A bioinformatics strategy for detecting the complexity of Chronic Obstructive Pulmonary Disease in Northern Chinese Han Population

Hua, Lin; An, Li; Li, Lin; Zhang, Yong-Biao; Wang, Chen

doi:10.1266/ggs.87.197

Cited by 3 publications

(11 citation statements)

References 46 publications

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“…Written informed consent was obtained from all participating subjects, and the study protocol was approved by the research ethics boards of all participating hospitals. The entry criteria were the same as those in our previous study Hua et al, 2012).…”

Section: Our Current Study Cohort: Chinese Han Populationmentioning

confidence: 99%

“…Illumina VeraCode technology on a BeadXpress platform (Illumina, San Diego, CA, USA) was used to perform SNP genotyping. Forty-four tagging SNPs (minor allele frequency >0.05) were genotyped to identify common variants of the four genes (EPHX1, GSTP1, SERPINE2, and TGFB1) under pair-wise mode with an r 2 threshold of 0.8 Hua et al, 2012). In this analysis, we focused on two SNPs (EPHX1 T337C and EPHX1 A416G) to explore whether the genetic variations in EPHX1 are associated with COPD in Chinese Han population.…”

Section: Our Current Study Cohort: Chinese Han Populationmentioning

confidence: 99%

“…Here, we applied three programs (VarionWatch (Hua et al, 2012), SIFT (Kumar et al, 2009), and PolyPhen-2 (Adzhubei et al, 2010)) to predict the functional effect scores of EPHX1 T337C and EPHX1 A416G. VarionWatch incorporates 6 databases and can use different criteria to predict the function of the variant.…”

Section: ) Prediction Of the Potential Functional Effect Scores Of Tmentioning

confidence: 99%

“…According to the naïve Bayes posterior probability calculated by PolyPhen-2, an nsSNP can be classified into 'benign' [0-0.2], 'possibly damaging' (0.2-0.85), or 'probably damaging' [0.85-1] groups. These three programs are described in detail in our previous study (Hua et al, 2012).…”

Section: ) Prediction Of the Potential Functional Effect Scores Of Tmentioning

confidence: 99%

“…These studies included 9 Caucasian populations (Rodriguez et al, 2002;Korytina et al, 2003;Hersh et al, 2005;Park et al, 2005;Brøgger et al, 2006;Chappell et al, 2008;Židzik et al, 2008;Penyige et al, 2010;Lee et al, 2011) and 10 Eastern Asian populations (Takeyabu et al, 2000;Yim et al, 2000;Yoshikawa et al, 2000;Zhang et al, 2002;Budhi et al, 2003;Park et al, 2003;Cheng et al, 2004;Xiao et al, 2004;Fu et al, 2007;Hua et al, 2012) ( Table 1). The total number of samples in the Caucasian and Eastern Asian populations were 47,048 (6471 cases vs 40,577 controls) and 2586 (1228 cases vs 1358 controls), respectively.…”

Section: Literature Searchmentioning

confidence: 99%

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Exploration of association between EPHX1 and chronic obstructive pulmonary disease on the basis of combined data mining

Liu¹,

Xia²,

Zhou³

et al. 2016

Genet. Mol. Res.

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ABSTRACT. Chronic obstructive pulmonary disease (COPD) is an important respiratory disease with high mortality. Although smoking is the major environmental risk factor for the development of COPD, only 10% of heavy smokers develop symptomatic disease, suggesting association between genetic susceptibilities and environmental influences. In recent years, as one of the most widely studied genes including tests for associations between a genetic variant and COPD, epoxide hydrolase 1 (EPHX1) was found to be involved in the metabolism of tobacco smoke, an important risk factor of COPD. However, genetic associations with COPD identified in studies on EPHX1 are controversial. To address this issue, except for performing the meta-analysis, which specially added our current study on two polymorphisms (T337C and A416G) of EPHX1, we performed combined data mining based on functional prediction algorithms of nonsynonymous single-nucleotide polymorphisms and gene-based variable threshold testing. Genetic variations in EPHX1 did not affect COPD in Caucasian and Eastern Asian population, which is supported by recent evidence. We found no association between EPHX1 and COPD; however, a minor effect of EPHX1 on COPD risk was not completely excluded; further replication studies with large samples are needed to confirm our findings.

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Section: Our Current Study Cohort: Chinese Han Populationmentioning

confidence: 99%

Section: Our Current Study Cohort: Chinese Han Populationmentioning

confidence: 99%

Section: ) Prediction Of the Potential Functional Effect Scores Of Tmentioning

confidence: 99%

Section: ) Prediction Of the Potential Functional Effect Scores Of Tmentioning

confidence: 99%

Section: Literature Searchmentioning

confidence: 99%

See 3 more Smart Citations

Exploration of association between EPHX1 and chronic obstructive pulmonary disease on the basis of combined data mining

Liu¹,

Xia²,

Zhou³

et al. 2016

Genet. Mol. Res.

