For More Information
Contact Aaron Thomas: (435) 757-5534;

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

The Fluidigm BioMark is a high throughput real-time PCR instrument that utilizes low volume microfluidics chips. With the accompanying loaders and Juno, our instrumentation can run the following BioMark chips:

  • 96.96 Gene expression and SNP Genotyping (96 samples, 96 assays)
  • 48.48 Gene expression and SNP Genotyping (48 samples, 48 assays)
  • FlexSix Gene Expression and SNP Genotyping (6 separate arrays of 12 samples/12 assays; can be run at different times)
  • 192.24 Gene expression and SNP Genotyping (192 samples, 24 assays)
  • 24.192 Gene expression and SNP Genotyping (24 samples, 192 assays)
  • LP 48.48 (48 samples, 48 assays; PCR product can be harvested for sequencing)
  • LP 192.24 (192 samples, 48 assays; PCR product can be harvested for sequencing)
  • 12.765 Digital Array (digital PCR, 12 samples)
  • 48.770 Digital Array (digital PCR, 48 samples)
  • 48.Atlas (Advanta RNA-Seq XT for automated library preparation, 48 RNA samples)

The BioMark is a user access self-service instrument. Users are charged $35 per run for instrument usage. Users must be trained before using the BioMark. Contact Dr. Aaron Thomas for training or other questions regarding access.

Supplies including chips and some reagents can be purchased from the Genomics Core, or can purchased directly from Fluidigm. Contact Dr. Aaron Thomas for chip/reagent pricing or with other questions.