Abstract
Objective
Lipid-associated genetic variants discovered through genome-wide association studies (GWAS) do not account for the majority of heritability estimated for these traits. Epidemiological studies have long indicated that certain environmental factors are capable of shaping lipid distributions. However, environmental modifiers of known genotype-phenotype associations are just recently emerging in the literature.
Research Methods & Procedures
We genotyped GWAS-identified variants in samples collected for the National Health and Nutrition Examination Surveys (NHANES). NHANES is a cross-sectional survey of Americans representing non-Hispanic whites (n=2,435), non-Hispanic blacks (n=1,407), and Mexican Americans (n=1,734). Along with lipid levels, NHANES contains an abundance of environmental variables, including serum vitamin A and E levels, both of which are antioxidants that may play a role in lipid metabolism. Gene-environment interactions were modeled between either vitamin A or ln(vitamin E) and 23 GWAS-identified lipid-associated variants for HDL-C, LDL-C, and ln(TG) levels.
Results
After adjusting for age, sex, and marginal effects, three SNPxvitamin A and six SNPxvitamin E interactions were identified at a significance threshold of p<2.2×10−3. The most significant interaction was APOB rs693xvitamin E (p=8.9×10−7) for LDL-C levels among Mexican Americans; this same interaction was significant in non-Hispanic whites (p=2.67×10−4) but not non-Hispanic Blacks (p=0.11). The nine significant interaction models individually explained 0.35–1.28% of the variation in one of the lipid traits.
Conclusions
Our results suggest that the vitamins A and E impact GWAS-identified associations for lipid traits; however, these significant interactions account for only a fraction of the overall variability observed for HDL-C, LDL-C, and TG levels in the general population.
Keywords: lipids, genetics, association, gene-environment interaction, antioxidants
INTRODUCTION
The importance of both genetics and environment in shaping an individual’s lipid profile is intuitively obvious. However, the search for gene-environment interactions that influence levels of HDL-C, LDL-C, and triglycerides has only been relatively recent. One driving force for expanding beyond the standard single-variant models is the observation that single-variant main effects do not account for the majority of the heritability attributed to additive genetics for most complex human traits [25]. For the lipid traits, heritability estimates are as high as 80% [17,31,36], yet the largest and most comprehensive lipid meta-analysis to date was only able to explain about 25–30% of the genetic variance [39]. The identification of gene-environment interactions may help find a proportion of this “missing heritability”.
Within a statistical framework, a gene-environment interaction describes the effect of a genotype and an environmental factor that deviates from their additive effects. Within a biological framework, the environment (or its by-product) modifies the function or amount of a gene product [18]. The latter approach to identify gene-environment interactions is difficult in outbred populations such as humans given that both genetic background and environmental exposures vary within and across populations. Model organisms are more suited to identify biological interactions, but it is difficult to automate these studies, and the findings of these experiments may not generalize to humans [32]. In contrast, methods to identify statistical interactions can be automated, making them an attractive option for detecting gene-environment interactions important for complex human traits [18].
A number of candidate environmental factors affect lipoprotein phenotypes, including diet and nutrition. More specifically, the fat-soluble micronutrients vitamin E and vitamin A may influence lipid metabolism by way of their antioxidant properties. For example, vitamin E may play a role in the prevention of atherosclerosis, through inhibition of oxidation of LDL. While one randomized control trial demonstrated an inverse association between vitamin E intake and relative risk of coronary artery disease [37], others were unable to replicate this protective effect, as reviewed in Nicolosi et al [30]. Discrepancies between studies may be due to the fact that vitamin E can also function as a prooxidant [38]. The antioxidant and anti-atherogenic properties of vitamin A are less studied, although it is known that high doses of vitamin A in the form of isotretinoin increase triglycerides and cholesterol levels and lower HDL-C levels [4,26,29,43].
Despite evidence that genetic variants and environmental factors are independently associated with lipid traits, relatively few studies have been published investigating the interaction between the two [3,10,11,16,22,40]. And, to our knowledge, no studies explicitly testing for interactions between lipid-associated SNPs and vitamin E or vitamin A have been published. We present here an investigation of the effects of 23 lipid-associated SNPs in the context of dietary intake of vitamins A and E using data from the National Health and Nutrition Examination Surveys (NHANES). Analysis of ~15,000 participants from this diverse population-based survey revealed nine significant interactions between lipid-associated SNPs and dietary intake of vitamins A and E. These significant interactions explained 0.35–0.39%, 0.67–1.28%, and 0.36–0.80% of the variability in HDL-C, LDL-C, and triglyceride levels, respectively. Overall, these data provide the first steps in finding the “missing heritability” for lipid traits by accounting for nutritional variables.
MATERIALS AND METHODS
Study population
Study samples were drawn from three National Health and Nutrition Examination Surveys (NHANES III, NHANES 1999–2000, and NHANES 2001–2002). Participant ascertainment and data collection for NHANES has been previously described [7,8]. Only fasting adults (age ≥ 18 years) were included in this analysis. Race/ethnicity was self-described.
All procedures were approved by the CDC Ethics Review Board and written informed consent was obtained from all participants. Because no identifying information was accessed by the investigators, this study was considered exempt from Human Subjects by Vanderbilt University’s Institutional Review Board.
Laboratory measurements
Serum HDL-C, triglycerides, and total cholesterol were measured using standard enzymatic methods. LDL-C was calculated using the Friedewald equation, with missing values assigned for samples with triglyceride levels greater than 400 mg/dl. Serum levels of vitamin E and vitamin A were measured with isocratic high-performance liquid chromatography [6,9].
