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Identification of significant regional genetic variations using continuous CNV values in aCGH data

Authors
 Ki-Yeol Kim  ;  Gui Youn Lee  ;  Jin Kim  ;  Hei-Cheul Jeung  ;  Hyun Cheol Chung  ;  Sun Young Rha 
Citation
 Genomics, Vol.94(5) : 317-323, 2009 
Journal Title
 Genomics 
ISSN
 0888-7543 
Issue Date
2009
MeSH
Analysis of Variance ; Chromosome Aberrations ; Colorectal Neoplasms/genetics ; Comparative Genomic Hybridization/methods* ; Comparative Genomic Hybridization/statistics & numerical data ; DNA/genetics ; Female ; Gene Dosage* ; Genetic Variation* ; Genome, Human/genetics* ; Genomics ; Humans ; Intestinal Mucosa/cytology ; Leukocytes, Mononuclear/cytology ; Male ; Models, Statistical ; Neoplasms ; Oligonucleotide Array Sequence Analysis/methods* ; Oligonucleotide Array Sequence Analysis/statistics & numerical data ; Sequence Analysis, DNA
Keywords
Array CGH ; Genomic variations ; Systematic aberrations ; Shifted ANOVA ; Chromosomal region
Abstract
Array comparative genomic hybridization (aCGH) provides a technique to survey the human genome for chromosomal aberrations in disease. The identification of genomic regions with aberrations may clarify the initiation and progression of cancer, improve diagnostic and prognostic accuracy, and guide therapy. The analysis of variance (ANOVA) model is widely used to detect differentially expressed genes after accounting for common sources of variation in microarray analysis. In this study, we propose a method, shifted ANOVA, to detect significantly altered regions. This method, based on the standard ANOVA, analyzes changes in copy number variation for regions. The selected regions have the group effect only, but no effect within samples and no interactive effects. The performance of the proposed method is evaluated from the homogeneity and classification accuracies of the selected regions. Shifted ANOVA may identify new candidate genes neighboring known because it detects significantly altered chromosomal regions, rather than independent probes.
Full Text
http://www.sciencedirect.com/science/article/pii/S0888754309001839
DOI
10.1016/j.ygeno.2009.08.006
Appears in Collections:
2. College of Dentistry (치과대학) > Dept. of Oral Pathology (구강병리학교실) > 1. Journal Papers
1. College of Medicine (의과대학) > Yonsei Biomedical Research Center (연세의생명연구원) > 1. Journal Papers
1. College of Medicine (의과대학) > Dept. of Internal Medicine (내과학교실) > 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
Kim, Jin(김진)
Rha, Sun Young(라선영) ORCID logo https://orcid.org/0000-0002-2512-4531
Lee, Gui Youn(이귀연)
Chung, Hyun Cheol(정현철) ORCID logo https://orcid.org/0000-0002-0920-9471
Jeung, Hei Cheul(정희철) ORCID logo https://orcid.org/0000-0003-0952-3679
URI
https://ir.ymlib.yonsei.ac.kr/handle/22282913/104621
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