Much of health sciences research involves seeing the unseen: the genetic and bioinformatic data that underlies human health and disease. At the University of Utah, generating that data involves top-quality tools. Part of the U’s research mission is acquiring and maintaining equipment and services that help scientists work at the frontier of what is known, where researchers gain an understanding of the genetic basis of human diseases, develop new treatments, and improve patient outcomes.
Among the formal facilities available to researchers are the Utah Center for Genetic Discovery (UCGD) and the DNA Sequencing and Genomics Core Facilities. At the heart of the UCGD mission is providing equipment and analysis for bioinformatic research along with modern computational power, including vast data storage key to bioinformatic research. The DNA Sequencing and Genomics Cores are in place to help researchers access and explore equipment they don’t have or are considering for their labs, and is an institutional partner ready to provide experienced insights in experimentation design.
Utah Center for Genetic Discovery (UCGD) Core
The UCGD Core supports research by providing expertise in bioinformatic analysis and access to shared computational infrastructure. UCGD helps investigate the genetic basis of human disease by offering whole exome and whole genome sequence analyses for research and clinical projects. The core includes 3088 CPU cores, 3 A100 GPUs, over 5.4 petabytes of disk storage, and an expansive library of computational software tools and workflows. The UCGD core can also provide storage allocations to support NIH-funded projects.
Key Services
- Genomics: Alignment and variant calling for next-generation sequencing datasets, joint genotyping, whole genome bisulfite sequencing analysis, disease gene discovery, structural variant calling, and more.
- Transcriptomics: Analysis of RNA microarrays, RNA-Seq data, identification of splicing aberrations, differential gene expression analysis, and single-cell dataset integration.
- Metabolomics/Lipidomics: Comparisons of individual metabolites or lipids, differential abundance analysis, and lipid ontology enrichment analysis.
- Image Analysis: Analysis of fluorescent microscopy images.
- Machine Learning: Custom deep learning networks and integration of clinical and omics data for predictive purposes.
- Development: Generation of parallelized pipelines, custom bioinformatics tools, and data visualizations.
Services with Impact
The UCGD supports a number of projects to identify the genetic cause of human disease in active clinical patients. These include the Penelope Program for rare and undiagnosed human diseases, which helped diagnose and lead to treatment for a patient with a rare disease.
Another UCGD supported project is the NeoSeq project for sick infants at the University of Utah NICU, which leads to diagnosis in almost half of cases and has identified causal genetic variants within as little as 6 hours of receiving genomic sequencing data.
Contact the UCGD Core
Press below to visit the UCGD website to learn more or contact the UCGD Core director, Carson Holt at carson.holt@genetics.utah.edu.
DNA Sequencing and Genomics Core Facilities
The DNA Sequencing and Genomics Cores have been developed to—as is the case with most cores—to ensure that scientists at the U have access to modern technology. Often times, labs are considering new equipment in the DNA and genomics research, and these cores allow researchers to rent equipment to generate data, get guidance on equipment they may want to acquire, and collaborate on designing novel research. These core facilities offer a range of services through modern equipment, such as: the Element Biosciences AVITI sequencer, P2 Solo nanopore sequencer, Sanger sequencer, Illumina iScan, PCR instruments, and more.
DNA Sequencing Core Key Services
- DNA Sequencing (Short Read): Provides higher data quality and better GC tolerance compared to Illumina sequencers using the Element Biosciences AVITI sequencer.
- DNA Sequencing (Long Read): Generates very long reads that are ideal for mapping new genomes and finding large structural changes, using Oxford Nanopore Sequencing via a P2 Solo device.
- Sanger Sequencing: The gold standard for accurately detecting small changes to DNA, used extensively for various research projects.
Genomics Core Key Services
- Microarray Analysis: Researchers can get a large-scale picture of gene activity using microarrays that measure methylation levels at hundreds of thousands of positions across the genome, or query genotype at many sites simultaneously, both using the Illumina iScan.
- Real-time PCR Instrumentation: Available for rent to help labs determine needs, with both standard and digital PCR instruments.
Services with Impact
Through these cores, more useful and timely data is generated. Derek Warner, director of the two cores notes that this was exemplified in a recent every-day-experience by a post-doctoral fellow being able to call 60% more repeat sequences than had been possible with previous equipment.
Collaborations have also allowed the DNA Sequencing Core to sequence the full genomes of mice produced in the Transgenic & Gene Targeting Mouse Core Facility to verify insertions and deletions. This ensures that the desired mutations are present without any off-target effects, providing researchers with clear and accurate results.
Contact the UCGD Core
Press below to visit the respective DNA Sequencing and Genomics Core Facilities websites. Or contact the director of the two cores, Derek Warner, at 801-581-4736 or dwarner@cores.utah.edu.