Genomics

The Genomics Core Facility at the University of Utah provides a variety of cost effective genotyping services to researchers on campus and around the world. SNP (single nucleotide polymorphism) genotyping and microsatellite (short tandem repeat) genotyping are the primary methods that our facility employs to provide genotyping analysis. Several platforms for both SNP genotyping and microsatellite genotyping are available to meet individual project needs, allowing cost effective results for projects ranging in scale from single sites to whole genomes. In addition to genotyping, these platforms can be used for copy number variation and whole genome methylation analysis. The Genomics Core Facility also offers training and real time PCR instrument access for researches interested in performing gene expression studies ranging from single targets to hundreds of genes.

Any researcher performing studies involving SNP genotyping, microsatellite STR genotyping, copy number variation, methylation, or gene expression is encouraged to contact the Genomics Core Facility to discuss the most appropriate and cost effective platform to achieve their study goals.

If you would like to make a reservation to use our equipment or services, please go to resource.cores.utah.edu. Our supply ordering system is currently listed under the DNA Sequencing Core Facility. This will change in the future. In the meantime, please click here to order from the DNA Sequencing Core.

SNP Genotyping

The Genomics Core Facility offers three platforms for genotyping single nucleotide polymorphisms (SNPs) and small genomic variations such as insertions and deletions. The appropriate platform will be selected based on the number of samples and SNPs. Applications of SNP genotyping include screening populations for known mutations and genome wide association studies.

WholeGenomeSNPGenotyping
Whole Genome SNP Genotyping

Ideal platform for genotyping thousands to millions of SNPs per sample using Illumina’s predesigned and custom bead chip arrays on the Illumina iScan system. Human, agricultural, and model organism chips are available.

Click here for additional information.

FocusedSNPGenotyping
Focused SNP Genotyping

Custom panels of SNPs for any organism can be selected for genotyping on the LifeTechnologies OpenArray system. This platform is ideal for studies that involve genotyping dozens to hundreds of SNPs on hundreds of samples.

For more information, please call Mike at (801)-585-2977.

IndividualSNPGenotyping
Individual SNP Genotyping

Predesigned and custom TaqMan SNP genotyping assays from LifeTechnologies are available for genotyping small numbers of SNPs on dozens to hundreds of samples. Assays can be designed for any organism.

For more information, please call Mike at (801)-585-2977.

Fragment Analysis

The Genomics Core Facility offers capillary electrophoresis-based fragment analysis on the Applied Biosystems 3730 platform. Fluorescently labeled PCR products up to 1200 base pairs in length can be accurately and consistently sized using a LIZ labeled size standard. Applications for fragment analysis include STR genotyping, identity and cell line verification, and tumor vs. normal studies.

str-genotyping-cropped
STR (microsatellite) Genotyping

Full service STR genotyping from PCR setup through analysis is available at the Genomics Core Facility. 1000+ fluorescently labeled human microsatellite markers are available for full genome scans, custom fine mapping projects, loss of heterozygosity (LOH) studies, and microsatellite instability (MSI) studies. Custom markers can be ordered for any organism.

For more information, please call Mike at (801)-585-2977.

capillary-electrophoresis-runs-cropped
Capillary Electrophoresis Runs

Users provide PCR products labeled with FAM, VIC, NED, or PET fluorescent tags for fragment sizing analysis on the 3730 capillary electrophoresis instrument.

For more information, please call Mike at (801)-585-2977.

Gene Expression Analysis

An Applied Biosystems 7900HT instrument and a Life Technologies QuantStudio 12K Flex instrument are available for researchers interested in performing real time PCR experiments for gene expression studies. Instrument and software training is available to all users and the instruments can be reserved in two hour time increments. Plate loading robots allow for 24 hour operation of both instruments. The most common plate formats are 96 well and 384 well, but the instruments are also capable of running TaqMan Array cards and OpenArrays from LifeTechnologies for higher throughput experiments involving hundreds of samples and genes.

Quantitative Real Time PCR

Users will isolate RNA from their samples, perform the reverse transcription step to generate cDNA, and set up the real time PCR reaction plates to be run on the Core Facility instruments. Instrument and software training is available to all users . Real time amplification measurements of target and endogenous control genes can be used to measure relative gene expression between various samples or groups.

Please contact the Genomics Core Facility for additional pricing and information about this service either by phone at (801)-585-2977 or email at mklein@genetics.utah.edu.

QuantitativeRealTimePCR
Methylation Analysis

The methylation of DNA at various sites in the human genome regulates the expression of genes and plays an important role in development, X chromosome inactivation, imprinting, and carcinogenesis. The Genomics Core Facility offers researchers a platform for measuring the degree of methylation at various sites throughout the human genome to compare groups or individual samples.

Whole Genome Methylation Analysis

Users provide bisulfite converted DNA for use on Illumina Infinium Human Methlyation 450 bead chip array. This BeadChip allows researchers to interrogate > 485,000 methylation sites per sample at single-nucleotide resolution. It covers 99% of RefSeq genes, with an average of 17 CpG sites per gene.

Please contact the Genomics Core Facility for additional pricing and information about this service either by phone at (801)-585-2977 or email at mklein@genetics.utah.edu.

WholeGenomeMethylationAnalysis
Hours of Operation

Monday-Friday 9am-5pm excluding University closure days

Location

Radiobiology Building (Building 585)
30 N. 2030 E. Room 110 RB
Salt Lake City, UT 84112

Staff

Derek Warner, Director
801-581-4736
dwarner@cores.utah.edu

Mike Klein, Manager
801-585-2977
mklein@cores.utah.edu

Reaction plates and optical sealers for real time PCR are available for purchase from the Genomics Core via the HSC Cores Scheduling System.

In the scheduling system, select “Genomics” on the menu on the left, then click “Order Real Time PCR supplies”.

The Genomics Core will not retain researcher’s data after delivery of the data to the requesting researcher.

Per NIH policy, it is the responsibility of the grant holder to store their data for at least the minimum time required by the grant (usually at least 3 years, but please check your grant conditions).

We request that all labs publishing work that relies at least partially on work we’ve performed acknowledge our core facility with something along the lines of:

Work was performed by the Genomics Core Facility, a part of the Health Sciences Cores at the University of Utah.

Thank you.