title: High level of chromosomal aberration in ovarian cancer genome correlates with poor clinical outcome.
abstract: OBJECTIVE
  Structural aberration in chromosomes characterizes almost all human solid cancers and analysis of those alterations may reveal the history of chromosomal instability. However, the clinical significance of massive chromosomal abnormality in ovarian high-grade serous carcinoma (HGSC) remains elusive. In this study, we addressed this issue by analyzing the genomic profiles in 455 ovarian HGSCs available from The Cancer Genome Atlas (TCGA).
  
  
  METHODS
  DNA copy number, mRNA expression, and clinical information were downloaded from the TCGA data portal. A chromosomal disruption index (CDI) was developed to summarize the extent of copy number aberrations across the entire genome. A Cox regression model was applied to identify factors associated with poor prognosis. Genes whose expression was associated with CDI were identified by a 2-stage multivariate linear regression and were used to find enriched pathways by Ingenuity Pathway Analysis.
  
  
  RESULTS
  Multivariate survival analysis showed that a higher CDI was significantly associated with a worse overall survival in patients. Interestingly, the pattern of DNA copy number alterations across all the chromosomes was similar between tumors with high and low CDI, suggesting they did not arise from different mechanisms. We also observed that expression of several genes was highly correlated with the CDI, even after adjusting for local copy number variation. We found that molecular pathways involving DNA damage response and mitosis were significantly enriched in these CDI-correlated genes.
  
  
  CONCLUSIONS
  Our results provide a new insight into the role of chromosomal rearrangement in the development of HGSC and the promise of applying CDI in risk-stratifying HGSC patients, perhaps for different clinical managements. The genes whose expression is correlated with CDI are worthy of further study to elucidate the mechanism of chromosomal instability in HGSC.
authors.affiliation: The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Lcope1@jhmi.edu
authors.forename: Leslie
authors.initials: L
authors.lastname: Cope
authors.forename: Ren-Chin
authors.initials: RC
authors.lastname: Wu
authors.forename: Ie-Ming
authors.initials: IeM
authors.lastname: Shih
authors.forename: Tian-Li
authors.initials: TL
authors.lastname: Wang
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D002869:Chromosome Aberrations; D018284:Cystadenocarcinoma, Serous / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D056915:DNA Copy Number Variations; D005260:Female; D015894:Genome, Human; D006801:Humans; D008875:Middle Aged; D010051:Ovarian Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D011379:Prognosis; D016019:Survival Analysis; D016896:Treatment Outcome