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Fast Screening Technology for Drug Emergency Management: Predicting Suspicious SNPs for ADR with Information Theory-based Models

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机构: [1] York Univ, Sch Informat Technol, Informat Retrieval & Knowledge Management Res Lab, Toronto, ON M3J 1P3, Canada [2] Guangzhou Univ Chinese Med, Sch Clin Med 2, Guangzhou 510120, Guangdong, Peoples R China
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关键词: Pharmacogenomics high throughput sequencing information theory single nucleotide polymorphism model

摘要:
Objective: The genetic polymorphism of Cytochrome P450 (CYP 450) is considered as one of the main causes for adverse drug reactions (ADRs). In order to explore the latent correlations between ADRs and potentially corresponding single-nucleotide polymorphism (SNPs) in CYP450, three algorithms based on information theory are used as the main method to predict the possible relation. Methods: The study uses a retrospective case-control study to explore the potential relation of ADRs to specific genomic locations and single-nucleotide polymorphism (SNP). The genomic data collected from 53 healthy volunteers are applied for the analysis, another group of genomic data collected from 30 healthy volunteers excluded from the study are used as the control group. The SNPs respective on five loci of CYP2D6* 2 * 10 * 14 and CYP1A2* 1C, * 1F are detected by the Applied Biosystem 3130xl. The raw data is processed by ChromasPro to detect the specific alleles on the above loci from each sample. The secondary data are reorganized and processed by R combined with the reports of ADRs from clinical reports. Three information theory based algorithms are implemented for the screening task: JMI, CMIM, and mRMR. If a SNP is selected by more than two algorithms, we are confident to conclude that it is related to the corresponding ADR. The selection results are compared with the control decision tree + LASSO regression model. Results: In the study group where ADRs occur, 10 SNPs are considered relevant to the occurrence of a specific ADR by the combined information theory model. In comparison, only 5 SNPs are considered relevant to a specific ADR by the decision tree + LASSO regression model. In addition, the new method detects more relevant pairs of SNP and ADR which are affected by both SNP and dosage. This implies that the new information theory based model is effective to discover correlations of ADRs and CYP 450 SNPs and is helpful in predicting the potential vulnerable genotype for some ADRs. Conclusion: The newly proposed information theory based model has superiority performance in detecting the relation between SNP and ADR compared to the decision tree + LASSO regression model. The new model is more sensitive to detect ADRs compared to the old method, while the old method is more reliable. Therefore, the selection criteria for selecting algorithms should depend on the pragmatic needs.

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出版当年[2017]版:
大类 | 4 区 化学
小类 | 4 区 生化研究方法 4 区 应用化学 4 区 药学
最新[2025]版:
大类 | 4 区 医学
小类 | 4 区 生化研究方法 4 区 应用化学 4 区 药学
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出版当年[2016]版:
Q3 CHEMISTRY, APPLIED Q4 PHARMACOLOGY & PHARMACY Q4 BIOCHEMICAL RESEARCH METHODS
最新[2023]版:
Q3 CHEMISTRY, APPLIED Q3 PHARMACOLOGY & PHARMACY Q4 BIOCHEMICAL RESEARCH METHODS

影响因子: 最新[2023版] 最新五年平均 出版当年[2016版] 出版当年五年平均 出版前一年[2015版] 出版后一年[2017版]

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第一作者机构: [1] York Univ, Sch Informat Technol, Informat Retrieval & Knowledge Management Res Lab, Toronto, ON M3J 1P3, Canada
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通讯机构: [1] York Univ, Sch Informat Technol, Informat Retrieval & Knowledge Management Res Lab, Toronto, ON M3J 1P3, Canada [*1]York Univ, Sch Informat Technol, Informat Retrieval & Knowledge Management Res Lab, Toronto, ON M3J 1P3, Canada [2] Guangzhou Univ Chinese Med, Sch Clin Med 2, Guangzhou 510120, Guangdong, Peoples R China [*2]Guangzhou Univ Chinese Med, Sch Clin Med 2, Guangzhou 510120, Guangdong, Peoples R China
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