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Molecular Diagnostics and Genetics |
1 Centre for Cardiovascular Genetics, Department of Medicine, British Heart Foundation Laboratories, Royal Free and University College Medical School, London, United Kingdom.
2 Medical Research Council Cardiovascular Group, Department of Environmental and Preventive Medicine, Wolfson Institute of Preventive Medicine, London, United Kingdom.
aAddress correspondence to this author at: Centre for Cardiovascular Genetics, Department of Medicine, British Heart Foundation Laboratories, Rayne Bldg., Royal Free and University College Medical School, 5 University St., London WC1E 6JF, United Kingdom. Fax 0107-679-6212; e-mail rmhaseh{at}ucl.ac.uk.
| Abstract |
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Methods: We followed middle-aged men in the prospective Northwick Park Heart Study II (NPHSII) for 10.8 years and analyzed complete trait and genotype information available on 2057 men (183 CHD events).
Results: Of the 12 genes previously associated with CHD risk, in stepwise multivariate risk analysis, uncoupling protein 2 (UCP2; P = 0.0001), apolipoprotein E (APOE; P = 0.0003), lipoprotein lipase (LPL; P = 0.007), and apolipoprotein AIV (APOA4; P = 0.04) remained in the model. Their combined area under the ROC curve (AROC) was 0.62 (0.580.66) [12.6% detection rate for a 5% false positive rate (DR5)]. The AROC for the CRFs age, triglyceride, cholesterol, systolic blood pressure, and smoking was 0.66 (0.610.70) (DR5 = 14.2%). Combining CRFs and genotypes significantly improved discrimination (P = 0.001). Inclusion of previously demonstrated interactions of smoking with LPL, interleukin-6 (IL6), and platelet/endothelial cell adhesion molecule (PECAM1) genotypes increased the AROC to 0.72 (0.680.76) for a DR5 of 19.1% (P = 0.01 vs CRF combined with genotypes).
Conclusions: For a modest panel of selected genotypes, CHD-risk estimates incorporating CRFs and genotyperisk factor interactions were more effective than risk estimates that used CRFs alone.
| Introduction |
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Inclusion of genotypes from selected candidate gene loci may improve the predictive accuracy of risk algorithms for CHD (6). Although many candidate genes for CHD have been tested (7), the optimal set of risk genotypes has yet to be identified. Only a relatively modest risk can be expected in association with any single genotype; published estimates are in the range 1.21.4 (6)(8)(9). Furthermore, given the multifactorial nature of CHD, lifestyle will set the operational context for genetic variants. Thus, a genotype may be associated with a high CHD risk only with exposure to a certain environment, for example, the reported interaction between smoking and apolipoprotein E genotype (APOE)2
(10). Thus, multiple-locus batteries of genotypes (11) may be significantly associated with CHD, but their usefulness over and above CRFs in risk prediction has not been demonstrated. A study using 5 genes involved in cancer risk suggested that only
20 genes are usually needed to explain 50% of the burden of a disease in the population if the predisposing genotypes are common (>25%), even if the individual risk ratios are relatively small (relative risk, 1.21.5) (12). To explore the use of genes in risk prediction for CHD, we used previously published NPHSII data on CRFs (4) and 14 common single-nucleotide polymorphisms (SNPs) in 12 candidate genes involved in determining plasma lipids, hemostasis, and vascular cell biology (13)(14)(15)(16)(17)(18)(19). We evaluated and compared ROC curves based on combinations of genotypes, CRFs, and previously demonstrated genotypeCRF interactions (17)(18)(20)(21)(22).
