Human Molecular Genetics Advance Access originally published online on January 13, 2005
Human Molecular Genetics 2005 14(5):639-643; doi:10.1093/hmg/ddi060
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Human Molecular Genetics, Vol. 14, No. 5 © Oxford University Press 2005; all rights reserved
Haplotypes produced from rare variants in the promoter and coding regions of angiotensinogen contribute to variation in angiotensinogen levels
1Department of Preventive Medicine and Epidemiology, Loyola University Medical Center, 2160 S. First Avenue, Maywood, IL 60153, USA, 2Department of Biological Anthropology, Oxford Unviersity, Oxford, UK, 3Department of Pediatrics, University College Hosptial, University of Ibadan, Ibadan, Nigeria and 4National Human Genome Research Center, College of Medicine, Howard University, Washington, DC, USA
* To whom correspondence should be addressed. Tel: +1 7083279058; Fax: +1 7083279009; Email: xzhu1{at}lumc.edu
Received November 18, 2004; Revised December 28, 2004; Accepted January 5, 2005
| ABSTRACT |
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The most efficient study design to map genes underlying complex traits will be determined by assumptions about whether the genetic effects are likely to be due to relatively few common variants or multiple rare variants. To examine the possibility that rare variants may influence blood pressure, we sequenced a 6.8 kb region of the angiotensinogen (AGT) gene in 29 male Nigerians with high plasma AGT levels and 28 with low levels. The frequency of haplotypes produced from rare variants in the promoter and coding regions was significantly different between the two groups, and it is unlikely that this difference was due to the manner in which the rare variants were selected. Further analysis suggested that most of the haplotypes produced by these rare variants are found on a haplotype background created by three common SNPs. Our study confirms in an additional trait that rare variants can influence the distribution of complex traits; whether these variants can be captured by common SNPs or haplotypes requires further investigation.
| INTRODUCTION |
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The relative frequency of variants that contribute to common human diseases continues to be a subject of intense speculation, in part because the evolutionary context in which these variants arose remains unknown (1
Rare variants are of recent origin and have a high probability of being lost due to random genetic draft. Potentially, however, variants which confer a selective advantage could be preserved at low frequencies more often than those in other portions of the phenotypic distribution, and this process could account for the observations reported earlier when discordant phenotypes were sampled. On the other hand, as most mutations are deleterious, over-representation of new variants at the bottom of the phenotype distribution could result simply from the fact that they most often confer loss of function.
Enzymatic pathways underlying blood-pressure regulation provide a model system for further investigation of these questions. Plasma angiotensinogen (AGT-P) is the substrate of the reninangiotensin system and has been correlated, albeit weakly, with blood pressure (12
14
). Variation at the angiotensinogen (AGT) locus is still incompletely described, but common variants have been associated with AGT-P and, also to a limited degree, with hypertension (12
,13
,15
). If low AGT-P confers some protection against the consequences of hypertension, we should observe an excess of haplotypes produced by rare mutations in association with lower levels of AGT-P. On the basis of an entirely different approach, prior evidence of natural selection has actually been reported for AGT in non-African populations (16
). It must be acknowledged, however, that the mechanism of selection over long time intervals is not entirely clear as the sequelae of hypertension occur late in life and most pre-modern societies have absent or very low prevalences of hypertension (17
).
| RESULTS |
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In the present study, we systematically examined the association of the rare haplotypes that resulted from low frequency variants in the promoter and coding regions in AGT with plasma levels of the gene product. We selected 57 males from the highest (N=29) and from the lowest (N=28) 20th percentiles of the AGT plasma level distribution in the population sample from Igbo-Ora, Nigeria. We reanalyzed the sequence data and its relation to AGT-P, age, systolic blood pressure (SBP) and diastolic blood pressure (DBP). A total of 93 SNPs were identified across the 6.8 kb sequence. The average nucleotide diversity,
, was 1.77x103, and
=2.29x103, which is slightly larger than the previous surveys (18
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In the low AGT-P group, we identified 11 haplotypes that were created by the 11 rare SNPs in the promoter region and the exonic SNP C3889T, compared with only three haplotypes in the high group (P-value of Fisher's exact test is 0.023, Table 2). Because C4072T has been found to be associated with AGT levels in the literature and is also relatively infrequent in Africans, we added this SNP to the analysis. One additional SNP A-6G had MAF <8.8% and was therefore included in the analysis. We then observed 19 rare haplotypes (H2H21) in the low group, compared with five in the high group (P-value of Fisher's exact test is 0.0009, Table 2). To estimate the effect of these rare haplotypes on the phenotype, we regressed AGT-P on the haplotypes assuming an additive model (i.e. all the rare haplotypes have the same effect on AGT-P and the effect is additive), with age and BMI as the covariates. Age and BMI were not significant and were then removed. As anticipated, the relationship was highly significant (excluding C4072T: ß=439.4±129.2, P=0.0013, including C4072T: ß=472.1±126.3, P=0.0004). For SBP and DBP, we observed marginal significance when C4072T was included and after adjustment for AGE and BMI (SBP: ß=8.49±4.45, P=0.06, DBP: ß=5.0±3.76, P=0.19); this weak effect could potentially be due to the small sample size.
