CHAPEL HILL, December 18, 2006–The Carolina Center for Exploratory Genetic Analysis (CCEGA), will present the results of its genetics “bake-off” at a meeting Feb. 2, 2007 in the Health Science Library building on the UNC-Chapel Hill campus. CCEGA is a collaborative project funded by the National Institutes of Health and led by the Renaissance Computing Institute (RENCI) and genetics department of the University of North Carolina at Chapel Hill.
The bake-off was organized by CCEGA researchers to test the value of various genetic association analysis tools and to put to use a genetic research tool developed at RENCI called the Genome Wide Association Simulator. The simulator allows researchers to create simulated datasets that are larger, and therefore more statistically valid, than data that comes from the typical laboratory experiments.
“When your data sets are small, it is very difficult to know if the results you are getting through analysis are accurate,” said Dan Reed, principal investigator for CCEGA and Director of RENCI. “Not only will the simulator give researchers more data to work with, but in doing so, it will help them evaluate their own analysis tools. This is a tool that could bring about best practices in the field and overall better analysis tools.”
The simulator creates its datasets based on real laboratory data from the HapMap project—an effort to catalog genetic similarities and differences among groups of people in the United States, Nigeria, Japan and China. The HapMap data chronicles single nucleotide polymosphisms (SNPs), which are the single changes among a DNA sequence that account for 90 percent of genetic variation.
The data created by the simulator scales up the HapMap data to a simulated sample of hundreds of thousands of individuals, accurately mimicking the crossover process, in which genetically similar regions of chromosomes entangle, interchange information and give rise to new chromosomes. By comparing SNPs in these new simulated DNA sequence models to the SNPs in models of known diseases, researchers can begin to isolate the SNPs that lead to diseases, including cancer, diabetes, hypertension and others. In addition, they can test the efficacy of their own analysis tools.
For several months, Kirk Wilhelmsen, an associate professor in the genetics department, Xiaojun Guan, a RENCI senior research scientist, and other members of the CCEGA research team have solicited participation in the bake-off among genetics and biomedical researchers and computer scientists on the UNC-Chapel Hill campus. Those who are testing their analysis tools with the Genome Wide Association Simulator have until Jan. 19, 2007 to submit their results.
RENCI, Catalyst for Innovation
The Renaissance Computing Institute brings together computer and discipline scientists, artists, humanists, industry leaders, entrepreneurs, state leaders and educators for collaborations designed to reshape science, the economy, the state of North Carolina and the world. RENCI leverages its expertise and resources in leading edge computing, networking and data technologies to ignite innovation and find solutions to previously intractable problems. Founded in 2004 as a major collaborative venture of Duke University, North Carolina State University, the University of North Carolina at Chapel Hill and the state of North Carolina, RENCI is a statewide virtual organization. For more, see www.renci.org.
kgreen at renci.org