Exploiting gene-environment interaction to detect genetic associations.
paper
Cited
Public
Unavailable
- Authors
- Kraft, Peter; Yen, Yu-Chun; Stram, Daniel O; Morrison, John; Gauderman, W James
- Year
- 2007
- Journal
- Human heredity
- PMID
- 17283440
- DOI
- 10.1159/000099183
Complex disease by definition results from the interplay of genetic and environmental factors. However, it is currently unclear how gene-environment interaction can best be used to locate complex disease susceptibility loci, particularly in the context of studies where between 1,000 and 1,000,000 markers are scanned for association with disease. We present a joint test of marginal association and gene-environment interaction for case-control data. We compare the power and sample size requirements of this joint test to other analyses: the marginal test of genetic association, the standard test for gene-environment interaction based on logistic regression, and the case-only test for interaction that exploits gene-environment independence. Although for many penetrance models the joint test of genetic marginal effect and interaction is not the most powerful, it is nearly optimal across all penetrance models we considered. In particular, it generally has better power than the marginal test when the genetic effect is restricted to exposed subjects and much better power than the tests of gene-environment interaction when the genetic effect is not restricted to a particular exposure level. This makes the joint test an attractive tool for large-scale association scans where the true gene-environment interaction model is unknown.
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| Genome-wide association studies and the clinic: a focus on breast cancer. | VΓ©ron A et al. | β | 2014 | β |
| Genome-wide association studies of obesity and metabolic syndrome. | Fall T et al. | β | 2014 | β |
| Genome-wide association study of bipolar disorder accounting for effect of body mass index identifies a new risk allele in TCF7L2. | Winham SJ et al. | β | 2014 | β |
| How genetic studies have advanced our understanding of age-related macular degeneration and their impact on patient care: a review. | Baird PN et al. | β | 2014 | β |
| Human leukocyte antigen class II variants and adult-onset asthma: does occupational allergen exposure play a role? | Smit LA et al. | β | 2014 | β |
| Identification of new genetic susceptibility loci for breast cancer through consideration of gene-environment interactions. | Schoeps A et al. | β | 2014 | β |
| Incorporating gene-environment interaction in testing for association with rare genetic variants. | Chen H et al. | β | 2014 | β |
| Integrative modeling of multiple genomic data from different types of genetic association studies. | Huang YT | β | 2014 | β |
| Interaction between genetic variants and exposure to Hurricane Katrina on post-traumatic stress and post-traumatic growth: a prospective analysis of low income adults. | Dunn EC et al. | β | 2014 | β |
| Lack of replication of the GRIN2A-by-coffee interaction in Parkinson disease. | Ahmed I et al. | β | 2014 | β |
| Mind the gap: why many geneticists and psychological scientists have discrepant views about gene-environment interaction (GΓE) research. | Duncan LE et al. | β | 2014 | β |
| Molecular insight in gastric cancer induction: an overview of cancer stemness genes. | Akhavan-Niaki H et al. | β | 2014 | β |
| Natural and orthogonal model for estimating gene-gene interactions applied to cutaneous melanoma. | Xiao F et al. | β | 2014 | β |
| On the choice of degrees of freedom for testing gene-gene interactions. | Ueki M | β | 2014 | β |
| Re: Association of polymorphism in cytochrome P450 2C9 with susceptibility to head and neck cancer and treatment outcome: Pragmatic use of Hardy-Weinberg equilibrium and statistical interaction analysis. | Singh SK | β | 2014 | β |
| Set-based joint test of interaction between SNPs in the VEGF pathway and exogenous estrogen finds association with age-related macular degeneration. | Courtenay MD et al. | β | 2014 | β |
| Testing departure from additivity in Tukey's model using shrinkage: application to a longitudinal setting. | Ko YA et al. | β | 2014 | β |
