A Computational Approach for Ultra-specific High-throughput HLA Typing
Abstract
The variations within an individual's HLA (Human Leukocyte Antigen) genes have been linked to many immunological events, e.g. susceptibility to disease, response to vaccines, and the success of blood, tissue, and organ transplants. Although the microarray format has the potential to achieve high-resolution typing, this has yet to be attained due to inefficiencies of current probe design strategies. The aim of the presented work is to develop a new technique for designing highly specific probe sets for high resolution microarray-based HLA typing. This approach includes: (1) new algorithms and data structures to identify probe subsequences that are present in the target genes which cannot be converted to subsequences within the background (the rest of the human genome and human associated microbial/viral genomes) by any combination of up to three base changes, and (2) an evolutionary programming-based algorithm to minimize the number of microarray probes, thus reducing the cost of typing.
Date: Friday, September 15, 2006
Time: 9:00 AM
Place: 550-PGH
Faculty, students, and the general public are invited.
Advisor: Dr. Yuriy Fofanov