SNP selection and genotyping
A total of 23 SNPs were considered in this analysis (Table 1). All SNPs were previously associated with HDL-C, LDL-C, and/or triglycerides in published (as of early 2009) candidate gene and genome-wide association studies [1,19,20,24,35,41] and were subsequently analyzed for single-SNP associations with lipid levels in a large meta-analysis by the Population Architecture using Genomics and Epidemiology (PAGE) study [13]. The 23 SNPs tested for gene-environment interactions were either accessed from existing data in the Genetic NHANES database [21] or were directly genotyped by the Epidemiological Architecture of Genes Linked to Environment (EAGLE), one of the four large population-based studies of the PAGE network, using Sequenom or Illumina BeadXpress. Genotyping was performed in the Vanderbilt DNA Resources Core and in the laboratory of Dr. Jonathan Haines. In addition to genotyping experimental NHANES samples, we genotyped blind duplicates provided by CDC and HapMap controls (n=360). All EAGLE SNPs considered here were genotyped in all three NHANES (NHANES III, NHANES 1999–2000, and NHANES 2001–2002), had minor allele frequencies >5% in all three racial/ethnic populations, passed CDC quality control metrics, and are available for secondary analyses through NCHS/CDC.
Table 1. List of 23 candidate gene and GWAS-identified SNPs genotyped in NHANES.
For each SNP (denoted by rs number), we list the chromosomal and genomic location (base-pair), the putative function of the SNP (based on SNP location), and the nearest gene of interest.
| SNP | Chr. | Build 37 location (bp) | Coded Allele | Function | Gene of Interest |
|---|---|---|---|---|---|
| rs11206510 | 1 | 55495789 | C | Intergenic | PCSK9 |
| rs1748195 | 1 | 63049343 | C | Intronic | ANGPTL3 |
| rs693 | 2 | 21231945 | T | Synonymous | APOB |
| rs754523 | 2 | 21311441 | C | Intergenic | APOB |
| rs780094 | 2 | 27740987 | A | Intronic | GCKR |
| rs12654264 | 5 | 74648353 | A | Intronic | HMGCR |
| rs1501908 | 5 | 156397919 | C | Intergenic | TIMD4 |
| rs2197089 | 8 | 19826123 | C | Downstream | LPL |
| rs2954029 | 8 | 126560154 | A | Intergenic | TRIB1 |
| rs4149268 | 9 | 107647220 | A | Intronic | ABCA1 |
| rs3890182 | 9 | 107647405 | A | Intronic | ABCA1 |
| rs1883025 | 9 | 107664051 | G | Intronic | ABCA1 |
| rs174547 | 11 | 61570533 | C | Intronic | FADS1 |
| rs3135506 | 11 | 116662157 | C | Non- synonymous | APOA1/C3/A4/A5 gene cluster |
| rs2338104 | 12 | 109894918 | C | Intronic | MMAB-MVK |
| rs4775041 | 15 | 58674445 | C | Intergenic | LIPC |
| rs9989419 | 16 | 56984889 | A | Upstream | CETP |
| rs3764261 | 16 | 56993074 | G | Upstream | CETP |
| rs2271293 | 16 | 67901820 | A | Intronic | LCAT |
| rs2156552 | 18 | 47181418 | A | Intergenic | LIPG |
| rs2967605 | 19 | 8469488 | G | Downstream | ANGPTL4 |
| rs6102059 | 20 | 39228784 | C | Intergenic | MAFB |
| rs7679 | 20 | 44576252 | C | Downstream | PLTP |
Statistical analysis
Regression modeling was used to investigate the effect of interactions between lipid-associated variants and vitamin levels on HDL-C, LDL-C, and triglycerides. Gene-environment interactions were modeled using a multiplicative interaction term between the environmental variable and the additively-encoded SNP. All models were adjusted for the main effect of the SNP and the environmental variable, along with age and sex. Triglycerides and vitamin E levels were natural-log transformed due to a skewed, non-normal distribution. HDL-C, LDL-C, and vitamin A levels were left as continuous and untransformed. All statistical analyses were conducted unweighted and remotely in SAS v9.2 (SAS Institute, Cary, NC) using the Analytic Data Research by Email (ANDRE) portal of the CDC Research Data Center in Hyattsville, MD. Associations were deemed significant if the p-value was less than or equal to the Bonferroni corrected threshold of 2.2×10−3 (=0.05/23 SNPs). Aggregate statistics related to this work will be available via dbGaP as part of the PAGE study.
RESULTS
Population characteristics
Table 2 displays descriptive statistics for the key variables in this study. Both vitamin A and vitamin E levels were significantly different among the three racial/ethnic groups (p<0.001, one-way ANOVA). Non-Hispanic whites had both higher mean vitamin A and vitamin E levels (60.6 ug/dl and 1,322 ug/dl, respectively) compared to non-Hispanic blacks (53.1 ug/dl and 1,002 ug/dl) and Mexican Americans (52.8 ug/dl and 1,135 ug/dl). Non-Hispanic blacks and Mexican Americans had similar mean vitamin A levels, although vitamin E levels are higher in Mexican Americans.
Table 2.
NHANES participant characteristics.
| Trait | Non-Hispanic Whites | Non-Hispanic Blacks | Mexican Americans |
|---|---|---|---|
| N | 2,435 | 1,407 | 1,734 |
| Age (years) | 51.9 ± 20 | 42.5 ± 17 | 42.8 ± 18 |
| Female (%) | 54 | 56 | 51 |
| Vitamin A (ug/dl) | 60.6 ± 16 | 53.1 ± 17 | 52.8 ± 15 |
| Vitamin E (ug/dl) | 1,322 ± 615 | 1,002 ± 379 | 1,135 ± 459 |
| HDL-C (mg/dl) | 51.3 ± 16 | 54.1 ± 17 | 48.3 ± 14 |
| LDL-C (mg/dl) | 126.9 ± 36 | 122.2 ± 39 | 120.9 ± 34 |
| Triglycerides (mg/dl) | 146.7 ± 93 | 107.0 ± 72 | 156.3 ± 104 |
Values are represented as mean ± sd unless otherwise indicated.