| The emerging molecular architecture of schizophrenia, polygenic risk scores and the clinical implications for GxE research. | Iyegbe C et al. | β | 2014 | β |
| The logistic regression model for gene-environment interactions using both case-parent trios and unrelated case-controls. | Guo CY et al. | β | 2014 | β |
| A nonparametric test to detect quantitative trait loci where the phenotypic distribution differs by genotypes. | Aschard H et al. | β | 2013 | β |
| Case-sibling studies that acknowledge unstudied parents and permit the inclusion of unmatched individuals. | Shi M et al. | β | 2013 | β |
| Comparisons of power of statistical methods for gene-environment interaction analyses. | Ege MJ et al. | β | 2013 | β |
| Confounding and heterogeneity in genetic association studies with admixed populations. | Liu J et al. | β | 2013 | β |
| Empirical hierarchical bayes approach to gene-environment interactions: development and application to genome-wide association studies of lung cancer in TRICL. | Sohns M et al. | β | 2013 | β |
| Environmental confounding in gene-environment interaction studies. | Vanderweele TJ et al. | β | 2013 | β |
| Gene-environment and gene-treatment interactions in type 2 diabetes: progress, pitfalls, and prospects. | Franks PW et al. | β | 2013 | β |
| Gene-environment interactions in cancer epidemiology: a National Cancer Institute Think Tank report. | Hutter CM et al. | β | 2013 | β |
| Gene-environment interactions in genome-wide association studies: current approaches and new directions. | Winham SJ et al. | β | 2013 | β |
| Gene Γ environment interactions in obesity: the state of the evidence. | Ahmad S et al. | β | 2013 | β |
| Genetic factors in nonsmokers with age-related macular degeneration revealed through genome-wide gene-environment interaction analysis. | Naj AC et al. | β | 2013 | β |
| Genome-wide investigation of gene-environment interactions in colorectal cancer. | Siegert S et al. | β | 2013 | β |
| Influence of serotonin transporter promoter variation on the effects of separation from parent/partner on depression. | FandiΓ±o-Losada A et al. | β | 2013 | β |
| Investigations of gene-disease associations: costs and benefits of environmental data. | Luo H et al. | β | 2013 | β |
| Meta-regression of gene-environment interaction in genome-wide association studies. | Xu X et al. | β | 2013 | β |
| Multivariate generalized multifactor dimensionality reduction to detect gene-gene interactions. | Choi J et al. | β | 2013 | β |
| Screening-testing approaches for gene-gene and gene-environment interactions using independent statistics. | Millstein J | β | 2013 | β |
| Strategy to control type I error increases power to identify genetic variation using the full biological trajectory. | Benke KS et al. | β | 2013 | β |
| The case-only test for gene-environment interaction is not uniformly powerful: an empirical example. | Wu C et al. | β | 2013 | β |
| Use of systems biology approaches to analysis of genome-wide association studies of myocardial infarction and blood cholesterol in the nurses' health study and health professionals' follow-up study. | Reilly D et al. | β | 2013 | β |
| Using Bayesian networks to discover relations between genes, environment, and disease. | Su C et al. | β | 2013 | β |
| Using shared genetic controls in studies of gene-environment interactions. | Chen YH et al. | β | 2013 | β |
| A comparison of case-control and case-only designs to investigate gene-environment interactions using breast cancer data. | Hassanzadeh J et al. | β | 2012 | β |
| A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance. | Manning AK et al. | β | 2012 | β |
| Allowing for sex differences increases power in a GWAS of multiplex Autism families. | Lu AT et al. | β | 2012 | β |
| A novel method to identify high order gene-gene interactions in genome-wide association studies: gene-based MDR. | Oh S et al. | β | 2012 | β |
| Beyond the fourth wave of genome-wide obesity association studies. | Sandholt CH et al. | β | 2012 | β |
| Challenges and opportunities in genome-wide environmental interaction (GWEI) studies. | Aschard H et al. | β | 2012 | β |
