title: Identification of genes with a correlation between copy number and expression in gastric cancer.
abstract: BACKGROUND
  To elucidate gene expression associated with copy number changes, we performed a genome-wide copy number and expression microarray analysis of 25 pairs of gastric tissues.
  
  
  METHODS
  We applied laser capture microdissection (LCM) to obtain samples for microarray experiments and profiled DNA copy number and gene expression using 244K CGH Microarray and Human Exon 1.0 ST Microarray.
  
  
  RESULTS
  Obviously, gain at 8q was detected at the highest frequency (70%) and 20q at the second (63%). We also identified molecular genetic divergences for different TNM-stages or histological subtypes of gastric cancers. Interestingly, the C20orf11 amplification and gain at 20q13.33 almost separated moderately differentiated (MD) gastric cancers from poorly differentiated (PD) type. A set of 163 genes showing the correlations between gene copy number and expression was selected and the identified genes were able to discriminate matched adjacent noncancerous samples from gastric cancer samples in an unsupervised two-way hierarchical clustering. Quantitative RT-PCR analysis for 4 genes (C20orf11, XPO5, PUF60, and PLOD3) of the 163 genes validated the microarray results. Notably, some candidate genes (MCM4 and YWHAZ) and its adjacent genes such as PRKDC, UBE2V2, ANKRD46, ZNF706, and GRHL2, were concordantly deregulated by genomic aberrations.
  
  
  CONCLUSIONS
  Taken together, our results reveal diverse chromosomal region alterations for different TNM-stages or histological subtypes of gastric cancers, which is helpful in researching clinicopathological classification, and highlight several interesting genes as potential biomarkers for gastric cancer.
authors.affiliation: State Key Laboratory of Medical Genomics and Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Cheng
authors.forename: Ping
authors.initials: P
authors.lastname: Wang
authors.forename: Sheng
authors.initials: S
authors.lastname: Yang
authors.forename: Yanqing
authors.initials: Y
authors.lastname: Yang
authors.forename: Qing
authors.initials: Q
authors.lastname: Zhang
authors.forename: Wen
authors.initials: W
authors.lastname: Zhang
authors.forename: Huasheng
authors.initials: H
authors.lastname: Xiao
authors.forename: Hengjun
authors.initials: H
authors.lastname: Gao
authors.forename: Qinghua
authors.initials: Q
authors.lastname: Zhang
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics; D002898:Chromosomes, Human, Pair 8 / Q000235:genetics; D056915:DNA Copy Number Variations / Q000235:genetics; D005753:Gastric Mucosa / Q000378:metabolism; D018628:Gene Dosage / Q000235:genetics*; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics*; D052138:Genes, Neoplasm / Q000235:genetics*; D055106:Genome-Wide Association Study; D006801:Humans; D061346:Laser Capture Microdissection; D009367:Neoplasm Staging; D013270:Stomach / Q000166:cytology / Q000473:pathology; D013274:Stomach Neoplasms / Q000175:diagnosis / Q000235:genetics* / Q000473:pathology
chemical_list: D014408:Biomarkers, Tumor