It is important to note that vitamins A and E were highly correlated with the majority of lipid levels in all three NHANES populations (Table 3). More specifically, vitamin A was associated with all three lipid traits in the majority of participants. For triglycerides, the amount of variance explained (R2) by vitamin A was as high as 14% in non-Hispanic whites. R2 was smaller for the other two lipid traits (max R2<5% between LDL-C and vitamin A in Mexican Americans; Table 3) although it was still larger than the average amount of variance explained by single common genetic variants (~3%). Vitamin E was also very strongly correlated with LDL-C and triglyceride levels (p<4.05×10−45) across all racial/ethnic groups. Furthermore, vitamin E levels explained 17–24% of the variance in LDL-C levels and 25–40% of the variance in triglyceride levels (Table 3).
Table 3. Associations between lipid traits and vitamins A and E.
The association of lipid traits and vitamin levels were performed using linear regression, adjusted for age and sex. Both triglycerides and vitamin E levels were natural-log transformed. Measures of variance explained (R2) are also provided for each association based on unadjusted regressions. Significant associations (p<0.01) are in bold.
| Vitamin A | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Lipid Trait | Non-Hispanic Whites | Non-Hispanic Blacks | Mexican American | ||||||
| Beta (SE) | p-value | R2 | Beta (SE) | p-value | R2 | Beta (SE) | p-value | R2 | |
| HDL-C | 0.05 (0.02) | 2.40E-03 | <0.01 | 0.08 (0.03) | 4.37E-03 | 0.01 | 0.06 (0.02) | 9.28E -03 | <0.01 |
| LDL-C | 0.24 (0.24) | 2.88E-05 | 0.02 | 0.17 (0.08) | 0.03 | 0.02 | 0.38 (0.07) | 1.58E-08 | 0.05 |
| TG | 0.01 (0.001) | 5.50E-56 | 0.14 | 0.01 (0.001) | 2.14E-27 | 0.11 | 0.01 (0.001) | 1.26E-30 | 0.12 |
| Vitamin E | |||||||||
| Lipid Trait | Non-Hispanic Whites | Non-Hispanic Blacks | Mexican American | ||||||
| Beta (SE) | p-value | R2 | Beta (SE) | p-value | R2 | Beta (SE) | p-value | R2 | |
| HDL-C | 1.25 (0.82) | 0.13 | <0.01 | 0.65 (1.53) | 0.67 | <0.01 | −2.18 (0.97) | 0.02 | <0.01 |
| LDL-C | 36.21 (2.29) | 1.03E-52 | 0.17 | 57.87 (3.88) | 4.05E-45 | 0.24 | 46.91 (2.83) | 2.04E-55 | 0.23 |
| TG | 0.68 (0.03) | 4.95E-116 | 0.26 | 0.78 (0.04) | 1.91E-68 | 0.25 | 1.01 (0.03) | 8.23E-151 | 0.40 |
SNPxVitamin interactions
We tested for gene-environment interaction effects between our 23 lipid-associated variants and vitamins A and E on HDL-C, LDL-C, and triglyceride levels. A total of nine gene-environment interactions were statistically significant at p<2.1×10−3 and are summarized in Table 4. Full association results are reported in Supplementary Tables S1–S6. The association between LDL-C and APOB rs693xvitamin E in Mexican Americans was the most significant at p=8.94×10−7. This same interaction was significant in non-Hispanic whites (p=2.67×10−4) but not in non-Hispanic blacks (p=0.11, Table S5). Additionally, other interactions with this APOB variant (rs693xvitamin A and rs693xvitamin E) were significantly associated with triglyceride levels among non-Hispanic whites at p=2.16×10−3 and 4.65×10−5, respectively.
Table 4. Significant SNPxenvironment interactions in NHANES.
Associations with significant interaction terms (p<2.17E-03, Bonferroni corrected p-value for 23 SNPs) are listed. Both triglycerides and vitamin E levels were natural-log transformed. Betas, standard errors (SE), and p-values for main effects of the SNP and the environment are represented, along with the amount of trait variance explained (R2) by interaction term.
| Interaction | Associated Lipid Trait | Population | SNP Main Effect | Environment Main Effect | SNPxEnvironment Interaction Effect | ||||
|---|---|---|---|---|---|---|---|---|---|
| Beta (SE) | P-value | Beta (SE) | P-value | Beta (SE) | P-value | R2 (%) | |||
| rs693xVitA | TG | Non-Hispanic Whites | −0.16 (0.06) | 6.11E-03 | 0.01 (0.001) | 1.01E-22 | 0.003 (0.001) | 2.16E-03 | 0.39 |
| rs693xVitE | LDL-C | Non-Hispanic Whites | −74.86 (21.54) | 5.22E-04 | 31.86 (2.76) | 1.39E-29 | 11.11 (3.04) | 2.67E-04 | 0.67 |
| rs693xVitE | LDL-C | Mexican Americans | −155.52 (31.82) | 1.17E-06 | 38.98 (3.25) | 2.51E-31 | 22.71 (4.60) | 8.94E-07 | 1.28 |
| rs693xVitE | TG | Non-Hispanic Whites | −0.99 (0.25) | 8.59E-09 | 0.60 (0.03) | 3.48E-62 | 0.14 (0.04) | 4.65E-05 | 0.60 |
| rs1748195xVitA | HDL-C | Non-Hispanic Whites | −5.15 (1.67) | 2.07E-03 | −0.05 (0.04) | 0.18 | 0.09 (0.03) | 1.16E-03 | 0.39 |
| rs1748195xVitE | HDL-C | Non-Hispanic Whites | −23.13 (7.55) | 2.22E-03 | −3.12 (0.65) | 0.06 | 3.28 (1.06) | 2.06E-03 | 0.35 |
| rs11206510xVitA | LDL-C | Mexican Americans | −30.58 (8.08) | 1.63E-04 | 0.25 (0.07) | 9.22E-04 | 0.58 (0.15) | 7.65E-05 | 1.26 |
| rs11206510xVitE | TG | Non-Hispanic Whites | 1.03 (0.33) | 1.63E-03 | 0.74 (0.03) | 1.89E-49 | −1.15 (0.05) | 1.27E-03 | 0.36 |
| rs3135506xVitE | TG | Non-Hispanic Blacks | −3.02 (0.85) | 4.16E-04 | 0.74 (0.04) | 1.14E-56 | 0.46 (0.12) | 2.45E-04 | 0.80 |
Interactions between ANGPTL3 rs1748195 and both vitamin A and E were associated with HDL-C levels in non-Hispanic whites (p=1.16×10−3 and p=2.06×10−3). The ANGPTL3 rs1748195xvitamin A interaction trended towards significance in non-Hispanic blacks (p=0.01) but was not associated with HDL-C in Mexican Americans (p=0.64, Table S1). Similarly, the rs1748195xvitamin E interaction was not associated with HDL-C in the other two populations.
