Application of simulation-based CYP26 SNP-environment barcodes for evaluating the occurrence of oral malignant disorders by odds ratio-based binary particle swarm optimization: A case-control study in the Taiwanese population

• Published in: PloS one Vol. 14; no. 8; p. e0220719
• Main Authors: Chen, Ping-Ho, Chuang, Li-Yeh, Wu, Kuo-Chuan, Wang, Yan-Hsiung, Shieh, Tien-Yu, Sheu, Jim Jinn-Chyuan, Chang, Hsueh-Wei, Yang, Cheng-Hong
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 29.08.2019; Public Library of Science (PLoS)
• Subjects: Adult; Alcohol use; Alcoholic beverages; Bar codes; Biology and Life Sciences; Breast cancer; Cancer; Cancer prevention; Cancer screening; Case studies; Case-Control Studies; Cell cycle; Chemical engineering; Chewing; Chromosomes; Cigarettes; Computer Simulation; Confidence intervals; Cytochrome; Cytochrome P-450; Cytochrome P450 Family 26 - genetics; Demographics; Dentistry; Diagnosis; Disorders; Drinking (Alcoholic beverages); EDTA; Environmental effects; Enzymes; Female; Gene expression; Gene-Environment Interaction; Genetic algorithms; Genetic polymorphisms; Health screening; Hospitals; Humans; Male; Medical research; Medicine and Health Sciences; Methods; Middle Aged; Minority & ethnic groups; Mouth cancer; Mouth Neoplasms - epidemiology; Mouth Neoplasms - genetics; Nucleotides; Odds Ratio; Optimization; Optimization theory; Oral cancer; Oral hygiene; Particle swarm optimization; Pharyngeal cancer; Pharyngeal Neoplasms - epidemiology; Pharyngeal Neoplasms - genetics; Pharynx; Physical Sciences; Polymorphism; Polymorphism, Single Nucleotide; Population genetics; Population studies; Prevention; Risk analysis; Risk Factors; Simulation; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Social factors; Social Sciences; Studies; Swarm intelligence; Taiwan - epidemiology; Throat cancer; Tuberculosis; Taiwan; Asia
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0220719

Genetic polymorphisms and social factors (alcohol consumption, betel quid (BQ) usage, and cigarette consumption), both separately or jointly, play a crucial role in the occurrence of oral malignant disorders such as oral and pharyngeal cancers and oral potentially malignant disorders (OPMD). Simultaneous analyses of multiple single nucleotide polymorphisms (SNPs) and environmental effects on oral malignant disorders are essential to examine, albeit challenging. Thus, we conducted a case-control study (N = 576) to analyze the risk of occurrence of oral malignant disorders by using binary particle swarm optimization (BPSO) with an odds ratio (OR)-based method. We demonstrated that a combination of SNPs (CYP26B1 rs887844 and CYP26C1 rs12256889) and socio-demographic factors (age, ethnicity, and BQ chewing), referred to as the combined effects of SNP-environment, correlated with maximal risk diversity of occurrence observed between the oral malignant disorder group and the control group. The risks were more prominent in the oral and pharyngeal cancers group (OR = 10.30; 95% confidence interval (CI) = 4.58-23.15) than in the OPMD group (OR = 5.42; 95% CI = 1.94-15.12). Simulation-based "SNP-environment barcodes" may be used to predict the risk of occurrence of oral malignant disorders. Applying simulation-based "SNP-environment barcodes" may provide insight into the importance of screening tests in preventing oral and pharyngeal cancers and OPMD.