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Identifying genes associated with chemotherapy response in ovarian carcinomas based on DNA copy number and expression profiles

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6 Author(s)
Fang-Han Hsu ; Department of Electrical and Computer Engineering, Texas A&M University, College Station, USA ; Erchin Serpedin ; Tzu-Hung Hsiao ; Alexander J. R. Bishop
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DNA copy number alterations (CNAs) may change transcription profiles and are reported to be associated with chemotherapy response. Using a recently concluded ovarian cancer study derived from the Cancer Genome Atlas (TCGA) Research Network, we selected 98 ovarian cancer samples derived from patients who were only treated with Paclitaxel/Carboplatin after the surgery. A statistical testing procedure was proposed to examine the genes with CNAs and correlated changes in expression level, and their associated response to chemotherapy in progression-free survival. Among 12,042 genes under consideration, 112 genes with CNAs and correlated gene expression levels were found to be associated with progression-free survival (PFS) significantly. The region containing many selected genes, 1p35.1-1p34.2, is closely examined as a candidate segment where CNAs are significantly associated with chemotherapeutic response to Paclitaxel/Carboplatin. Biological processes and molecular functions associated with chemotherapy response were further proposed based on a gene ontology enrichment analysis.

Published in:

2011 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS)

Date of Conference:

4-6 Dec. 2011