Two interactions with a variant in PCSK9 are also listed in Table 5.4. The PCSK9 rs11206510xvitamin A interaction was associated with LDL-C in Mexican Americans at p=7.65×10−5. In addition, the PCSK9 rs11206510xvitamin E interaction was associated with transformed triglycerides in non-Hispanic whites at p=1.27×10−3. Lastly, the only significant gene-environment interaction observed in non-Hispanic blacks was between the APOA1/C3/A4/A5 cluster variant rs3135506 and vitamin E, which was associated with triglyceride levels at p=2.45×10−4.
The nine significant interaction models individually explained 0.35–1.28% of the variation in one of the lipid traits. Interactions rs693xvitamin E and rs11206510xvitamin A had the greatest R2 values and contributed to 1.28% and 1.26%, respectively, of the variation in LDL-C among Mexican Americans. The seven other interaction terms had R2 values <1%.
DISCUSSION
In this study we have identified three novel SNPxvitamin A and six novel SNPxvitamin E interactions. A majority of the significant interactions were associated with triglycerides (4/9) and were among non-Hispanic whites (6/9). Our most significant finding (APOB rs693xvitamin E), however, explained less than 1.3% of the variance in LDL-C among Mexican Americans, a trait that is up to 80% heritable. In comparison, the effect of age and sex together accounted for 5.9% of the variance in LDL-C among Mexican Americans.
All of the genes implicated here play key roles in lipid metabolism. The gene products of APOB, apoB-48 and apo-100, are the main apolipoproteins of chylomicrons and LDL particles, respectively. ANGPTL3 encodes a protein which can suppress lipoprotein lipase (LPL) activity, leading to increases in plasma triglycerides and HDL-C. PCSK9 encodes protein convertase subtilisin kexin 9, a protein that binds the LDL receptor and induces its degradation. Lastly, the APOA1/C3/A4/A5 gene cluster lies within a 17kb region on chromosome 11. Proteins made by this gene cluster are major constituents of very low density lipoprotein (VLDL) and/or HDL, act to inhibit LPL activity, and influence dietary fat absorption and chylomicron synthesis [12].
Both vitamin E and A are incorporated into lipoproteins and are delivered to peripheral tissues. Additionally, both are found exclusively in plasma lipoproteins (VLDL, LDL, and HDL) [5]. The interdependence of these vitamins and lipids (as demonstrated in Table 3) suggests that the interactions described in this study may be either just reflective of the strong correlation between vitamins and lipids or biological relevance. In support of the latter interpretation, micronutrients such as vitamin A and E have previously been implicated in affecting the gene expression of import lipid-metabolizing genes [15,16,27,28,33]. For example, Mooradian et al demonstrated that high concentrations of vitamin E were associated with significant decreases in apoA-I expression (which is sensitive to the oxidative state of the cell) in hepatic HepG2 cells by reducing apoA-I promoter activity [27].
It has been argued that gene-environment heterogeneity may be, in part, to blame for the lack of replication among GWAS studies and among different ancestral populations [23,32]. In the single-SNP PAGE meta-analysis detailed in Dumitrescu et al [14], APOB rs693 was strongly associated in European Americans (p=3.38×10−21), marginally associated with LDL-C in African Americans (p=0.02), but not associated in Mexican Americans/Hispanics (p=0.18). However, in this analysis, which represents a subset of the PAGE study sample, the main effect of rs693 was significantly associated in Mexican Americans (p=1.17×10−6, Table 4) after adjusting for the interaction with vitamin E. Accounting for environmental modifiers in genetic studies of lipid levels may not only uncover new biology, it may also improve the generalizabilty of findings from genome-wide association studies.
In interpreting our findings, we should consider several aspects. First, NHANES is a cross-sectional study and, therefore, we are unable to determine the temporal sequence of our results. Second, the issue of sample size and the ‘curse of dimensionality’ [2] is relevant to this study. As the number of factors under study increases (as with the addition of interaction terms), so do the number of strata. With a set sample size, increasing the number of terms in the model quickly increases the degrees of freedom and reduces the per-stratum sample size, thus decreasing statistical power. For this reason, even with relatively large sample sizes in NHANES, we had to restrict our analysis to SNPs with minor allele frequencies greater than 5%. To better study less-common variants, collaborative studies and/or other non-regression based approaches (such as multifactor dimensionality reduction) [34] may be appropriate, although they are not without their own limitations. Lastly, other potential confounding environmental factors, such as physical activity and alcohol consumption, were not included in the analysis.