| Materials and Methods |
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genotype analysis
Genotypes were determined for 12 genes: uncoupling protein 2 (UCP2), 866G>A (15); apolipoprotein (apo) E (APOE)
2,
3,
4 (20); lipoprotein lipase (LPL) D9N (21), apoAIV (APOA4) T347S (13); interleukin-6 (IL6), 174G>C (22); platelet endothelial cell adhesion molecule-1 (PECAM1) G650R (17); angiotensin type 1 receptor (AGTR1) 1166A>C (18); angiotensin type 2 receptor (AGTR2) 1675G>A (18); bradykinin type 1 receptor (BDKRB1) 699G>C (16); bradykinin type 2 receptor (BDKRB2) +9/9 (16); peroxisome proliferator-activated receptor-
(PPARA); intron 7 and L162V (19); and factor VII (F7) A670C (14) (see Table 1A and 1B in the online Data Supplement for references for genotyping methods and Table 1C in the online Data Supplement for genotype distributions and allele frequencies).
statistical analysis
We log-transformed serum triglyceride (TG) data before statistical analysis. Associations with CHD risk were assessed with Cox proportional hazards models, and hazard ratios (HR; 95% confidence interval) were derived. Analyses were stratified by recruitment center. Coefficients and HRs for systolic BP, TG, and cholesterol were adjusted for regression to the mean by correction factors obtained by the Rosner intraclass correlation coefficient method from repeat measurements made within 6 weeks on a subset of 228 men in NPHSII (5). For the conventional model, a score was derived based on age, TG, cholesterol, smoking, and systolic BP (5). For the genotype-only and genotype-plus-CRF models, scores were obtained by weighting according to the ß coefficients presented in Table 2
. Thus, for the genotype score, those negative for all risk genotypes were scored as 0, and for those positive for any genotype, the coefficient associated with each positive genotype was added to the score. This method gives more weight to the more strongly associated genotypes and thus should yield better predictions than those obtained by basing estimates simply on the number of risk genotypes. Only genotypes and interactions previously shown to be statistically significant in NPHSII were considered for entry into the models. Genotypes were selected for inclusion in the model by a stepwise procedure. Departure from a multiplicative model was then assessed by adding interaction terms into the model. Because of low power to pick up interaction effects, a significance level of P = 0.1 was used. In addition to models including the individual genotypes, models were also fitted according to the number of risk genotypes carried by each study participant, and HRs were obtained for participants carrying any 1, 2, 3, or more risk genotypes. The ability of the several algorithms to predict CHD was assessed using the area under the ROC curve (AROC). The ROC curve was produced by plotting the sensitivity (true positive rate) against 1 specificity (false-positive rate) for all possible scores. Differences in the areas under the curves were tested with an algorithm suggested by Cooper et al. (5). We also calculated the Harrell C index, which extends the ROC analysis to the case of right-censored survival data. Confidence intervals were calculated as described (23). Detection rates (or sensitivities) for a 5% false-positive rate were calculated by interpolation (DR5). It was not appropriate to use a random 50% of the sample to derive the best-fit model and the 2nd 50% as a test cohort, because the number of cases available limits the power to detect the expected modest effects associated with the SNPs.
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| Results |
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genotype and risk
To reduce the possibility of type I errors due to multiple comparisons, we did not examine the complete list of genes and previously determined genotypes examined for CHD risk associations in NPHSI (see Table 1 in the online Data Supplement). We examined only the 12 candidate genes (see Materials and Methods) that showed statistically significant CHD-associated risk. Only UCP2, APOE, LPL, and APO4 were independently associated with risk in the stepwise regression procedure (Table 2
), with no evidence for greater-than-additive effects for any pairwise combination (see Table 3 in the online Data Supplement). The AROC for this 4-genotype model was 0.62 (0.580.66), with a DR5 of 12.6%, not statistically significantly different from that obtained using CRFs alone (P = 0.20) (Fig. 1A
). Compared with the risk associated with homozygosity for the common alleles, the risk associated with the less frequent alleles was modest, with HRs ranging from 1.38 to 2.41 and 0.35 for the protective e2 allele. These HRs were similar and remained statistically significant after adjustment for CRFs.
