Identification of novel gastric cancer-associated cnvs by integrated analysis of microarray

Chan Hee Park, SunYoung Rha, Hei Cheul Jeung, Seung Hui Kang, Dong Hyuk Ki, Won Suk Lee, Sung Hoon Noh, Hyuncheol Chung

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

Background: Microarray-CGH facilitates analysis of cancer-associated genomic differences between normal and tumor tissues and provides a genome-wide assessment of copy number variations (CNVs). Methods: To identify CNVs and their clinical significance in gastric cancer, Microarray-CGH was performed to identify CNVs with genomic DNA (gDNA) from normal placenta tissue, peripheral blood mononuclear cells (PBMCs), and normal gastric tissue. Results: A total of 20 CNVs, including 8 novel CNVs, were identified by Microarray-CGH. Among the 20 CNVs, 5 showed an aberration frequency of over 50%. In addition, mRNA expression of W72437 (TFIIH), AI968311 (GAGE10), AI352361, and AA169807 (PTCH1) in normal tissues and AA485362 (GPX1), AI201652, and AI968311 (GAGE10) in cancer tissues was associated with DNA change. As a whole, incidences of oncogene-like, suppressor-like, and innocent CNVs were 13.8%, 13.2%, and 73.0%, respectively (gain 11.4%, loss 11.8%). AA936795 (C19orf61) appeared as an oncogene-like CNV (9/30, 30%), A1352361 (13/30, 43%), and AA281797 (LOC728340, 10/30, 33%) appeared as tumor suppressor-related CNVs. Conclusions: This study identified gastric cancer-associated and innocent CNVs in gDNA isolated from placenta tissue and PBMC, which are generally used as reference samples in Microarray-CGH. These novel CNVs may be used for gastric cancer-specific gene selection in comparative analysis of genomics.

Original languageEnglish
Pages (from-to)454-461
Number of pages8
JournalJournal of Surgical Oncology
Volume102
Issue number5
DOIs
Publication statusPublished - 2010 Oct 1

Fingerprint

Microarray Analysis
Stomach Neoplasms
Oncogenes
Placenta
DNA
Blood Cells
Neoplasms
Neoplasm Genes
Genomics
Stomach
Genome
Messenger RNA
Incidence

All Science Journal Classification (ASJC) codes

  • Surgery
  • Oncology

Cite this

Park, Chan Hee ; Rha, SunYoung ; Jeung, Hei Cheul ; Kang, Seung Hui ; Ki, Dong Hyuk ; Lee, Won Suk ; Noh, Sung Hoon ; Chung, Hyuncheol. / Identification of novel gastric cancer-associated cnvs by integrated analysis of microarray. In: Journal of Surgical Oncology. 2010 ; Vol. 102, No. 5. pp. 454-461.
@article{a611113b94114a3b837876317d8d4366,
title = "Identification of novel gastric cancer-associated cnvs by integrated analysis of microarray",
abstract = "Background: Microarray-CGH facilitates analysis of cancer-associated genomic differences between normal and tumor tissues and provides a genome-wide assessment of copy number variations (CNVs). Methods: To identify CNVs and their clinical significance in gastric cancer, Microarray-CGH was performed to identify CNVs with genomic DNA (gDNA) from normal placenta tissue, peripheral blood mononuclear cells (PBMCs), and normal gastric tissue. Results: A total of 20 CNVs, including 8 novel CNVs, were identified by Microarray-CGH. Among the 20 CNVs, 5 showed an aberration frequency of over 50{\%}. In addition, mRNA expression of W72437 (TFIIH), AI968311 (GAGE10), AI352361, and AA169807 (PTCH1) in normal tissues and AA485362 (GPX1), AI201652, and AI968311 (GAGE10) in cancer tissues was associated with DNA change. As a whole, incidences of oncogene-like, suppressor-like, and innocent CNVs were 13.8{\%}, 13.2{\%}, and 73.0{\%}, respectively (gain 11.4{\%}, loss 11.8{\%}). AA936795 (C19orf61) appeared as an oncogene-like CNV (9/30, 30{\%}), A1352361 (13/30, 43{\%}), and AA281797 (LOC728340, 10/30, 33{\%}) appeared as tumor suppressor-related CNVs. Conclusions: This study identified gastric cancer-associated and innocent CNVs in gDNA isolated from placenta tissue and PBMC, which are generally used as reference samples in Microarray-CGH. These novel CNVs may be used for gastric cancer-specific gene selection in comparative analysis of genomics.",
author = "Park, {Chan Hee} and SunYoung Rha and Jeung, {Hei Cheul} and Kang, {Seung Hui} and Ki, {Dong Hyuk} and Lee, {Won Suk} and Noh, {Sung Hoon} and Hyuncheol Chung",
year = "2010",
month = "10",
day = "1",
doi = "10.1002/jso.21585",
language = "English",
volume = "102",
pages = "454--461",
journal = "Journal of Surgical Oncology",
issn = "0022-4790",
publisher = "Wiley-Liss Inc.",
number = "5",

