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Genomics Core marks two decades of growth

Image with caption: Jim Eudy, PhD

Jim Eudy, PhD

The Genomics Core turns 20 this year, and director Jim Eudy, PhD, has been with it every step of the way.

Today, the core offers a variety of services to users, including next generation DNA sequencing (NGS), NanoString technology for profiling panels of genes, single cell genomics and Sanger sequencing. In 2020 alone, the core provided services to approximately 167 different laboratories at all University of Nebraska campuses, as well as other academic research institutions throughout the state.

In 2001, the core was created in response to the development of DNA microarrays, which allowed researchers to measure the activity of many different genes in the genome simultaneously.

"That was a big technological advancement for the study of genetics," Dr. Eudy said. "There are approximately 22,000 genes in the genome -- so being able to measure the gene activity levels in those individual genes simultaneously was a major breakthrough."

UNMC recognized the implications, and the core -- originally housed at the Munroe-Meyer Institute -- was created. Initial funding came from the Nebraska INBRE Project, which purchased the core's first DNA microarray machine and has been a longtime supporter of the core, and the Center for Molecular Human Genetics at MMI. (Shelley Smith, PhD, and her Centers for Biomedical Research Excellence grant also provided important early support, Dr. Eudy said.)

"Like many of our cores, this core's growth and ability to continue to evolve to meet customer needs also has received critical support from Nebraska Research Initiative funding," said Tess Kuenstling as Director of Research Resources.

As DNA sequencing technology advanced, the center's capabilities grew, and, in 2004, the core merged with the UNMC Department of Genetics, Cell Biology and Anatomy, eventually moving to the Durham Research Center.

With the development of DNA microarray technology, increased statistical analysis of data was needed. Dr. Eudy credits UNMC's biostatisticians, particularly Lynette Smith, PhD, with helping researchers maximize the impact of the newly available data.

Next generation DNA sequencing (NGS) began in 2010, with funding Dr. Eudy obtained from a National Institutes of Health grant purchase of an "Illumina Genome Analyzer IIa," and the hiring of Alok Dhar, PhD, who was key in integrating the Illumina's capabilities into the core's services.

"Next generation sequencing revolutionized what was possible in genetics on a global scale," Dr. Eudy said, adding that applications included not only humans and other animals in the context of health and disease, but plants in the context of agriculture and conservation.

"At the medical center, we focused on biomedical research," he said. "But when we worked with colleagues at the University of Nebraska-Lincoln, we worked with plants and agricultural systems and the landscape of what was possible changed."

With the arrival of NGS, the first genome-wide RNAseq experiments began immediately along with large scale DNA sequencing applications. Again, interdepartmental collaboration was key.

"The datasets generated by NGS are quite large, and the analysis often requires coding and a great deal of computational understanding," Dr. Eudy said. "As the genomics core was bringing on the NGS technology, UNMC was investing in and developing its bioinformatics infrastructure."

Today, the genomics core collaborates with UNMC's Bioinformatics and Systems Biology Core, directed by Babu Guda, PhD, to provide analytical support to researchers who utilize the NGS technology in the genomics core

"Since 2010, the field of NGS has grown tremendously, as has the sequencing technology and the applications," Dr. Eudy said. "Initially, around 10 to 15 researchers accessed the NGS services annually. Today, the core provides services to approximately 160 different laboratories throughout the state of Nebraska, and approximately 90 of those researchers are accessing the NGS component of the lab."

Research includes infectious disease, cancer, vision, cardiology, pulmonary and agriculture studies. Going forward, Dr. Eudy expects to see advances that impact personalized medicine, liquid biopsies to identify cancer and more.

"The advancement in technology is amazing," Dr. Eudy said, reflecting on 20 years. "I'm not sure many people would have foreseen how profoundly different it would be today."

But the success of the core also is due to its people, said Jennifer Larsen, MD, vice chancellor for research at UNMC.

"While cores depend in part on their advanced technologies, their success depends not only on their leadership but the considerable expertise of the staff in the core, as well," Dr. Larsen said. "They not only help investigators achieve the best scientific results, but play an important role in the education of our graduate and other students, as well."

Current services and support

Current services provided at the UNMC Genomics Core include:
  • RNAseq -- The core provides genome-wide RNAseq to identify genes expressed during various biological processes. This yields insights into the biological underpinnings of a normal and disease-related processes. This is the most widely used application.

  • DNASeq -- Sequencing of DNA to identify mutations related to cancer, hearing and other disease states. This is at the level of panels of genes all the way up to entire human, plant and microbial genomes.

  • Metagenomics -- Sequencing of mixtures of microbial specimens to identify all the bacterial, fungal and viral components of the mixture. Shifts or changes in the quantities and relative ratios of the organisms can be reflective of, and contribute to, the state of disease or health.

  • Single Cell Genomics -- The newest technology to come to the lab is 10x Genomics, which provides the ability to perform genome-wide RNAseq and DNA applications on individual cells - up to 10,000 single cells at a time. This is an amazing development that yields high resolution understanding of the cells that comprise a given tissue in either disease or healthy states. Prior, these experiments were performed on tissues, which are comprised of various types of different cells.

Support

Current funds for the operation of the core comes from a variety of sources, including the Nebraska Research Initiative, large NIH infrastructure grants including Nebraska INBRE, the Fred & Pamela Buffett Cancer Center, funds from the UNMC Office of the Vice Chancellor for Research and user fees.

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