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

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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.

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Acknowledgments

This work was supported by Priority Research Centers Program through the National Research Foundation of Korea(NRF), funded by the Ministry of Education, Science and Technology (2009-0094030).

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Authors and Affiliations

  1. Oral Cancer Research Institute, College of Dentistry, Yonsei University, Seoul, 120-752, Republic of Korea

    Ki-Yeol Kim, Jin Kim & In-Ho Cha

  2. Department of Oral and Maxillofacial Surgery, College of Dentistry, Yonsei University, Seoul, 120-752, Republic of Korea

    Hyung Jun Kim, Woong Nam & In-Ho Cha

Authors
  1. Ki-Yeol Kim
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  2. Jin Kim
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  3. Hyung Jun Kim
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  4. Woong Nam
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  5. In-Ho Cha
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Correspondence to In-Ho Cha.

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Kim, KY., Kim, J., Kim, H.J. et al. A method for detecting significant genomic regions associated with oral squamous cell carcinoma using aCGH. Med Biol Eng Comput 48, 459–468 (2010). https://doi.org/10.1007/s11517-010-0595-0

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  • DOI: https://doi.org/10.1007/s11517-010-0595-0

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