title: Identification of recurrent focal copy number variations and their putative targeted driver genes in ovarian cancer.
abstract: BACKGROUND
  Genomic regions with recurrent DNA copy number variations (CNVs) are generally believed to encode oncogenes and tumor suppressor genes (TSGs) that drive cancer growth. However, it remains a challenge to delineate the key cancer driver genes from the regions encoding a large number of genes.
  
  
  RESULTS
  In this study, we developed a new approach to CNV analysis based on spectral decomposition of CNV profiles into focal CNVs and broad CNVs. We performed an analysis of CNV data of 587 serous ovarian cancer samples on multiple platforms. We identified a number of novel focal regions, such as focal gain of ESR1, focal loss of LSAMP, prognostic site at 3q26.2 and losses of sub-telomere regions in multiple chromosomes. Furthermore, we performed network modularity analysis to examine the relationships among genes encoded in the focal CNV regions. Our results also showed that the recurrent focal gains were significantly associated with the known oncogenes and recurrent losses associated with TSGs and the CNVs had a greater effect on the mRNA expression of the driver genes than that of the non-driver genes.
  
  
  CONCLUSIONS
  Our results demonstrate that spectral decomposition of CNV profiles offers a new way of understanding the role of CNVs in cancer.
authors.affiliation: Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, 1400 Pressler St, Unit 1410, Houston, TX, 77401, USA.|Department of Statistics, Rice University, Houston, TX, USA.|Department of Biophysics, College of Bioinformatics Sciences and Technology, Harbin Medical University, Harbin, China.
authors.forename: Liangcai
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Department of Biostatistics, The University of Texas MD Anderson Cancer Center, 1400 Pressler St, Unit 1410, Houston, TX, 77401, USA.|Department of Statistics, Rice University, Houston, TX, USA.
authors.forename: Ying
authors.initials: Y
authors.lastname: Yuan
authors.affiliation: Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
authors.forename: Karen H
authors.initials: KH
authors.lastname: Lu
authors.affiliation: Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, 1400 Pressler St, Unit 1410, Houston, TX, 77401, USA. lzhangli@mdanderson.org.
authors.forename: Li
authors.initials: L
authors.lastname: Zhang
mesh_terms: D056915:DNA Copy Number Variations / Q000235:genetics*; D005260:Female; D023281:Genomics / Q000379:methods*; D006801:Humans; D009857:Oncogenes / Q000235:genetics*; D010051:Ovarian Neoplasms / Q000235:genetics*
keywords: Cancer; Copy number variations; Focal and broad CNV; Oncogenes and tumor suppressor genes