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 language | English |
|---|---|
| Pages (from-to) | 459-468 |
| Number of pages | 10 |
| Journal | Medical and Biological Engineering and Computing |
| Volume | 48 |
| Issue number | 5 |
| DOIs | |
| Publication status | Published - 2010 May 1 |
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All Science Journal Classification (ASJC) codes
- Biomedical Engineering
- Computer Science Applications
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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 journal › Article
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.
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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 -