Oral Clefts, Maternal Smoking, and TGFA: A Meta-Analysis of Gene-Environment Interaction

2005 ◽  
Vol 42 (1) ◽  
pp. 58-63 ◽  
Author(s):  
Joanna S. Zeiger ◽  
Terri H. Beaty ◽  
Kung-Yee Liang
Keyword(s):  
Logistic Regression ◽  
Maternal Smoking ◽  
Meta Analysis ◽  
Case Control ◽  
Environment Interaction ◽  
Oral Clefts ◽  
Gene Environment Interaction ◽  
Gene Environment ◽  
Increased Risk ◽  
Polytomous Logistic Regression

Objective A meta-analysis was performed to examine the association among maternal cigarette smoking, infant genotype at the Taq1 site in the transforming growth factor α (TGFA) locus, and risk of nonsyndromic oral clefts, both cleft palate (CP) and cleft lip with or without cleft palate (CL/P). Design Five published case-control studies were included in the meta-analyis. Pooled Mantel-Haenszel odds ratios (OR) and 95% confidence intervals (CIs) were computed. Gene-environment interaction was also assessed by using the pooled data in a case-only analysis and polytomous logistic regression. Results Among nonsmoking mothers, there was no evidence of any increased risk for CP if the infant carried the TGFA Taq1 C2 allele. If the mother reported smoking, however, there was an overall increased risk for CP if the infant carried the C2 allele (ORsmokers = 1.95; 95% CI = 1.22 to 3.10). TGFA genotype did not increase risk to CL/P, regardless of maternal smoking status. Polytomous logistic regression revealed a significant overall smoking effect for CL/P (OR = 1.64, 95% CI = 1.33 to 2.02) and CP (OR = 1.42, 95% CI = 1.06 to 1.90). Conclusions While maternal smoking was a consistent risk factor for both CL/P and CP across all studies, the suggestive evidence for gene-environment interaction between the infant's genotype at the Taq1 marker in TGFA and maternal smoking was limited to CP. Furthermore, evidence for such gene-environment interaction was strongest in a case-control study drawn from a birth defect registry where infants with non-cleft defects served as controls.

Testing for Interaction between Maternal Smoking and TGFA Genotype among Oral Cleft Cases Born in Maryland 1992–1996

1997 ◽  
Vol 34 (5) ◽  
pp. 447-454 ◽  
Author(s):  
Terri H. Beaty ◽  
Nancy E. Maestri ◽  
Jacqueline B. Hetmanski ◽  
Diego F. Wyszynski ◽  
Craig A. Vanderkolk ◽  
...  
Keyword(s):  
Birth Defects ◽  
Maternal Smoking ◽  
Case Control Study ◽  
Case Control ◽  
Comprehensive Treatment ◽  
Environment Interaction ◽  
Oral Clefts ◽  
Oral Cleft ◽  
Increased Risk ◽  
Control Study

Objective: Infants born in Maryland between June 1992 and June 1996 were used in a case-control study of nonsyndromic oral clefts to test for effects of maternal smoking and a polymorphic genetic marker at the transforming growth factor alpha (TGFA) locus, both of which have been reported to be risk factors for these common birth defects. Design and Setting: Cases were infants with an oral cleft ascertained through three comprehensive treatment centers, with additional ascertainment through a registry of birth defects maintained by the Maryland Health Department. Controls were healthy infants. Medical history information on infants and mothers were collected, along with DNA samples Patients, Participants: Among 286 cases contacted (72% ascertainment), there were 192 nonsyndromic isolated oral clefts (106 M; 86 F) available for this case-control study. Main Outcome Measures: The largest group of 149 Caucasian nonsyndromic cases and 86 controls was used to test for association with maternal smoking and genotype at the Taq1 polymorphism in TGFA. Results: While this modest sample had limited statistical power to detect gene-environment interaction, there was a significant marginal Increase In risk of having an oral cleft If the mother smoked (odds ratio = 1.75, 95%CI = 1.01 to 3.02). We could not demonstrate statistical interaction between maternal smoking and TGFA genotype in this study, however, and the observed increase in the C2 allele among cases was not statistically significant. Conclusions: We could not confirm either the reported association between oral clefts and TGFA genotype or its interaction with maternal smoking. However, these data do show an increased risk if the mother smoked during pregnancy, and this effect was greatest among infants with a bilateral cleft and no close family history of clefts.

