August 31, 2017

The Grand Challenge: using supercomputers to speed diagnosis and treatment

By Sharon Rosen

If you are a cancer patient who has exhausted all standard treatment options, a one day turnaround of your DNA testing results could make a big difference in your search for new, individualized treatment options. Mayo Clinic envisions just that: using supercomputers that are so fast and efficient they can interpret your DNA sequence in hours so providers can quickly apply them to individualized patient care.

Right now, it can take several days to weeks for computer systems to analyze DNA sequences looking for new treatment options. This is time that many patients with advanced cancer do not have. Researchers at Mayo Clinic Center for Individualized Medicine and the University of Illinois at Urbana-Champaign (Illinois) are collaborating on a research effort known as the Grand Challenge project, employing supercomputers that are many times faster than typical home or business computers so that analysis and interpretation of a complete human genome sequence can be completed in just one day.

The goals of the project are to develop methods within the next two years to automate and speed:

  • Analysis of DNA sequence to identify genetic variations that may be linked to disease – right now it can take days. The goal is to do it in hours.
  • Interpretation of genetic data so massive that it’s like sifting through a huge haystack and finding the needle with the clues to health and disease – right now we only understand the impact of 2 to 3 percent of the genetic variations that are discovered.

Keith Stewart, M.B., Ch.B.

According to Keith Stewart, M.B., Ch.B., the project addresses the need to move genomics from a manual exercise to an automated process that delivers information physicians can use in making a diagnosis or finding precise therapies.

“Eventually we hope to sequence the genome for all Mayo patients, incorporating those results in their electronic health record to inform future medical care.  This would enable us to harness the promise of genomics and better prevent, diagnose, treat and even cure disease,” says Dr. Stewart, Carlson and Nelson Endowed Director, Center for Individualized Medicine, and Vasek and Anna Maria Polak Professor of Cancer Research.

First pilot study – searching for genetic factors linked to a rare congenital heart disease

The research team will start developing and testing new genomic computational models using genomic data from approximately 300 people from families that have been affected with hypoplastic left heart syndrome (HLHS), a rare congenital heart disease, according to Eric Wieben, Ph.D., director, Medical Genome Faculty, and co-director, Clinomics Program, in the Center for Individualized Medicine.

Eric Wieben, Ph.D.

“Thanks to the foresight and effort of Timothy Nelson, M.D., Ph.D., and Timothy Olson, M.D., in the Center for Regenerative Medicine and the support of the Wanek family, we have genomic sequencing data on those affected by HLHS. This defined data set provides an initial testing ground to refine our computer models, before scaling them for larger numbers of patients. We know that HLHS patients and their family members share common underlying genetic characteristics linked to the disease, making them an ideal group to test new analytical models. To date, we have only been able to find genetic factors linked to a few of the HLHS cases. With new sequencing and computational models, we hope to solve that mystery for more families, potentially leading to the development of new targeted treatments for this serious heart condition,” says Dr. Wieben.

Research collaboration key to success

Mathieu Wiepert

Mathieu Wiepert, who provides IT support for the Center for Individualized Medicine and other Mayo research programs, says the Grand Challenge is just one project of the Mayo Clinic & Illinois Alliance for Technology-based Healthcare, a collaboration to develop additional technology and capacity to meet the big data challenge in health care.

“Our collaboration with University of Illinois faculty is critical to solving this and other big data challenges being faced in medicine today. We each have complementary strengths – Mayo with expertise in clinical medicine and genomics and Illinois with expertise in computer science and engineering. By collaborating, we can make a real difference for patients, providing critical answers faster, allowing them to get the care they need sooner,” says Wiepert.

Learn more about ongoing efforts to improve genomic data analysis

Register for the 2017 Individualizing Medicine Conference

Learn more about precision medicine and how that can be applied to improve diagnosis and treatment for many conditions at Individualizing Medicine 2017: Advancing Care Through Genomics.

The Mayo Clinic Center for Individualized Medicine, is hosting the sixth annual genomics conference, October 9–10, in Rochester, Minnesota.

Mayo Clinic Center for Individualized Medicine is hosting the conference with support from the Jackson Family Foundation.





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