A major strength of the study is that NHANES systematically collects environmental exposures in a diverse population. It is important to keep in mind that, beyond sample size, the power to detect gene-environment interactions is influenced by the accuracy of the measurement of the outcome and the environmental exposure [42]. In general, environmental variables are notoriously difficult to collect and quantify. Most environmental factors are assessed by questionnaire, which can lead to certain biases, including under-reporting of risky behaviors. Therefore, biomarkers as quantitative measures of the environmental exposures are preferred. Measures of dietary intake may be assessed by collection of daily food diaries or 24-hour dietary recalls. From these recall data, calculation of fat, vitamin, and mineral content is available in NHANES but these estimates are subject to poor recall. However, serum vitamin A and E levels are easily measured from a blood draw and may be used as a measure of dietary compliance.
CONCLUSION
The results presented here highlight the fact that effect sizes of gene-environment interactions tend to be small and large sample sizes are needed to detect them. Nevertheless, understanding the mechanism of the interaction between these lipid-associated variants and environmental factors, such as smoking and dietary vitamin E and A intake, is imperative to determining the etiology of a poor lipid profile and could, therefore, have implications in clinical care.
Supplementary Material
Acknowledgments
Genotyping in NHANES was supported in part by The Population Architecture Using Genomics and Epidemiology (PAGE) study, which is funded by the National Human Genome Research Institute (NHGRI). Data included in this report were resulted from the Epidemiologic Architecture for Genes Linked to Environment (EAGLE) Study, as part of the NHGRI PAGE study (U01HG004798-01). We at EAGLE would like to thank Dr. Geraldine McQuillan and Jody McLean for their help in accessing the Genetic NHANES data. The Vanderbilt University Center for Human Genetics Research, Computational Genomics Core provided computational and/or analytical support for this work. The NHANES DNA samples are stored and plated by the Vanderbilt DNA Resources Core, managed by Cara Sutcliffe. The findings and conclusions in this report are those of the authors and do not necessarily represent the views of the National Institutes for Health or the Centers for Disease Control and Prevention.
Footnotes
LD and DCC contributed to conception and design of the study, interpretation of data, and drafting the manuscript. PM, MA, NS-B,, HJ, NI, and HD contributed to the collection of the data, and RG and KBG contributed to the analysis of the data.
Reference List
- 1.Aulchenko YS, Ripatti S, Lindqvist I, Boomsma D, Heid IM, Pramstaller PP, Penninx BW, Janssens AC, Wilson JF, Spector T, Martin NG, Pedersen NL, Kyvik KO, Kaprio J, Hofman A, Freimer NB, Jarvelin MR, Gyllensten U, Campbell H, Rudan I, Johansson A, Marroni F, Hayward C, Vitart V, Jonasson I, Pattaro C, Wright A, Hastie N, Pichler I, Hicks AA, Falchi M, Willemsen G, Hottenga JJ, de Geus EJ, Montgomery GW, Whitfield J, Magnusson P, Saharinen J, Perola M, Silander K, Isaacs A, Sijbrands EJ, Uitterlinden AG, Witteman JC, Oostra BA, Elliott P, Ruokonen A, Sabatti C, Gieger C, Meitinger T, Kronenberg F, Doring A, Wichmann HE, Smit JH, McCarthy MI, van Duijn CM, Peltonen L. Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. Nat Genet. 2009;41(1):47–55. doi: 10.1038/ng.269. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2.Bellman R. Adaptive Control Processes. Princeton University Press; 1961. [Google Scholar]
- 3.Bernstein MS, Costanza MC, James RW, Morris MA, Cambien F, Raoux S, Morabia A. Physical activity may modulate effects of ApoE genotype on lipid profile. Arterioscler Thromb Vasc Biol. 2002;22(1):133–40. doi: 10.1161/hq0102.101819. [DOI] [PubMed] [Google Scholar]
- 4.Bershad S, Rubinstein A, Paterniti JR, Le NA, Poliak SC, Heller B, Ginsberg HN, Fleischmajer R, Brown WV. Changes in plasma lipids and lipoproteins during isotretinoin therapy for acne. N Engl J Med. 1985;313(16):981–5. doi: 10.1056/NEJM198510173131604. [DOI] [PubMed] [Google Scholar]
- 5.Borel P, Moussa M, Reboul E, Lyan B, Defoort C, Vincent-Baudry S, Maillot M, Gastaldi M, Darmon M, Portugal H, Planells R, Lairon D. Human plasma levels of vitamin E and carotenoids are associated with genetic polymorphisms in genes involved in lipid metabolism. J Nutr. 2007;137(12):2653–9. doi: 10.1093/jn/137.12.2653. [DOI] [PubMed] [Google Scholar]
- 6.Center for Disease Control and Prevention. The Third National Health and Nutrition Examination Survey, 1988–94. Reference manuals and reports (CD ROM) US Department of Health and Human Services National Center for Health Statistics; 1996. [Google Scholar]
