title: The development of a mini-array for estimating the disease state of gastric adenocarcinoma by array CGH.
abstract: BACKGROUND
  The treatment strategy usually depends on the disease state in the individual patient. However, it is difficult to estimate the disease state before treatment in many patients. The purpose of this study was to develop a BAC (bacterial artificial chromosome) mini-array allowing for the estimation of node metastasis, liver metastasis, peritoneal dissemination and the depth of tumor invasion in gastric cancers.
  
  
  METHODS
  Initially, the DNA copy number aberrations (DCNAs) were analyzed by array-based comparative genomic hybridization (aCGH) in 83 gastric adenocarcinomas as a training-sample set. Next, two independent analytical methods were applied to the aCGH data to identify the BAC clones with DNA copy number aberrations that were linked with the disease states. One of the methods, a decision-tree model classifier, identified 6, 4, 4, 4, and 7 clones for estimating lymph node metastasis, liver metastasis, peritoneal dissemination, depth of tumor invasion, and histological type, respectively. In the other method, a clone-by-clone comparison of the frequency of the DNA copy number aberrations selected 26 clones to estimate the disease states.
  
  
  RESULTS
  By spotting these 50 clones together with 26 frequently or rarely involved clones and 62 reference clones, a mini-array was made to estimate the above parameters, and the diagnostic performance of the mini-array was evaluated for an independent set of 30 gastric cancers (blinded - sample set). In comparison to the clinicopathological features, the overall accuracy was 66.7% for node metastasis, 86.7% for liver metastasis, 86.7% for peritoneal dissemination, and 96.7% for depth of tumor invasion. The intratumoral heterogeneity barely affected the diagnostic performance of the mini-array.
  
  
  CONCLUSIONS
  These results suggest that the mini-array makes it possible to determine an optimal treatment for each of the patients with gastric adenocarcinoma.
authors.affiliation: Department of Pathology, Yamaguchi University School of Medicine, Ube, Japan. tfuruya@yamaguchi-u.ac.jp
authors.forename: Tomoko
authors.initials: T
authors.lastname: Furuya
authors.forename: Tetsuji
authors.initials: T
authors.lastname: Uchiyama
authors.forename: Atsushi
authors.initials: A
authors.lastname: Adachi
authors.forename: Takae
authors.initials: T
authors.lastname: Okada
authors.forename: Motonao
authors.initials: M
authors.lastname: Nakao
authors.forename: Atsunori
authors.initials: A
authors.lastname: Oga
authors.forename: Song-Ju
authors.initials: SJ
authors.lastname: Yang
authors.forename: Shigeto
authors.initials: S
authors.lastname: Kawauchi
authors.forename: Kohsuke
authors.initials: K
authors.lastname: Sasaki
mesh_terms: D000230:Adenocarcinoma / Q000235:genetics / Q000473:pathology / Q000556:secondary; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D055028:Comparative Genomic Hybridization / Q000379:methods*; D005260:Female; D018628:Gene Dosage / Q000235:genetics; D006801:Humans; D008113:Liver Neoplasms / Q000556:secondary; D008297:Male; D008875:Middle Aged; D013274:Stomach Neoplasms / Q000235:genetics / Q000473:pathology; D046888:Tissue Array Analysis / Q000379:methods*