Genotyping

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For More Information
Contact Aaron Thomas: (435) 757-5534; aaron.thomas@usu.edu

The Genotyping laboratory, is a core facility of the Center for Integrated BioSystems at Utah State University. It is equipped with a Fluidigm BioMark™ system, a Fluidigm Access Array™ system, and an Illumina MiSeq next-generation sequencing system.

Two units comprising the CIB Genotyping core are the Fluidigm BioMark™ application service and the Cattle MHC Typing service. The first application provides custom services available to run real-time PCR, SNP genotyping, and digital PCR assays in a high-throughput, low volume fluidics chip. The MHC Typing service provides Major Histocompatibility Complex (MHC) Typing of cattle. Services offer high-throughput genomic DNA sequencing to determine MHC class I and class II haplotypes of cattle.

The CIB Genotyping facility provides consultation and guidance to researchers in designing and performing genetic studies, and genotyping data for their research projects. Services are offered as fee for service. For more information, please contact Dr. Aaron Thomas.

Cattle MHC Typing

Full service involves high-resolution genotyping at the MHC locus performed by PCR amplification of the most polymorphic regions of the MHC genes. Due to the duplicated nature of the MHC genes and the high levels of polymorphism found in MHC genes, the Illumina MiSeq System is employed for targeted exon sequencing.

After sequencing, the alleles present in each sample are identified based on the sequences obtained and the haplotype(s) of each sample are determined. This service requires 1 ug of genomic DNA at a concentration of at least 50 ng/ul, and the data returned are the haplotype(s) for each sample.

The MHC typing service is currently offered only for bovine samples. However, our reagents should work with sheep and bison samples. Typing of other species may also be possible. If you are interested in MHC genotyping, please contact Dr. Aaron Thomas.

mhc typing

Fluidigm BioMark

Custom services for those working on animal, plant, or human genetics are available using the technology of the BioMark™ instrument to run real-time PCR, SNP genotyping, and digital PCR assays in a high-throughput, low volume fluidics chip.

Two-Tiered Services Are Available

Level 1-Full Service

  • Lab staff runs equipment for customer.
  • Customer supplies primers, TaqMan® probes, samples, etc. in 96 well plates at appropriate concentration.
  • Project details must be coordinated in advance with Dr. Aaron Thomas.

Level 2-User Access-Self Service

  • User runs equipment after completing training and certification with lab.
  • Equipment to be scheduled in advance through Outlook “CIB BioMark™ ” calendar or with Dr. Aaron Thomas.
  • Supplies including chips and some reagents are available through core lab which includes list of reagents/chips. (CIB core lab gets bulk pricing or customer can contact Fluidigm directly for bulk pricing on large numbers of chips)

BioMark