| Literature DB >> 19341499 |
Matthew B Lanktree1, Robert A Hegele.
Abstract
Despite the recent success of genome-wide association studies (GWASs) in identifying loci consistently associated with coronary artery disease (CAD), a large proportion of the genetic components of CAD and its metabolic risk factors, including plasma lipids, type 2 diabetes and body mass index, remain unattributed. Gene-gene and gene-environment interactions might produce a meaningful improvement in quantification of the genetic determinants of CAD. Testing for gene-gene and gene-environment interactions is thus a new frontier for large-scale GWASs of CAD. There are several anecdotal examples of monogenic susceptibility to CAD in which the phenotype was worsened by an adverse environment. In addition, small-scale candidate gene association studies with functional hypotheses have identified gene-environment interactions. For future evaluation of gene-gene and gene-environment interactions to achieve the same success as the single gene associations reported in recent GWASs, it will be important to pre-specify agreed standards of study design and statistical power, environmental exposure measurement, phenomic characterization and analytical strategies. Here we discuss these issues, particularly in relation to the investigation and potential clinical utility of gene-gene and gene-environment interactions in CAD.Entities:
Year: 2009 PMID: 19341499 PMCID: PMC2664961 DOI: 10.1186/gm28
Source DB: PubMed Journal: Genome Med ISSN: 1756-994X Impact factor: 11.117
Figure 1The pathophysiology of coronary artery disease (CAD) is affected by environmental and genetic factors and their interactions. Pathogenic mechanisms contributing to plaque development and subsequent CAD can be affected both negatively and positively by environmental exposures and genes. Environmental exposures can be either discrete (presence or absence) or continuous. Typically, CAD associated mutations and polymorphisms are found in genes encoding proteins that have key roles in intermediate pathways. Neither the environmental nor genetic lists shown here are comprehensive.
Figure 2Putative gene-environment interactions. For even the simplest case, a dichotomous genetic risk factor (for example, carriers versus non-carriers) and a dichotomous environmental risk factor (for example, present versus absent), several types of interactions are possible. If both the gene and environment have main effects (odds ratios > 1), and thus could be identified independently, a synergistic interaction would result in an effect size larger than a simple additive effect. A second possibility is that an environmental factor could have no main effect but could modify the effect of a genetic factor that does have a main effect, creating a larger than expected combined effect. The inverse is also possible, in which a modifier gene with no main effect of its own increases the effect size of an environmental risk factor. A fourth possibility is that neither the gene nor the environment has a detectable main effect, and interaction is required to produce a measurable effect. A fifth possibility is for a gene and an environmental factor to have redundant effects, in which case the combination of factors produces no increase in risk. These types of interactions can be extended to include different effect sizes or gene-gene interactions.
Box 1. Glossary of statistical termsSummary of strategies to detect gene-gene and gene-environment interactions
| Analytical strategy | Advantages | Disadvantages | References |
|---|---|---|---|
| Examine the effect of the cumulative number of risk alleles at multiple loci | Simple; shows independence of loci | No interaction measured | [ |
| Compare effect of risk allele in sample subgrouped by environmental exposure or additional genotype | Simple | Substantial loss of power in subgroups | [ |
| Identify risk allele whose association with phenotype is modulated by inclusion of environmental or genetic covariate | Easy to implement | Multiple comparisons | [ |
| Inclusion of interaction term in regression model | Direct modeling of gene-gene or gene-environment interaction | Need to define multiple terms in model; possibility of over-fitting; multiple comparisons | [ |
| Non-linear statistical classification techniques, including Bayesian networks, neural networks and support vector machines | Large volumes of data in model-free manner | Difficult to interpret; require validation datasets | [ |
Potential biases in gene-gene and gene-environment investigations of coronary artery disease (CAD)
| Bias | General description | Application to CAD |
|---|---|---|
| Selection bias | Skew in the selection of study participants | Patients with strong family history may self-select for study participation; patients with strong family history may be more likely to be referred to tertiary care and research centers |
| Survivor bias (prevalence-incidence bias) | Selection of study participants may miss mild disease or severe fatal cases | Patients whose first myocardial infarction is fatal are less likely to be studied |
| Recall bias | Patients are more likely to recall an environmental exposure if it was linked to a negative outcome | Patients with CAD may be more likely to remember an environmental exposure because of its negative consequences |
| Respondent bias | Patients answer in the way they believe they should answer, not the true answer | Patients with CAD and knowledge of potential CAD risk factors will be more motivated to report those exposures |
| Family information bias | Individuals become more aware of exposure if it is prevalent in their family | Many CAD risk factors and environmental exposures cluster in families |
| Exposure suspicion bias | Disease status can affect the amount of environmental exposure history collected | If data collection is not standardized, investigators may more thoroughly query patients with CAD |
| Publication bias | Statistically significant findings are more likely to be published | Gene-gene and gene-environment interaction findings in CAD are more likely to be published if significant |
| Measurement bias | Systematic errors of measurement | Platform- or laboratory-dependent genotyping errors; errors of laboratory values; errors of environmental exposure measurement |
| Population stratification | Differences in allele frequencies between groups resulting from ancestry not outcome status | CAD prevalence varies between ethnicities; but this can be tested and corrected for using methodological and statistical techniques |
Box 2. Factors affecting the statistical power of a study of gene-gene or gene-environment interactionsExamples of replicated gene-gene and gene-environment interactions in CAD
| Gene | Environment | Interaction | Independently associated with CAD? | References |
|---|---|---|---|---|
| Lifestyle | Rare mutations have larger effect in less active people with high-fat diet | LDLR: yes; lifestyle: yes | [ | |
| Smoking | Elevated CAD risk in smokers with null mutations | GSTM1, GSTT1: weak; smoking: yes | [ | |
| Smoking | Exaggerated smoking-associated CAD risk in carriers of APOE ε4 | APOE: yes; smoking: yes | [ | |
| Alcohol consumption | Slow-metabolizing γ2 allele homozygotes have the greatest CAD protection | ADH1C: weak; alcohol: yes | [ | |
| Strenuous exercise | Carriers of 455A allele have exaggerated increase in fibrinogen after exercise | FGB: no; exercise: yes | [ | |
| Plasma fibrinogen | Leu34 is protective for CAD in people with high fibrinogen levels | F13A1: no; fibrinogen: yes | [ | |
| Unclear multi-locus epistatic interactions | ACE: no; AGT: no | [ | ||
| Greater negative effect of rare LPL alleles in APOE ε4 carriers | LPL: yes; APOE: yes | [ |
Abbreviations: ACE, acetylcholine esterase; ADH1C, alcohol dehydrogenase 1C; AGT, angiotensinogen; APOE, apolipoprotein E; FGB, fibrinogen beta chain; F13A1, coagulation factor XIII, subunit A1; GSTM1, glutathione S-transferase mu 1; GSTT1, glutathione S-transferase theta 1; LDLR, low-density lipoprotein receptor; LPL, lipoprotein lipase.