title: Discovery and validation of prognostic markers in gastric cancer by genome-wide expression profiling.
abstract: OBJECTIVE
  To develop a prognostic gene set that can predict patient overall survival status based on the whole genome expression analysis.
  
  
  METHODS
  Using Illumina HumanWG-6 BeadChip followed by semi-supervised analysis, we analyzed the expression of 47,296 transcripts in two batches of gastric cancer patients who underwent surgical resection. Thirty-nine samples in the first batch were used as the training set to discover candidate markers correlated to overall survival, and thirty-three samples in the second batch were used for validation.
  
  
  RESULTS
  A panel of ten genes were identified as prognostic marker in the first batch samples and classified patients into a low- and a high-risk group with significantly different survival times (P = 0.000047). This prognostic marker was then verified in an independent validation sample batch (P = 0.0009). By comparing with the traditional Tumor-node-metastasis (TNM) staging system, this ten-gene prognostic marker showed consistent prognosis results. It was the only independent prognostic value by multivariate Cox regression analysis (P = 0.007). Interestingly, six of these ten genes are ribosomal proteins, suggesting a possible association between the deregulation of ribosome related gene expression and the poor prognosis.
  
  
  CONCLUSIONS
  A ten-gene marker correlated with overall prognosis, including 6 ribosomal proteins, was identified and verified, which may complement the predictive value of TNM staging system.
authors.affiliation: Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China.
authors.forename: Yue-Zheng
authors.initials: YZ
authors.lastname: Zhang
authors.forename: Lian-Hai
authors.initials: LH
authors.lastname: Zhang
authors.forename: Yang
authors.initials: Y
authors.lastname: Gao
authors.forename: Chao-Hua
authors.initials: CH
authors.lastname: Li
authors.forename: Shu-Qin
authors.initials: SQ
authors.lastname: Jia
authors.forename: Ni
authors.initials: N
authors.lastname: Liu
authors.forename: Feng
authors.initials: F
authors.lastname: Cheng
authors.forename: De-Yun
authors.initials: DY
authors.lastname: Niu
authors.forename: William Cs
authors.initials: WC
authors.lastname: Cho
authors.forename: Jia-Fu
authors.initials: JF
authors.lastname: Ji
authors.forename: Chang-Qing
authors.initials: CQ
authors.lastname: Zeng
mesh_terms: D000368:Aged; D014408:Biomarkers, Tumor / Q000235:genetics*; D005260:Female; D020869:Gene Expression Profiling / Q000592:standards*; D015894:Genome, Human; D055106:Genome-Wide Association Study; D006801:Humans; D053208:Kaplan-Meier Estimate; D008297:Male; D008875:Middle Aged; D020411:Oligonucleotide Array Sequence Analysis / Q000592:standards*; D011379:Prognosis; D015203:Reproducibility of Results; D013274:Stomach Neoplasms / Q000175:diagnosis* / Q000235:genetics* / Q000473:pathology / Q000601:surgery
chemical_list: D014408:Biomarkers, Tumor