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conventional plus genotype risk factors
When both genotype data and CRFs were included in the score, the AROC increased to 0.70 (0.660.74) with a DR5 of 18.0%, a significant improvement over the score obtained with conventional factors alone (P <0.001). The predictive accuracy of these 4-gene genotypes was not significantly different in study participants in the lowest, middle, or top tertile of CRF score [0.65 (0.550.75), 0.63 (0.550.72), and 0.60 (0.530.67), respectively; P = 0.66]. Adding APOE genotype alone significantly improved the AROC [0.68 (0.640.72); P <0.01 vs CRFs only], but none of the other genotypes singly or in pairwise combinations did so (see Table 4 in the online Data Supplement). Study participants did not differ significantly in age, TG, systolic BP, or smoking habit according to the number of genetic risk factors. Mean (SD) serum cholesterol, however, was significantly lower in those with no genetic risk factors than in all other groups [5.30 (1.04) vs 5.77 (1.00) mmol/L, respectively; P <0.001], due in part to the higher prevalence of the cholesterol-lowering
2
3 genotype in this group (see Table 5 in the online Data Supplement). With CHD event rates in men with none of the risk genotypes (9.0% of the sample) as reference, the CRF-adjusted HRs for those carrying any 1 (53.3%), any 2 (33.4%), or any 3 (4.3%) genotypes were 3.17 (1.168.60), 4.58 (1.6712.56), and 12.05 (4.1235.24), respectively (no study participant was found to have all 4 risk genotypes).
risk score with geneenvironment interactions
Several of the gene variants have shown evidence for interaction with smoking [LPL (21), APOE (20), IL6 (22), PECAM1 (17)] or a baseline systolic BP of
160 mmHg [AGTR2 (18), BDKRB2 (16)], and we included these interactions in a 3rd model. The reported interactions with increased systolic BP did not significantly improve the model (P >0.2 for both). However, as shown in Table 3
, in a model including the CRFs and the reported smoking interactions, UCP2, APOE, and APO4 were retained in the model, as was the interaction term between smoking and LPL; 2 additional genotypes also added to the model, PECAM1 and IL6. The AROC for this model was 0.72 (0.680.76) with a DR5 of 19.1% (Fig. 1B
), which was a significant improvement (P = 0.01) on the model based on CRFs and genotypes alone. These estimates were not materially altered in any way when we accounted for those having CHD events by use of the Harrell C index, which takes into account the censored data (see Table 6 in the online Data Supplement). For LPL, IL6, and PECAM1, significant risk was found only in smokers, with the highest HR of 8.02 observed in LPL N9 smokers, compared with LPL D9 nonsmokers, although the prevalence of this group was low (0.9%). For IL6, men carrying 1 or more copy of the 174C allele, nonsmokers had no significant evidence for higher CHD risk than GG men, but smokers had a 1.81-fold higher risk. For PECAM1, nonsmokers homozygous for the common G allele had the lowest risk (and were set as the reference group) but smokers had the highest risk [3.1 (1.79, 5.36)], whereas men carrying the R allele had a much smaller increase in risk, only 30%, if they smoked.
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A KaplanMeier survival plot of the combined effects of these variants and their interactions on survival is presented in Fig. 2
. No significant differences in age, serum cholesterol, or TG were observed between the 5 groups of men with different numbers of genetic risk factors (i.e., either a risk genotype alone or a genotypesmoking risk factor; Table 4
).
