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

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.