Please tell us about yourself

The Center for Individualized Medicine and the University of Illinois are teaming up to translate data-heavy genomics research into customized clinical care.

Fifty thousand. That’s how many people have enrolled in the Mayo Clinic Biobank, a collection of samples and health information donated by Mayo Clinic patients for use in ongoing biomedical research. Multiply that number by 180,000, or the number of exons — regions of DNA that direct the human body to make essential proteins—contained in a single human genome, and you get 9 billion. Through statistical analysis, researchers and physicians at the Mayo Clinic for Individualized Medicine (CIM) are using those 9 billion data points to translate genomic medicine into clinical practice.

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But they can’t do it with just pencil and paper. Crunching that much data requires high-performance computers and people who can run them — like Arjun Athreya. A third-year Ph.D. candidate in Electrical and Computer Engineering at the University of Illinois at Urbana–Champaign (UIUC), Arjun is supporting pharmacogenomics research at CIM this summer through an institutional partnership that brings together top thinkers in technology and medicine.

What did you study?

Arjun did his Telecommunication Engineering from R.V. College of Engineering, Bangalore and Masters in Computer & Wireless Networks from Carnegie Mellon University.

Tell us about your work

For Athreya, Mayo Clinic offers the opportunity to take his background in electrical and computer engineering to advance technology used in individualizing treatment management of patients with major depressive disorder. The work of the team he served on has been encapsulated in a clinician-friendly web interface they hope will be made available to all primary care centers and hospitals that are willing to follow assessments recommended by measurement-based psychiatry.

 “What I learned is that modern health science—and even beyond healthcare—is now ‘team science,’ a phrase I borrow from my mentor Dr. Richard Weinshilboum,” said Athreya. “It means multiple disciplines and thinking philosophies are needed to address a complex problem, and by working together as a team, we are bound to achieve what we could not have done individually.”

For young statisticians, computer scientists and engineers intrigued by the growing possibilities for big data in health care, the chance to collaborate on cutting-edge research at Mayo Clinicholds obvious appeal. “You can’t be working on medical data and not know what people at Mayo are doing, or miss an opportunity to work with their clinical experts,”says Athreya, who has an M.S. in Electrical and Computer Engineering from Carnegie Mellon University and is advised by Ravishankar Iyer, Ph.D., and Zbigniew Kalbarczyk, Ph.D., both of UIUC’s Coordinated Science Lab.

Likewise, Mayo researchers need the informatics infrastructure and powerful minds housed at UIUC, a world leader in engineering and computational sciences. Without this technology expertise, says Athreya, teasing out biological patterns from the chaos of numbers would be daunting.

“When you look at analyzing these data, a lot of these experiments can take hours to days to complete,” he says. “Today it might seem trivial when we say something takes hours to run for one patient, but if every hospital and every clinic starts to do this for every patient that comes in, the scale becomes pretty messy very quickly.”

If engineers can write more sophisticated software programs and make them run on the right kind of hardware, they can reduce the entire computation time needed for data analysis in experiments, Athreya explains. Millions or billions of unintelligible data points can quickly assume meaning. That makes research in individualized medicine more efficient, which ultimately translates into clinical care that better meets the patient’s needs.

For a glimpse at the Alliance’s integrated approach to research, consider Athreya’s contributions to cancer treatment studies in CIM’s Pharmacogenomics Program, which is led by Richard Weinshilboum, M.D., and Liewei Wang, M.D., Ph.D. To understand why standard drugs work effectively in some cancer patients but not in others, CIM investigators are collaborating with UIUC researchers like Athreya to study how variations in genes affect patients’ response to medications.

How does your work benefit the society?

Within the Pharmacogenomics Program, Athreya is working with Krishna Kalari, Ph.D., to develop and apply computational models to statistically analyze the impact of metformin, a drug used to manage type 2 diabetes that also shows promise in treatment of certain breast cancers. Their models are helping CIM researchers identify genetic mutations in tumors that affect a patient’s response to metformin. The goal, says Athreya, is to “narrow down the impact of the drug to specific genetic biomarkers. Then we will know which patients would respond to this drug.”

Though the CIM research on metformin will continue after he returns to UIUC, Athreya says his summer at Mayo has given him a lasting gift: greater appreciation for how his analytical skills can harmonize with the knowledge of health care experts.

“There were times when from our engineering perspective, we generated some results that made no sense to us,” he says. “And then the physicians and biologists looked at it and they said, ‘We know exactly what this is saying, and we can narrow down our research base.’ Those moments when we put up some results and there is a huge biological story behind what they see, those moments are pretty exciting.”

In those moments, he says, he sees the power of data to transform medicine.

What inspires you?

 “What I learned is that modern health science—and even beyond healthcare—is now ‘team science,’ a phrase I borrow from my mentor Dr. Richard Weinshilboum,” said Athreya. “It means multiple disciplines and thinking philosophies are needed to address a complex problem, and by working together as a team, we are bound to achieve what we could not have done individually.”

Using team science to advance and transform healthcare is what the Mayo Clinic and Illinois Alliance is all about. Richard Weinshilboum, M.D., professor of pharmacology and medicine and Dasburg Professor of Cancer Genomics Research at Mayo Clinic, said, “I’ve been at Mayo Clinic for a long time, and this alliance—institution to institution—has been the most positive and most productive I’ve seen.” With the explosion of big data in medicine—from data-loaded electronic health records, to digital imaging data, to the genomic revolution—Dr. Weinshilboum believes the alliance responds to the need to combine medical and computational expertise. It allows burgeoning leaders from both Illinois and Mayo Clinic to physically interact and learn from each other.

That mutual learning has translated to real results for Arthreya and his team. While there are effective medications for treating depression, matching the right patients with the right drugs has been a clinical challenge. Patients may go through several trials of treatment, over the course of several months, before they see remission from depressive symptoms. By applying computation techniques to the large Mayo Clinic patient datasets, the team has seen large improvements in drug response prediction rates. Especially for suicidal patients, this can mean the difference between life and death.

“Not often do we engineers get an opportunity to be so close to the point of impact our technology has as when a clinician uses our technology to tailor diagnoses/treatment for a patient,” said Athreya.