}

Identification of novel gastric cancer-associated cnvs by integrated analysis of microarray. / Park, Chan Hee; Rha, SunYoung; Jeung, Hei Cheul; Kang, Seung Hui; Ki, Dong Hyuk; Lee, Won Suk; Noh, Sung Hoon; Chung, Hyuncheol.

In: Journal of Surgical Oncology, Vol. 102, No. 5, 01.10.2010, p. 454-461.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Identification of novel gastric cancer-associated cnvs by integrated analysis of microarray

AU - Park, Chan Hee

AU - Rha, SunYoung

AU - Jeung, Hei Cheul

AU - Kang, Seung Hui

AU - Ki, Dong Hyuk

AU - Lee, Won Suk

AU - Noh, Sung Hoon

AU - Chung, Hyuncheol

PY - 2010/10/1

Y1 - 2010/10/1

N2 - Background: Microarray-CGH facilitates analysis of cancer-associated genomic differences between normal and tumor tissues and provides a genome-wide assessment of copy number variations (CNVs). Methods: To identify CNVs and their clinical significance in gastric cancer, Microarray-CGH was performed to identify CNVs with genomic DNA (gDNA) from normal placenta tissue, peripheral blood mononuclear cells (PBMCs), and normal gastric tissue. Results: A total of 20 CNVs, including 8 novel CNVs, were identified by Microarray-CGH. Among the 20 CNVs, 5 showed an aberration frequency of over 50%. In addition, mRNA expression of W72437 (TFIIH), AI968311 (GAGE10), AI352361, and AA169807 (PTCH1) in normal tissues and AA485362 (GPX1), AI201652, and AI968311 (GAGE10) in cancer tissues was associated with DNA change. As a whole, incidences of oncogene-like, suppressor-like, and innocent CNVs were 13.8%, 13.2%, and 73.0%, respectively (gain 11.4%, loss 11.8%). AA936795 (C19orf61) appeared as an oncogene-like CNV (9/30, 30%), A1352361 (13/30, 43%), and AA281797 (LOC728340, 10/30, 33%) appeared as tumor suppressor-related CNVs. Conclusions: This study identified gastric cancer-associated and innocent CNVs in gDNA isolated from placenta tissue and PBMC, which are generally used as reference samples in Microarray-CGH. These novel CNVs may be used for gastric cancer-specific gene selection in comparative analysis of genomics.

AB - Background: Microarray-CGH facilitates analysis of cancer-associated genomic differences between normal and tumor tissues and provides a genome-wide assessment of copy number variations (CNVs). Methods: To identify CNVs and their clinical significance in gastric cancer, Microarray-CGH was performed to identify CNVs with genomic DNA (gDNA) from normal placenta tissue, peripheral blood mononuclear cells (PBMCs), and normal gastric tissue. Results: A total of 20 CNVs, including 8 novel CNVs, were identified by Microarray-CGH. Among the 20 CNVs, 5 showed an aberration frequency of over 50%. In addition, mRNA expression of W72437 (TFIIH), AI968311 (GAGE10), AI352361, and AA169807 (PTCH1) in normal tissues and AA485362 (GPX1), AI201652, and AI968311 (GAGE10) in cancer tissues was associated with DNA change. As a whole, incidences of oncogene-like, suppressor-like, and innocent CNVs were 13.8%, 13.2%, and 73.0%, respectively (gain 11.4%, loss 11.8%). AA936795 (C19orf61) appeared as an oncogene-like CNV (9/30, 30%), A1352361 (13/30, 43%), and AA281797 (LOC728340, 10/30, 33%) appeared as tumor suppressor-related CNVs. Conclusions: This study identified gastric cancer-associated and innocent CNVs in gDNA isolated from placenta tissue and PBMC, which are generally used as reference samples in Microarray-CGH. These novel CNVs may be used for gastric cancer-specific gene selection in comparative analysis of genomics.

UR - http://www.scopus.com/inward/record.url?scp=77957327697&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=77957327697&partnerID=8YFLogxK

U2 - 10.1002/jso.21585

DO - 10.1002/jso.21585

M3 - Article

VL - 102

SP - 454

EP - 461

JO - Journal of Surgical Oncology

JF - Journal of Surgical Oncology

SN - 0022-4790

IS - 5

ER -