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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  ;  In-Ho Cha 
 Medical & Biological Engineering & Computing, Vol.48(5) : 459-468, 2010 
Journal Title
 Medical & Biological Engineering & Computing 
Issue Date
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
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1. Journal Papers (연구논문) > 2. College of Dentistry (치과대학) > Dept. of Oral Pathology (구강병리학교실)
1. Journal Papers (연구논문) > 5. Research Institutes (연구소) > Oral Cancer Research Institute (구강종양연구소)
1. Journal Papers (연구논문) > 2. College of Dentistry (치과대학) > Dept. of Oral and Maxillofacial Surgery (구강악안면외과학교실)
Yonsei Authors
김기열(Kim, Ki Yeol) ORCID logo https://orcid.org/0000-0001-5357-1067
김진(Kim, Jin)
김형준(Kim, Hyung Jun) ORCID logo https://orcid.org/0000-0001-8247-4004
남웅(Nam, Woong) ORCID logo https://orcid.org/0000-0003-0146-3624
차인호(Cha, In Ho) ORCID logo https://orcid.org/0000-0001-8259-2190
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