A preliminary result of three-dimensional microarray technology to gene analysis with endoscopic ultrasound-guided fine-needle aspiration specimens and pancreatic juices

Koji Nonogaki, Akihiro Itoh, Hiroki Kawashima, Eizaburo Ohno, Takuya Ishikawa, Hiroshi Matsubara, Yuya Itoh, Yosuke Nakamura, Masanao Nakamura, Ryoji Miyahara, Naoki Omiya, Masatoshi Ishigami, Yoshiaki Katano, Hidemi Goto, Yoshiki Hirooka

Research output: Contribution to journalArticle

4 Citations (Scopus)

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.

Original languageEnglish
Article number36
JournalJournal of Experimental and Clinical Cancer Research
Volume29
Issue number1
DOIs
Publication statusPublished - 01-12-2010
Externally publishedYes

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Endoscopic Ultrasound-Guided Fine Needle Aspiration
Pancreatic Juice
Technology
RNA
Genes
Gene Expression
Mutation
RNA Stability
Codon
Nucleic Acids
Neoplasms

All Science Journal Classification (ASJC) codes

  • Oncology
  • Cancer Research

Cite this

Nonogaki, Koji ; Itoh, Akihiro ; Kawashima, Hiroki ; Ohno, Eizaburo ; Ishikawa, Takuya ; Matsubara, Hiroshi ; Itoh, Yuya ; Nakamura, Yosuke ; Nakamura, Masanao ; Miyahara, Ryoji ; Omiya, Naoki ; Ishigami, Masatoshi ; Katano, Yoshiaki ; Goto, Hidemi ; Hirooka, Yoshiki. / A preliminary result of three-dimensional microarray technology to gene analysis with endoscopic ultrasound-guided fine-needle aspiration specimens and pancreatic juices. In: Journal of Experimental and Clinical Cancer Research. 2010 ; Vol. 29, No. 1.
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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.",
author = "Koji Nonogaki and Akihiro Itoh and Hiroki Kawashima and Eizaburo Ohno and Takuya Ishikawa and Hiroshi Matsubara and Yuya Itoh and Yosuke Nakamura and Masanao Nakamura and Ryoji Miyahara and Naoki Omiya and Masatoshi Ishigami and Yoshiaki Katano and Hidemi Goto and Yoshiki Hirooka",
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Nonogaki, K, Itoh, A, Kawashima, H, Ohno, E, Ishikawa, T, Matsubara, H, Itoh, Y, Nakamura, Y, Nakamura, M, Miyahara, R, Omiya, N, Ishigami, M, Katano, Y, Goto, H & Hirooka, Y 2010, 'A preliminary result of three-dimensional microarray technology to gene analysis with endoscopic ultrasound-guided fine-needle aspiration specimens and pancreatic juices', Journal of Experimental and Clinical Cancer Research, vol. 29, no. 1, 36. https://doi.org/10.1186/1756-9966-29-36

A preliminary result of three-dimensional microarray technology to gene analysis with endoscopic ultrasound-guided fine-needle aspiration specimens and pancreatic juices. / Nonogaki, Koji; Itoh, Akihiro; Kawashima, Hiroki; Ohno, Eizaburo; Ishikawa, Takuya; Matsubara, Hiroshi; Itoh, Yuya; Nakamura, Yosuke; Nakamura, Masanao; Miyahara, Ryoji; Omiya, Naoki; Ishigami, Masatoshi; Katano, Yoshiaki; Goto, Hidemi; Hirooka, Yoshiki.

In: Journal of Experimental and Clinical Cancer Research, Vol. 29, No. 1, 36, 01.12.2010.

Research output: Contribution to journalArticle

TY - JOUR

T1 - A preliminary result of three-dimensional microarray technology to gene analysis with endoscopic ultrasound-guided fine-needle aspiration specimens and pancreatic juices

AU - Nonogaki, Koji

AU - Itoh, Akihiro

AU - Kawashima, Hiroki

AU - Ohno, Eizaburo

AU - Ishikawa, Takuya

AU - Matsubara, Hiroshi

AU - Itoh, Yuya

AU - Nakamura, Yosuke

AU - Nakamura, Masanao

AU - Miyahara, Ryoji

AU - Omiya, Naoki

AU - Ishigami, Masatoshi

AU - Katano, Yoshiaki

AU - Goto, Hidemi

AU - Hirooka, Yoshiki

PY - 2010/12/1

Y1 - 2010/12/1

N2 - 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.

AB - 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.

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