| Circadian genes and breast cancer susceptibility in rotating shift workers. | Monsees GM et al. | β | 2012 | β |
| Concealed effects of gene-environment interactions in genome-wide association. | Handel AE et al. | β | 2012 | β |
| Design and analysis issues in gene and environment studies. | Liu CY et al. | β | 2012 | β |
| Does accounting for gene-environment interactions help uncover association between rare variants and complex diseases? | Kazma R et al. | β | 2012 | β |
| Effects of interleukin-10 polymorphisms, Helicobacter pylori infection, and smoking on the risk of noncardia gastric cancer. | Kim J et al. | β | 2012 | β |
| Evidence of gene-environment interaction for the RUNX2 gene and environmental tobacco smoke in controlling the risk of cleft lip with/without cleft palate. | Wu T et al. | β | 2012 | β |
| Gene Γ environment interaction models in psychiatric genetics. | Karg K et al. | β | 2012 | β |
| Gene-environment interactions in asthma and allergic diseases: challenges and perspectives. | Kauffmann F et al. | β | 2012 | β |
| Gene-environment interactions in genome-wide association studies: a comparative study of tests applied to empirical studies of type 2 diabetes. | Cornelis MC et al. | β | 2012 | β |
| Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function. | Hancock DB et al. | β | 2012 | β |
| hOGG1 Ser326Cys polymorphism is associated with risk of bladder cancer in a Chinese population: a case-control study. | Ma L et al. | β | 2012 | β |
| Improved statistics for genome-wide interaction analysis. | Ueki M et al. | β | 2012 | β |
| Inclusion of gene-gene and gene-environment interactions unlikely to dramatically improve risk prediction for complex diseases. | Aschard H et al. | β | 2012 | β |
| Informed conditioning on clinical covariates increases power in case-control association studies. | Zaitlen N et al. | β | 2012 | β |
| Invited commentary: GE-Whiz! Ratcheting gene-environment studies up to the whole genome and the whole exposome. | Thomas DC et al. | β | 2012 | β |
| On lung function and interactions using genome-wide data. | MelΓ©n E et al. | β | 2012 | β |
| Population-based case-control association studies. | Hancock DB et al. | β | 2012 | β |
| Simultaneously testing for marginal genetic association and gene-environment interaction. | Dai JY et al. | β | 2012 | β |
| Testing gene-environment interaction in large-scale case-control association studies: possible choices and comparisons. | Mukherjee B et al. | β | 2012 | β |
| A fast algorithm to optimize SNP prioritization for gene-gene and gene-environment interactions. | Deng WQ et al. | β | 2011 | β |
| Application of a novel score test for genetic association incorporating gene-gene interaction suggests functionality for prostate cancer susceptibility regions. | Ciampa J et al. | β | 2011 | β |
| Characterizing associations and SNP-environment interactions for GWAS-identified prostate cancer risk markers--results from BPC3. | Lindstrom S et al. | β | 2011 | β |
| Entropy based genetic association tests and gene-gene interaction tests. | de Andrade M et al. | β | 2011 | β |
| Evidence for gene-environment interaction in a genome wide study of nonsyndromic cleft palate. | Beaty TH et al. | β | 2011 | β |
| Gene-environment interactions: early life stress and risk for depressive and anxiety disorders. | Nugent NR et al. | β | 2011 | β |
| Gene Γ environment interactions in type 2 diabetes. | Franks PW | β | 2011 | β |
| Genetic association and gene-environment interaction: a new method for overcoming the lack of exposure information in controls. | Kazma R et al. | β | 2011 | β |
| Genome-wide gene-environment study identifies glutamate receptor gene GRIN2A as a Parkinson's disease modifier gene via interaction with coffee. | Hamza TH et al. | β | 2011 | β |
| Genotype-environment interactions in microsatellite stable/microsatellite instability-low colorectal cancer: results from a genome-wide association study. | Figueiredo JC et al. | β | 2011 | β |
| Large-scale exploration of gene-gene interactions in prostate cancer using a multistage genome-wide association study. | Ciampa J et al. | β | 2011 | β |
