title: A preliminary result of three-dimensional microarray technology to gene analysis with endoscopic ultrasound-guided fine-needle aspiration specimens and pancreatic juices.
abstract: BACKGROUND
  Analysis of gene expression and gene mutation may add information to be different from ordinary pathological tissue diagnosis. Since samples obtained endoscopically are very small, it is desired that more sensitive technology is developed for gene analysis. We investigated whether gene expression and gene mutation analysis by newly developed ultra-sensitive three-dimensional (3D) microarray is possible using small amount samples from endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA) specimens and pancreatic juices.
  
  
  METHODS
  Small amount samples from 17 EUS-FNA specimens and 16 pancreatic juices were obtained. After nucleic acid extraction, the samples were amplified with labeling and analyzed by the 3D microarray.
  
  
  RESULTS
  The analyzable rate with the microarray was 46% (6/13) in EUS-FNA specimens of RNAlater storage, and RNA degradations were observed in all the samples of frozen storage. In pancreatic juices, the analyzable rate was 67% (4/6) in frozen storage samples and 20% (2/10) in RNAlater storage. EUS-FNA specimens were classified into cancer and non-cancer by gene expression analysis and K-ras codon 12 mutations were also detected using the 3D microarray.
  
  
  CONCLUSIONS
  Gene analysis from small amount samples obtained endoscopically was possible by newly developed 3D microarray technology. High quality RNA from EUS-FNA samples were obtained and remained in good condition only using RNA stabilizer. In contrast, high quality RNA from pancreatic juice samples were obtained only in frozen storage without RNA stabilizer.
authors.affiliation: Department of Gastroenterology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku, Nagoya 4668550, Japan.
authors.forename: Koji
authors.initials: K
authors.lastname: Nonogaki
authors.forename: Akihiro
authors.initials: A
authors.lastname: Itoh
authors.forename: Hiroki
authors.initials: H
authors.lastname: Kawashima
authors.forename: Eizaburo
authors.initials: E
authors.lastname: Ohno
authors.forename: Takuya
authors.initials: T
authors.lastname: Ishikawa
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Matsubara
authors.forename: Yuya
authors.initials: Y
authors.lastname: Itoh
authors.forename: Yosuke
authors.initials: Y
authors.lastname: Nakamura
authors.forename: Masanao
authors.initials: M
authors.lastname: Nakamura
authors.forename: Ryoji
authors.initials: R
authors.lastname: Miyahara
authors.forename: Naoki
authors.initials: N
authors.lastname: Ohmiya
authors.forename: Masatoshi
authors.initials: M
authors.lastname: Ishigami
authors.forename: Yoshiaki
authors.initials: Y
authors.lastname: Katano
authors.forename: Hidemi
authors.initials: H
authors.lastname: Goto
authors.forename: Yoshiki
authors.initials: Y
authors.lastname: Hirooka
mesh_terms: D000465:Algorithms; D044963:Biopsy, Fine-Needle / Q000379:methods*; D016000:Cluster Analysis; D004247:DNA / Q000378:metabolism; D004252:DNA Mutational Analysis; D004724:Endoscopy / Q000379:methods*; D019160:Endosonography / Q000379:methods*; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D009696:Nucleic Acids / Q000737:chemistry; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010189:Pancreatic Juice / Q000378:metabolism; D010190:Pancreatic Neoplasms / Q000378:metabolism*; D012313:RNA / Q000378:metabolism
chemical_list: D009696:Nucleic Acids; D012313:RNA; D004247:DNA