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.

<h4>Introduction</h4>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 ma...

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Main Authors: 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
Format: Article
Language:English
Published: Public Library of Science (PLoS) 2019-01-01
Series:PLoS ONE
Online Access:https://doi.org/10.1371/journal.pone.0220719
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author 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
author_facet 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
author_sort Ping-Ho Chen
collection DOAJ
description <h4>Introduction</h4>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).<h4>Material and methods</h4>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.<h4>Results</h4>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).<h4>Conclusions</h4>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.
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spelling doaj.art-87e5a25b5bf24790af28590992bd9d9d2022-12-21T18:27:27ZengPublic Library of Science (PLoS)PLoS ONE1932-62032019-01-01148e022071910.1371/journal.pone.0220719Application 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 ChenLi-Yeh ChuangKuo-Chuan WuYan-Hsiung WangTien-Yu ShiehJim Jinn-Chyuan SheuHsueh-Wei ChangCheng-Hong Yang<h4>Introduction</h4>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).<h4>Material and methods</h4>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.<h4>Results</h4>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).<h4>Conclusions</h4>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.https://doi.org/10.1371/journal.pone.0220719
spellingShingle 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
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
title 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.
title_full 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.
title_fullStr 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.
title_full_unstemmed 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.
title_short 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.
title_sort 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
url https://doi.org/10.1371/journal.pone.0220719
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