| Meta-analysis of gene-environment interaction: joint estimation of SNP and SNP Γ environment regression coefficients. | Manning AK et al. | β | 2011 | β |
| On the robustness of tests of genetic associations incorporating gene-environment interaction when the environmental exposure is misspecified. | Tchetgen Tchetgen EJ et al. | β | 2011 | β |
| Polymorphisms in genes involved in the NF-ΞΊB signalling pathway are associated with bone mineral density, geometry and turnover in men. | Roshandel D et al. | β | 2011 | β |
| Population stratification bias: more widespread than previously thought. | Kraft P | β | 2011 | β |
| Robust discovery of genetic associations incorporating gene-environment interaction and independence. | Tchetgen Tchetgen E | β | 2011 | β |
| Sample size requirements to detect gene-environment interactions in genome-wide association studies. | Murcray CE et al. | β | 2011 | β |
| Studying gene and gene-environment effects of uncommon and common variants on continuous traits: a marker-set approach using gene-trait similarity regression. | Tzeng JY et al. | β | 2011 | β |
| Tests for compositional epistasis under single interaction-parameter models. | VanderWeele TJ et al. | β | 2011 | β |
| To stratify or not to stratify: power considerations for population-based genome-wide association studies of quantitative traits. | Behrens G et al. | β | 2011 | β |
| Varying coefficient model for gene-environment interaction: a non-linear look. | Ma S et al. | β | 2011 | β |
| A comparison of sample size and power in case-only association studies of gene-environment interaction. | Clarke GM et al. | β | 2010 | β |
| Bayesian mixture modeling of gene-environment and gene-gene interactions. | Wakefield J et al. | β | 2010 | β |
| Case-control studies of gene-environment interaction: Bayesian design and analysis. | Mukherjee B et al. | β | 2010 | β |
| Effect of including environmental data in investigations of gene-disease associations in the presence of qualitative interactions. | Williamson E et al. | β | 2010 | β |
| Evidence of gene-environment interaction for the IRF6 gene and maternal multivitamin supplementation in controlling the risk of cleft lip with/without cleft palate. | Wu T et al. | β | 2010 | β |
| Fetal genotype for the xenobiotic metabolizing enzyme NQO1 influences intrauterine growth among infants whose mothers smoked during pregnancy. | Price TS et al. | β | 2010 | β |
| Gene--environment-wide association studies: emerging approaches. | Thomas D | β | 2010 | β |
| Genetic education and the challenge of genomic medicine: development of core competences to support preparation of health professionals in Europe. | Skirton H et al. | β | 2010 | β |
| Genetics of post-traumatic stress disorder: review and recommendations for genome-wide association studies. | Cornelis MC et al. | β | 2010 | β |
| Genome-wide conditional search for epistatic disease-predisposing variants in human association studies. | Wang G et al. | β | 2010 | β |
| Genome-wide meta-analysis of joint tests for genetic and gene-environment interaction effects. | Aschard H et al. | β | 2010 | β |
| Incorporating age at onset of smoking into genetic models for nicotine dependence: evidence for interaction with multiple genes. | Grucza RA et al. | β | 2010 | β |
| Methods for investigating gene-environment interactions in candidate pathway and genome-wide association studies. | Thomas D | β | 2010 | β |
| Methods: genetic epidemiology. | Benke KS et al. | β | 2010 | β |
| On the use of sibling recurrence risks to select environmental factors liable to interact with genetic risk factors. | Kazma R et al. | β | 2010 | β |
| Ordered subset analysis for case-control studies. | Qin X et al. | β | 2010 | β |
| The Gene, Environment Association Studies consortium (GENEVA): maximizing the knowledge obtained from GWAS by collaboration across studies of multiple conditions. | Cornelis MC et al. | β | 2010 | β |
| Transferrin receptor-1 gene polymorphisms are associated with type 2 diabetes. | FernΓ‘ndez-Real JM et al. | β | 2010 | β |
| Using principal components of genetic variation for robust and powerful detection of gene-gene interactions in case-control and case-only studies. | Bhattacharjee S et al. | β | 2010 | β |
