American Statistical Association
New York City
Metropolitan Area Chapter

Mailman School of Public Health
Columbia University
Department of Biostatistics Special Seminar



DETECTING GENE-GENE INTERACTIONS
IN GENOME-WIDE CASE-CONTROL STUDIES

by

Weichuan Yu, Ph.D.
Hong Kong University of Science and Technology
http://www.ece.ust.hk/~eeyu


Abstract

Gene-gene interactions have long been recognized to be fundamentally important to understand genetic causes of complex disease traits. At present, identifying gene-gene interactions from genome-wide case-control studies is computationally and methodologically challenging. In this talk, we introduce a new method, named ‘Boolean Operation Based Screening and Testing’ (BOOST). To discover unknown gene-gene interactions that underlie complex diseases, BOOST allows examining all pair-wise interactions in genome-wide case-control studies in a remarkably fast manner. We have carried out interaction analyses on seven data sets from the Wellcome Trust Case Control Consortium (WTCCC). Each analysis took less than 60 hours on a standard 3.0 GHz desktop with 4G memory running Windows XP system. The interaction patterns identified from the type 1 diabetes data set display significant difference from those identified from the rheumatoid arthritis data set, while both data sets share a very similar hit region in the WTCCC report. BOOST has also identified many undiscovered interactions between genes in the major histocompatibility complex (MHC) region in the type 1 diabetes data set. In the coming era of large-scale interaction mapping in genome-wide case-control studies, our method can serve as a computationally and statistically useful tool.

Biographical Note

Weichuan Yu received his Ph.D. in Computer Vision and Image Analysis from the University of Kiel, Germany in 2001. He was a postdoctoral associate at Yale University from 2001 to 2004 and a research faculty member in the Center for Statistical Genomics and Proteomics at Yale University from 2004 to 2006. He has been an assistant professor in the Department of Electronic and Computer Engineering at the Hong Kong University of Science and Technology since August 2006. He is interested in computational analysis problems with biological and medical applications. He has published papers on a variety of topics including bioinformatics, computational biology, biomedical imaging, signal processing, pattern recognition and computer vision. His long-term goal is to develop mathematical, computational, and statistical methods to address challenges in biological and medical data analysis.


Date: Thursday, July 8, 2010
Time: 11:00 A.M. - 12:00 P.M.
Location: Mailman School of Public Health
Department of Biostatistics
722 West 168th Street
Biostatistics Conference Room
6th Floor - Room 627
New York, New York

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