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Phenotype prediction of deleterious nonsynonymous single nucleotide polymorphisms in human alcohol metabolism-related genes: a bioinformatics study
Wang, Lin-Lin3,4; Yang, An-Kui5,6; Li, Yong3; Liu, Jun-Ping7; Zhou, Shu-Feng1,2
关键词Alcohol Metabolism Bioinformatics Phenotype Single Nucleotide Polymorphisms
刊名ALCOHOL
2010-08-01
DOI10.1016/j.alcohol.2010.05.009
44期:5页:425-438
收录类别SCI
文章类型Article
WOS标题词Science & Technology
类目[WOS]Substance Abuse ; Pharmacology & Pharmacy ; Toxicology
研究领域[WOS]Substance Abuse ; Pharmacology & Pharmacy ; Toxicology
关键词[WOS]SJOGREN-LARSSON-SYNDROME ; ALDEHYDE DEHYDROGENASE GENE ; SUCCINATE SEMIALDEHYDE DEHYDROGENASE ; AMINO-ACID SUBSTITUTIONS ; AFFECT PROTEIN FUNCTION ; FALDH GENE ; ESOPHAGEAL CANCER ; MUTATION DATABASE ; ENZYME GENES ; ALDH5A1 GENE
英文摘要

Nonsynonymous single nucleotide polymorphisms (nsSNPs) are thought as potential disease modifiers because they alter the encoded amino acid sequence and are likely to affect the function of the proteins accounting for susceptibility to disease. Distinguishing the functionally significant nsSNPs from tolerant nsSNPs is helpful to characterize the genetic basis of human diseases and assess individual susceptibility to diseases. Many nsSNPs have been found in alcohol metabolism-related genes but there is poor knowledge on the relationship between the genotype and phenotype of nsSNPs in these genes. In this study, we have identified a total of 203 nsSNPs in 29 human alcohol metabolism-related genes from the National Center for Biotechnology Information (NCBI) dbSNP and SWISS-Prot databases. Using the PolyPhen and SIFT algorithms, 43% of nsSNPs in alcohol metabolism-related genes were predicted to have functional impacts on protein function with a significant concordance of the prediction results between the two algorithms. The prediction accuracy is about 77-81% of all the nsSNPs based on the results of in vivo and in vitro studies. These amino acid substitutions are supposed to be the pathogenetic basis for the alteration of metabolism enzyme activity and the association with disease susceptivity. The phenotype of nsSNPs predicted as deleterious needs to be clarified in further studies and the prediction of nsSNPs in human alcohol metabolism-related genes would be useful hints for further genotype phenotype studies on the individual difference in susceptivity to alcohol-related diseases. (C) 2010 Elsevier Inc. All rights reserved.

语种英语
WOS记录号WOS:000282412200005
引用统计
被引频次:7[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符http://ir.bjmu.edu.cn/handle/400002259/54852
专题北京大学公共卫生学院
作者单位1.RMIT Univ, Sch Hlth Sci, Bundoora, Vic 3083, Australia
2.RMIT Univ, Hlth Innovat Res Inst, Bundoora, Vic 3083, Australia
3.Peking Univ, Sch Publ Hlth, Dept Food Hyg & Nutr, Beijing 100191, Peoples R China
4.Peking Univ, Inst Reprod & Child Hlth, Beijing 100191, Peoples R China
5.Sun Yat Sen Univ, Ctr Canc, Dept Head & Neck Surg, Guangzhou 510060, Guangdong, Peoples R China
6.Sun Yat Sen Univ, Ctr Canc, State Key Lab Oncol S China, Guangzhou 510060, Guangdong, Peoples R China
7.Monash Univ, Dept Immunol, Cent & Eastern Clin Sch, Prahran, Vic 3181, Australia
推荐引用方式
GB/T 7714
Wang, Lin-Lin,Yang, An-Kui,Li, Yong,et al. Phenotype prediction of deleterious nonsynonymous single nucleotide polymorphisms in human alcohol metabolism-related genes: a bioinformatics study[J]. ALCOHOL,2010,44(5):425-438.
APA Wang, Lin-Lin,Yang, An-Kui,Li, Yong,Liu, Jun-Ping,&Zhou, Shu-Feng.(2010).Phenotype prediction of deleterious nonsynonymous single nucleotide polymorphisms in human alcohol metabolism-related genes: a bioinformatics study.ALCOHOL,44(5),425-438.
MLA Wang, Lin-Lin,et al."Phenotype prediction of deleterious nonsynonymous single nucleotide polymorphisms in human alcohol metabolism-related genes: a bioinformatics study".ALCOHOL 44.5(2010):425-438.
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