A method for detecting significant genomic regions associated with oral squamous cell carcinoma using aCGH

Ki Yeol Kim, Jin Kim, Hyung Jun Kim, Woong Nam, Inho Cha

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

Array comparative genomic hybridization (aCGH) provides a genome-wide technique for identifying chromosomal aberrations in human diseases, including cancer. Chromosomal aberrations in cancers are defined as regions that contain an increased or decreased DNA copy number, relative to normal samples. The identification of genomic regions associated with systematic aberrations provides insights into initiation and progression of cancer, and improves diagnosis, prognosis, and therapy strategies. The McNemar test can be used to detect differentially expressed genes after discretization of gene expressions in a microarray experiment for the matched dataset. In this study, we propose a method to detect significantly altered DNA regions, shifted McNemar test, which is based on the standard McNemar test and takes into account changes in copy number variations and the region size throughout the whole genome. In addition, this novel method can be used to detect genomic regions associated with the progress of oral squamous cell carcinoma (OSCC). The performance of the proposed method was evaluated based on the homogeneity within the selected regions and the classification accuracies of the selected regions. This method might be useful for identifying new candidate genes that neighbor known genes based on the whole-genomic variation because it detects significant chromosomal regions, not independent probes.

Original languageEnglish
Pages (from-to)459-468
Number of pages10
JournalMedical and Biological Engineering and Computing
Volume48
Issue number5
DOIs
Publication statusPublished - 2010 May 1

Fingerprint

Comparative Genomic Hybridization
Squamous Cell Carcinoma
Genes
Aberrations
Chromosome Aberrations
Genome
DNA
Neoplasms
Microarrays
Gene expression
Gene Expression
Epithelial Cells
Experiments
Therapeutics

All Science Journal Classification (ASJC) codes

  • Biomedical Engineering
  • Computer Science Applications

Cite this

@article{1714682bd56043b0beed061ce293983c,
title = "A method for detecting significant genomic regions associated with oral squamous cell carcinoma using aCGH",
abstract = "Array comparative genomic hybridization (aCGH) provides a genome-wide technique for identifying chromosomal aberrations in human diseases, including cancer. Chromosomal aberrations in cancers are defined as regions that contain an increased or decreased DNA copy number, relative to normal samples. The identification of genomic regions associated with systematic aberrations provides insights into initiation and progression of cancer, and improves diagnosis, prognosis, and therapy strategies. The McNemar test can be used to detect differentially expressed genes after discretization of gene expressions in a microarray experiment for the matched dataset. In this study, we propose a method to detect significantly altered DNA regions, shifted McNemar test, which is based on the standard McNemar test and takes into account changes in copy number variations and the region size throughout the whole genome. In addition, this novel method can be used to detect genomic regions associated with the progress of oral squamous cell carcinoma (OSCC). The performance of the proposed method was evaluated based on the homogeneity within the selected regions and the classification accuracies of the selected regions. This method might be useful for identifying new candidate genes that neighbor known genes based on the whole-genomic variation because it detects significant chromosomal regions, not independent probes.",
author = "Kim, {Ki Yeol} and Jin Kim and Kim, {Hyung Jun} and Woong Nam and Inho Cha",
year = "2010",
month = "5",
day = "1",
doi = "10.1007/s11517-010-0595-0",
language = "English",
volume = "48",
pages = "459--468",
journal = "Medical and Biological Engineering and Computing",
issn = "0140-0118",
publisher = "Springer Verlag",
number = "5",

}

A method for detecting significant genomic regions associated with oral squamous cell carcinoma using aCGH. / Kim, Ki Yeol; Kim, Jin; Kim, Hyung Jun; Nam, Woong; Cha, Inho.

In: Medical and Biological Engineering and Computing, Vol. 48, No. 5, 01.05.2010, p. 459-468.

Research output: Contribution to journalArticle

TY - JOUR

T1 - A method for detecting significant genomic regions associated with oral squamous cell carcinoma using aCGH

AU - Kim, Ki Yeol

AU - Kim, Jin

AU - Kim, Hyung Jun

AU - Nam, Woong

AU - Cha, Inho

PY - 2010/5/1

Y1 - 2010/5/1

N2 - Array comparative genomic hybridization (aCGH) provides a genome-wide technique for identifying chromosomal aberrations in human diseases, including cancer. Chromosomal aberrations in cancers are defined as regions that contain an increased or decreased DNA copy number, relative to normal samples. The identification of genomic regions associated with systematic aberrations provides insights into initiation and progression of cancer, and improves diagnosis, prognosis, and therapy strategies. The McNemar test can be used to detect differentially expressed genes after discretization of gene expressions in a microarray experiment for the matched dataset. In this study, we propose a method to detect significantly altered DNA regions, shifted McNemar test, which is based on the standard McNemar test and takes into account changes in copy number variations and the region size throughout the whole genome. In addition, this novel method can be used to detect genomic regions associated with the progress of oral squamous cell carcinoma (OSCC). The performance of the proposed method was evaluated based on the homogeneity within the selected regions and the classification accuracies of the selected regions. This method might be useful for identifying new candidate genes that neighbor known genes based on the whole-genomic variation because it detects significant chromosomal regions, not independent probes.

AB - Array comparative genomic hybridization (aCGH) provides a genome-wide technique for identifying chromosomal aberrations in human diseases, including cancer. Chromosomal aberrations in cancers are defined as regions that contain an increased or decreased DNA copy number, relative to normal samples. The identification of genomic regions associated with systematic aberrations provides insights into initiation and progression of cancer, and improves diagnosis, prognosis, and therapy strategies. The McNemar test can be used to detect differentially expressed genes after discretization of gene expressions in a microarray experiment for the matched dataset. In this study, we propose a method to detect significantly altered DNA regions, shifted McNemar test, which is based on the standard McNemar test and takes into account changes in copy number variations and the region size throughout the whole genome. In addition, this novel method can be used to detect genomic regions associated with the progress of oral squamous cell carcinoma (OSCC). The performance of the proposed method was evaluated based on the homogeneity within the selected regions and the classification accuracies of the selected regions. This method might be useful for identifying new candidate genes that neighbor known genes based on the whole-genomic variation because it detects significant chromosomal regions, not independent probes.

UR - http://www.scopus.com/inward/record.url?scp=77955588483&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=77955588483&partnerID=8YFLogxK

U2 - 10.1007/s11517-010-0595-0

DO - 10.1007/s11517-010-0595-0

M3 - Article

C2 - 20306232

AN - SCOPUS:77955588483

VL - 48

SP - 459

EP - 468

JO - Medical and Biological Engineering and Computing

JF - Medical and Biological Engineering and Computing

SN - 0140-0118

IS - 5

ER -