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Structural analysis of a 50 kb region on 17q23

Akman, Begüm H
17q23 amplicon is one of the many chromosomal regions that undergo amplification in breast tumors. Such amplicons harbor proto-oncogenes that may be overexpressed due to gene amplifications. Copy number analysis in breast cancer cell lines and breast tumors identified several independently amplified regions within the 17q23 amplicon, suggesting that a number of genes are selected for amplification as they may independently contribute to tumor formation and progression. To characterize distinct amplicons on 17q23 and localize putative oncogenes, various studies are done on this region. In order to better understand the role of 17q23 amplification in breast cancer, characterizing unidentified genes or ESTs (Expressed Sequence Tags) on the 17q23 amplicon is crucial. In this study, in silico analysis of human (H.sapiens), chimpanzee (P.troglodytes), and mouse (M.musculus) genomes were performed to examine sequence homology between these 3 species for the purpose of identifying novel genes. The objective of this study was to analyze a 50 kb region between TBX2 and TBX4 genes and characterize the EST T02811 located on that region. Analysis and comparisons of these three genomes were established based on genomic sequences and availability of ESTs with gene prediction programs (BLAST, Pipmaker, Vista, GENSCAN etc.). Based on our results, we prepared a homology map between these 3 species, including positions of ESTs that may indicate novel genes. In this 50 kb region, we found in silico and experimantal evidence for the presence of an unidentified gene. We managed to extend the 313 bp EST T02811 size to 1423 bp which we think is as of yet incomplete. Further studies are needed to characterize this novel gene as a potential oncogene candidate. Characterizing the roles of such candidate oncogenes in amplicons will provide a better understanding of genomic amplicon regions and their roles in tumorigenesis.