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

Authors
 Ki-Yeol Kim  ;  Jin Kim  ;  Hyung Jun Kim  ;  Woong Nam  ;  In-Ho Cha 
Citation
 MEDICAL & BIOLOGICAL ENGINEERING & COMPUTING, Vol.48(5) : 459-468, 2010 
Journal Title
 MEDICAL & BIOLOGICAL ENGINEERING & COMPUTING 
ISSN
 0140-0118 
Issue Date
2010
MeSH
Aged ; Carcinoma, Squamous Cell/genetics* ; Chromosome Aberrations* ; Comparative Genomic Hybridization/methods ; Disease Progression ; Female ; Humans ; Male ; Middle Aged ; Mouth Neoplasms/genetics* ; Precancerous Conditions/genetics
Keywords
Shifted McNemar ; Oral squamous cell carcinoma ; aCGH ; Genomic variations ; Systematic aberrations ; Significant chromosomal region
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
Full Text
http://link.springer.com/article/10.1007%2Fs11517-010-0595-0
DOI
10.1007/s11517-010-0595-0
Appears in Collections:
2. College of Dentistry (치과대학) > Dept. of Oral Pathology (구강병리학교실) > 1. Journal Papers
5. Research Institutes (연구소) > Oral Cancer Research Institute (구강종양연구소) > 1. Journal Papers
2. College of Dentistry (치과대학) > Dept. of Oral and Maxillofacial Surgery (구강악안면외과학교실) > 1. Journal Papers
Yonsei Authors
Kim, Ki Yeol(김기열) ORCID logo https://orcid.org/0000-0001-5357-1067
Kim, Jin(김진)
Kim, Hyung Jun(김형준) ORCID logo https://orcid.org/0000-0001-8247-4004
Nam, Woong(남웅) ORCID logo https://orcid.org/0000-0003-0146-3624
Cha, In Ho(차인호) ORCID logo https://orcid.org/0000-0001-8259-2190
URI
https://ir.ymlib.yonsei.ac.kr/handle/22282913/100855
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