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| Discussion |
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The primary aim of this study was to examine whether common SNPs in any of 12 candidate genes, individually or in combination, could meet the criterion of enhancing event prediction. Our a priori hypothesis was that risk prediction would not be significantly improved, because of the low reported risk associated with any particular SNP, the low prevalence of risk genotypes, and the fact that many of the genes will be influencing CHD through factors already in the CRF algorithm. Thus, although metaanalysis demonstrates a significant impact of CETP genotype on risk, this effect was considerably attenuated (and no longer statistically significant) by adjustment for HDL concentrations (9), demonstrating that CHD-risk genotypes will not necessarily improve prediction over CRFs. APOE did so singly, however, and the combination of SNPs in the genes for UCP2, APOA4, and LPL with APOE improved prediction further. The inclusion of reported interactions between certain genotypes (LPL, IL6, and PECAM1) and smoking improved the model still further, with a final 19.1% specificity of prediction, for a false-positive rate of 5%. These results suggest that it may be possible to develop a relatively small, clinically useful set of SNPs that can enhance CHD risk prediction based on CRFs alone. The set of SNPs (and their interactions with smoking) that gave the best prediction in NPHSII are unlikely to be universally applicable, and without validation in larger data sets cannot be considered for clinical practice. Although others have reported multilocus genotype assays for CHD risk (11), and at least 1 report suggests that inclusion of a limited set of candidate SNPs may improve prediction of stroke risk (25), to our knowledge our study is the first demonstration of the predictive value of a combined SNP genotype for CHD risk. For cancer risk, such an approach has yielded variable results (26)(27).
We have suggested that data from large metaanalyses be used to select genotypes for inclusion in risk algorithms (6). For the genes examined here, only metaanalysis confirmation for APOE (28) and for LPL (29) have been reported. Such confirmation is particularly important in regard to geneenvironment interactions but has not been reported for any of the genes studied here. In this analysis, the previously reported interaction of APOE and smoking in determining risk of CHD (20), although not seen in all studies (30), appears relatively robust (31)(32). In stepwise regression analysis, however, it was not statistically significant (P = 0.12) and was therefore not retained in the final model. Thus, considerable caution must be exercised and many additional data are required before such SNPs and their interactions can be accepted for risk prediction.
Our data suggest that although the risk associated with any 1 genotype included here is modest, in combination, they may be associated with a clinically significant risk. Because the allele frequency for many of these variants is high, many men carry several alleles associated with CHD risk. Compared with the 9.0% of men carrying none of the risk alleles, the observed 10-year HR for CHD in the 33% of men with 2 risk alleles was >4-fold higher, and in the 4.3% with 3 risk alleles, it was 12-fold higher (see Table 5 in the online Data Supplement). This risk is comparable to that seen in untreated familial hypercholesterolemia (33). For the 29% of men in NPHSII who were smokers, the proportion with a similarly increased HR attributable to the combination of smoking and their genotype is even larger (11.7%; Table 4
). To put the magnitude of the genetic contributions to risk prediction in context, the contributions of cholesterol and systolic BP to the AROC were 2.5% and 0.7%, respectively, and the genotype and genotypesmoking contributions were 4.1% and 6.4%.
mechanism of chd risk effects
All SNPs included in the final model were functional in that the base change creating the SNP alters the amino-acid sequence and function of the cognate protein [LPL (34), APOE (35), APO4(36), PECAM1 (17)] or the control of transcription and gene expression [UCP2 (37), IL6(38)]. In contrast, nonfunctional SNPs are likely to have little or no utility unless they show complete or strong linkage disequilibrium with a functional SNP. The CHD-risk mechanism of action of the functional SNPs is thus attributable to modulation of the anti- or proatherogenic actions of the cognate proteins, with the APOE effect probably related to the associated atherogenicity of plasma lipoproteins (28)(35), the influence of UCP2 on oxidative stress (39), the reverse cholesterol metabolism and lipid oxidation effects of APOA4 (40), the influence of LPL (34) and PECAM1 (41) on monocyte adhesion and entry into the developing plaque, and the modulation by IL6 of IL-6 plasma and tissue concentrations and thus damage to endothelial or other vascular wall cells (reviewed in Ref. (42).
