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

Ping-Ho Chen; Li-Yeh Chuang; Kuo-Chuan Wu; Yan-Hsiung Wang; Tien-Yu Shieh; Jim Jinn-Chyuan Sheu; Hsueh-Wei Chang; Cheng-Hong Yang

doi:10.1371/journal.pone.0220719

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

PLoS One. 2019 Aug 29;14(8):e0220719. doi: 10.1371/journal.pone.0220719. eCollection 2019.

Authors

Ping-Ho Chen^{1

2

3}, Li-Yeh Chuang^{4

5}, Kuo-Chuan Wu^{6

7}, Yan-Hsiung Wang^{1

8}, Tien-Yu Shieh⁹, Jim Jinn-Chyuan Sheu^{3

10

11

12}, Hsueh-Wei Chang^{3

13

14

15}, Cheng-Hong Yang^{6

16}

Affiliations

¹ School of Dentistry, College of Dental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.
² Center for Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan.
³ Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan.
⁴ Department of Chemical Engineering, I-Shou University, Kaohsiung, Taiwan.
⁵ Institute of Biotechnology and Chemical Engineering, I-Shou University, Kaohsiung, Taiwan.
⁶ Department of Electronic Engineering, National Kaohsiung University of Science and Technology, Kaohsiung, Taiwan.
⁷ Department of Computer Science and Information Engineering, National Kaohsiung University of Sciences and Technology, Kaohsiung, Taiwan.
⁸ Orthopaedic Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan.
⁹ Global Center of Excellence for Oral Health Research and Development, Kaohsiung, Taiwan.
¹⁰ Institute of Biopharmaceutical Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan.
¹¹ School of Chinese Medicine, China Medical University, Taichung, Taiwan.
¹² Department of Health and Nutrition Biotechnology, Asia University, Taichung, Taiwan.
¹³ Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung, Taiwan.
¹⁴ Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.
¹⁵ Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan.
¹⁶ Ph. D. Program in Biomedical Engineering, Kaohsiung Medical University, Kaohsiung, Taiwan.

Abstract

Introduction: 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).

Material and methods: 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.

Results: 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).

Conclusions: 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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Adult
Case-Control Studies
Computer Simulation
Cytochrome P450 Family 26 / genetics*
Female
Gene-Environment Interaction*
Humans
Male
Middle Aged
Mouth Neoplasms / epidemiology
Mouth Neoplasms / genetics*
Odds Ratio
Pharyngeal Neoplasms / epidemiology
Pharyngeal Neoplasms / genetics*
Polymorphism, Single Nucleotide*
Risk Factors
Taiwan / epidemiology

Substances

Cytochrome P450 Family 26

Grants and funding

This study design, data collection, analysis, interpretation and manuscript writing were supported by the Kaohsiung Medical University Research Foundation (KMU-M106020, KMU-M108022), the Ministry of Science and Technology (MOST 106-2314-B-037-014- and MOST 108-2320-B-037-015-MY3), NSYSU-KMU JOINT RESEARCH PROJECT, (#NSYSUKMU 105-P021), Chimei-KMU jointed project (108CM-KMU-11), ChangHua Christian Hospital-KMU Fund (108-CCH-KMU-008), and Ministry of Health and Welfare (MOHW) Health and welfare surcharge of tobacco products (MOHW108-TDU-B-212-124016), Taiwan. This study is supported partially by Kaohsiung Medical University Research Center Grant (KMU-TC108A04). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.