title: Evaluation and integration of genetic signature for prediction risk of nasopharyngeal carcinoma in Southern China.
abstract: Genetic factors, as well as environmental factors, play a role in development of nasopharyngeal carcinoma (NPC). A number of single nucleotide polymorphisms (SNPs) have been reported to be associated with NPC. To confirm these genetic associations with NPC, two independent case-control studies from Southern China comprising 1166 NPC cases and 2340 controls were conducted. Seven SNPs in ITGA9 at 3p21.3 and 9 SNPs within the 6p21.3 HLA region were genotyped. To explore the potential clinical application of these genetic markers in NPC, we further evaluate the predictive/diagnostic role of significant SNPs by calculating the area under the curve (AUC).
  
  
  RESULTS
  The reported associations between ITGA9 variants and NPC were not replicated. Multiple loci of GABBR1, HLA-F, HLA-A, and HCG9 were statistically significant in both cohorts (P(combined) range from 5.96 × 10(-17) to 0.02). We show for the first time that these factors influence NPC development independent of environmental risk factors. This study also indicated that the SNP alone cannot serve as a predictive/diagnostic marker for NPC. Integrating the most significant SNP with IgA antibodies status to EBV, which is presently used as screening/diagnostic marker for NPC in Chinese populations, did not improve the AUC estimate for diagnosis of NPC.
authors.affiliation: Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325000, China ; State Key Laboratory for Infectious Diseases Prevention and Control, Institute for Viral Disease Control and Prevention, Chinese CDC, Beijing 10052, China ; ICF International, Atlanta, GA 30329, USA.
authors.forename: Xiuchan
authors.identifier: 0000-0002-5622-5669
authors.initials: X
authors.lastname: Guo
authors.affiliation: Basic Research Laboratory, Frederick National Laboratory, Leidos Biomedical Research, Inc., National Cancer Institute, Frederick, MD 21702, USA.
authors.forename: Cheryl A
authors.initials: CA
authors.lastname: Winkler
authors.affiliation: Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325000, China.
authors.forename: Ji
authors.initials: J
authors.lastname: Li
authors.affiliation: Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199004, Russia.
authors.forename: Li
authors.initials: L
authors.lastname: Guan
authors.affiliation: College of Life Science and Bio-Engineering, Beijing University of Technology, Beijing 100022, China ; Cancer Center, Wuzhou Red Cross Hospital, Guangxi 543002, China.
authors.forename: Minzhong
authors.initials: M
authors.lastname: Tang
authors.affiliation: Cangwu Institute for Nasopharyngeal Carcinoma Control and Prevention, Wuzhou, Guangxi 543100, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Liao
authors.affiliation: Cancer Center, Wuzhou Red Cross Hospital, Guangxi 543002, China.
authors.forename: Hong
authors.initials: H
authors.lastname: Deng
authors.affiliation: Institut Pasteur, 75724 Paris, France.
authors.forename: Guy
authors.initials: G
authors.lastname: de Thé
authors.affiliation: State Key Laboratory for Infectious Diseases Prevention and Control, Institute for Viral Disease Control and Prevention, Chinese CDC, Beijing 10052, China ; College of Life Science and Bio-Engineering, Beijing University of Technology, Beijing 100022, China.
authors.forename: Yi
authors.initials: Y
authors.lastname: Zeng
authors.affiliation: Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199004, Russia.
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: O'Brien
mesh_terms: D002277:Carcinoma; D002681:China / Q000453:epidemiology; D005260:Female; D005819:Genetic Markers / Q000235:genetics; D020022:Genetic Predisposition to Disease / Q000453:epidemiology* / Q000235:genetics*; D006801:Humans; D008297:Male; D008875:Middle Aged; D000077274:Nasopharyngeal Carcinoma; D009303:Nasopharyngeal Neoplasms / Q000175:diagnosis / Q000453:epidemiology* / Q000235:genetics*; D009363:Neoplasm Proteins / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D015995:Prevalence; D011379:Prognosis; D015203:Reproducibility of Results; D018570:Risk Assessment / Q000379:methods; D012680:Sensitivity and Specificity
chemical_list: D005819:Genetic Markers; D009363:Neoplasm Proteins