scholarly journals Meta-analysis of gene-environment interaction exploiting gene-environment independence across multiple case-control studies

2017 ◽  
Vol 36 (24) ◽  
pp. 3895-3909 ◽  
Author(s):  
Jason P. Estes ◽  
John D. Rice ◽  
Shi Li ◽  
Heather M. Stringham ◽  
Michael Boehnke ◽  
...  
Keyword(s):  
Meta Analysis ◽  
Case Control ◽  
Environment Interaction ◽  
Case Control Studies ◽  
Gene Environment Interaction ◽  
Gene Environment ◽  
Multiple Case

Association Between Tfeb Gene Polymorphism, Gene–environment Interaction, and Fatty Liver Disease: a Case–control Study in China

2021 ◽  
Author(s):  
Chunbao Mo ◽  
Tingyu Mai ◽  
Jiansheng Cai ◽  
Haoyu He ◽  
Huaxiang Lu ◽  
...  
Keyword(s):  
Liver Disease ◽  
Fatty Liver ◽  
Fatty Liver Disease ◽  
Case Control Study ◽  
Case Control ◽  
Environment Interaction ◽  
Additive Interaction ◽  
Gene Environment Interaction ◽  
Gene Environment ◽  
Control Study

Abstract Background: Fatty liver disease (FLD) is a serious public health problem that is rapidly increasing. Evidences indicated that the transcription factor EB (TFEB) gene may be involved in the pathophysiology of FLD; however, whether TEFB polymorphism is association with FLD remains unclear.Objectives: To explore the association among TFEB polymorphism, gene–environment interaction, and FLD and provide epidemiological evidence for clarifying the genetic factors of FLD.Methods: This study is a case–control study. Sequenom MassARRAY was applied in genotyping. Logical regression was used to analyze the association between TFEB polymorphism and FLD, and the gene–environment interaction in FLD was evaluated by multiplication and additive interaction models.Results: (1) The alleles and genotypes of each single nucleotide polymorphism of TFEB in the case and control groups were evenly distributed; no statistically substantial difference was observed. (2) Logistic regression analysis indicated that TFEB polymorphism is not remarkably associated with FLD. (3) In the multiplicative interaction model, rs1015149, rs1062966, and rs11754668 had remarkable interaction with smoking amount. Rs1062966 and rs11754668 also had a considerable interaction with body mass index and alcohol intake, respectively. However, no remarkable additive interaction was observed.Conclusion: TFEB polymorphism is not directly associated with FLD susceptibility, but the risk can be changed through gene–environment interaction.

An Overview of the RELIEF Algorithm and Advancements

2016 ◽  
Author(s):  
Alexandre Todorov
Keyword(s):  
Machine Learning ◽  
Logistic Regression ◽  
Learning Algorithm ◽  
Simulated Data ◽  
Environment Interaction ◽  
Machine Learning Algorithm ◽  
Gene Environment Interaction ◽  
Snp Data ◽  
Relief Algorithm ◽  
Gene Environment

The aim of the RELIEF algorithm is to filter out features (e.g., genes, environmental factors) that are relevant to a trait of interest, starting from a set of that may include thousands of irrelevant features. Though widely used in many fields, its application to the study of gene-environment interaction studies has been limited thus far. We provide here an overview of this machine learning algorithm and some of its variants. Using simulated data, we then compare of the performance of RELIEF to that of logistic regression for screening for gene-environment interactions in SNP data. Even though performance degrades in larger sets of markers, RELIEF remains a competitive alternative to logistic regression, and shows clear promise as a tool for the study of gene-environment interactions. Areas for further improvements of the algorithm are then suggested.

scholarly journals Case-Control Studies of Gene-Environment Interaction: Bayesian Design and Analysis

Biometrics ◽  
2009 ◽  
Vol 66 (3) ◽  
pp. 934-948 ◽  
Author(s):  
Bhramar Mukherjee ◽  
Jaeil Ahn ◽  
Stephen B. Gruber ◽  
Malay Ghosh ◽  
Nilanjan Chatterjee
Keyword(s):  
Case Control ◽  
Environment Interaction ◽  
Case Control Studies ◽  
Bayesian Design ◽  
Gene Environment Interaction ◽  
Gene Environment

scholarly journals Effect of polygenic risk scores on depression in childhood trauma