- 7.Centers for Disease Control and Prevention. Third National Health and Nutrition Examination Survey, 1988–94, Plan and Operations Procedures Manuals. Hyattsville, Md: US Department of Health and Human Services (DHHS), National Center for Health Statistics, Centers for Disease Control and Prevention; 1996. Ref Type: Audiovisual Material. [Google Scholar]
- 8.Centers for Disease Control and Prevention. National Health and Nutrition Examination Survey (NHANES) DNA Samples: Guidelines for Proposals to Use Samples and Cost Schedule. Federal Register. 2010;75(108):32191–5. [Google Scholar]
- 9.Centers for Disease Control and Prevention (CDC), National Center for Health Statistics NCHS. National Health and Nutrition Examination Survey Data. Centers for Disease Control and Prevention. Hyattsville, MD: U.S. Department of Health and Human Services; 2002. Ref Type: Electronic Citation. [Google Scholar]
- 10.Corella D, Guillen M, Saiz C, Portoles O, Sabater A, Cortina S, Folch J, Gonzalez JI, Ordovas JM. Environmental factors modulate the effect of the APOE genetic polymorphism on plasma lipid concentrations: ecogenetic studies in a Mediterranean Spanish population. Metabolism. 2001;50(8):936–44. doi: 10.1053/meta.2001.24867. [DOI] [PubMed] [Google Scholar]
- 11.Corella D, Tucker K, Lahoz C, Coltell O, Cupples LA, Wilson PW, Schaefer EJ, Ordovas JM. Alcohol drinking determines the effect of the APOE locus on LDL-cholesterol concentrations in men: the Framingham Offspring Study. Am J Clin Nutr. 2001;73(4):736–45. doi: 10.1093/ajcn/73.4.736. [DOI] [PubMed] [Google Scholar]
- 12.Delgado-Lista J, Perez-Jimenez F, Ruano J, Perez-Martinez P, Fuentes F, Criado-Garcia J, Parnell LD, Garcia-Rios A, Ordovas JM, Lopez-Miranda J. Effects of variations in the APOA1/C3/A4/A5 gene cluster on different parameters of postprandial lipid metabolism in healthy young men. J Lipid Res. 2010;51(1):63–73. doi: 10.1194/jlr.M800527-JLR200. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13.Dumitrescu L, Carty CL, Taylor K, Schumacher FR, Hindorff LA, Ambite JL, Anderson G, Best LG, Brown-Gentry K, Buzkova P, Carlson CS, Cochran B, Cole SA, Devereux RB, Duggan D, Eaton CB, Fronage M, Franceschini N, Haessler J, Howard BV, Johnson KC, Laston S, Kolonel LN, Lee ET, MacCluer JW, Manolio TA, Pendergrass SA, Quibrera M, Shohet RV, Wilkens LR, Haiman CA, Le Marchand L, Buyske S, Kooperberg C, North KE, Crawford DC. Genetic determinants of lipid traits in diverse populations from the Population Architecture using Genomics and Epidemiology (PAGE) Study. PLoS Genetics. 2011 doi: 10.1371/journal.pgen.1002138. In Press. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 14.Dumitrescu L, Ritchie MD, Brown-Gentry K, Pulley J, Basford M, Denny J, Oksenberg JR, Roden DM, Haines JL, Crawford DC. Assessing the accuracy of ancestry reported in a biorepository linked to electronic medical records for genetic association studies. Genet Med. 2010;12(10):648–50. doi: 10.1097/GIM.0b013e3181efe2df. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 15.Gatica LV, Vega VA, Zirulnik F, Oliveros LB, Gimenez MS. Alterations in the lipid metabolism of rat aorta: effects of vitamin a deficiency. J Vasc Res. 2006;43(6):602–10. doi: 10.1159/000096247. [DOI] [PubMed] [Google Scholar]
- 16.Hagberg JM, Wilund KR, Ferrell RE. APO E gene and gene-environment effects on plasma lipoprotein-lipid levels. Physiol Genomics. 2000;4(2):101–8. doi: 10.1152/physiolgenomics.2000.4.2.101. [DOI] [PubMed] [Google Scholar]
- 17.Heller DA, de FU, Pedersen NL, Dahlen G, McClearn GE. Genetic and environmental influences on serum lipid levels in twins. N Engl J Med. 1993;328(16):1150–6. doi: 10.1056/NEJM199304223281603. [DOI] [PubMed] [Google Scholar]
- 18.Hunter DJ. Gene-environment interactions in human diseases. Nat Rev Genet. 2005;6(4):287–98. doi: 10.1038/nrg1578. [DOI] [PubMed] [Google Scholar]
- 19.Kathiresan S, Melander O, Guiducci C, Surti A, Burtt NP, Rieder MJ, Cooper GM, Roos C, Voight BF, Havulinna AS, Wahlstrand B, Hedner T, Corella D, Tai ES, Ordovas JM, Berglund G, Vartiainen E, Jousilahti P, Hedblad B, Taskinen MR, Newton-Cheh C, Salomaa V, Peltonen L, Groop L, Altshuler DM, Orho-Melander M. Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans. Nat Genet. 2008;40(2):189–97. doi: 10.1038/ng.75. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 20.Kathiresan S, Willer CJ, Peloso GM, Demissie S, Musunuru K, Schadt EE, Kaplan L, Bennett D, Li Y, Tanaka T, Voight BF, Bonnycastle LL, Jackson AU, Crawford G, Surti A, Guiducci C, Burtt NP, Parish S, Clarke R, Zelenika D, Kubalanza KA, Morken MA, Scott LJ, Stringham HM, Galan P, Swift AJ, Kuusisto J, Bergman RN, Sundvall J, Laakso M, Ferrucci L, Scheet P, Sanna S, Uda M, Yang Q, Lunetta KL, Dupuis J, De Bakker PI, O’Donnell CJ, Chambers JC, Kooner JS, Hercberg S, Meneton P, Lakatta EG, Scuteri A, Schlessinger D, Tuomilehto J, Collins FS, Groop L, Altshuler D, Collins R, Lathrop GM, Melander O, Salomaa V, Peltonen L, Orho-Melander M, Ordovas JM, Boehnke M, Abecasis GR, Mohlke KL, Cupples LA. Common variants at 30 loci contribute to polygenic dyslipidemia. Nat Genet. 