| What's the best statistic for a simple test of genetic association in a case-control study? | Kuo CL et al. | β | 2010 | β |
| Alcohol and colorectal cancer: the role of alcohol dehydrogenase 1C polymorphism. | Homann N et al. | β | 2009 | β |
| A partial least-square approach for modeling gene-gene and gene-environment interactions when multiple markers are genotyped. | Wang T et al. | β | 2009 | β |
| Assessment of sex-specific effects in a genome-wide association study of rheumatoid arthritis. | Zhuang JJ et al. | β | 2009 | β |
| Detecting gene-environment interactions in genome-wide association data. | Engelman CD et al. | β | 2009 | β |
| Detecting gene-gene interactions that underlie human diseases. | Cordell HJ | β | 2009 | β |
| Estimation and testing of gene-environment interactions in family-based association studies. | Cordell HJ | β | 2009 | β |
| Gene-environment interaction in genome-wide association studies. | Murcray CE et al. | β | 2009 | β |
| Gene-environment interaction tests for dichotomous traits in trios and sibships. | Hoffmann TJ et al. | β | 2009 | β |
| Genome-wide association scans for secondary traits using case-control samples. | Monsees GM et al. | β | 2009 | β |
| Independent and additive interactive effects among tumor necrosis factor-alpha polymorphisms, substance use habits, and chronic hepatitis B and hepatitis C virus infection on risk for hepatocellular carcinoma. | Jeng JE et al. | β | 2009 | β |
| Invited commentary: from genome-wide association studies to gene-environment-wide interaction studies--challenges and opportunities. | Khoury MJ et al. | β | 2009 | β |
| MDR1 variants and risk of Parkinson disease. Association with pesticide exposure? | Zschiedrich K et al. | β | 2009 | β |
| Methodological Issues in Multistage Genome-wide Association Studies. | Thomas DC et al. | β | 2009 | β |
| Smoking modifies the relationship between XRCC1 haplotypes and HPV16-negative head and neck squamous cell carcinoma. | Applebaum KM et al. | β | 2009 | β |
| Structures and Assumptions: Strategies to Harness Gene Γ Gene and Gene Γ Environment Interactions in GWAS. | Kooperberg C et al. | β | 2009 | β |
| Testing in semiparametric models with interaction, with applications to gene-environment interactions. | Maity A et al. | β | 2009 | β |
| The impact of gene-environment dependence and misclassification in genetic association studies incorporating gene-environment interactions. | LindstrΓΆm S et al. | β | 2009 | β |
| Two-stage analysis for gene-environment interaction utilizing both case-only and family-based analysis. | Chen YH et al. | β | 2009 | β |
| Biostatistical aspects of genome-wide association studies. | Ziegler A et al. | β | 2008 | β |
| Gene-environment interactions for complex traits: definitions, methodological requirements and challenges. | Dempfle A et al. | β | 2008 | β |
| Nicotinic acetylcholine receptor beta2 subunit gene implicated in a systems-based candidate gene study of smoking cessation. | Conti DV et al. | β | 2008 | β |
| Population stratification bias in the case-only study for gene-environment interactions. | Wang LY et al. | β | 2008 | β |
| Sample size requirements for indirect association studies of gene-environment interactions (G x E). | Hein R et al. | β | 2008 | β |
| Study designs for genome-wide association studies. | Kraft P et al. | β | 2008 | β |
| Tests for gene-environment interaction from case-control data: a novel study of type I error, power and designs. | Mukherjee B et al. | β | 2008 | β |
| Chronic lymphocytic leukaemia: an overview of aetiology in light of recent developments in classification and pathogenesis. | Linet MS et al. | β | 2007 | β |
| Evidence of potential interaction of chemokine genes in susceptibility to systemic sclerosis. | Lee EB et al. | β | 2007 | β |
| Genes, environment, health, and disease: facing up to complexity. | Manolio TA et al. | β | 2007 | β |
| Investigating gene environment interaction in complex diseases: increasing power by selective sampling for environmental exposure. | Boks MP et al. | β | 2007 | β |
| The contribution of gene-environment interaction to psychopathology. | Thapar A et al. | β | 2007 | β |