Environmental Factor, December 2007, National Institute of Environmental Health Sciences
Conference Promotes Bioinformatics in Genomics Fields
By Eddy Ball
NIEHS is helping to open new lines of interdisciplinary communication with its sponsorship of the first in a series of international conferences emphasizing the application of bioinformatics in the fields of toxicogenomics and environmental genomics. The two-day meeting, called the First International Conference on Toxicogenomics Integrated with Environmental Sciences (TIES), was held October 25 and 26 and drew more than 200 scientists to the McKimmon Center at North Carolina State University (NCSU).
The conference featured what NIEHS Bioinformatics Manager and TIES-2007 Organizing Committee member Pierre Bushel, Ph.D., described as "a diverse panel of scientists with a range of expertise, cutting-edge research and technological advances in genomics, toxicogenomics, genetics, proteomics and bioinformatics." The program also included a student oral presentation competition, poster session and a special session on reports from the FDA-led MicroArray Quality Consortium (MAQC).
Delivering the meeting's opening remarks, William Slikker, Ph.D., director of the Food and Drug Administration (FDA) National Center for Toxicological Research (NCTR), reflected on the convergence of recent American and European initiatives. "Certainly this [meeting] is one of the first times that all of these kinds of facets are being brought together in an international conference," he said.
The agenda brought together researchers from the NCTR, several current and former NIEHS grantees, and investigators from universities and institutes across the United States and worldwide. Topics ranged from population gene expression studies that challenge the notion of wild type and strategies for integrating genetics and exposure data, to statistical applications for microarray platforms and the issues of prediction and explanation in biomarker discovery.
NIEHS grantees included keynote speakers Kenneth Ramos, Ph.D., of the University of Louisville, who spoke on genetic regulation of mammalian retroelements, and David Threadgill, Ph.D., of the University of North Carolina (UNC), who addressed the integration of genetics and environmental exposure data. Randy Jirtle, Ph.D., of Duke University, delivered the dinner keynote talk on "Epigenetics: The Link between Fetal Exposure and Adult Disease Susceptibility." Other NIEHS grantees included Ivan Rusyn, Ph.D., of UNC, reporting on liver toxicology, and Daniel Liebler, Ph.D., of Vanderbilt University, exploring protein damage and its consequences.
Four students participated in the student oral presentation competition, with ClarLynda Williams of NCSU winning first place for her work with the Environmental Protection Agency (EPA) Distributed Structure Searchable Toxicity Database Network (DSSTox) Project . Placing second through fourth, respectively, were Yunjung Kim of NCSU, Venus Welch of Tuskegee University, a 2007 NIEHS Summers of Discovery intern (see related Spotlight story), and D. Ryan Georgianna of NCSU.
The special session on MAQC confronted some of the persistent technical issues surrounding the adoption of DNA microarray platforms by the regulatory community. The platform offers researchers and regulators a tool that can evaluate simultaneously the relative expression of thousands of genes, but questions about analytical consistency have long hindered widespread adoption of the methodology.
Currently in Phase II, the MAQC was formed in 2005 to assess the key factors contributing to variability and reproducibility of microarray data among different sites and platforms. The consortium brought together researchers from government, industry and academia to pursue development of a new set of standards and guidelines for the use of DNA microarray data.
The MAQC sessions featured presentations by Weida Tong, Ph.D., director of the Center for Toxicoinformatics at NCTR and technical representatives from several companies involved in microarray applications, including Expression Analysis, Panomics, SAS, Affymetrix, Agilent and Cogenics. The presentations reported on the consortium's studies of in-lab reproducibility and between-lab reproducibility, correlation of alternative platform results and the overlap of differentially expressed genes among different microarray platforms.
Jointly sponsored by NIEHS, NCSU and NCTR, the conference also received support from JMP Genomics and Rosetta Biosoftware. The meeting set the stage for a second conference scheduled for Spring 2009 at Zhejiang University in HangZhou, China and a meeting planned for 2010 in Germany.