Vui King Vincent-Chong1,2, Iman Salahshourifar1, Rozaimi Razali3, Arif Anwar3, Rosnah Binti Zain1,2. 1. Oral Cancer Research and Coordinating Center, Faculty of Dentistry, University of Malaya, Lembah Pantai, Kuala Lumpur, Malaysia. 2. Department of Oro-maxillofacial Surgical and Medical Sciences, Faculty of Dentistry, University of Malaya, Lembah Pantai, Kuala Lumpur, Malaysia. 3. Sengenics Sdn Bhd, High Impact Research (HIR) Building, University of Malaya, Lembah Pantai, Kuala Lumpur, Malaysia.
Abstract
BACKGROUND: This purpose of this meta-analysis study was to identify the most frequent and potentially significant copy number alteration (CNA) in oral carcinogenesis. METHODS: Seven oral squamous cell carcinoma (OSCC)-related publications, corresponding to 312 samples, were identified for this meta-analysis. The data were analyzed in a 4-step process that included the genome assembly coordination of multiple platforms, assignment of chromosomal position anchors, calling gains and losses, and functional annotation analysis. RESULTS: Gains were more frequent than losses in the entire dataset. High-frequency gains were identified in chromosomes 5p, 14q, 11q, 7p, 17q, 20q, 8q, and 3q, whereas high-frequency losses were identified in chromosomes 3p, 8p, 6p, 18q, and 4q. Ingenuity pathway analysis showed that the top biological function was associated with immortalization of the epithelial cells (p = 1.93E-04). CONCLUSION: This study has identified multiple recurrent CNAs that are involved in various biological annotations associated with oral carcinogenesis.
BACKGROUND: This purpose of this meta-analysis study was to identify the most frequent and potentially significant copy number alteration (CNA) in oral carcinogenesis. METHODS: Seven oral squamous cell carcinoma (OSCC)-related publications, corresponding to 312 samples, were identified for this meta-analysis. The data were analyzed in a 4-step process that included the genome assembly coordination of multiple platforms, assignment of chromosomal position anchors, calling gains and losses, and functional annotation analysis. RESULTS: Gains were more frequent than losses in the entire dataset. High-frequency gains were identified in chromosomes 5p, 14q, 11q, 7p, 17q, 20q, 8q, and 3q, whereas high-frequency losses were identified in chromosomes 3p, 8p, 6p, 18q, and 4q. Ingenuity pathway analysis showed that the top biological function was associated with immortalization of the epithelial cells (p = 1.93E-04). CONCLUSION: This study has identified multiple recurrent CNAs that are involved in various biological annotations associated with oral carcinogenesis.
Authors: Vui King Vincent-Chong; Iman Salahshourifar; Kar Mun Woo; Arif Anwar; Rozaimi Razali; Ranganath Gudimella; Zainal Ariff Abdul Rahman; Siti Mazlipah Ismail; Thomas George Kallarakkal; Anand Ramanathan; Wan Mahadzir Wan Mustafa; Mannil Thomas Abraham; Keng Kiong Tay; Rosnah Binti Zain Journal: PLoS One Date: 2017-04-06 Impact factor: 3.240