August 20, 2019

Genomics and computer science intersect to improve patient care

By Sharon Rosen

Computational genomics is a field that brings high-performance computing resources to drive precision medicine research toward new discoveries. However, when over 50 Mayo Clinic physicians, researchers and students gathered in June to participate in the Computational Genomics Course, the emphasis was on the needs of the patient.

The annual week-long intensive course is sponsored by the Mayo Clinic and Illinois Alliance for Technology-Based Healthcare. The collaboration between Mayo Clinic and the University of Illinois at Urbana Champaign provides an overview of the latest tools of the genomics trade used to rapidly analyze the vast amounts of data generated by DNA testing.

Participants in this year's course from Mayo Clinic and the Carl R. Woese Institute for Genomic Biology at Illinois gained a better understanding of the computational processes used to analyze genomics data. University of Illinois faculty led hands-on lab exercises in a variety of subject areas, including genome sequencing and assembly, polymorphism and variant analysis, epigenomics and data visualization.

Educating the next generation of researchers and physicians

Timothy Curry, M.D., Ph.D.

“The Center for Individualized Medicine’s mission includes educating the next generation of researchers and physicians about the rapidly advancing field of genomics. This course offers attendees practical experience, providing them with tools and insights about how genomics can foster the development of new diagnostic tests and therapies for individualized care,” says Timothy Curry, M.D., Ph.D., director, Mayo Clinic Center for Individualized Medicine Education Program.

Nidhi Jalan Sakrikar, Ph.D., a course participant, wanted to learn how to improve care for patients with liver disease.  Dr. Sakrikar is a research associate working with Robert Huebert, M.D., and his research team. The team aims to develop new therapies for patients with liver and biliary diseases.

Nidhi Jalan Sakrikar, Ph.D.

“My research involves using genomics sequencing on samples from patients with primary sclerosing cholangitis,” says Dr. Sakrikar. “The techniques covered in the Computational Genomics course will help me curate all of the research data into one comprehensive data set that we hope will reveal some new therapeutic targets to treat these patients, especially those that do not respond to standard therapies.”

Justin Nguyen, M.D. , also wanted to learn how to improve care for patients with liver disease, but from the physician side.

Justin Nguyen, M.D.

 “As a liver transplant surgeon, one of my goals is to optimize how to make the liver work better,” says Dr. Nguyen.  “This course really offered me a new perspective and better tools to dive deep into the genetic and molecular levels of the liver to achieve better outcomes for patients.”

Computational genomics — a rapidly evolving science

Michael Kalmbach

Mike Kalmbach, a Mayo Clinic lead analyst and programmer in Bioinformatics Systems and teaching assistant for the course, often consults with participants, offering advice on how to use computational genomics to advance research projects.

“Computational genomics offers participants a glimpse into the possibilities of this evolving science,” says Kalmbach. “We’re at the very beginning with genomics we have much more to learn, but what we’ve been able to do already to improve our understanding of health and disease showcases how this science can guide more precise medical care.”

Mayo Clinic Center for Individualized Medicine sponsored the course with support from the Brandt Family Foundation.

The latest advances in cancer care

Join us for Individualizing Medicine 2019 Conference: Precision Cancer Care through Immunotherapy and Genomics on Sept. 20-21, in Scottsdale, Arizona. 

The conference brings together experts from Mayo Clinic and across the country to present and discuss case-based approaches to using genomics and new immunotherapies that oncologists and their teams can bring back to their own patients.

Other key conference themes include:

  • CAR-T cell therapy
  • Clonality
  • Pharmacogenomics
  • Lineage Plasticity
  • National Cancer Institute match

Preview the conference program.


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Tags: #CIMCon19, #computational genomics, #Mayo Clinic and Illinois Alliance for Technology-Based Healthcare, #Michael Kalmbach, center for individualized medicine, Dr. Justin Nguyen, Dr. Nidhi Jalan Sakrikar, Dr. Timothy Curry, education, mayo clinic, Precision Medicine, Research, University of Illinois at Urbana-Champaign

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