Iyer leads search for new computer platform to speed genomic data interpretation

8/2/2016 Kim Gudeman, CSL

The new center seeks to develop a new platform for generating, interpreting, and applying genomic data for a variety of applications, such as enabling patient-specific treatment of cancer and other diseases.

Written by Kim Gudeman, CSL

The human genome consists of three billion nucleotides that, when strung together, offer a glimpse into the basic processes of life as well as risk for disease. However, breakthroughs in the use of this genomic information have been limited due to the difficulty in quickly and accurately analyzing a rapidly expanding amount of genomic data.  

The University of Illinois at Urbana-Champaign is leading a new center that seeks to develop a new platform for generating, interpreting, and applying genomic data for a wide variety of applications. Working with colleagues at Mayo Clinic, researchers in the Center for Computational Biotechnology and Genomic Medicine (CCBGM) will advance pressing societal issues, such as enabling patient-specific treatment of cancer and other diseases, understanding and modifying microbial communities related to human health and agriculture, and supporting humanity’s growing need for food by improving the efficiency of plant and animal agriculture.

The center is funded for five years through the National Science Foundation’s Industry/University Cooperative Research Centers program.

Ravishankar K. Iyer
Ravishankar K. Iyer
“The big picture goal is to apply computational genomics across the life sciences industry, but currently it’s challenged by our inability to generate, interpret, and apply genomic data quickly, efficiently, and accurately,” said Ravishankar K Iyer, principal investigator, ECE ILLINOIS faculty, and George and Ann Fisher Distinguished Professor of Engineering at Illinois. “The amount of data is increasing at such a rapid rate that our ability to apply computing to a wide range of genomic problems is still very limited.”

CCBGM will seek to address those challenges by developing new computer platforms that can more efficiently scale to the rapidly growing volume, velocity, and variety of genomic data. It will focus on scaling the computation of epistatic interactions (interactions between two or more genes or DNA variants), generating lists of genomic features, and developing information-compression algorithms for genomic data storage and transfer.

Researchers also will work to enhance the capability of computers to evaluate data and provide actionable intelligence for treatment. This will enable physicians to determine genome-specific treatments for patients with cancer and other diseases, and to help agriculture biotech companies improve seed for crops.

Liewei Wang
Liewei Wang
“Incorporating these latest technologies in the era of big data in medicine and biology will help physicians and scientists at Mayo, along with the broader medical community, improve patient care and health-care delivery, and be part of the innovation,” said Dr. Liewei Wang, professor in the Mayo Dept. of Molecular Pharmacology and Experimental Therapeutics (MPET), who is Co-PI and the Mayo site lead for CCBGM.

To enable these advancements, researchers will design new architectures that can optimize genomic analysis workflows, providing unprecedented speed and energy efficiency while preserving the accuracy of the analytics.

“Like physics in the 1960s, medicine is now on the cusp of enormous breakthroughs,” said Dr. Richard Weinshilboum, professor of medicine and pharmacology at Mayo. “The Human Genome Project and recent advancements in DNA sequencing technology have made precision medicine possible. This new center will bring together physicians, engineers, and life scientists who will utterly transform the way we treat patients in the future.”

The center is part of CompGen, an Illinois initiative of the Carl R. Woese Institute for Genomic Biology and the Coordinated Science Laboratory, which leverages big data and large-scale parallel systems to impact genomic research. Through the CompGen initiative, researchers have built a new instrument that will serve as the computational engine of CCBGM. The research is part of a growing partnership with Mayo, which is collaborating with Illinois on a $9.34 million, four-year Big Data to Knowledge (BD2K) grant funded by the National Institutes of Health, also under the auspices of CompGen.

The center researchers also will collaborate with colleagues at the University of Chicago.

As an I/UCRC, industry will play a large role in the center. Currently, CCBGM has nine member companies that will help select the center’s projects and steer its course.

“We are very excited to work with some of the leading companies in computing technology, pharmaceuticals, and agricultural biotechnology to create the computational breakthroughs that are necessary to realize the fruits of the genomic revolution,” said Dr. Rashid Robinson, Swanlund Chair of Entomology and Neuroscience at Illinois and Director of the Carl R. Woese Institute for Genomic Biology.

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This story was published August 2, 2016.