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Exploring the interaction among EPHX1, GSTP1, SERPINE2, and TGFB1 contributing to the quantitative traits of chronic obstructive pulmonary disease in Chinese Han population

Lin

Yang

et al. 2016

Hum Genomics

Self Cite

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BackgroundCurrently, the majority of genetic association studies on chronic obstructive pulmonary disease (COPD) risk focused on identifying the individual effects of single nucleotide polymorphisms (SNPs) as well as their interaction effects on the disease. However, conventional genetic studies often use binary disease status as the primary phenotype, but for COPD, many quantitative traits have the potential correlation with the disease status and closely reflect pathological changes.MethodHere, we genotyped 44 SNPs from four genes (EPHX1, GSTP1, SERPINE2, and TGFB1) in 310 patients and 203 controls which belonged to the Chinese Han population to test the two-way and three-way genetic interactions with COPD-related quantitative traits using recently developed generalized multifactor dimensionality reduction (GMDR) and quantitative multifactor dimensionality reduction (QMDR) algorithms.ResultsBased on the 310 patients and the whole samples of 513 subjects, the best gene-gene interactions models were detected for four lung-function-related quantitative traits. For the forced expiratory volume in 1 s (FEV1), the best interaction was seen from EPHX1, SERPINE2, and GSTP1. For FEV1%pre, the forced vital capacity (FVC), and FEV1/FVC, the best interactions were seen from SERPINE2 and TGFB1.ConclusionThe results of this study provide further evidence for the genotype combinations at risk of developing COPD in Chinese Han population and improve the understanding on the genetic etiology of COPD and COPD-related quantitative traits.Electronic supplementary materialThe online version of this article (doi:10.1186/s40246-016-0076-0) contains supplementary material, which is available to authorized users.

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<p>Association among genetic polymorphisms of GSTP1, HO-1, and SOD-3 and chronic obstructive pulmonary disease susceptibility</p>

Du¹,

Zhang²,

Xu³

et al. 2019

COPD

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BackgroundChronic obstructive pulmonary disease (COPD) is a progressive lung disease characterized by incomplete reversible airﬂow limitation, which is associated with emphysema and chronic inflammation. Oxidative/antioxidant imbalance is one of the mechanisms of the current pathogenesis of COPD and several recent studies have attempted to uncover genetic causes of COPD and its progression. GST, HO-1, and SOD-3 are important susceptibility genes related to COPD.MethodsA total of 300 blood samples were included in two groups: Control group and COPD group. We genotyped 4 single nucleotide polymorphisms (SNPs) from these 3 genes in 150 COPD patients and 150 controls to analyze genetic polymorphisms and interactions with COPD-related quantitative traits using correlation analysis and multivariate logistic regression analysis.ResultsThe results indicated that genotype distributions and allele frequencies of GSTP1, HO-1, and SOD-3 were significantly different between the COPD and the control group, while there is no correlation between the polymorphism of GSTP1, HO-1, SOD3, and the different stages of COPD. Furthermore, multivariate logistic regression analysis indicated that COPD GSTP1-exon5 SNP and HO-1 (GT)n SNP are high-risk factors for COPD and there was interaction between GSTP1 exon5 SNPS and HO-1 (GT)n SNP. More important, the genotypes, AG, GG of GSTP1 exon5 and L/M*S, L/L of HO-1 (GT)n associated with increased 8-iso-prostaglandin F (2 alpha) (8-iso-PGF2) and malondialdehyde (MDA) concentration and decreased catalase (CAT) activity.ConclusionCollectively, this study shows that genetic polymorphisms of GSTP1, HO-1, and SOD-3 are associated with COPD susceptibility.

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A bioinformatics strategy for detecting the complexity of Chronic Obstructive Pulmonary Disease in Northern Chinese Han Population

Cited by 3 publications

References 46 publications

Exploration of association between EPHX1 and chronic obstructive pulmonary disease on the basis of combined data mining

Exploration of association between EPHX1 and chronic obstructive pulmonary disease on the basis of combined data mining

Exploring the interaction among EPHX1, GSTP1, SERPINE2, and TGFB1 contributing to the quantitative traits of chronic obstructive pulmonary disease in Chinese Han population

<p>Association among genetic polymorphisms of GSTP1, HO-1, and SOD-3 and chronic obstructive pulmonary disease susceptibility</p>

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