title: Integrative analysis of array-comparative genomic hybridisation and matched gene expression profiling data reveals novel genes with prognostic significance in oesophageal adenocarcinoma.
abstract: OBJECTIVE
  The incidence of oesophageal adenocarcinoma (OAC) has been increasing rapidly with a dismal survival rate of less than 20%. Understanding the genomic aberrations and biology of this cancer may enhance disease interventions. This study aimed to use genome-wide genomic and expression data to enhance the understanding of OAC pathogenesis and identify groups with differential outcomes.
  
  
  METHODS
  Array-comparative genomic hybridisation (aCGH) analysis was carried out on 56 fresh frozen OAC resection samples with long-term clinical follow-up data. Samples with aberrations were further analysed with whole-genome single-nucleotide polymorphism arrays to confirm aCGH findings. Matched gene expression microarray data were used to identify genes with high copy number-expression correlations. Nested-multiplex PCR on DNA from microdissected specimens and fluorescence in situ hybridisation assays were used for target validation. Immunohistochemistry on the same cohort and independent samples (n=371) was used for subsequent validation. Kaplan-Meier survival analyses were performed based on aCGH data after unsupervised K-means clustering (K=5, 50 iterations) and immunohistochemistry data.
  
  
  RESULTS
  aCGH identified 17 common regions (>5% samples) of gains and 11 common regions of losses, including novel regions in OAC (loci 11p13 and 21q21.2). Integration of aCGH data with matched gene expression microarray data highlighted genes with high copy number-expression correlations: two deletions (p16/CDKN2A, MBNL1) and four gains (EGFR, WT1, NEIL2, MTMR9). Immunohistochemistry demonstrated protein over-expression of targets with gains: EGFR (10%), WT1 (20%), NEIL2 (14%) and MTMR9 (25%). These targets individually (p<0.060) and in combination had prognostic significance (p=0.008). On the genomic level, K-means clustering identified a cluster (32% of cohort) with differential log(2) ratios of 16 CGH probes (p<4×10(-7)) and a worse prognosis (median survival=1.37 years; p=0.015).
  
  
  CONCLUSIONS
  Integration of aCGH and gene expression data identified copy number aberrations and novel genes with prognostic potential in OAC.
authors.affiliation: MRC Cancer Cell Unit, Hutchison-MRC Research Centre, Cambridge, UK.
authors.forename: X Y
authors.initials: XY
authors.lastname: Goh
authors.forename: J R E
authors.initials: JR
authors.lastname: Rees
authors.forename: A L
authors.initials: AL
authors.lastname: Paterson
authors.forename: S F
authors.initials: SF
authors.lastname: Chin
authors.forename: J C
authors.initials: JC
authors.lastname: Marioni
authors.forename: V
authors.initials: V
authors.lastname: Save
authors.forename: M
authors.initials: M
authors.lastname: O'Donovan
authors.forename: P P
authors.initials: PP
authors.lastname: Eijk
authors.forename: D
authors.initials: D
authors.lastname: Alderson
authors.forename: B
authors.initials: B
authors.lastname: Ylstra
authors.forename: C
authors.initials: C
authors.lastname: Caldas
authors.forename: R C
authors.initials: RC
authors.lastname: Fitzgerald
mesh_terms: D000230:Adenocarcinoma / Q000235:genetics* / Q000401:mortality / Q000473:pathology; D000368:Aged; D000369:Aged, 80 and over; D014408:Biomarkers, Tumor / Q000096:biosynthesis / Q000235:genetics; D055028:Comparative Genomic Hybridization / Q000379:methods*; D004273:DNA, Neoplasm / Q000235:genetics*; D066246:ErbB Receptors / Q000096:biosynthesis / Q000235:genetics*; D004938:Esophageal Neoplasms / Q000235:genetics* / Q000401:mortality / Q000473:pathology; D005260:Female; D005500:Follow-Up Studies; D020869:Gene Expression Profiling / Q000379:methods*; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D007150:Immunohistochemistry; D053208:Kaplan-Meier Estimate; D008297:Male; D046228:Microarray Analysis; D008875:Middle Aged; D016133:Polymerase Chain Reaction; D011379:Prognosis; D012189:Retrospective Studies; D015996:Survival Rate; D013997:Time Factors; D006113:United Kingdom / Q000453:epidemiology
chemical_list: D014408:Biomarkers, Tumor; D004273:DNA, Neoplasm; C512478:EGFR protein, human; D066246:ErbB Receptors