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Discrete Stationary Wavelet Transform of Array CGH Data for Biomarkers Identification of Hepatocellular Carcinoma

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Hepatocellular carcinoma is considered as one of the common malignant tumors in the world, chronic hepatitis and liver cirrhosis have been recognized as important risk factors for the development of hepatocellular carcinoma. Hepatocellular carcinoma is the third most common cause of cancer mortality worldwide. The outcome of hepatocellular carcinoma patients still dismal because it is difficult to detect the disease at its early stage. Genomic DNA copy number alterations are associated with many complex diseases such as hepatocellular carcinoma. Copy number alterations are important for both the basic understanding of hepatocellular carcinoma and its diagnosis. Array-based comparative genomic hybridization is a technique used to identify copy number changes in genomic DNA. The aim of this work is to apply discrete stationary wavelet transform technique to a number of human chromosomes for analyzing array-based comparative genomic hybridization data to evaluate the prognosis of hepatocellular carcinoma patients in order to identify genome-wide alternations in copy number from the genomic data. A number of 67 samples of hepatocellular carcinoma patients on specific chromosome regions were tested, and then discrete stationary wavelet transform algorithm is applied to detect genomic DNA alternations in copy number. Results provided that a gain of 1q is detected in 55% and a gain of 20q is detected in 67% of hepatocellular carcinoma cases. Also, a loss of 4q is detected in 67%, a loss and gain of 8q, 8p is detected in 87%, a loss of 13q is detected in 72%, loss in 16q is detected in 75%, and loss of 17q is detected in 33% of hepatocellular carcinoma cases.
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Keywords: ARRAY-BASED COMPARATIVE GENOMIC; COPY NUMBER ALTERNATION; DISCRETE STATIONARY WAVELET TRANSFORM AND ARRAY-COMPARATIVE GENOMIC HYBRIDIZATION; HEPATOCELLULAR CARCINOMA

Document Type: Research Article

Publication date: December 1, 2012

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  • Journal of Bioinformatics and Intelligent Control (JBIC) is an international journal that publishes research articles in areas of the bioinformatics and intelligent control. JBIC is aimed to provide an international forum for the exchange of ideas and new scientific and technological findings to disseminate information and promote the transfer of knowledge between professionals in academia and industry. The journal publishes original research papers; review papers; technical reports and notes; short communications focused on emerging new developments in these research areas.
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