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To test whether the difference in the haplotype frequencies created by the rare SNPs is due to the process we used to select them, we repeated the analyses using the haplotypes created by rare intronic SNPs, which are relatively likely to be neutral. A total of 46 SNPs with an MAF <5% were observed in the introns, as were 50 SNPs with frequencies <9%. We randomly chose 12 SNPs from among the 46 and compared the haplotype frequencies created by these 12 SNPs between the high and the low AGT-P groups. This procedure was repeated 10 000 times, and each time we recorded the P-value of Fisher's exact test. We observed a P-value <0.023 on only nine occasions. Similarly, when we selected 14 SNPs from the full set of 50, we observed seven instances of a P-value <0.0009. These simulation results confirm that the significant difference in rare haplotypes in the promoter regions and the exons is unlikely to be due to random variation in the selection of the rare SNPs.
We then tested whether a subset of common SNPs in AGT could distinguish the haplotypes created by the rare promoter and coding SNPs from the remaining haplotypes. After excluding the rare SNPs, 29 SNPs remained, and their pairwise r2 values are presented in Figure 1, as summarized by the software Haploview. We also created a pseudo-SNP (SNP 30 in Fig. 1) which has a value of 1 if one of (H2H11) is presented, otherwise 0. The pseudo-SNP was in lower LD with all the common SNPs, which is not unexpected. By setting the criterion r2>0.7 in the method proposed by Carlson et al. (19
), we identified 16 bins. In each bin, the SNP having the maximum correlation with the pseudo-SNP was selected as the htSNP. To select a subset of htSNPs in AGT to distinguish the haplotypes created by the rare promoter and coding SNPs from the remaining haplotypes, we first defined a dependent variable y which has a value of 1 if one of (H2H11) is presented, otherwise 0. We then performed stepwise linear regression using y as the dependent variable and htSNPs as independent variables. The final model included SNPs 217, 172, 2186, 5593 and 6420. From these five SNPs, we selected SNPs 217, 172 and 2186, which had the smallest variance, given the rare haplotypes. In other words, there is only one major haplotype which carries most of the rare SNPs in the promoter and coding regions. Among the 24 rare haplotypes produced by the rare promoter and coding SNPs, 19 carried haplotype GCT created by SNPs 217, 172 and 2186, compared with only three in the remaining haplotypes, suggesting that in this instance common SNPs could potentially have captured the variation due to the rare variants (Table 3). The frequencies of the haplotypes that included these three common SNPs were significantly different between the high and the low AGT groups (P=0.035, Fisher's exact test).
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| DISCUSSION |
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Our study provides evidence that rare sequence variants could have an important influence on variation of blood-pressure regulating phenotypes, in support of the finding by Cohen et al. (10
Our additional finding that most of the rare mutations occurred on haplotype GCT formed by three common SNPs suggests that htSNPs may in some instances capture the haplotype variation due to rare variants, as suggested by Lin et al. (25
). However, whether this occurs frequently or has a biological basis remains unknown. Furthermore, our analysis proceeded backwards, aggregating the rare SNPs onto haplotypes; prospectively many possible combinations of SNPs would have to be examined to identify the underlying pattern. Owing to the need to consider a large number of htSNPs, the multiple comparisons adjustment that would be required with this approach would greatly reduce the statistical power of an association study. To generalize, our results suggest that htSNPS, like those that will be provided by efforts such as the HapMap, might miss a substantial proportion of the variants which underlie complex disease.
| MATERIALS AND METHODS |
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Data collection and genotyping
All the participants were recruited from Igbo-Ora, a rural community in southwest Nigeria. Study protocols were reviewed and approved by the institutional review boards at University College Hospital, Ibadan, and Loyola University Medical School. Written informed consent was obtained from the participants. The detailed sampling frame was described in our previous studies (26
Statistical methods
We compared haplotypes resulting from rare variants in the promoter and coding regions between high and low AGT-P levels by Fisher's exact test of a 2x2 table. To determine whether the observed significance difference of the rare haplotype frequencies between high and low AGT-P levels was because of the selection of SNPs, we carried out 10 000 simulations by examining the haplotype frequencies resulting from rare intronic SNPs. In each simulation, we randomly selected the same number of intronic SNPs and compared the rare haplotype frequencies between the high and the low AGT-P levels. To obtain an empirical P-value, we counted the number of simulations in which the Fisher's exact test P-value was less than the observed P-value when the rare promoter and coding SNPs were compared.
Pairwise LD between common SNPs was measured by r2 (29
). To select htSNPs, we applied one of the accepted methods, [the method of Carlson et al. (19
)] which clusters the SNPs into different bins according to the r2 values. We used a criteria r2
0.7 to define the bins.
| ELECTRONIC DATABASE INFORMATION |
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Accession numbers and URLs for data presented herein are as follows:
Haploviewhttp://www.broad.mit.edu/mpg/haploview/
| ACKNOWLEDGEMENTS |
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We thank Donghui Kan for his assistance in programming. We also thank two anonymous reviews for their helpful comments to further improve the performance of the paper. The work was supported by National Institutes of Health, grant numbers HL074166, HL45508 from NHLBI.
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