JSM 2005 - Toronto

Abstract #304085

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Legend: = Applied Session, = Theme Session, = Presenter
Activity Number: 355
Type: Topic Contributed
Date/Time: Wednesday, August 10, 2005 : 8:30 AM to 10:20 AM
Sponsor: Biometrics Section
Abstract - #304085
Title: Detection of Genomic Changes and the Association with Clinical Parameters
Author(s): Chiang-Ching Huang*+
Companies: Northwestern University
Address: 925 E Bailey Rd, Naperville, IL, 60565, United States
Keywords: Transcriptome map ; microarray ; cancer ; Hidden Markov Chain
Abstract:

The study of transcriptome maps has become an active research area to better understand the gene expression pattern in relationship to chromosomal position. In cancer research, several abnormal expression regions found through transcriptome maps have been linked to genomic alterations such as deletions, amplification, and LOH. To facilitate the search for these regions using gene-expression data, we developed a type of hidden Markov model in a penalization framework. Our method provides probabilistic inference for expression status for all the genes in the genome. We applied our method to a lung cancer microarray experiment and demonstrated that several regions identified are consistent with those reported in the literature. Moreover, we found the pattern of these abnormal expression regions has strong association with clinical parameters such as stage and differentiation. This finding suggests genes in these regions have a major role in carcinogenesis. Our method offers a valuable technique to pinpoint these regions.

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Revised March 2005