Genome-wide haplotype association analysis identifies SERPINB9, SERPINE2, GAK, and HSP90B1 as novel risk genes for oral squamous cell carcinoma
- 207 Downloads
The oral squamous cell carcinoma (OSCC) is one of the most common malignant epithelial neoplasms and considered to be caused by the genetic damage. In addition, smoking habit and excessive alcohol consumption have been estimated to be the main risk factors. Although the association between OSCC and genetic susceptibility loci has been observed in many different populations, most of these studies simply focused on the single nucleotide polymorphism. Therefore, we made a contrast analysis between the 112 OSCC patients from the GEO database and 245 normal samples from the HapMap project. First, we performed a genome-wide haplotype association study by comparing the frequency of the haplotypes in the case–control experiment. Then, we mapped the haplotypes to the corresponding genes, screened the risk genes according to significant haplotypes (P < 1E−04), and prioritized the OSCC genes based on their similarity to the known OSCC susceptibility genes. We filtered four OSCC genes including SERPINB9, SERPINE2, GAK, and HSP90B1 through the gene global prioritization score (P < 0.005). SERPINB9 ranked first in the candidate gene list and contained a significant haplotype TAGGA (P value = 3.12E−11). The second risk gene was SERPINE2 with the haplotype GGGCCCTTT, which was closely similar to the SERPINB9.
KeywordsOSCC Haplotype Association study Risk gene
This work was supported in part by grants from the National Natural Science Foundation of China (grant numbers 31200934, 61300116, and 81300945) and the Natural Science Foundation of Heilongjiang Province (grant numbers C201206 and QC2013C063).
Conflicts of interest
- 4.Basnaker M, Sr S, Bnvs S. Expression of endoglin (CD-105) and microvessel density in oral dysplasia and squamous cell carcinoma. J Clin Diagnostic Res: JCDR. 2014;8:ZC91–94.Google Scholar
- 6.Montgomery DC: Introduction to statistical quality control. John Wiley & Sons, 2007Google Scholar
- 10.Barrett JC. Haploview: visualization and analysis of SNP genotype data. Cold Spring Harbor Protocols 2009;2009:pdb. ip71.Google Scholar
- 16.Beaglehole JC, Banks J. The ‘Endeavour’ journal of Joseph Banks 1768–1771. Angus & Robertson Limited, 1962.Google Scholar
- 17.Goodridge D, Sloan J, LeDoyen Y, McKenzie J, Knight W, Gayari M. Risk-assessment scores, prevention strategies, and the incidence of pressure ulcers among the elderly in four canadian health-care facilities. Can J Nursing Res= Revue canadienne de Recherche en Sci Infirmieres. 1997;30:23–44.Google Scholar
- 20.Mayr E. Change of genetic environment and evolution. 1954.Google Scholar
- 22.Silverman GA, Bird PI, Carrell RW, Coughlin PB, Gettins PG, Irving JI, et al. The serpins are an expanding superfamily of structurally similar but funtionally diverse proteins: evolution, mechanism of inhibition, novel functions, and a revised nomenclature. J Biol Chem. 2001.Google Scholar