2009;41(1):56–65. doi: 10.1038/ng.291. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 21.Keebler ME, Sanders CL, Surti A, Guiducci C, Burtt NP, Kathiresan S. Association of blood lipids with common DNA sequence variants at 19 genetic loci in the multiethnic United States National Health and Nutrition Examination Survey III. Circ Cardiovasc Genet. 2009;2(3):238–43. doi: 10.1161/CIRCGENETICS.108.829473. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 22.Lai CQ, Corella D, Demissie S, Cupples LA, Adiconis X, Zhu Y, Parnell LD, Tucker KL, Ordovas JM. Dietary intake of n-6 fatty acids modulates effect of apolipoprotein A5 gene on plasma fasting triglycerides, remnant lipoprotein concentrations, and lipoprotein particle size: the Framingham Heart Study. Circulation. 2006;113(17):2062–70. doi: 10.1161/CIRCULATIONAHA.105.577296. [DOI] [PubMed] [Google Scholar]
- 23.Lasky-Su J, Lyon HN, Emilsson V, Heid IM, Molony C, Raby BA, Lazarus R, Klanderman B, Soto-Quiros ME, Avila L, Silverman EK, Thorleifsson G, Thorsteinsdottir U, Kronenberg F, Vollmert C, Illig T, Fox CS, Levy D, Laird N, Ding X, McQueen MB, Butler J, Ardlie K, Papoutsakis C, Dedoussis G, O’Donnell CJ, Wichmann HE, Celedon JC, Schadt E, Hirschhorn J, Weiss ST, Stefansson K, Lange C. On the replication of genetic associations: timing can be everything! Am J Hum Genet. 2008;82(4):849–58. doi: 10.1016/j.ajhg.2008.01.018. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 24.Lu Y, Dolle ME, Imholz S, van ‘t SR, Verschuren WM, Wijmenga C, Feskens EJ, Boer JM. Multiple genetic variants along candidate pathways influence plasma high-density lipoprotein cholesterol concentrations. J Lipid Res. 2008;49(12):2582–9. doi: 10.1194/jlr.M800232-JLR200. [DOI] [PubMed] [Google Scholar]
- 25.Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, McCarthy MI, Ramos EM, Cardon LR, Chakravarti A, Cho JH, Guttmacher AE, Kong A, Kruglyak L, Mardis E, Rotimi CN, Slatkin M, Valle D, Whittemore AS, Boehnke M, Clark AG, Eichler EE, Gibson G, Haines JL, Mackay TF, McCarroll SA, Visscher PM. Finding the missing heritability of complex diseases. Nature. 2009;461(7265):747–53. doi: 10.1038/nature08494. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 26.Marsden J. Hyperlipidaemia due to isotretinoin and etretinate: possible mechanisms and consequences. Br J Dermatol. 1986;114(4):401–7. doi: 10.1111/j.1365-2133.1986.tb02842.x. [DOI] [PubMed] [Google Scholar]
- 27.Mooradian AD, Haas MJ, Wadud K. Ascorbic acid and alpha-tocopherol down-regulate apolipoprotein A-I gene expression in HepG2 and Caco-2 cell lines. Metabolism. 2006;55(2):159–67. doi: 10.1016/j.metabol.2005.08.008. [DOI] [PubMed] [Google Scholar]
- 28.Mooradian AD, Haas MJ, Wong NC. The effect of select nutrients on serum high-density lipoprotein cholesterol and apolipoprotein A-I levels. Endocr Rev. 2006;27(1):2–16. doi: 10.1210/er.2005-0013. [DOI] [PubMed] [Google Scholar]
- 29.Murray JC, Gilgor RS, Lazarus GS. Serum triglyceride elevation following high-dose vitamin A treatment for pityriasis rubra pilaris. Arch Dermatol. 1983;119(8):675–6. [PubMed] [Google Scholar]
- 30.Nicolosi RJ, Wilson TA, Lawton C, Handelman GJ. Dietary effects on cardiovascular disease risk factors: beyond saturated fatty acids and cholesterol. J Am Coll Nutr. 2001;20(5 Suppl):421S–7S. doi: 10.1080/07315724.2001.10719179. [DOI] [PubMed] [Google Scholar]
- 31.O’Connell DL, Heller RF, Roberts DC, Allen JR, Knapp JC, Steele PL, Silove D. Twin study of genetic and environmental effects on lipid levels. Genet Epidemiol. 1988;5(5):323–41. doi: 10.1002/gepi.1370050504. [DOI] [PubMed] [Google Scholar]
- 32.Ober C, Vercelli D. Gene-environment interactions in human disease: nuisance or opportunity? Trends Genet. 2011 doi: 10.1016/j.tig.2010.12.004. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 33.Oliveros LB, Domeniconi MA, Vega VA, Gatica LV, Brigada AM, Gimenez MS. Vitamin A deficiency modifies lipid metabolism in rat liver. Br J Nutr. 2007;97(2):263–72. doi: 10.1017/S0007114507182659. [DOI] [PubMed] [Google Scholar]
- 34.Ritchie MD, Hahn LW, Roodi N, Bailey LR, Dupont WD, Parl FF, Moore JH. Multi-factor dimensionality reduction reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer. Am J Hum Genet. 2001;69(1):138–47. doi: 10.1086/321276. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 35.Sandhu MS, Waterworth DM, Debenham SL, Wheeler E, Papadakis K, Zhao JH, Song K, Yuan X, Johnson T, Ashford S, Inouye M, Luben R, Sims M, Hadley D, McArdle W, Barter P, Kesaniemi YA, Mahley RW, McPherson R, Grundy SM, Bingham SA, Khaw KT, Loos RJ, Waeber G, Barroso I, Strachan DP, Deloukas P, Vollenweider P, Wareham NJ, Mooser V. LDL-cholesterol concentrations: a genome-wide association study. Lancet. 2008;371(9611):483–91. doi: 10.1016/S0140-6736(08)60208-1. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 36.Snieder H, van Doornen LJ, Boomsma DI. Dissecting the genetic architecture of lipids, lipoproteins, and apolipoproteins: lessons from twin studies. Arterioscler Thromb Vasc Biol. 1999;19(12):2826–34. doi: 10.1161/01.atv.19.12.2826. [DOI] [PubMed] [Google Scholar]
