible, high quality, high throughput SNP Genotyping to the University of Minnesota research community, including Fairview University Medical Center. SNP genotyping is performed using MALDI-TOF (Matrix-assisted laser desorption ionization - time of flight) mass spectrometry. SNP genotyping by MALDI-TOF mass spectrometry is performed using the Sequenom mass spectrometry system. Our service includes primer and assay design through to production of genotypes. All steps involved are highly automated. In this method, multiplexed PCR and then a mini-sequencing reaction are performed in a single well. The size of reaction products is determined directly by MALDI-TOF mass spectrometry, yielding genotype information. Multiplexing permits determination of up to 12 SNPs in a single well of a 384 well plate. Specialized equipment for this work includes a Biomek multi-pipettor robot, a Multimek multi-pipettor robot, a nanoliter plotting robot for spotting the extension products onto chips, and the mass spectrometer.
  

• Affymetrix GenChip MegAllele System
  BioMedical Genomics Center has the next-generation tools with the ability to genotype virtually any set of targeted SNPs by utilizing the Affymetrix GeneChip MegAllele System by offering flexible multiplexing from 3,000-10,000 SNPs per individual assay. Using Molecular Inversion Probe technology (ParAllele) is invaluable as a high-throughput SNP genotyping method for both targeted and whole genome SNP analysis projects as well as allele quantitation.

Project Design

Because of the unique characteristics of any genotyping project and the high quality we aim for, we meet with each investigator who wishes to use our service.

• If using the Sequenom System the mass spec methods are discussed. Primer and assay design will be carried out and a test genotyping run performed. A second meeting will occur after this trial run to discuss results. Depending on those results, we will either proceed with full-scale genotyping or consider alternative genotyping methods as necessary.  Genotype results are provided to the user in electronic format. Extensive bioinformatics support for our laboratory is in place and refinements are planned.
  

• For the Affymetrix MegAllele system we discuss the ParAllele True Tag Arraychips available in 3K to 10K.  You can choose form a set of application specific assays to designing your own panel. Comprehensive MegAllele software package allows easy management of project information.