2014 ◽  
Vol 205 (2) ◽  
pp. 113-119 ◽  
Author(s):  
Wouter J. Peyrot ◽  
Yuri Milaneschi ◽  
Abdel Abdellaoui ◽  
Patrick F. Sullivan ◽  
Jouke J. Hottenga ◽  
...  
Keyword(s):  
Childhood Trauma ◽  
Meta Analysis ◽  
Genetic Effect ◽  
Risk Scores ◽  
Environment Interaction ◽  
Polygenic Risk ◽  
Gene Environment Interaction ◽  
Gene Environment ◽  
Genome Wide ◽  
Direct Genetic Effect

BackgroundResearch on gene×environment interaction in major depressive disorder (MDD) has thus far primarily focused on candidate genes, although genetic effects are known to be polygenic.AimsTo test whether the effect of polygenic risk scores on MDD is moderated by childhood trauma.MethodThe study sample consisted of 1645 participants with a DSM-IV diagnosis of MDD and 340 screened controls from The Netherlands. Chronic or remitted episodes (severe MDD) were present in 956 participants. The occurrence of childhood trauma was assessed with the Childhood Trauma Interview and the polygenic risk scores were based on genome-wide meta-analysis results from the Psychiatric Genomics Consortium.ResultsThe polygenic risk scores and childhood trauma independently affected MDD risk, and evidence was found for interaction as departure from both multiplicativity and additivity, indicating that the effect of polygenic risk scores on depression is increased in the presence of childhood trauma. The interaction effects were similar in predicting all MDD risk and severe MDD risk, and explained a proportion of variation in MDD risk comparable to the polygenic risk scores themselves.ConclusionsThe interaction effect found between polygenic risk scores and childhood trauma implies that (1) studies on direct genetic effect on MDD gain power by focusing on individuals exposed to childhood trauma, and that (2) individuals with both high polygenic risk scores and exposure to childhood trauma are particularly at risk for developing MDD.

scholarly journals Interaction between ELMO1 gene polymorphisms and environment factors on susceptibility to diabetic nephropathy in Chinese Han population

2019 ◽  
Vol 11 (1) ◽  
Author(s):  
Yi Hou ◽  
Yong Gao ◽  
Yan Zhang ◽  
Si-Tong Lin ◽  
Yue Yu ◽  
...  
Keyword(s):  
Diabetic Nephropathy ◽  
Alcohol Drinking ◽  
Control Group ◽  
Environment Interaction ◽  
Nucleotide Polymorphisms ◽  
Chinese Han ◽  
Gene Environment Interaction ◽  
Gene Environment ◽  
Increased Risk ◽  
Significant Gene

Abstract Background The association of diabetic nephropathy (DN) risk with single nucleotide polymorphisms (SNPs) within Engulfment and Cell Motility 1 (ELMO1) gene and gene–environment synergistic effect have not been extensively examined in, therefore, the purpose of this study is to explore the association between multiple SNPs in ELMO1 gene, and the relationship between gene–environment synergy effect and the risk of DN. Methods Genotyping for 4 SNPs was performed with polymerase chain reaction (PCR) and following restriction fragment length polymorphism (RFLP) methods. Hardy–Weinberg balance of the control group was tested by SNPstats (online software: http://bioinfo.iconologia.net/snpstats). The best combination of four SNPs of ELMO1 gene and environmental factors was screened by GMDR model. Logistic regression was used to calculating the OR values between different genotypes of ELMO1 gene and DN. Results The rs741301-G allele and the rs10255208-GG genotype were associated with an increased risk of DN risk, adjusted ORs (95% CI) were 1.75 (1.19–2.28) and 1.41 (1.06–1.92), respectively, both p-values were < 0.001. We also found that the others SNPs-rs1345365 and rs7782979 were not significantly associated with susceptibility to DN. GMDR model found a significant gene–alcohol drinking interaction combination (p = 0.0107), but no significant gene–hypertension interaction combinations. Alcohol drinkers with rs741301-AG/GG genotype also have the highest DN risk, compared to never drinkers with rs741301-AA genotype, OR (95% CI) 3.52 (1.93–4.98). Conclusions The rs741301-G allele and the rs10255208-GG genotype, gene–environment interaction between rs741301 and alcohol drinking were all associated with increased DN risk.

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