- 37.Stephens NG, Parsons A, Schofield PM, Kelly F, Cheeseman K, Mitchinson MJ. Randomised controlled trial of vitamin E in patients with coronary disease: Cambridge Heart Antioxidant Study (CHAOS) Lancet. 1996;347(9004):781–6. doi: 10.1016/s0140-6736(96)90866-1. [DOI] [PubMed] [Google Scholar]
- 38.Stocker R. The ambivalence of vitamin E in atherogenesis. Trends Biochem Sci. 1999;24(6):219–23. doi: 10.1016/s0968-0004(99)01404-8. [DOI] [PubMed] [Google Scholar]
- 39.Teslovich TM, Musunuru K, Smith AV, Edmondson AC, Stylianou IM, Koseki M, Pirruccello JP, Ripatti S, Chasman DI, Willer CJ, Johansen CT, Fouchier SW, Isaacs A, Peloso GM, Barbalic M, Ricketts SL, Bis JC, Aulchenko YS, Thorleifsson G, Feitosa MF, Chambers J, Orho-Melander M, Melander O, Johnson T, Li X, Guo X, Li M, Shin CY, Jin GM, Jin KY, Lee JY, Park T, Kim K, Sim X, Twee-Hee OR, Croteau-Chonka DC, Lange LA, Smith JD, Song K, Hua ZJ, Yuan X, Luan J, Lamina C, Ziegler A, Zhang W, Zee RY, Wright AF, Witteman JC, Wilson JF, Willemsen G, Wichmann HE, Whitfield JB, Waterworth DM, Wareham NJ, Waeber G, Vollenweider P, Voight BF, Vitart V, Uitterlinden AG, Uda M, Tuomilehto J, Thompson JR, Tanaka T, Surakka I, Stringham HM, Spector TD, Soranzo N, Smit JH, Sinisalo J, Silander K, Sijbrands EJ, Scuteri A, Scott J, Schlessinger D, Sanna S, Salomaa V, Saharinen J, Sabatti C, Ruokonen A, Rudan I, Rose LM, Roberts R, Rieder M, Psaty BM, Pramstaller PP, Pichler I, Perola M, Penninx BW, Pedersen NL, Pattaro C, Parker AN, Pare G, Oostra BA, O’Donnell CJ, Nieminen MS, Nickerson DA, Montgomery GW, Meitinger T, McPherson R, McCarthy MI, McArdle W, Masson D, Martin NG, Marroni F, Mangino M, Magnusson PK, Lucas G, Luben R, Loos RJ, Lokki ML, Lettre G, Langenberg C, Launer LJ, Lakatta EG, Laaksonen R, Kyvik KO, Kronenberg F, Konig IR, Khaw KT, Kaprio J, Kaplan LM, Johansson A, Jarvelin MR, Janssens AC, Ingelsson E, Igl W, Kees HG, Hottenga JJ, Hofman A, Hicks AA, Hengstenberg C, Heid IM, Hayward C, Havulinna AS, Hastie ND, Harris TB, Haritunians T, Hall AS, Gyllensten U, Guiducci C, Groop LC, Gonzalez E, Gieger C, Freimer NB, Ferrucci L, Erdmann J, Elliott P, Ejebe KG, Doring A, Dominiczak AF, Demissie S, Deloukas P, de Geus EJ, de FU, Crawford G, Collins FS, Chen YD, Caulfield MJ, Campbell H, Burtt NP, Bonnycastle LL, Boomsma DI, Boekholdt SM, Bergman RN, Barroso I, Bandinelli S, Ballantyne CM, Assimes TL, Quertermous T, Altshuler D, Seielstad M, Wong TY, Tai ES, Feranil AB, Kuzawa CW, Adair LS, Taylor HA, Jr, Borecki IB, Gabriel SB, Wilson JG, Holm H, Thorsteinsdottir U, Gudnason V, Krauss RM, Mohlke KL, Ordovas JM, Munroe PB, Kooner JS, Tall AR, Hegele RA, Kastelein JJ, Schadt EE, Rotter JI, Boerwinkle E, Strachan DP, Mooser V, Stefansson K, Reilly MP, Samani NJ, Schunkert H, Cupples LA, Sandhu MS, Ridker PM, Rader DJ, van Duijn CM, Peltonen L, Abecasis GR, Boehnke M, Kathiresan S. Biological, clinical and population relevance of 95 loci for blood lipids. Nature. 2010;466(7307):707–13. doi: 10.1038/nature09270. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 40.Weinberg RB. Apolipoprotein A-IV polymorphisms and diet-gene interactions. Curr Opin Lipidol. 2002;13(2):125–34. doi: 10.1097/00041433-200204000-00003. [DOI] [PubMed] [Google Scholar]
- 41.Willer CJ, Sanna S, Jackson AU, Scuteri A, Bonnycastle LL, Clarke R, Heath SC, Timpson NJ, Najjar SS, Stringham HM, Strait J, Duren WL, Maschio A, Busonero F, Mulas A, Albai G, Swift AJ, Morken MA, Narisu N, Bennett D, Parish S, Shen H, Galan P, Meneton P, Hercberg S, Zelenika D, Chen WM, Li Y, Scott LJ, Scheet PA, Sundvall J, Watanabe RM, Nagaraja R, Ebrahim S, Lawlor DA, Ben-Shlomo Y, vey-Smith G, Shuldiner AR, Collins R, Bergman RN, Uda M, Tuomilehto J, Cao A, Collins FS, Lakatta E, Lathrop GM, Boehnke M, Schlessinger D, Mohlke KL, Abecasis GR. Newly identified loci that influence lipid concentrations and risk of coronary artery disease. Nat Genet. 2008;40(2):161–9. doi: 10.1038/ng.76. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 42.Wong MY, Day NE, Luan JA, Chan KP, Wareham NJ. The detection of gene-environment interaction for continuous traits: should we deal with measurement error by bigger studies or better measurement? Int J Epidemiol. 2003;32(1):51–7. doi: 10.1093/ije/dyg002. [DOI] [PubMed] [Google Scholar]
- 43.Zech LA, Gross EG, Peck GL, Brewer HB. Changes in plasma cholesterol and triglyceride levels after treatment with oral isotretinoin. A prospective study. Arch Dermatol. 1983;119(12):987–93. [PubMed] [Google Scholar]
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