limitations to the study
One limitation to our findings is that evaluating the effects on CHD risk of the combined genotypes in the same sample in which they were originally tested likely leads to overestimation of their predictive power. Both the Framingham (1) and PROCAM (2) risk algorithms, however, were developed in the same sample in which the constituent CRFs were originally tested, with PROCAM based on 325 events in 5389 men followed for 10 years, and Framingham based on 383 events in 2489 men followed for 12 years (i.e., of a magnitude similar to NPHSII). Therefore, although the actual risk estimates seen here are unlikely to be extrapolated to other studies, we believe that this limitation did not affected the exploration of whether a modest panel of SNPs can add significantly to the CHD-predictive power of classical risk factors. We and others (43) have argued that correction for multiple comparisons is too conservative in hypothesis-deriving analyses such as these, but for some of the genotypes, the statistical significance is high and likely to be a true effect.
The number of CHD events was a major limitation in our study, restricting the power of detection to a risk of >1.7-fold for a variant with a carrier frequency of 10% (
= 0.05; ß = 0.2). To decrease the potential problem of multiple testing, we included in the modeling only those genes showing a statistically significant effect on risk in NPHSII, excluding 13 other genes (26 SNPs; see Table 1C in the online Data Supplement). Thus, several genotypes with modest effects on CHD risk confirmed by metaanalysis [e.g., ENOS (8) and CETP (9)] were not statistically significant in NPHSII (see Table 1B in the online Data Supplement) and were therefore not included in the current analysis. We also acknowledge the limitations set by the limited number of SNPs examined. Other genes reported to influence CHD risk (7), such as those for lymphotoxin
(44) or the Toll-like receptor 4 (45), may also improve predictive power, but studies larger than NPHSII will be needed to test this possibility. Simulations in NPHSII show that the AROC for conventional factors would improve by
3% (P = 0.03) after addition of a genotype of 10% frequency associated with a 3-fold risk, a level unlikely for common genetic variants for which estimates are usually <2-fold (6)(28)(29).
In summary, we explored the potential scope of genetic approaches to risk assessment in CHD and examined the potential predictive utility of genotype interactions with CRFs, such as smoking. For mathematical reasons, adding independent risk factors to risk prediction is associated with diminishing returns (24), and with risk factors of modest screening performance (DR5
15%), all independent of each other,
15 such factors would be required to increase the DR5 to 80%. Our genetic risk factor results for 5 classical factors and 10 genes indicate that this goal is feasible. For the genotypes included here, if the true HR values are lower, their individual contribution to the ROC will be smaller, and for the combined genetic contribution to improve the predictive power of the CRFs, more genotypes of modest effect would have to be included. Thus, to have a similar improvement for AROC, 12 SNPS with a 10% genotype frequency and a 1.5-fold risk would be required, whereas for a 30% frequency, 3 SNPs with a 1.5-fold risk would be required. Nevertheless, these findings confirm the reported utility of a relatively small set of common SNPs of modest effect on risk to explain a significant proportion of the burden of disease (12), suggesting that a relatively small number of selected SNPs can be used with CRFs to identify high-risk individuals who would derive the most benefit from correction of modifiable risk factors through lifestyle interventions or medications. Thus, these data demonstrate that the discovery of independent gene SNPs or haplotypes of modest predictive power to add to the classical risk score algorithm may have clinical utility in CHD risk prediction and management.
| Acknowledgments |
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| Footnotes |
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2 Human genes: APOE, apolipoprotein E; UCP2, uncoupling protein 2 (mitochondrial, proton carrier); LPL, lipoprotein lipase; APOA4, apolipoprotein A-IV; IL6, interleukin 6 (interferon ß2); PECAM1 platelet/endothelial cell adhesion molecule (CD31 antigen); AGTR1, angiotensin II receptor, type 1; AGTR2, angiotensin II receptor, type 2; BDKRB1, bradykinin receptor B1; BDKRB2, bradykinin receptor B2; PPARA, peroxisome proliferator-activated receptor-
; F7, coagulation factor VII (serum prothrombin conversion accelerator); CETP, cholesteryl ester transfer protein. ![]()
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