Researchers earn NSF grant to solve evolutionary riddle

An interdisciplinary team of researchers at the College of Science and Technology has been awarded a five-year, $3.2 million grant from the National Science Foundation to investigate a fundamental riddle of evolution and genetics: Why, over time, are some genetic mutations that negatively effect the function and behavior of organisms not eliminated from the gene pool?

To answer that question, the Temple researchers are exploring an evolutionary phenomenon called epistasis. This involves pairs or even more complex groupings of deleterious genes that suppress or neutralize each other’s effects. While epistasis has been long known, science has yet to test if this is the predominant mode of evolution and resilience.

“Our hypothesis is that epistasis is the predominant mode of evolution and resilience. If proven to be true, it would have profound impacts on the fields of genetics, human evolution and synthetic biology,” says Sudhir Kumar, principal investigator and Laura H. Carnell Professor of Biology and director of Temple’s Institute for Genomics and Evolutionary Medicine.

The researchers are utilizing big-data statistics, sophisticated modeling and machine learning to analyze as many as hundreds of thousands of available human genomes in their search for relevant mutated gene pairs. Analyzing complex networks of epistasis requires massive computational power, and the group will use graphics processing units (GPUs), commonly used in computer gaming, to accurately sort out which genes affect which other genes. 

“It’s extremely fast and it enables us to tackle problems on a genome-wide scale,” says co-principal investigator Ron Levy, Professor of Chemistry, Laura H. Carnell Professor of Biophysics and Computational Biology and the director of Temple’s Center for Biophysics and Computational Biology. “So far, we’re the first researchers in the country using GPU to analyze epistasis, the key for genotype to phenotype mapping.”

The NSF has also awarded approximately $300,00 more to a collaborator, Jeffrey Townsend, Elihu Professor of Biostatistics at Yale University, who will investigate the epistasis hypothesis in yeast cells in his laboratory.

Temple’s research team also includes Slobodan Vucetic, professor of computer science and director of the Center for Cognitive Computing; Vincenzo Carnevale, research associate professor of biology; and Allan Haldane, research associate professor of physics.

Byproducts of the research will include software packages of methods and tools for molecular epistasis analysis, as well as online curricula for both high school and college students.

-Bruce E. Beans