Expression-based identification of OHNC genomic changes

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Oral/head and neck cancer (OHNC) is the 6th most common cancer worldwide. Approximately 38,000 new cases of oral cancer are diagnosed in the U.S. each year. Like most human cancers, oral/head and neck cancer is characterized by chromosomal alterations. The advent of DNA microarrays has produced a massive corpus of data on gene expression dynamics associated with various disease states, but comparatively little research has been done to identify chromosomal structural abnormalities that might underlie those expression changes. The present studies seek to develop an easily usable statistical framework for identifying chromosomal alterations based on widely available gene expression data. Specifically, these studies seek to: AIM 1) Map the boundaries of structural insertions or deletions within an abnormal chromosome AIM 2) Identify chromosomes showing spatially organized abnormalities in gene expression AIM 3) Discover chromosomal alterations in oral/head and neck cancer using clinical gene expression data. These studies will provide a comprehensive and clinically useful framework for mapping chromosomal abnormalities based on statistical techniques we have recently developed to identify chromosomal break points based on gene expression data. In addition to opening archival expression data to structural analysis, these techniques can provide a "value-added" layer of data analysis to nominate incoming gene expression data for more direct analyses of chromosomal abnormality through fluorescence in situ hybridization (FISH), loss of heterozygosity (LOH), or comparative genomic hybridization (CGH).