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Combined genomic expressions as a diagnostic factor for oral squamous cell carcinoma

Authors
 Ki-Yeol Kim  ;  Xianglan Zhang  ;  In-Ho Cha 
Citation
 Genomics, Vol.103(5-6) : 317-322, 2014 
Journal Title
 Genomics 
ISSN
 0888-7543 
Issue Date
2014
MeSH
Adolescent ; Adult ; Aged ; Aged, 80 and over ; Biomarkers, Tumor/genetics* ; Biomarkers, Tumor/metabolism ; Carcinoma, Squamous Cell/diagnosis* ; Carcinoma, Squamous Cell/genetics ; Carcinoma, Squamous Cell/metabolism ; Case-Control Studies ; Female ; Gene Expression Profiling* ; Humans ; Male ; Middle Aged ; Mouth Neoplasms/diagnosis* ; Mouth Neoplasms/genetics ; Mouth Neoplasms/metabolism ; Sensitivity and Specificity ; Transcriptome ; Young Adult
Keywords
Combined biomarker ; Combined gene expression ; Microarray dataset ; Oral squamous cell carcinoma
Abstract
Trends in genetics are transforming in order to identify differential coexpressions of correlated gene expression rather than the significant individual gene. Moreover, it is known that a combined biomarker pattern improves the discrimination of a specific cancer. The identification of the combined biomarker is also necessary for the early detection of invasive oral squamous cell carcinoma (OSCC). To identify the combined biomarker that could improve the discrimination of OSCC, we explored an appropriate number of genes in a combined gene set in order to attain the highest level of accuracy. After detecting a significant gene set, including the pre-defined number of genes, a combined expression was identified using the weights of genes in a gene set. We used the Principal Component Analysis (PCA) for the weight calculation. In this process, we used three public microarray datasets. One dataset was used for identifying the combined biomarker, and the other two datasets were used for validation. The discrimination accuracy was measured by the out-of-bag (OOB) error. There was no relation between the significance and the discrimination accuracy in each individual gene. The identified gene set included both significant and insignificant genes. One of the most significant gene sets in the classification of normal and OSCC included MMP1, SOCS3 and ACOX1. Furthermore, in the case of oral dysplasia and OSCC discrimination, two combined biomarkers were identified. The combined expression revealed good performance in the validation datasets. The combined genomic expression achieved better performance in the discrimination of different conditions than a single significant gene. Therefore, it could be expected that accurate diagnosis for cancer could be possible with a combined biomarker.
Full Text
http://www.sciencedirect.com/science/article/pii/S0888754313002231
DOI
10.1016/j.ygeno.2013.11.007
Appears in Collections:
2. College of Dentistry (치과대학) > Dept. of Oral and Maxillofacial Surgery (구강악안면외과학교실) > 1. Journal Papers
5. Research Institutes (연구소) > Oral Cancer Research Institute (구강종양연구소) > 1. Journal Papers
Yonsei Authors
Kim, Ki Yeol(김기열) ORCID logo https://orcid.org/0000-0001-5357-1067
Zhang, Xiang Lan(장향란)
Cha, In Ho(차인호) ORCID logo https://orcid.org/0000-0001-8259-2190
URI
https://ir.ymlib.yonsei.ac.kr/handle/22282913/98823
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